bluuebunny/crossref_metadata_2025 huggingface dataset:
Ceramide-induced BOK promotes mitochondrial fission in preeclampsia
Authors: Ausman Jonathan , Abbade Joelcio , Ermini Leonardo , Farrell Abby , Tagliaferro Andrea , Post Martin , Caniggia Isabella
Published: February 2018

Mitochondria are in a constant balance of fusing and dividing in response to cellular cues. Fusion creates healthy mitochondria, whereas fission results in removal of non-functional organelles. Changes in mitochondrial dynamics typify several human diseases. However, the contribution of mitochondrial dynamics to preeclampsia, a hypertensive disorder of pregnancy characterized by placental cell autophagy and death, remains unknown. Herein, we show that the mitochondrial dynamic balance in preeclamptic placentae is tilted toward fission (increased DRP1 expression/activation and decreased OPA1 expression). Increased phosphorylation of DRP1 (p-DRP1) in mitochondrial isolates from preeclamptic placentae and transmission electron microscopy corroborated augmented mitochondrial fragmentation in cytotrophoblast cells of PE placentae. Increased fission was accompanied by build-up of ceramides (CERs) in mitochondria from preeclamptic placentae relative to controls. Treatment of human choriocarcinoma JEG3 cells and primary isolated cytrophoblast cells with CER 16:0 enhanced mitochondrial fission. Loss- and gain-of-function experiments showed that Bcl-2 member BOK, whose expression is increased by CER, positively regulated p-DRP1/DRP1 and MFN2 expression, and localized mitochondrial fission events to the ER/MAM compartments. We also identified that the BH3 and transmembrane domains of BOK were vital for BOK regulation of fission. Moreover, we found that full-length PTEN-induced putative kinase 1 (PINK1) and Parkin, were elevated in mitochondria from PE placentae, implicating mitophagy as the process that degrades excess mitochondria fragments produced from CER/BOK-induced fission in preeclampsia. In summary, our study uncovered a novel CER/BOK-induced regulation of mitochondrial fission and its functional consequence for heightened trophoblast cell autophagy in preeclampsia.
Magnolol restores the activity of meropenem against NDM-1-producing Escherichia coli by inhibiting the activity of metallo-beta-lactamase
Authors: Liu Shui , Zhou Yonglin , Niu Xiaodi , Wang Tingting , Li Jiyun , Liu Zhongjie , Wang Jianfeng , Tang Shusheng , Wang Yang , Deng Xuming
Published: February 2018

The emergence of plasmid-mediated New Delhi metallo-β-lactamase-1 (NDM-1) in carbapenem-resistant Gram-negative pathogens is an increasing clinical threat. Here we report the discovery of an NDM-1 inhibitor, magnolol, through enzyme inhibition screening. We showed that magnolol significantly inhibited NDM enzyme activity (IC50 = 6.47 µg/mL), and it restored the activity of meropenem against Escherichia coli ZC-YN3, an NDM-1-producing E. coli isolate, in in vitro antibacterial activity assays. Magnolol lacked direct antibacterial activity, but compared with meropenem alone, it reduced the MICs of meropenem against E. coli ZC-YN3 by 4-fold and killed almost all the bacteria within 3 h. Molecular modeling and a mutational analysis demonstrated that magnolol binds directly to the catalytic pocket (residues 110 to 200) of NDM-1, thereby blocking the binding of the substrate to NDM-1 and leading to its inactivation. Our results demonstrate that the combination of magnolol and meropenem may have the potential to treat infections caused by NDM-1-positive, carbapenem-resistant Gram-negative pathogens.
Mycobacterium fortuitum-induced ER-Mitochondrial calcium dynamics promotes calpain/caspase-12/caspase-9 mediated apoptosis in fish macrophages
Authors: Datta Debika , Khatri Preeti , Singh Ambika , Saha Dhira Rani , Verma Gaurav , Raman Rajagopal , Mazumder Shibnath
Published: February 2018

Mycobacterium fortuitum is a natural fish pathogen. It induces apoptosis in headkidney macrophages (HKM) of catfish, Clarias sp though the mechanism remains largely unknown. We observed M. fortuitum triggers calcium (Ca2+) insult in the sub-cellular compartments which elicits pro-apototic ER-stress factor CHOP. Alleviating ER-stress inhibited CHOP and attenuated HKM apoptosis implicating ER-stress in the pathogenesis of M. fortuitum. ER-stress promoted calpain activation and silencing the protease inhibited caspase-12 activation. The study documents the primal role of calpain/caspase-12 axis on caspase-9 activation in M. fortuitum-pathogenesis. Mobilization of Ca2+ from ER to mitochondria led to increased mitochondrial Ca2+ (Ca2+)m load,, mitochondrial permeability transition (MPT) pore opening, altered mitochondrial membrane potential (ΔΨm) and cytochrome c release eventually activating the caspase-9/-3 cascade. Ultra-structural studies revealed close apposition of ER and mitochondria and pre-treatment with (Ca2+)m-uniporter (MUP) blocker ruthenium red, reduced Ca2+ overload suggesting (Ca2+)m fluxes are MUP-driven and the ER-mitochondria tethering orchestrates the process. This is the first report implicating role of sub-cellular Ca2+ in the pathogenesis of M. fortuitum. We summarize, the dynamics of Ca2+ in sub-cellular compartments incites ER-stress and mitochondrial dysfunction, leading to activation of pro-apoptotic calpain/caspase-12/caspase-9 axis in M. fortuitum-infected HKM.
A dual mechanism promotes switching of the Stormorken STIM1 R304W mutant into the activated state
Authors: Fahrner Marc , Stadlbauer Michael , Muik Martin , Rathner Petr , Stathopulos Peter , Ikura Mitsu , Müller Norbert , Romanin Christoph
Published: February 2018

