bluuebunny/crossref_metadata_2025 huggingface dataset:
Dicamba-Tolerant Soybean Combined Cover Crop to Control Palmer amaranth
Authors: Montgomery Garret B. , McClure Angela T. , Hayes Robert M. , Walker Forbes R. , Senseman Scott A. , Steckel Lawrence E.
Published: November 2017

A study was conducted to evaluate the response of glyphosate- and dicamba-tolerant (GDT) soybean and weed control from cover crop different termination intervals before and after soybean planting. Cover crop biomass was highest when terminated at planting, decreased with the 7- and 14-d preplant (DPP) and day-after-planting (DAP) timings, and again at the 14 DPP and DAP timings. Glyphosate+dicamba provided total control of cover crops by 21 DAP. Cover crop termination timing did not influence soybean population or yield. Palmer amaranth control at the 21 and 28 d after termination (DAT) was 97% to 99%. Differences in Palmer amaranth control were not detected among herbicide programs or termination intervals at the end of season rating, and all treatments provided ≥97% control. Although differences in Palmer amaranth control were not apparent at the end of the season, the delay in cover crop affected the number of days until 10-cm Palmer amaranth was present. When utilizing a wheat+hairy vetch cover crop in DGT soybeans, producers should delay cover crop termination until 11 to 14 DPP and make at least one POST application of glyphosate+dicamba+an additional herbicide mode of action (MOA) to maximize Palmer amaranth control and soybean yields.
Physiologie der eosinophilen Granulozyten
Authors: Sokollik Christiane , Simon Hans-Uwe
Published: November 2017

Zusammenfassung. Eosinophile Granulozyten gehören zu den Leukozyten und sind im Blutausstrich durch ihre pinken Granula und den brillenförmigen doppelt- gelappten Kern gut identifizierbar. Sie spielen bei allergischen Erkrankungen und parasitären Infektionen eine Rolle. Nach ihrer Aktivierung setzen sie aus ihren Granula toxische Proteine frei. Sie können auch mit diesen Proteinen beladene extrazelluläre mitochondriale DNA-Netze zur Pathogenbekämpfung auswerfen. Über verschiedenste Mediatoren stehen sie im engen Zusammenspiel mit anderen Zellen der Immunabwehr, modulieren deren Reaktion und fördern die Gewebshomöostase. Mit zunehmendem Wissen wird mehr und mehr deutlich, dass Eosinophile nicht nur Effektorzellen sind, sondern regulatorisch an Immun-, Entwicklungs- und Heilungsprozessen beteiligt sind.
Eosinophilie und Parasiten
Authors: Marti Hanspeter , Hatz Christoph
Published: November 2017

Zusammenfassung. Eine Eosinophilie bei Reisenden oder Migranten aus tropischen oder subtropischen Gebieten ist oft assoziiert mit einem Wurmbefall. Da die oft wenig spezifische Klinik in vielen Fällen nicht weiterhilft, sind spezifische Abklärungen vonnöten. Stuhluntersuchungen allein sind bei schwachen Infektionen oder wegen der unregelmässigen Ausscheidung der Eier oder Larven oft nicht sensitiv genug und sollten mittels serologischen Abklärungen ergänzt werden.
Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis
Authors: Huot Bethany , Castroverde Christian Danve M. , Velásquez André C. , Hubbard Emily , Pulman Jane A. , Yao Jian , Childs Kevin L. , Tsuda Kenichi , Montgomery Beronda L. , He Sheng Yang
Published: November 2017

Environmental conditions profoundly affect plant disease development; however, the underlying molecular bases are not well understood. Here we show that elevated temperature significantly increases the susceptibility of Arabidopsis to Pseudomonas syringae pv. tomato (Pst) DC3000 independently of the phyB/PIF thermosensing pathway. Instead, elevated temperature promotes translocation of bacterial effector proteins into plant cells and causes a loss of ICS1-mediated salicylic acid (SA) biosynthesis. Global transcriptome analysis reveals a major temperature-sensitive node of SA signalling, impacting ~60% of benzothiadiazole (BTH)-regulated genes, including ICS1 and the canonical SA marker gene, PR1. Remarkably, BTH can effectively protect Arabidopsis against Pst DC3000 infection at elevated temperature despite the lack of ICS1 and PR1 expression. Our results highlight the broad impact of a major climate condition on the enigmatic molecular interplay between temperature, SA defence and function of a central bacterial virulence system in the context of a widely studied susceptible plant–pathogen interaction.
Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment
Authors: Gu Yanyun , Wang Xiaokai , Li Junhua , Zhang Yifei , Zhong Huanzi , Liu Ruixin , Zhang Dongya , Feng Qiang , Xie Xiaoyan , Hong Jie , Ren Huahui , Liu Wei , Ma Jing , Su Qing , Zhang Hongmei , Yang Jialin , Wang Xiaoling , Zhao Xinjie , Gu Weiqiong , Bi Yufang , Peng Yongde , Xu Xiaoqiang , Xia Huihua , Li Fang , Xu Xun , Yang Huanming , Xu Guowang , Madsen Lise , Kristiansen Karsten , Ning Guang , Wang Weiqing
Published: November 2017

