bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptide density targets and impedes triple negative breast cancer metastasis
Authors: Liu Daxing , Guo Peng , McCarthy Craig , Wang Biran , Tao Yu , Auguste Debra 
Published: June 2018

AbstractThe C-X-C chemokine receptor type 4 (CXCR4, CD184) pathway is a key regulator of cancer metastasis. Existing therapeutics that block CXCR4 signaling are dependent on single molecule-receptor interactions or silencing CXCR4 expression. CXCR4 localizes in lipid rafts and forms dimers therefore CXCR4 targeting and signaling may depend on ligand density. Herein, we report liposomes presenting a CXCR4 binding peptide (DV1) as a three-dimensional molecular array, ranging from 9k to 74k molecules μm−2, target triple negative breast cancer (TNBC). TNBC cells exhibit a maxima in binding and uptake of DV1-functionalized liposomes (L-DV1) in vitro at a specific density, which yields a significant reduction in cell migration. This density inhibits metastasis from a primary tumor for 27 days, resulting from peptide density dependent gene regulation. We show that complementing cell membrane receptor expression may be a strategy for targeting cells and regulating signaling.
Large second harmonic generation in alloyed TMDs and boron nitride nanostructures
Authors: Lucking Michael C. , Beach Kory , Terrones Humberto 
Published: June 2018

AbstractFirst principles methods are used to explicitly calculate the nonlinear susceptibility (χ(2)(2ω, ω, ω)) representing the second harmonic generation (SHG) of two dimensional semiconducting materials, namely transition metal dichalcogenides (TMDs) and Boron Nitride (BN). It is found that alloying TMDs improves their second harmonic response, with MoTeS alloys exhibiting the highest of all hexagonal alloys at low photon energies. Moreover, careful examination of the relationship between the concentration of Se in MoxSeySz alloys shows that the SHG intensity can be tuned by modifying the stoichiometry. In addition, materials with curvature can have large second harmonic susceptibility. Of all the calculated monolayer structures, the hypothetical TMD Haeckelites NbSSe and Nb0.5Ta0.5S2 exhibit the highest χ(2), while one of the porous 3D structures constructed from 2D hBN exhibits a larger χ(2) than known large band gap 3-D materials.
MicroRNA interactome analysis predicts post-transcriptional regulation of ADRB2 and PPP3R1 in the hypercholesterolemic myocardium
Authors: Ágg Bence , Baranyai Tamás , Makkos András , Vető Borbála , Faragó Nóra , Zvara Ágnes , Giricz Zoltán , Veres Dániel V. , Csermely Péter , Arányi Tamás , Puskás László G. , Varga Zoltán V. , Ferdinandy Péter 
Published: June 2018

AbstractLittle is known about the molecular mechanism including microRNAs (miRNA) in hypercholesterolemia-induced cardiac dysfunction. We aimed to explore novel hypercholesterolemia-induced pathway alterations in the heart by an unbiased approach based on miRNA omics, target prediction and validation. With miRNA microarray we identified forty-seven upregulated and ten downregulated miRNAs in hypercholesterolemic rat hearts compared to the normocholesterolemic group. Eleven mRNAs with at least 4 interacting upregulated miRNAs were selected by a network theoretical approach, out of which 3 mRNAs (beta-2 adrenergic receptor [Adrb2], calcineurin B type 1 [Ppp3r1] and calcium/calmodulin-dependent serine protein kinase [Cask]) were validated with qRT-PCR and Western blot. In hypercholesterolemic hearts, the expression of Adrb2 mRNA was significantly decreased. ADRB2 and PPP3R1 protein were significantly downregulated in hypercholesterolemic hearts. The direct interaction of Adrb2 with upregulated miRNAs was demonstrated by luciferase reporter assay. Gene ontology analysis revealed that the majority of the predicted mRNA changes may contribute to the hypercholesterolemia-induced cardiac dysfunction. In summary, the present unbiased target prediction approach based on global cardiac miRNA expression profiling revealed for the first time in the literature that both the mRNA and protein product of Adrb2 and PPP3R1 protein are decreased in the hypercholesterolemic heart.
The extensive networks of frequent population mobility in the Samoan Islands and their implications for infectious disease transmission
Authors: Xu Zhijing , Lau Colleen L. , Zhou Xiaoyan , Fuimaono Saipale , Soares Magalhães Ricardo J. , Graves Patricia M. 
Published: June 2018