STIM1 and Orai1 are key components of the Ca2+-release activated Ca2+ (CRAC) current. Orai1, which represents the subunit forming the CRAC channel complex, is activated by the ER resident Ca2+ sensor STIM1. The genetically inherited Stormorken syndrome disease has been associated with the STIM1 single point R304W mutant. The resulting constitutive activation of Orai1 mainly involves the CRAC-activating domain CAD/SOAR of STIM1, the exposure of which is regulated by the molecular interplay between three cytosolic STIM1 coiled-coil (CC) domains. Here we present a dual mechanism by which STIM1 R304W attains the pathophysiological, constitutive activity eliciting the Stormorken syndrome. The R304W mutation induces a helical elongation within the CC1 domain, which together with an increased CC1 homomerization, destabilize the resting state of STIM1. This culminates, even in the absence of store depletion, in structural extension and CAD/SOAR exposure of STIM1 R304W leading to constitutive CRAC channel activation and Stormorken disease.
Agrochemicals increase risk of human schistosomiasis by supporting higher densities of intermediate hosts
Authors: Halstead Neal T. , Hoover Christopher M. , Arakala Arathi , Civitello David J. , De Leo Giulio A. , Gambhir Manoj , Johnson Steve A. , Jouanard Nicolas , Loerns Kristin A. , McMahon Taegan A. , Ndione Raphael A. , Nguyen Karena , Raffel Thomas R. , Remais Justin V. , Riveau Gilles , Sokolow Susanne H. , Rohr Jason R.
Published: February 2018

Schistosomiasis is a snail-borne parasitic disease that ranks among the most important water-based diseases of humans in developing countries. Increased prevalence and spread of human schistosomiasis to non-endemic areas has been consistently linked with water resource management related to agricultural expansion. However, the role of agrochemical pollution in human schistosome transmission remains unexplored, despite strong evidence of agrochemicals increasing snail-borne diseases of wildlife and a projected 2- to 5-fold increase in global agrochemical use by 2050. Using a field mesocosm experiment, we show that environmentally relevant concentrations of fertilizer, a herbicide, and an insecticide, individually and as mixtures, increase densities of schistosome-infected snails by increasing the algae snails eat and decreasing densities of snail predators. Epidemiological models indicate that these agrochemical effects can increase transmission of schistosomes. Identifying agricultural practices or agrochemicals that minimize disease risk will be critical to meeting growing food demands while improving human wellbeing.
How ligand binds to the type 1 insulin-like growth factor receptor
Authors: Xu Yibin , Kong Geoffrey K.-W. , Menting John G. , Margetts Mai B. , Delaine Carlie A. , Jenkin Lauren M. , Kiselyov Vladislav V. , De Meyts Pierre , Forbes Briony E. , Lawrence Michael C.
Published: February 2018

Human type 1 insulin-like growth factor receptor is a homodimeric receptor tyrosine kinase that signals into pathways directing normal cellular growth, differentiation and proliferation, with aberrant signalling implicated in cancer. Insulin-like growth factor binding is understood to relax conformational restraints within the homodimer, initiating transphosphorylation of the tyrosine kinase domains. However, no three-dimensional structures exist for the receptor ectodomain to inform atomic-level understanding of these events. Here, we present crystal structures of the ectodomain in apo form and in complex with insulin-like growth factor I, the latter obtained by crystal soaking. These structures not only provide a wealth of detail of the growth factor interaction with the receptor’s primary ligand-binding site but also indicate that ligand binding separates receptor domains by a mechanism of induced fit. Our findings are of importance to the design of agents targeting IGF-1R and its partner protein, the human insulin receptor.
Cardiolipin exposure on the outer mitochondrial membrane modulates α-synuclein
Authors: Ryan Tammy , Bamm Vladimir V. , Stykel Morgan G. , Coackley Carla L. , Humphries Kayla M. , Jamieson-Williams Rhiannon , Ambasudhan Rajesh , Mosser Dick D. , Lipton Stuart A. , Harauz George , Ryan Scott D.
Published: February 2018

Neuronal loss in Parkinson’s disease (PD) is associated with aberrant mitochondrial function and impaired proteostasis. Identifying the mechanisms that link these pathologies is critical to furthering our understanding of PD pathogenesis. Using human pluripotent stem cells (hPSCs) that allow comparison of cells expressing mutant SNCA (encoding α-synuclein (α-syn)) with isogenic controls, or SNCA-transgenic mice, we show that SNCA-mutant neurons display fragmented mitochondria and accumulate α-syn deposits that cluster to mitochondrial membranes in response to exposure of cardiolipin on the mitochondrial surface. Whereas exposed cardiolipin specifically binds to and facilitates refolding of α-syn fibrils, prolonged cardiolipin exposure in SNCA-mutants initiates recruitment of LC3 to the mitochondria and mitophagy. Moreover, we find that co-culture of SNCA-mutant neurons with their isogenic controls results in transmission of α-syn pathology coincident with mitochondrial pathology in control neurons. Transmission of pathology is effectively blocked using an anti-α-syn monoclonal antibody (mAb), consistent with cell-to-cell seeding of α-syn.
Clonally diverse CD38+HLA-DR+CD8+ T cells persist during fatal H7N9 disease
Authors: Wang Zhongfang , Zhu Lingyan , Nguyen Thi H. O. , Wan Yanmin , Sant Sneha , Quiñones-Parra Sergio M. , Crawford Jeremy Chase , Eltahla Auda A. , Rizzetto Simone , Bull Rowena A. , Qiu Chenli , Koutsakos Marios , Clemens E. Bridie , Loh Liyen , Chen Tianyue , Liu Lu , Cao Pengxing , Ren Yanqin , Kedzierski Lukasz , Kotsimbos Tom , McCaw James M. , La Gruta Nicole L. , Turner Stephen J. , Cheng Allen C. , Luciani Fabio , Zhang Xiaoyan , Doherty Peter C. , Thomas Paul G. , Xu Jianqing , Kedzierska Katherine
Published: February 2018