Antidiabetic medication may modulate the gut microbiota and thereby alter plasma and faecal bile acid (BA) composition, which may improve metabolic health. Here we show that treatment with Acarbose, but not Glipizide, increases the ratio between primary BAs and secondary BAs and plasma levels of unconjugated BAs in treatment-naive type 2 diabetes (T2D) patients, which may beneficially affect metabolism. Acarbose increases the relative abundances of Lactobacillus and Bifidobacterium in the gut microbiota and depletes Bacteroides, thereby changing the relative abundance of microbial genes involved in BA metabolism. Treatment outcomes of Acarbose are dependent on gut microbiota compositions prior to treatment. Compared to patients with a gut microbiota dominated by Prevotella, those with a high abundance of Bacteroides exhibit more changes in plasma BAs and greater improvement in metabolic parameters after Acarbose treatment. Our work highlights the potential for stratification of T2D patients based on their gut microbiota prior to treatment.
A protein interaction mechanism for suppressing the mechanosensitive Piezo channels
Authors: Zhang Tingxin , Chi Shaopeng , Jiang Fan , Zhao Qiancheng , Xiao Bailong
Published: November 2017

Piezo proteins are bona fide mammalian mechanotransduction channels for various cell types including endothelial cells. The mouse Piezo1 of 2547 residues forms a three-bladed, propeller-like homo-trimer comprising a central pore-module and three propeller-structures that might serve as mechanotransduction-modules. However, the mechanogating and regulation of Piezo channels remain unclear. Here we identify the sarcoplasmic /endoplasmic-reticulum Ca2+ ATPase (SERCA), including the widely expressed SERCA2, as Piezo interacting proteins. SERCA2 strategically suppresses Piezo1 via acting on a 14-residue-constituted intracellular linker connecting the pore-module and mechanotransduction-module. Mutating the linker impairs mechanogating and SERCA2-mediated modulation of Piezo1. Furthermore, the synthetic linker-peptide disrupts the modulatory effects of SERCA2, demonstrating the key role of the linker in mechanogating and regulation. Importantly, the SERCA2-mediated regulation affects Piezo1-dependent migration of endothelial cells. Collectively, we identify SERCA-mediated regulation of Piezos and the functional significance of the linker, providing important insights into the mechanogating and regulation mechanisms of Piezo channels.
Cellular microRNA networks regulate host dependency of hepatitis C virus infection
Authors: Li Qisheng , Lowey Brianna , Sodroski Catherine , Krishnamurthy Siddharth , Alao Hawwa , Cha Helen , Chiu Stephan , El-Diwany Ramy , Ghany Marc G. , Liang T. Jake
Published: November 2017

Cellular microRNAs (miRNAs) have been shown to regulate hepatitis C virus (HCV) replication, yet a systematic interrogation of the repertoire of miRNAs impacting HCV life cycle is lacking. Here we apply integrative functional genomics strategies to elucidate global HCV–miRNA interactions. Through genome-wide miRNA mimic and hairpin inhibitor phenotypic screens, and miRNA–mRNA transcriptomics analyses, we identify three proviral and nine antiviral miRNAs that interact with HCV. These miRNAs are functionally linked to particular steps of HCV life cycle and related viral host dependencies. Further mechanistic studies demonstrate that miR-25, let-7, and miR-130 families repress essential HCV co-factors, thus restricting viral infection at multiple stages. HCV subverts the antiviral actions of these miRNAs by dampening their expression in cell culture models and HCV-infected human livers. This comprehensive HCV–miRNA interaction map provides fundamental insights into HCV-mediated pathogenesis and unveils molecular pathways linking RNA biology to viral infections.
Baicalein ameliorates TNBS-induced colitis by suppressing TLR4/MyD88 signaling cascade and NLRP3 inflammasome activation in mice
Authors: Luo Xiaoping , Yu Zhilun , Deng Chao , Zhang Jingjing , Ren Gaiyan , Sun Aning , Mani Sridhar , Wang Zhengtao , Dou Wei
Published: November 2017

Baicalein (5,6,7-trihydroxyflavone), a predominant bioactive component isolated from the root of Scutellaria baicalensis Georgi, has established potent anti-inflammatory activity via multi-targeted mechanisms. However, little is known about the effect of baicalein on 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis, which shares pathology related to human Crohn’s disease (CD). The present study demonstrated that baicalein alleviated the severity of TNBS-induced colitis in mice by decreasing the activity of myeloperoxidase (MPO) and the expression of pro-inflammatory mediators. The decline in the activation of nuclear factor-kappa B (NF-κB) and p38 mitogen-activated protein kinase (MAPK) correlated with a decrease in the expression of mucosal toll-like receptor 4 (TLR4) and its adaptor myeloid differentiation factor 88 (MyD88). In vitro, baicalein down-regulated the TLR4/MyD88 signaling cascades (NF-κB and MAPKs) in lipopolysaccharide (LPS)-stimulated macrophages. At the upstream level, baicalein bound to the hydrophobic region of the myeloid differentiation protein-2 (MD-2) pocket and inhibited the formation of the LPS-induced MD-2/TLR4 complex. Furthermore, baicalein reduced NOD-like receptor 3 (NLRP3) inflammasome activation and downstream interleukin-1β expression in a dose-dependent manner. Our study provided evidence for the first time that baicalein attenuated TNBS-induced colitis, at least in part, via inhibition of TLR4/MyD88 signaling cascade as well as inactivation of NLRP3 inflammasome.
Synthesis and implication of novel poly(acrylic acid)/nanosorbent embedded hydrogel composite for lead ion removal
Authors: Bhatia Mayuri , Rajulapati Satish Babu , Sonawane Shirish , Girdhar Amandeep
Published: November 2017