Severe influenza A virus (IAV) infection is associated with immune dysfunction. Here, we show circulating CD8+ T-cell profiles from patients hospitalized with avian H7N9, seasonal IAV, and influenza vaccinees. Patient survival reflects an early, transient prevalence of highly activated CD38+HLA-DR+PD-1+ CD8+ T cells, whereas the prolonged persistence of this set is found in ultimately fatal cases. Single-cell T cell receptor (TCR)-αβ analyses of activated CD38+HLA-DR+CD8+ T cells show similar TCRαβ diversity but differential clonal expansion kinetics in surviving and fatal H7N9 patients. Delayed clonal expansion associated with an early dichotomy at a transcriptome level (as detected by single-cell RNAseq) is found in CD38+HLA-DR+CD8+ T cells from patients who succumbed to the disease, suggesting a divergent differentiation pathway of CD38+HLA-DR+CD8+ T cells from the outset during fatal disease. Our study proposes that effective expansion of cross-reactive influenza-specific TCRαβ clonotypes with appropriate transcriptome signatures is needed for early protection against severe influenza disease.
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
Authors: Numanagić Ibrahim , Malikić Salem , Ford Michael , Qin Xiang , Toji Lorraine , Radovich Milan , Skaar Todd C. , Pratt Victoria M. , Berger Bonnie , Scherer Steve , Sahinalp S. Cenk
Published: February 2018

High-throughput sequencing provides the means to determine the allelic decomposition for any gene of interest—the number of copies and the exact sequence content of each copy of a gene. Although many clinically and functionally important genes are highly polymorphic and have undergone structural alterations, no high-throughput sequencing data analysis tool has yet been designed to effectively solve the full allelic decomposition problem. Here we introduce a combinatorial optimization framework that successfully resolves this challenging problem, including for genes with structural alterations. We provide an associated computational tool Aldy that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data. For a large diverse sequencing data set, Aldy identifies multiple rare and novel alleles for several important pharmacogenes, significantly improving upon the accuracy and utility of current genotyping assays. As more data sets become available, we expect Aldy to become an essential component of genotyping toolkits.
High spin cycles: topping the spin record for a single molecule verging on quantum criticality
Authors: Baniodeh Amer , Magnani Nicola , Lan Yanhua , Buth Gernot , Anson Christopher E. , Richter Johannes , Affronte Marco , Schnack Jürgen , Powell Annie K.
Published: February 2018

The cyclisation of a short chain into a ring provides fascinating scenarios in terms of transforming a finite array of spins into a quasi-infinite structure. If frustration is present, theory predicts interesting quantum critical points, where the ground state and thus low-temperature properties of a material change drastically upon even a small variation of appropriate external parameters. This can be visualised as achieving a very high and pointed summit where the way down has an infinity of possibilities, which by any parameter change will be rapidly chosen, in order to reach the final ground state. Here we report a mixed 3d/4f cyclic coordination cluster that turns out to be very near or even at such a quantum critical point. It has a ground state spin of S = 60, the largest ever observed for a molecule (120 times that of a single electron). [Fe10Gd10(Me-tea)10(Me-teaH)10(NO3)10]·20MeCN forms a nano-torus with alternating gadolinium and iron ions with a nearest neighbour Fe–Gd coupling and a frustrating next-nearest neighbour Fe–Fe coupling. Such a spin arrangement corresponds to a cyclic delta or saw-tooth chain, which can exhibit unusual frustration effects. In the present case, the quantum critical point bears a ‘flatland’ of tens of thousands of energetically degenerate states between which transitions are possible at no energy costs with profound caloric consequences. Entropy-wise the energy flatland translates into the pointed summit overlooking the entropy landscape. Going downhill several target states can be reached depending on the applied physical procedure which offers new prospects for addressability.
Indomethacin Disrupts Autophagic Flux by Inducing Lysosomal Dysfunction in Gastric Cancer Cells and Increases Their Sensitivity to Cytotoxic Drugs
Authors: Vallecillo-Hernández Jorge , Barrachina Maria Dolores , Ortiz-Masiá Dolores , Coll Sandra , Esplugues Juan Vicente , Calatayud Sara , Hernández Carlos
Published: February 2018