Lead stands second among the deadly heavy metal pollutants owing to the incompetent mechanism possessed by the human body for its removal. A polymeric hydrogel in the form of composite was prepared using acrylic acid (monomer) and novel nanofiller that possess super adsorbent properties with restricted gel seepage into flowing ionic liquid. The filler used is an adsorbent which is biocompatible, biodegradable, economical, abundant, non-hazardous and easy to synthesize. The invariably porous nanofiller, the Nanobentonite(clay), was synthesized using ion exchange reaction by creating acidic environment for accelerated dispersion with exfoliation by CTAB to enhance cation exchange capacity. NanobentoFnite was capable of removing >97% lead ion in batch adsorption study and followed pseudo-second order kinetic model. Freundlich isotherm suggested a removal capacity of ~20 mg/g. Thus, the successfully experimented adsorbent was implicated as filler to form polyacrylic acid nanoclay hydrogel polymerized in ultrasonic bath. The amount of filler was varied from 0.25 to 2 wt% to get 94% removal, analyzed using ICP-OES. The prepared adsorbents were characterized before and after adsorption using TEM, FESEM, XRD, FTIR and DSC to understand the structural changes and metal-sorbent interaction. Thus, the novel nanosorbent/composite are promiscuous and competent in terms of availability, reusability and longevity to remove heavy metal ions.
Metabolic regulatory oscillations in intertidal green seaweed Ulva lactuca against tidal cycles
Authors: Gupta Vishal , Kushwaha Hemant R
Published: November 2017

The survival of wetland plant species largely relies on physiological adaptations essential for submergence and desiccation. Intertidal seaweeds, unlike terrestrial plants, have unique adaptations to submergence and can also sustain desiccation arising from tidal rhythms. This study determined the differential metabolic regulations in the inter-tidal seaweed species Ulva lactuca against the submergence and desiccation. During desiccation, the relative water content of the algal thalli declined with concomitant increase in reactive oxygen species (ROS) and lipid peroxidation. Nevertheless, the trends reversed during recovery on re-submergence and attained homeostasis. Metabolite profiling of U. lactuca revealed desiccation induced balance in energy reserve utilization by adjusting carbohydrate metabolism and switch over to ammonia metabolism. Upon re-submergence, thalli showed an increase in fermentative metabolites, pyruvate-alanine conversion, and the GABA shunt. Prolonged submergence induced substrate level phosphorylation mediated sugar biosynthesis while continuing the alternative carbon flux through fermentative metabolism, an increase in osmoprotectants glycine and betaine, sulfur bearing compounds cysteine and hypotaurine, and phenolic compound coniferaldehyde. The determined metabolic regulations in U. lactuca for submergence tolerance provide insights into potential evolutionarily conserved protective mechanisms across the green lineage and also highlights the possible role of sulfur oxoforms as strong free radical scavengers.
Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons
Authors: Fowler Nicholas J. , Blanford Christopher F. , de Visser Sam P. , Warwicker Jim
Published: November 2017

Large-scale characterisation of cysteine modification is enabling study of the physicochemical determinants of reactivity. We find that location of cysteine at the amino terminus of an α-helix, associated with activity in thioredoxins, is under-represented in human protein structures, perhaps indicative of selection against background reactivity. An amino-terminal helix location underpins the covalent linkage for one class of kinase inhibitors. Cysteine targets for S-palmitoylation, S-glutathionylation, and S-nitrosylation show little correlation with pKa values predicted from structures, although flanking sequences of S-palmitoylated sites are enriched in positively-charged amino acids, which could facilitate palmitoyl group transfer to substrate cysteine. A surprisingly large fraction of modified sites, across the three modifications, would be buried in native protein structure. Furthermore, modified cysteines are (on average) closer to lysine ubiquitinations than are unmodified cysteines, indicating that cysteine redox biology could be associated with protein degradation and degron recognition.
Specific Features of SVZ Neurogenesis After Cortical Ischemia: a Longitudinal Study
Authors: Palma-Tortosa S. , García-Culebras A. , Moraga A. , Hurtado O. , Perez-Ruiz A. , Durán-Laforet V. , Parra J. de la , Cuartero M. I. , Pradillo J. M. , Moro M. A. , Lizasoain I.
Published: November 2017

Stroke is a devastating disease with an increasing prevalence. Part of the current development in stroke therapy is focused in the chronic phase, where neurorepair mechanisms such as neurogenesis, are involved. In the adult brain, one of the regions where neurogenesis takes place is the subventricular zone (SVZ) of the lateral ventricles. Given the possibility to develop pharmacological therapies to stimulate this process, we have performed a longitudinal analysis of neurogenesis in a model of cortical ischemia in mice. Our results show an initial decrease of SVZ proliferation at 24 h, followed by a recovery leading to an increase at 14d and a second decrease 28d after stroke. Coinciding with the 24 h proliferation decrease, an increase in the eutopic neuroblast migration towards the olfactory bulb was observed. The analysis of the neuroblast ectopic migration from the SVZ toward the lesion showed an increase in this process from day 14 after the insult. Finally, our data revealed an increased number of new cortical neurons in the peri-infarct cortex 65d after the insult. In summary, we report here critical check-points about post-stroke neurogenesis after cortical infarcts, important for the pharmacological modulation of this process in stroke patients.
Publisher Correction: Sex-Dependent Effects of Caloric Restriction on the Ageing of an Ambush Feeding Copepod
Authors: Saiz Enric , Calbet Albert , Griffell Kaiene
Published: November 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
Publisher Correction: Seismic evidence for a possible deep crustal hot zone beneath Southwest Washington
Authors: Flinders Ashton F. , Shen Yang
Published: November 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has beenfixed in the paper.
Quantitative analysis of intra- and inter-individual variability of human beta-cell mass
Authors: Olehnik Scott K. , Fowler Jonas L. , Avramovich Gil , Hara Manami
Published: November 2017

Pancreatic beta-cell mass is a critical determinant of the progression of diabetes. The loss of beta-cells in various types of diabetes has been documented in comparison to age, sex and body mass index (BMI) matched control subjects. However, the underlying heterogeneity of beta-cell mass in healthy individuals has not been considered. In this study, the inter-individual heterogeneity in beta-cell/islet mass was examined among 10 cases of age-matched non-diabetic male subjects in relation to BMI, pancreas weight, and the percent ratio, volume and number of islets in the whole pancreas. Beta-cell/islet mass was measured using a large-scale unbiased quantification method. In contrast to previous studies, we found no clinically relevant correlation between beta-cell/islet mass and age, BMI or pancreas weight, with large differences in beta-cell/islet mass and islet number among the individuals. Our method extracts the comprehensive information out of individual pancreas providing multifaceted parameters to study the intrinsic heterogeneity of the human pancreas.
Circulating microparticles in acute diabetic Charcot foot exhibit a high content of inflammatory cytokines, and support monocyte-to-osteoclast cell induction
Authors: Pasquier Jennifer , Thomas Binitha , Hoarau-Véchot Jessica , Odeh Tala , Robay Amal , Chidiac Omar , Dargham Soha R. , Turjoman Rebal , Halama Anna , Fakhro Khalid , Menzies Robert , Jayyousi Amin , Zirie Mahmoud , Al Suwaidi Jassim , Rafii Arash , Malik Rayaz A. , Talal Talal , Abi Khalil Charbel
Published: November 2017

Circulating microparticles (MPs) are major mediators in cardiovascular complications of type 2 diabetes (T2D); however, their contribution to Charcot foot (CF) disease is not known. Here, we purified and assessed the origin, concentration and content of circulating MPs from 33 individuals: 11 with T2D and acute CF, 11 T2D patients with equivalent neuropathy and 11 non-diabetic controls. First, we demonstrated that there were no differences in the distribution of MPs of endothelial, platelet origin among the 3 groups. However, MPs from leukocytes and monocytes origin were increased in CF patients. Moreover, we demonstrated that monocytes-derived MPs originated more frequently from intermediate and non-classical monocytes in CF patients. Five cytokines (G-CSF, GM-CSF, IL-1-ra, IL-2 and IL-16) were significantly increased in MPs from acute CF patients. Applying ingenuity pathways analysis, we found that those cytokines interacted well and induced the activation of pathways that are involved in osteoclast formation. Further, we treated THP-1 monocytes and monocytes sorted from healthy patients with CF-derived MPs during their differentiation into osteoclasts, which increased their differentiation into multinucleated osteoclast-like cells. Altogether, our study suggests that circulating MPs in CF disease have a high content of inflammatory cytokines and could increase osteoclast differentiation in vitro.
SNX27 links DGKζ to the control of transcriptional and metabolic programs in T lymphocytes
Authors: Tello-Lafoz M. , Rodríguez-Rodríguez C. , Kinna G. , Loo L. S. , Hong W. , Collins B. M. , Teasdale R. D. , Mérida I.
Published: November 2017

Sorting nexin 27 (SNX27) recycles PSD-95, Dlg1, ZO-1 (PDZ) domain-interacting membrane proteins and is essential to sustain adequate brain functions. Here we define a fundamental SNX27 function in T lymphocytes controlling antigen-induced transcriptional activation and metabolic reprogramming. SNX27 limits the activation of diacylglycerol (DAG)-based signals through its high affinity PDZ-interacting cargo DAG kinase ζ (DGKζ). SNX27 silencing in human T cells enhanced T cell receptor (TCR)-stimulated activator protein 1 (AP-1)- and nuclear factor κB (NF-κB)-mediated transcription. Transcription did not increase upon DGKζ silencing, suggesting that DGKζ function is dependent on SNX27. The enhanced transcriptional activation in SNX27-silenced cells contrasted with defective activation of the mammalian target of rapamycin (mTOR) pathway. The analysis ofSnx27−/−mice supported a role for SNX27 in the control of T cell growth. This study broadens our understanding of SNX27 as an integrator of lipid-based signals with the control of transcription and metabolic pathways.
STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array
Authors: Hochgerner Hannah , Lönnerberg Peter , Hodge Rebecca , Mikes Jaromir , Heskol Abeer , Hubschle Hermann , Lin Philip , Picelli Simone , La Manno Gioele , Ratz Michael , Dunne Jude , Husain Syed , Lein Ed , Srinivasan Maithreyan , Zeisel Amit , Linnarsson Sten
Published: November 2017

Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.
A new A-P compartment boundary and organizer in holometabolous insect wings
Authors: Abbasi Roohollah , Marcus Jeffrey M.
Published: November 2017