NSAIDs inhibit tumorigenesis in gastrointestinal tissues and have been proposed as coadjuvant agents to chemotherapy. The ability of cancer epithelial cells to adapt to the tumour environment and to resist cytotoxic agents seems to depend on rescue mechanisms such as autophagy. In the present study we aimed to determine whether an NSAID with sensitizing properties such as indomethacin modulates autophagy in gastric cancer epithelial cells. We observed that indomethacin causes lysosomal dysfunction in AGS cells and promotes the accumulation of autophagy substrates without altering mTOR activity. Indomethacin enhanced the inhibitory effects of the lysosomotropic agent chloroquine on lysosome activity and autophagy, but lacked any effect when both functions were maximally reduced with another lysosome inhibitor (bafilomycin B1). Indomethacin, alone and in combination with chloroquine, also hindered the autophagic flux stimulated by the antineoplastic drug oxaliplatin and enhanced its toxic effect, increasing the rate of apoptosis/necrosis and undermining cell viability. In summary, our results indicate that indomethacin disrupts autophagic flux by disturbing the normal functioning of lysosomes and, by doing so, increases the sensitivity of gastric cancer cells to cytotoxic agents, an effect that could be used to overcome cancer cell resistance to antineoplastic regimes.
Skew in ovarian activation depends on domicile size in phyllode-glueing thrips
Authors: Gilbert J. D. J. , Wells A. , Simpson S. J.
Published: February 2018

Costs and benefits of group living are a fundamental topic in behavioural ecology. Resource availability affects individuals’ breeding prospects alone and in groups, as well as how reproduction is distributed within groups (“reproductive skew”). Here, in facultatively social thrips, we provide correlational evidence that breeding resources are associated with (1) whether solitary or social living is favoured, and (2) the degree of ovarian skew.Dunatothrips aneurae(Thysanoptera, Phlaeothripidae) cooperatively build silk “domiciles” on Australian Acacias, feeding exclusively from internal phyllode surfaces.Per capitaproductivity scaled differently with group size depending on domicile volume — females in small domiciles did better alone than in groups, whereas in large domiciles single and group-nesting females did equally well. Ovarian dissections revealed that in small domiciles some females were nonreproductive, indicating ovarian (i.e. reproductive) skew. Skew increased as domicile size decreased and group size increased. Breeders had smaller oocyte volume in smaller domiciles, especially those containing nonreproductives. These findings suggest group formation and reproductive skew inD. aneuraemay be influenced by reproductive competition for breeding resources. Nonreproductive females in small domiciles may be reproductively suppressed, subfertile, or accumulating resources to reproduce.
Oligonucleotide conjugated multi-functional adeno-associated viruses
Authors: Katrekar Dhruva , Moreno Ana M. , Chen Genghao , Worlikar Atharv , Mali Prashant
Published: February 2018

Recombinant adeno-associated viruses (AAVs) are among the most commonly used vehicles for in vivo gene delivery. However, their tropism is limited, and additionally their efficacy can be negatively affected by prevalence of neutralizing antibodies in sera. Methodologies to systematically engineer AAV capsid properties would thus be of great relevance. In this regard, we develop here multi-functional AAVs by engineering precision tethering of oligonucleotides onto the AAV surface, and thereby enabling a spectrum of nucleic-acid programmable functionalities. Towards this, we engineered genetically encoded incorporation of unnatural amino acids (UAA) bearing bio-orthogonal chemical handles onto capsid proteins. Via these we enabled site-specific coupling of oligonucleotides onto the AAV capsid surface using facile click chemistry. The resulting oligo-AAVs could be sequence specifically labeled, and also patterned in 2D using DNA array substrates. Additionally, we utilized these oligo conjugations to engineer viral shielding by lipid-based cloaks that efficaciously protected the AAV particles from neutralizing serum. We confirmed these ‘cloaked AAVs’ retained full functionality via their ability to transduce a range of cell types, and also enable robust delivery of CRISPR-Cas9 effectors. Taken together, we anticipate this programmable oligo-AAV system will have broad utility in synthetic biology and AAV engineering applications.
Increased mechanical loading through controlled swimming exercise induces bone formation and mineralization in adult zebrafish
Authors: Suniaga Santiago , Rolvien Tim , vom Scheidt Annika , Fiedler Imke A. K. , Bale Hrishikesh A. , Huysseune Ann , Witten P. Eckhard , Amling Michael , Busse Björn
Published: February 2018

Exercise promotes gain in bone mass through adaptive responses of the vertebrate skeleton. This mechanism counteracts age- and disease-related skeletal degradation, but remains to be fully understood. In life sciences, zebrafish emerged as a vertebrate model that can provide new insights into the complex mechanisms governing bone quality. To test the hypothesis that musculoskeletal exercise induces bone adaptation in adult zebrafish and to characterize bone reorganization, animals were subjected to increased physical exercise for four weeks in a swim tunnel experiment. Cellular, structural and compositional changes of loaded vertebrae were quantified using integrated high-resolution analyses. Exercise triggered rapid bone adaptation with substantial increases in bone-forming osteoblasts, bone volume and mineralization. Clearly, modeling processes in zebrafish bone resemble processes in human bone. This study highlights how exercise experiments in adult zebrafish foster in-depth insight into aging-related bone diseases and can thus catalyze the search for appropriate prevention and new treatment options.
Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme
Authors: Gonska Nathalie , Young David , Yuki Riki , Okamoto Takuya , Hisano Tamao , Antonyuk Svetlana , Hasnain S. Samar , Muramoto Kazumasa , Shiro Yoshitsugu , Tosha Takehiko , Ädelroth Pia
Published: February 2018

Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O2-reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 Å crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.
Activation of AMPK inhibits TGF-β1-induced airway smooth muscle cells proliferation and its potential mechanisms
Authors: Pan Yilin , Liu Lu , Li Shaojun , Wang Ke , Ke Rui , Shi Wenhua , Wang Jian , Yan Xin , Zhang Qianqian , Wang Qingting , Chai Limin , Xie Xinming , Li Manxiang
Published: February 2018