Decades of research on the highly modified wings of Drosophila melanogaster has suggested that insect wings are divided into two Anterior-Posterior (A-P) compartments separated by an axis of symmetry. This axis of symmetry is created by a developmental organizer that establishes symmetrical patterns of gene expression that in turn pattern the A-P axis of the wing. Butterflies possess more typical insect wings and butterfly wing colour patterns provide many landmarks for studies of wing structure and development. Using eyespot colour pattern variation in Vanessa butterflies, here we show an additional A-P axis of symmetry running between wing sectors 3 and 4. Boundaries of Drosophila mitotic clones suggest the existence of a previously undetected Far-Posterior (F-P) compartment boundary that coincides with this additional A-P axis. A similar compartment boundary is evident in butterfly mosaic gynandromorphs. We suggest that this additional compartment boundary and its associated developmental organizer create an axis of wing colour pattern symmetry and a gene expression-based combinatorial code, permitting each insect wing compartment to acquire a unique identity and allowing for the individuation of butterfly eyespots.
Genetic Architecture and Candidate Genes Identified for Follicle Number in Chicken
Authors: Shen Manman , Sun Hongyan , Qu Liang , Ma Meng , Dou Taocun , Lu Jian , Guo Jun , Hu Yuping , Wang Xingguo , Li Yongfeng , Wang Kehua , Yang Ning
Published: November 2017

Follicular development has a major impact on reproductive performance. Most previous researchers focused on molecular mechanisms of follicular development. The genetic architecture underlying the number of follicle, however, has yet not to be thoroughly defined in chicken. Here we report a genome-wide association study for the genetic architecture determining the numbers of follicles in a large F2 resource population. The results showed heritability were low to moderate (0.05–0.28) for number of pre-ovulatory follicles (POF), small yellow follicles (SYF) and atresia follicles (AF). The highly significant SNPs associated with SYF were mainly located on GGA17 and GGA28. Only four significant SNPs were identified for POF on GGA1. The variance partitioned across chromosomes and chromosome lengths had a linear relationship for SYF (R2 = 0.58). The enriched genes created by the closest correspondent significant SNPs were found to be involved in biological pathways related to cell proliferation, cell cycle and cell survival. Two promising candidate genes, AMH and RGS3, were suggested to be prognostic biomarkers for SYF. In conclusion, this study offers the first evidence of genetic variance and positional candidate genes which influence the number of SYF in chicken. These identified informative SNPs may facilitate selection for an improved reproductive performance of laying hens.
A new structural arrangement in proteins involving lysine NH3
+ group and carbonyl
Authors: Rogacheva Olga N. , Izmailov Sergei A. , Slipchenko Lyudmila V. , Skrynnikov Nikolai R.
Published: November 2017

Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3+ group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3+ group (angle Cε-Nζ-O close to 180°, distance Nζ-O ca. 2.7-3.0 Å). Typically, this linear arrangement coexists with three regular hydrogen bonds formed by lysine NH3+ group (angle Cε-Nζ-acceptor atom close to 109°, distance Nζ-acceptor atom ca. 2.7-3.0 Å). Our DFT calculations using polarizable continuum environment suggest that this newly identified linear interaction makes an appreciable contribution to protein’s energy balance, up to 2 kcal/mol. In the context of protein structure, linear interactions play a role in capping the C-termini of α-helices and 310-helices. Of note, linear interaction involving conserved lysine is consistently found in the P-loop of numerous NTPase domains, where it stabilizes the substrate-binding conformation of the P-loop. Linear interaction NH3+ – carbonyl represents an interesting example of ion-dipole interactions that has so far received little attention compared to ion-ion interactions (salt bridges) and dipole-dipole interactions (hydrogen bonds), but nevertheless represents a distinctive element of protein architecture.
A sensitive and rapid immunoassay for Mycoplasma pneumoniae in children with pneumonia based on single-walled carbon nanotubes
Authors: Song Ming , Zhang Ying , Li Shi , Zhang Chunsheng , Tao Mingming , Tang Ying , Jiang Zhuquan , Cai Sulan , Xu Wei , Xu Weizhuo
Published: November 2017

Mycoplasma pneumoniae(MP) is a leading pathogen of respiratory infection, especially community-acquired pneumonia (CAP), in children worldwide. However, its diagnosis is frequently ineffective because bacterial culture and serology test are usually positive 1–2 weeks or more after the disease onset. To achieve a better detection efficiency, the single-walled carbon nanotubes(SWCNT) were coupled with the colloidal gold-monoclonal antibody immunochromatographic strips(CGIC). Interestingly, the SWCNT/CGIC assay allowed MP identification, with a detection limit of 1 × 102 copies/ml. Using referenced throat swabs of 97 MP and 40 non-MP cases, the assay yielded 72.2% sensitivity, 100.0% specificity, 100.0% positive predictive value (PPV), 59.7% negative predictive value (NPV). In summary, our assay was far more effective than any conventional methods for the diagnosis of acute MP. The ease of use, rapid and stability further enhance its feasibility for clinical use on-site.
Risk of non-cardiac surgery after percutaneous coronary intervention with drug-eluting stents
Authors: Park Sun-Kyung , Jung Dhong Eun , Jung Sung Ae , Kim Won Ho , Bahk Jae-Hyon
Published: November 2017

Elective non-cardiac surgery (NCS) should optimally be delayed one year after implantation of a drug-eluting stent (DES). Dual antiplatelet therapy or at least aspirin is recommended to be continued considering the relative risk of stent thrombosis especially during the 4 weeks after DES implantation. However, these recommendations were supported by insufficient evidence. We investigated predictors for postoperative major adverse cardiovascular and cerebral event (MACCE) in 1582 patients undergoing non-cardiac surgery after DES implantation. 96 patients (6.1%) developed postoperative MACCE. In the propensity score-matched analysis, aspirin maintenance was not associated with MACCE (odds ratio [OR] 0.78, 95% confidence interval [CI] 0.48–1.27, P = 0.320) and was associated with increased risk of major bleeding (OR 1.84, 95% CI 1.02–3.32, P = 0.044). When patients who underwent NCS within one month after DES implantation were matched with those who underwent NCS thereafter, the risk of MACCE was higher when surgery was done within 30 days after PCI (OR 2.21, 95% CI 1.05–4.66, P = 0.036). Maintenance of aspirin did not decrease MACCE after NCS in patients with DES and only increased the risk of major bleeding. NCS within one month after DES implantation was associated with higher incidence of MACCE. However, prospective trials are required to validate our results.
Subcutaneous white adipocytes express a light sensitive signaling pathway mediated via a melanopsin/TRPC channel axis
Authors: Ondrusova Katarina , Fatehi Mohammad , Barr Amy , Czarnecka Zofia , Long Wentong , Suzuki Kunimasa , Campbell Scott , Philippaert Koenraad , Hubert Matthew , Tredget Edward , Kwan Peter , Touret Nicolas , Wabitsch Martin , Lee Kevin Y. , Light Peter E.
Published: November 2017