The aims of the present study were to examine signaling mechanisms underlying transforming growth factor β1 (TGF-β1)-induced airway smooth muscle cells (ASMCs) proliferation and to determine the effect of adenosine monophosphate-activated protein kinase (AMPK) activation on TGF-β1-induced ASMCs proliferation and its potential mechanisms. TGF-β1 reduced microRNA-206 (miR-206) level by activating Smad2/3, and this in turn up-regulated histone deacetylase 4 (HDAC4) and consequently increased cyclin D1 protein leading to ASMCs proliferation. Prior incubation of ASMCs with metformin induced AMPK activation and blocked TGF-β1-induced cell proliferation. Activation of AMPK slightly attenuated TGF-β1-induced miR-206 suppression, but dramatically suppressed TGF-β1-caused HDAC4 up-expression and significantly increased HDAC4 phosphorylation finally leading to reduction of up-regulated cyclin D1 protein expression. Our study suggests that activation of AMPK modulates miR-206/HDAC4/cyclin D1 signaling pathway, particularly targeting on HDAC4, to suppress ASMCs proliferation and therefore has a potential value in the prevention and treatment of asthma by alleviating airway remodeling.
A rice class-XIV kinesin enters the nucleus in response to cold
Authors: Xu Xiaolu , Walter Wilhelm J. , Liu Qiong , Machens Isabel , Nick Peter
Published: February 2018

Higher plants possess a large number of kinesins, but lack the minus-end directed dynein motors. However, the kinesin class XIV has strongly expanded, and minus-end directed motors from this class may have taken over functions of cytoplasmic dyneins. In this study, we address the functional aspects of a novel rice homologue of the Arabidopsis class-XIV kinesins ATK1 and ATK5. Since a loss-of-function rice mutant of this kinesin is not viable, the function was studied in tobacco BY-2 as heterologous system. OsDLK-GFP stably expressed in BY-2 cells decorates cortical microtubules, but also can shift into the nucleus of interphase cells. Because of this peculiar localisation, we coined the name Dual Localisation Kinesin (DLK). The nuclear import of this protein is strongly and reversibly promoted in response to cold. During mitosis, OsDLK is repartitioned between spindle and phragmoplast. Motility assays in vitro using show that OsDLK can convey mutual sliding of microtubules and moves at a velocity comparable to other class-XIV kinesins. When tobacco cells overexpressing OsDLK are synchronised, they exhibit a delayed entry into metaphase, while the later phases of mitosis are accelerated. The data are discussed in relation to additional functions of this kinesin type, beyond their transport along microtubules.
A comparative analysis of surface and bulk contributions to second-harmonic generation in centrosymmetric nanoparticles
Authors: Timbrell Daniel , You Jian Wei , Kivshar Yuri S. , Panoiu Nicolae C.
Published: February 2018

Second-harmonic generation (SHG) from nanoparticles made of centrosymmetric materials provides an effective tool to characterize many important properties of photonic structures at the subwavelength scale. Here we study the relative contribution of surface and bulk effects to SHG for plasmonic and dielectric nanostructures made of centrosymmetric materials in both dispersive and non-dispersive regimes. Our calculations of the far-fields generated by the nonlinear surface and bulk currents reveal that the size of the nanoparticle strongly influences the amount and relative contributions of the surface and bulk SHG effects. Importantly, our study reveals that, whereas for plasmonic nanoparticles the surface contribution is always dominant, the bulk and surface SHG effects can become comparable for dielectric nanoparticles, and thus they both should be taken into account when analyzing nonlinear optical properties of all-dielectric nanostructures.
Elastic net regularized regression for time-series analysis of plasma metabolome stability under sub-optimal freezing condition
Authors: Gonzales Gerard Bryan , De Saeger Sarah
Published: February 2018

In this paper, the stability of the plasma metabolome at −20 °C for up to 30 days was evaluated using liquid chromatography-high resolution mass spectrometric metabolomics analysis. To follow the time-series deterioration of the plasma metabolome, the use of an elastic net regularized regression model for the prediction of storage time at −20 °C based on the plasma metabolomic profile, and the selection and ranking of metabolites with high temporal changes was demonstrated using the glmnet package in R. Out of 1229 (positive mode) and 1483 (negative mode) metabolite features, the elastic net model extracted 32 metabolites of interest in both positive and negative modes. L-gamma-glutamyl-L-(iso)leucine (tentative identification) was found to have the highest time-dependent change and significantly increased proportionally to the storage time of plasma at −20 °C (R2 = 0.6378 [positive mode], R2 = 0.7893 [negative mode], p-value < 0.00001). Based on the temporal profiles of the extracted metabolites by the model, results show only minimal deterioration of the plasma metabolome at −20 °C up to 1 month. However, majority of the changes appeared at around 12–15 days of storage. This allows scientists to better plan logistics and storage strategies for samples obtained from low-resource settings, where −80 °C storage is not guaranteed.
Inhibition of Heat Shock proteins HSP90 and HSP70 induce oxidative stress, suppressing cotton fiber development
Authors: Sable Anshulika , Rai Krishan M. , Choudhary Amit , Yadav Vikash K. , Agarwal Sudhir K. , Sawant Samir V.
Published: February 2018