Subcutaneous white adipose tissue (scWAT) is the major fat depot in humans and is a central player in regulating whole body metabolism. Skin exposure to UV wavelengths from sunlight is required for Vitamin D synthesis and pigmentation, although it is plausible that longer visible wavelengths that penetrate the skin may regulate scWAT function. In this regard, we discovered a novel blue light-sensitive current in human scWAT that is mediated by melanopsin coupled to transient receptor potential canonical cation channels. This pathway is activated at physiological intensities of light that penetrate the skin on a sunny day. Daily exposure of differentiated adipocytes to blue light resulted in decreased lipid droplet size, increased basal lipolytic rate and alterations in adiponectin and leptin secretion. Our results suggest that scWAT function may be directly under the influence of ambient sunlight exposure and may have important implications for our current understanding of adipocyte biology. (150 words)
A fast approach to detect gene–gene synergy
Authors: Xing Pengwei , Chen Yuan , Gao Jun , Bai Lianyang , Yuan Zheming
Published: November 2017

Selecting informative genes, including individually discriminant genes and synergic genes, from expression data has been useful for medical diagnosis and prognosis. Detecting synergic genes is more difficult than selecting individually discriminant genes. Several efforts have recently been made to detect gene-gene synergies, such as dendrogram-based I(X1; X2; Y) (mutual information), doublets (gene pairs) and MIC(X1; X2; Y) based on the maximal information coefficient. It is unclear whether dendrogram-based I(X1; X2; Y) and doublets can capture synergies efficiently. Although MIC(X1; X2; Y) can capture a wide range of interaction, it has a high computational cost triggered by its 3-D search. In this paper, we developed a simple and fast approach based on abs conversion type (i.e. Z = |X1 − X2|) and t-test, to detect interactions in simulation and real-world datasets. Our results showed that dendrogram-based I(X1; X2; Y) and doublets are helpless for discovering pair-wise gene interactions, our approach can discover typical pair-wise synergic genes efficiently. These synergic genes can reach comparable accuracy to the individually discriminant genes using the same number of genes. Classifier cannot learn well if synergic genes have not been converted properly. Combining individually discriminant and synergic genes can improve the prediction performance.
Persistent inhibition of pore-based cell migration by sub-toxic doses of miuraenamide, an actin filament stabilizer
Authors: Moser Christina , Rüdiger Daniel , Förster Florian , von Blume Julia , Yu Peng , Kuster Bernhard , Kazmaier Uli , Vollmar Angelika M. , Zahler Stefan
Published: November 2017

Opposed to tubulin-binding agents, actin-binding small molecules have not yet become part of clinical tumor treatment, most likely due to the fear of general cytotoxicity. Addressing this problem, we investigated the long-term efficacy of sub-toxic doses of miuraenamide, an actin filament stabilizing natural compound, on tumor cell (SKOV3) migration. No cytotoxic effects or persistent morphological changes occurred at a concentration of miuraenamide of 20 nM. After 72 h treatment with this concentration, nuclear stiffness was increased, causing reduced migration through pores in a Boyden chamber, while cell migration and chemotaxis per se were unaltered. A concomitant time-resolved proteomic approach showed down regulation of a protein cluster after 56 h treatment. This cluster correlated best with the Wnt signaling pathway. A further analysis of the actin associated MRTF/SRF signaling showed a surprising reduction of SRF-regulated proteins. In contrast to acute effects of actin-binding compounds on actin at high concentrations, long-term low-dose treatment elicits much more subtle but still functionally relevant changes beyond simple destruction of the cytoskeleton. These range from biophysical parameters to regulation of protein expression, and may help to better understand the complex biology of actin, as well as to initiate alternative regimes for the testing of actin-targeting drugs.
Linear magnetoelectric effect in göthite, α-FeOOH
Authors: Ter-Oganessian N. V. , Guda A. A. , Sakhnenko V. P.
Published: November 2017

By means of symmetry analysis, density functional theory calculations, and Monte Carlo simulations we show that goethite, α-FeOOH, is a linear magnetoelectric below its Néel temperature TN = 400 K. The experimentally observed magnetic field induced spin-flop phase transition results in either change of direction of electric polarization or its suppression. Estimated value of magnetoelectric coefficient is 0.57 μC · m−2 · T−1. The abundance of goethite in nature makes it arguably the most widespread magnetoelectric material.
Fishing for cures: The alLURE of using zebrafish to develop precision oncology therapies
Authors: Astone Matteo , Dankert Erin N. , Alam Sk. Kayum , Hoeppner Luke H.
Published: November 2017

Zebrafish have proven to be a valuable model to study human cancer biology with the ultimate aim of developing new therapies. Danio rerio are amenable to in vivo imaging, high-throughput drug screening, mutagenesis, and transgenesis, and they share histological and genetic similarities with Homo sapiens. The significance of zebrafish in the field of precision oncology is rapidly emerging. Indeed, modeling cancer in zebrafish has already been used to identify tumor biomarkers, define therapeutic targets and provide an in vivo platform for drug discovery. New zebrafish studies are starting to pave the way to direct individualized clinical applications. Patient-derived cancer cell xenograft models have demonstrated the feasibility of using zebrafish as a real-time avatar of prognosis and drug response to identify the most ideal therapy for an individual patient. Genetic cancer modeling in zebrafish, now facilitated by rapidly evolving genome editing techniques, represents another innovative approach to recapitulate human oncogenesis and develop individualized treatments. Utilizing zebrafish to design customizable precision therapies will improve the clinical outcome of patients afflicted with cancer.
Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project
Authors: de Hoogt Ronald , Estrada Marta F. , Vidic Suzana , Davies Emma J. , Osswald Annika , Barbier Michael , Santo Vítor E. , Gjerde Kjersti , van Zoggel Hanneke J. A. A. , Blom Sami , Dong Meng , Närhi Katja , Boghaert Erwin , Brito Catarina , Chong Yolanda , Sommergruber Wolfgang , van der Kuip Heiko , van Weerden Wytske M. , Verschuren Emmy W. , Hickman John , Graeser Ralph
Published: November 2017

Two-dimensional (2D) culture of cancer cells in vitro does not recapitulate the three-dimensional (3D) architecture, heterogeneity and complexity of human tumors. More representative models are required that better reflect key aspects of tumor biology. These are essential studies of cancer biology and immunology as well as for target validation and drug discovery. The Innovative Medicines Initiative (IMI) consortium PREDECT (www.predect.eu) characterized in vitro models of three solid tumor types with the goal to capture elements of tumor complexity and heterogeneity. 2D culture and 3D mono- and stromal co-cultures of increasing complexity, and precision-cut tumor slice models were established. Robust protocols for the generation of these platforms are described. Tissue microarrays were prepared from all the models, permitting immunohistochemical analysis of individual cells, capturing heterogeneity. 3D cultures were also characterized using image analysis. Detailed step-by-step protocols, exemplary datasets from the 2D, 3D, and slice models, and refined analytical methods were established and are presented.
Making Maquette Models of Bioenergetic Structures
Authors: Moser Christopher C. , Ennist Nathan M. , Mancini Joshua A. , Dutton P. L.
Published: November 2017

A practical understanding of first-principles directed protein folding in de novo protein design and the factors that control intraprotein electron tunnelling in both natural and artificial proteins allows the planned design of artificial counterparts of natural bioenergetic proteins. Such designs allow reverse engineering of natural proteins to separate out protein elements that are important for function from those that are remnants of the legacy of evolution. Furthermore, these practical understandings allow us to go beyond natural protein designs that are dedicated to natural cellular needs, to engineer robust novel electron-transfer systems directed instead towards human needs such as solar energy trapping in renewable fuels.
Structure and Function of Respiratory Complex I
Authors: Zickermann Volker
Published: November 2017

Proton-pumping NADH : ubiquinone oxidoreductase (respiratory complex I) is a very large and intricate membrane protein complex with a key role in aerobic energy metabolism. Complex I dysfunction causes a number of hereditary and degenerative disorders. The enzyme complex comprises fourteen central subunits that are conserved from bacteria to humans; some 30 additional accessory subunits are typically found in complex I from eukaryotes. The structure of complex I was determined by X-ray crystallography and electron microscopy. The central subunits can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. Electron transfer and proton translocation are spatially separated and the ubiquinone reduction site is found in the hydrophilic peripheral arm of the enzyme complex. Functional studies, structure determination and computational approaches have tremendously advanced our understanding of redox-linked proton translocation by respiratory complex I. However, molecular details and even fundamental issues of the coupling mechanism remain unresolved or speculative. This review discusses the structural basis of current mechanistic models.
Coupling Hydride Transfer to Proton Pumping: the Swiveling Mechanism of Transhydrogenase
Authors: Hong Sangjin , Leung Josephine H. , Sun Chang , Mahinthichichan Paween , Schurig-Briccio Lici , Padyatti Pius S. , Gennis Robert B.
Published: November 2017

The membrane-bound nicotinamide nucleotide transhydrogenase is a key enzyme for the maintenance of metabolic balance in mammalian cells as well as in many bacteria. The enzyme resides in the mitochondrial inner membrane in eukaryotic cells or the cytoplasmic membrane in bacteria. Under normal physiological conditions, the transhydrogenase utilizes the proton motive force to drive hydride transfer from NADH to NADP+, thus generating NADPH. Among other functions, NADPH is critical for the cellular defense against reactive oxygen species. Although not the only source of NADPH, the transhydrogenase is often important, depending on cell type and physiological state. People with the most severe mutations in the Nnt gene, encoding transhydrogenase, suffer from familial glucocorticoid deficiency. Recent X-ray structures of the transhydrogenase from the hyperthermophilic bacterium Thermus thermophilus have provided key insights into how this enzyme couples proton flux across the membrane to hydride transfer. The central hypothesis from these studies focuses on the proposal that large motions of the NADP(H) binding domain (dIII), swiveling between alternating states during the catalytic cycle, are responsible for gating the proton channel in response to the redox state of bound NADP+/NADPH.
Life and Death of Cytochrome c Oxidase: Influence of Subunit III on the D pathway, Proton Backflow and Suicide Inactivation
Authors: Ferguson-Miller Shelagh , Hosler Jonathan
Published: November 2017