Cotton fiber is a specialized unicellular structure useful for the study of cellular differentiation and development. Heat shock proteins (HSPs) have been shown to be involved in various developmental processes. Microarray data analysis of five Gossypium hirsutum genotypes revealed high transcript levels of GhHSP90 and GhHSP70 genes at different stages of fiber development, indicating their importance in the process. Further, we identified 26 and 55 members of HSP90 and HSP70 gene families in G. hirsutum. The treatment of specific inhibitors novobiocin (Nov; HSP90) and pifithrin/2-phenylethynesulfonamide (Pif; HSP70) in in-vitro cultured ovules resulted in a fewer number of fiber initials and retardation in fiber elongation. The molecular chaperone assay using bacterially expressed recombinant GhHSP90-7 and GhHSP70-8 proteins further confirmed the specificity of inhibitors. HSP inhibition disturbs the H2O2 balance that leads to the generation of oxidative stress, which consequently results in autophagy in the epidermal layer of the cotton ovule. Transmission electron microscopy (TEM) of inhibitor-treated ovule also corroborates autophagosome formation along with disrupted mitochondrial cristae. The perturbations in transcript profile of HSP inhibited ovules show differential regulation of different stress and fiber development-related genes and pathways. Altogether, our results indicate that HSP90 and HSP70 families play a crucial role in cotton fiber differentiation and development by maintaining cellular homeostasis.
Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
Authors: Dyavar Shetty Ravi , Ye Zhen , Byrareddy Siddappa N. , Scarsi Kimberly K. , Winchester Lee C. , Weinhold Jonathan A. , Fletcher Courtney V. , Podany Anthony T.
Published: February 2018

Quantification of antiretroviral (ARV) drug concentrations in peripheral blood mononuclear cells (PBMCs) and tissue isolated mononuclear cells (TIMCs) from lymph node (LNMC) and rectum (RMC) is an important measure of bio-distribution. Normalization of drug concentrations is critical to represent tissue drug concentrations and to analyze both intra-individual and inter-individual variability in drug distribution. However, a molecular method to normalize intracellular drug concentrations in PBMCs and TIMCs methanol extracts is currently unavailable. In this study, a novel droplet digital PCR (ddPCR) assay was designed to amplify RPP30 gene sequence conserved in human and non-human primates (NHP). Genomic DNA (gDNA) isolated from 70 percent methanol embedded PBMCs and TIMCs was used as ddPCR template to quantitate precise RPP30 copies to derive cell counts. The novel molecular method quantitated RPP30 copies in human and rhesus macaque gDNA templates with greater accuracy and precision than qPCR. RPP30 ddPCR derived cell counts are strongly correlated with automated cytometer based cell counts in PBMC (R = 0.90, p = 0.001 and n = 20); LNMC (R = 0.85 p = 0.0001 and n = 22) and RMC (R = 0.92, p = 0.0001 and n = 20) and achieved comparable normalized drug concentrations. Therefore, the RPP30 ddPCR assay is an important normalization method in drug bio-distribution and pharmacokinetic studies in humans and NHPs.
Targeting Ligand Specificity Linked to Tumor Tissue Topological Heterogeneity via Single-Cell Micro-Pharmacological Modeling
Authors: Karolak Aleksandra , Estrella Veronica C. , Huynh Amanda S. , Chen Tingan , Vagner Josef , Morse David L. , Rejniak Katarzyna A.
Published: February 2018

Targeted therapy has held promise to be a successful anticancer treatment due to its specificity towards tumor cells that express the target receptors. However, not all targeting drugs used in the clinic are equally effective in tumor eradication. To examine which biochemical and biophysical properties of targeted agents are pivotal for their effective distribution inside the tumor and their efficient cellular uptake, we combine mathematical micro-pharmacological modeling with in vivo imaging of targeted human xenograft tumors in SCID mice. The mathematical model calibrated to experimental data was used to explore properties of the targeting ligand (diffusion and affinity) and ligand release schemes (rates and concentrations) with a goal to identify the properties of cells and ligands that enable high receptor saturation. By accounting for heterogeneities typical of in vivo tumors, our model was able to identify cell- and tissue-level barriers to efficient drug uptake. This work provides a base for utilizing experimentally measurable properties of a ligand-targeted agent and patient-specific attributes of the tumor tissue to support the development of novel targeted imaging agents and for improvement in their delivery to individual tumor cells.
Human Epicardial Adipose Tissue cTGF Expression is an Independent Risk Factor for Atrial Fibrillation and Highly Associated with Atrial Fibrosis
Authors: Wang Qing , Xi Wang , Yin Liang , Wang Jing , Shen Hua , Gao Yang , Min Jie , Zhang Yufeng , Wang Zhinong
Published: February 2018

Epicardial adipose tissue (EAT) is associated with the incidence, perpetuation, and recurrence of atrial fibrillation (AF), with elusive underlying mechanisms. We analyzed adipokine expression in samples from 20 patients with sinus rhythm (SR) and 16 with AF. Quantitative real-time PCR showed that connective tissue growth factor (cTGF) expression was significantly higher in EAT than in subcutaneous adipose tissue (SAT) or paracardial adipose tissue (PAT) from patients with AF, and in EAT from patients with SR (P < 0.001). Galectin-3 expression was significantly higher in EAT than in SAT or PAT (P < 0.001), with no significant differences between patients with AF and SR (P > 0.05). Leptin and vaspin expression were lower in EAT than in PAT (P < 0.001). Trichrome staining showed that the fibrosis was much more severe in patients with AF than SR (P < 0.001). We found a linear relationship between cTGF mRNA expression level and collagen volume fraction (y = 1.471x + 27.330, P < 0.001), and logistic regression showed that cTGF level was an independent risk factor for AF (OR 2.369, P = 0.027). In conclusion, highly expressed in EAT, cTGF is associated with atrial fibrosis, and can be an important risk factor for AF.
Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model
Authors: Wang Fuyuan , Meng Jingjing , Zhang Li , Johnson Timothy , Chen Chi , Roy Sabita
Published: February 2018