The two most conserved subunits of the catalytic core of cytochrome c oxidase (CcO) are subunits I and III. Although equally conserved, subunit III contains no redox centers and can be removed from CcO without substantial loss of activity. Progress in deciphering its elusive function is detailed in this chapter, including evidence for its role in modulating the pH dependence of CcO activity, preventing turnover-based suicide inactivation of CcO, increasing the efficiency of proton pumping, enhancing proton backflow, providing antenna residues for proton uptake and facilitating the entry of oxygen.
Structure, Mechanism and Regulation of ATP Synthases
Authors: Walker John E.
Published: November 2017

The ATP synthases, also known as F-ATPases or F1Fo-ATPases, are multisubunit enzyme complexes found in energy transducing membranes in eubacteria, chloroplasts and mitochondria. They make ATP from ADP and phosphate under aerobic conditions using a proton-motive force, Δp, generated by respiration or photosynthesis, as a source of energy. The ATP synthases from these diverse sources have many common conserved structural features and mechanistic similarities, and all the enzymes operate by a rotary mechanism, where a rotor driven by the transmembrane proton motive force, transmits energy mechanically into the catalytic sites to drive the binding of substrates, and the formation and release of ATP. However, as enzymes from a wider range of species become investigated, significant differences are being uncovered, most notably in the energy cost of making each ATP molecule, and in the ways that the enzymes from various sources are regulated. Differences between the structures and regulatory mechanisms of the human enzyme, and the ATP synthases in bacterial and fungal pathogens, once understood in molecular detail, have the potential to be exploited systematically in the development of new drugs to combat antibiotic resistance in these microbes.
Carbene-catalyzed LUMO activation of alkyne esters for access to functional pyridines
Authors: Mou Chengli , Wu Jichang , Huang Zhijian , Sun Jun , Jin Zhichao , Chi Yonggui Robin
Published: November 2017

A carbene-catalyzed activation of alkyne ester for quick access to functional pyridines is reported. The reaction involves a previously unexplored unsaturated acyl azolium intermediate bearing a carbon–carbon triple bond that shall exhibit rich chemical reactivities.
Microscopic understanding of the conformational features of a protein–DNA complex
Authors: Mondal Sandip , Chakraborty Kaushik , Bandyopadhyay Sanjoy
Published: November 2017

Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.
Analysis of dispersive interactions at polymer/TiAlN interfaces by means of dynamic force spectroscopy
Authors: Wiesing M. , de los Arcos T. , Gebhard M. , Devi A. , Grundmeier G.
Published: November 2017

Dispersion forces due to polarizable subsurface layers govern TiAlN/polymer interactions and decrease by 50% when oxidizing TiAlN to form TiAlO.
Retraction: The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation
Authors: Mohrmann Hendrik , Dragelj Jovan , Baserga Federico , Knapp Ernst-Walter , Stripp Sven T. , Heberle Joachim
Published: November 2017

Retraction of ‘The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation’ by Hendrik Mohrmann et al., Phys. Chem. Chem. Phys., 2017, DOI: 10.1039/c7cp06480b.
Low temperature growth of gallium oxide thin films via plasma enhanced atomic layer deposition
Authors: O'Donoghue Richard , Rechmann Julian , Aghaee Morteza , Rogalla Detlef , Becker Hans-Werner , Creatore Mariadriana , Wieck Andreas Dirk , Devi Anjana
Published: November 2017

Lowest temperature to date for the ALD growth of Ga2O3 thin films and the 2nd highest GPC regarding Ga2O3 ALD.
Unexpected catalytic performance of Fe–M–C (M = N, P, and S) electrocatalysts towards oxygen reduction reaction: surface heteroatoms boost the activity of Fe2M/graphene nanocomposites
Authors: Chen Yan-Ru , Wang Qin , Bai Xue , Yan Zhen , Ning Yunkun , He Feng , Wu Zhijian , Zhang Jun
Published: November 2017

Heteroatoms-multi-doped Fe2M/graphene hybrids catalysts are fabricatedviaa facile strategy as highly efficient electrocatalysts toward the oxygen reduction reaction.
A unique non-interpenetrated open-framework chalcogenide with a large cavity
Authors: Luo Min , Yang Huajun , Wang Wei , Xue Chaozhuang , Wu Tao
Published: November 2017

A unique non-interpenetrated open-framework chalcogenide with a large cavity was reported.
Predicting the frequency of extreme air quality events
Authors: Brown Richard J. C. , Harris Peter M.
Published: November 2017

A new method for predicting the frequency of extreme air quality events is proposed.
Accurate density functional theory (DFT) protocol for screening and designing chain transfer and branching agents for LDPE systems
Authors: Konstantinov Ivan , Ewart Sean , Brown Hayley , Eddy Christopher , Mendenhall Jonathan , Munjal Sarat
Published: November 2017

This work emphasizes the importance of considering multiple reaction pathways when estimating the rate parameters for free radical polymerization using DFT.
Human ability to discriminate surface chemistry by touch
Authors: Carpenter Cody W. , Dhong Charles , Root Nicholas B. , Rodriquez Daniel , Abdo Emily E. , Skelil Kyle , Alkhadra Mohammad A. , Ramírez Julian , Ramachandran Vilayanur S. , Lipomi Darren J.
Published: November 2017

Human ability to discriminate between hydrophilic and hydrophobic surfaces is attributed to differences in vibrational frequencies generated while sliding at particular velocities and normal forces.