Opioid analgesics are frequently prescribed in the United States and worldwide. However, serious comorbidities, such as dependence, tolerance, immunosuppression and gastrointestinal disorders limit their long-term use. In the current study, a morphine-murine model was used to investigate the role of the gut microbiome and metabolome as a potential mechanism contributing to the negative consequences associated with opioid use. Results reveal a significant shift in the gut microbiome and metabolome within one day following morphine treatment compared to that observed after placebo. Morphine-induced gut microbial dysbiosis exhibited distinct characteristic signatures, including significant increase in communities associated with pathogenic function, decrease in communities associated with stress tolerance and significant impairment in bile acids and morphine-3-glucuronide/morphine biotransformation in the gut. Moreover, expansion of Enterococcus faecalis was strongly correlated with gut dysbiosis following morphine treatment, and alterations in deoxycholic acid (DCA) and phosphatidylethanolamines (PEs) were associated with opioid-induced metabolomic changes. Collectively, these results indicate that morphine induced distinct alterations in the gut microbiome and metabolome, contributing to negative consequences associated with opioid use. Therapeutics directed at maintaining microbiome homeostasis during opioid use may reduce the comorbidities associated with opioid use for pain management.
Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207
Authors: Basharat Zarrin , Yasmin Azra , He Tongtong , Tong Yigang
Published: February 2018

Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.
Acute Kidney Injury in Trauma Patients Admitted to Critical Care: Development and Validation of a Diagnostic Prediction Model
Authors: Haines Ryan W. , Lin Shih-Pin , Hewson Russell , Kirwan Christopher J. , Torrance Hew D. , O’Dwyer Michael J. , West Anita , Brohi Karim , Pearse Rupert M. , Zolfaghari Parjam , Prowle John R.
Published: February 2018

Acute Kidney Injury (AKI) complicating major trauma is associated with increased mortality and morbidity. Traumatic AKI has specific risk factors and predictable time-course facilitating diagnostic modelling. In a single centre, retrospective observational study we developed risk prediction models for AKI after trauma based on data around intensive care admission. Models predicting AKI were developed using data from 830 patients, using data reduction followed by logistic regression, and were independently validated in a further 564 patients. AKI occurred in 163/830 (19.6%) with 42 (5.1%) receiving renal replacement therapy (RRT). First serum creatinine and phosphate, units of blood transfused in first 24 h, age and Charlson score discriminated need for RRT and AKI early after trauma. For RRT c-statistics were good to excellent: development: 0.92 (0.88–0.96), validation: 0.91 (0.86–0.97). Modelling AKI stage 2–3, c-statistics were also good, development: 0.81 (0.75–0.88) and validation: 0.83 (0.74–0.92). The model predicting AKI stage 1–3 performed moderately, development: c-statistic 0.77 (0.72–0.81), validation: 0.70 (0.64–0.77). Despite good discrimination of need for RRT, positive predictive values (PPV) at the optimal cut-off were only 23.0% (13.7–42.7) in development. However, PPV for the alternative endpoint of RRT and/or death improved to 41.2% (34.8–48.1) highlighting death as a clinically relevant endpoint to RRT.
Influent factors of gestational vitamin D deficiency and its relation to an increased risk of preterm delivery in Chinese population
Authors: Chen Yuan-Hua , Fu Lin , Hao Jia-Hu , Wang Hua , Zhang Cheng , Tao Fang-Biao , Xu De-Xiang
Published: February 2018

Gestational vitamin D deficiency (VDD) has been linked with adverse pregnant outcomes. To investigate influent factors of gestational VDD and its relation to the incidence of preterm delivery, total 3598 eligible mother-and-singleton-offspring pairs were recruited. For serum 25(OH)D concentration, 941 pregnant women were sufficient, 1260 insufficient, and 1397 deficient. Further analysis showed that VDD was more prevalent in winter than in other seasons. Underweight but not overweight was a risk factor for gestational VDD. Multivitamin use reduced risk of gestational VDD. Interestingly, 8.23% delivered preterm infants among subjects with VDD (adjusted RR: 4.02; 95% CI: 2.33, 6.92) and 3.81% among subjects with gestational vitamin D insufficiency (VDI) (adjusted RR: 2.07; 95% CI: 1.16, 3.71). Moreover, 2.59% delivered early preterm infants among subjects with VDD (adjusted RR: 2.97; 95% CI: 1.41, 6.24) and 0.49% among subjects with VDI (adjusted RR: 0.54; 95% CI: 0.19, 1.51). The incidence of late preterm delivery was 5.64% among subjects with VDD (adjusted RR: 3.90; 95% CI: 2.26, 6.72) and 3.32% among subjects with VDI (adjusted RR: 2.09; 95% CI: 1.17, 3.74). In conclusion, pre-pregnancy BMI, seasonality and multivitamin use are influent factors of gestational vitamin D status. Gestational VDD is associated with an increased risk of preterm delivery in Chinese population.
Magnetic properties and magnetocrystalline anisotropy of Nd2Fe17, Nd2Fe17X3, and related compounds
Authors: Pandey Tribhuwan , Parker David S.
Published: February 2018

The electronic and magnetic properties of Nd2Fe17 and Nd2Fe17X3 (X = C or N) compounds have been calculated using the first-principles density functional calculations. Among these, the nitrogen and carbon interstitial compounds exhibit all of the required properties such as a saturation moment of 1.6 T, Curie temperature of 700–750 K, however easy magnetic axis lies in the planar direction making them less attractive for permanent magnet applications. The calculated magnetocrystalline anisotropy energy is found to be −2.7 MJ/m3 for Nd2Fe17C3 and −4.7 MJ/m3 for Nd2Fe17N3. We further explored the possibility of changing the easy axis direction through La/Ce alloying at Nd site. Although the MAE is found to be smaller in magnitude for all the La/Ce alloys it still maintains planar direction.
Prediabetes and diabetes in a cohort of Qatari women screened for polycystic ovary syndrome
Authors: Dargham Soha R. , Shewehy Abeer El , Dakroury Youssra , Kilpatrick Eric S. , Atkin Stephen L.
Published: February 2018

Polycystic ovary syndrome (PCOS) is associated with an increased risk of type 2 diabetes mellitus (T2DM) but its association with prediabetes and T2DM is unknown in Qatar. A cross sectional analysis of 3,017 Qatari subjects from the Qatar Biobank, identified 749 women aged 18–40 years, 720 of whom were assessed by the National Institute for Health (NIH) Guidelines for PCOS. Prediabetes (HbA1c 5.7–6.4% and/or impaired fasting glucose (IFG): fasting plasma glucose (FPG) 100–125 mg/dL (5.6–6.9 mmol/L)), and T2DM (fasting plasma glucose > 125 mg/dL (≥7 mmol/L), and/or HbA1c ≥ 6.5%) were determined. The prevalence of prediabetes was 10.6% and the prevalence of undiagnosed diabetes was found to be 4.0% in the total population. Overall, 12.1% of 720 women had PCOS, of whom FPG and HbA1c were available in 62 women with PCOS: 19.4% had prediabetes and 9.7% had diabetes. An adverse cardiovascular risk profile for IFG women compared to normal women was found. Women with PCOS alone had a similar adverse cardiovascular profile as those with IFG alone and T2DM. Thus, the risk of prediabetes and diabetes is increased in Qatari women with PCOS, with an adverse cardiovascular risk profile similar to that seen in prediabetes and T2DM.
Light Emission from Plasmonic Nanostructures Enhanced with Fluorescent Nanodiamonds
Authors: Zhao Jingyi , Cheng Yuqing , Shen Hongming , Hui Yuen Yung , Wen Te , Chang Huan-Cheng , Gong Qihuang , Lu Guowei
Published: February 2018

In the surface-enhanced fluorescence (SEF) process, it is well known that the plasmonic nanostructure can enhance the light emission of fluorescent emitters. With the help of atomic force microscopy, a hybrid system consisting of a fluorescent nanodiamond and a gold nanoparticle was assembled step-by-step for in situ optical measurements. We demonstrate that fluorescent emitters can also enhance the light emission from gold nanoparticles which is judged through the intrinsic anti-Stokes emission owing to the nanostructures. The light emission intensity, spectral shape, and lifetime of the hybrid system were dependent on the coupling configuration. The interaction between gold nanoparticles and fluorescent emitter was modelled based on the concept of a quantised optical cavity by considering the nanodiamond and the nanoparticle as a two-level energy system and a nanoresonator, respectively. The theoretical calculations reveal that the dielectric antenna effect can enhance the local field felt by the nanoparticle, which contributes more to the light emission enhancement of the nanoparticles rather than the plasmonic coupling effect. The findings reveal that the SEF is a mutually enhancing process. This suggests the hybrid system should be considered as an entity to analyse and optimise surface-enhanced spectroscopy.
The efficacy of Ranolazine on E1784K is altered by temperature and calcium
Authors: Abdelsayed Mena , Ruprai Manpreet , Ruben Peter C.
Published: February 2018

E1784K is the most common mixed syndrome SCN5a mutation underpinning both Brugada syndrome type 1 (BrS1) and Long-QT syndrome type 3 (LQT3). The charge reversal mutant enhances the late sodium current (INa) passed by the cardiac voltage-gated sodium channel (NaV1.5), delaying cardiac repolarization. Exercise-induced triggers, like elevated temperature and cytosolic calcium, exacerbate E1784K late INa. In this study, we tested the effects of Ranolazine, the late INa blocker, on voltage-dependent and kinetic properties of E1784K at elevated temperature and cytosolic calcium. We used whole-cell patch clamp to measure INa from wild type and E1784K channels expressed in HEK293 cells. At elevated temperature, Ranolazine attenuated gain-of-function in E1784K by decreasing late INa, hyperpolarizing steady-state fast inactivation, and increasing use-dependent inactivation. Both elevated temperature and cytosolic calcium hampered the capacity of Ranolazine to suppress E1784K late INa. In-silico action potential (AP) simulations were done using a modified O’Hara Rudy (ORd) cardiac model. Simulations showed that Ranolazine failed to shorten AP duration, an effect augmented at febrile temperatures. The drug-channel interaction is clearly affected by external triggers, as reported previously with ischemia. Determining drug efficacy under various physiological states in SCN5a cohorts is crucial for accurate management of arrhythmias.