AbstractPopulation mobility has been demonstrated to contribute to the persistent transmission and global diffusion of epidemics. In the Pacific Islands, population mobility is particularly important for emerging infectious diseases, disease elimination programs, and diseases spread by close contact. The extent of population mobility between American Samoa villages, Samoa districts and other countries was investigated based on travel data collected during community surveys in American Samoa in 2010 and 2014. Within American Samoa, workers commuted daily across the whole of the main island of Tutuila, with work hubs drawing from villages across the island. Of the 670 adult workers surveyed, 37% had traveled overseas in the past year, with 68% of trips to Samoa. Of children aged 8–13 years (n = 337), 57% had traveled overseas, with 55% of trips to Samoa. An extensive network of connections between American Samoa villages and Samoa districts was demonstrated, with most trips lasting one week to one month. Our study showed that populations in the Samoan islands are highly mobile, and quantified the extent and destinations of their travels. Our findings offer insight into the impact of population mobility on the transmission of infectious diseases and data to refine existing models of disease transmission in the Pacific islands.
Identifying Recrudescent Plasmodium falciparum in Treated Malaria Patients by Real-time PCR and High Resolution Melt Analysis of Genetic Diversity
Authors: Beshir Khalid B. , Diallo Nouhoum , Sutherland Colin J. 
Published: June 2018

AbstractRecurrent parasitaemia during follow up of clinical trials of antimalarial drug efficacy results from either recrudescence of parasites surviving treatment or from parasites newly emerging from the hepatic stage of infection. Nested PCR is used to distinguish these two possibilities and the technique is difficult to standardise. There is risk of both false positive and false negative results, leading to misclassification errors. The high-resolution melt (HRM) assay was developed with pairs of conserved primers targeting blocks of merozoite surface protein 1 and 2 (msp1 and msp2) genes, and polymorphisms were compared using sequence-confirmed Plasmodium falciparum DNA samples from laboratory isolates. In this study, the HRM dissociation profiles of msp1 and msp2 amplicons were determined and validated against parasite isolates from malaria patients. The msp1 and msp2 profiles of both laboratory and clinical isolates were reproducibly differentiated by HRM. These rapid assays are performed in a closed-tube system, and so avoid cross-contamination while increasing throughput, which are two major advantages. The HRM assays offer significant gains in simplicity, speed and interpretation of results, and reduced analysis cost, for studies that require discrimination of parasite clones. Assay performance in large-scale studies utilizing DNA samples derived from filter-paper bloodspots should now be evaluated.
Flow of CO2 from soil may not correspond with CO2 concentration in soil
Authors: Frouz Jan , Bujalský Luděk 
Published: June 2018

AbstractThe relationship between CO2flow from soil and soil CO2concentration was investigated at 72 permanent sampling points at two forested post-mining sites in the northwest of the Czechia. Based on the entire data set (72 points sampled monthly during the growing season), CO2flow from the soil was positively correlated with soil CO2concentration. CO2concentration in deeper soil layers was positively correlated with root biomass and negatively correlated with soil microbial respiration. In individual sampling points relationship between CO2flow and soil CO2concentration varied from being significantly positive (30% of points) to significantly negative (7%) but mostly being non-significant (63%). The positive correlation occurred at points with high root biomass in deeper soil layers, while the negative correlation occurred at points with high soil microbial respiration per cm3of soil. Laboratory experiments showed that the CO2produced by microbial respiration can reduce microbial respiration but that CO2produced by root respiration did not reduce root respiration. The results indicate that when soil ventilation is poor, microbial respiration can sufficiently increase soil CO2concentration so as to reduce microbial respiration, which greatly increases the variability in the relationship between CO2flow from soil and soil CO2concentration.
Processing and Structure of the Lantibiotic Peptide Nso From the Human Gut Bacterium Blautia obeum A2-162 analysed by Mass Spectrometry
Authors: Gherghisan-Filip Cristina , Saalbach Gerhard , Hatziioanou Diane , Narbad Arjan , Mayer Melinda J. 
Published: June 2018

AbstractA previously reported gene cluster encoding four nisin-like peptides, three with the same sequence (NsoA1-3) and the unique NsoA4, produced antimicrobial activity in the presence of trypsin after heterologous expression in Lactococcus lactis. Protein extracts were separated by SDS gel electrophoresis or immunoprecipitation using an antibody to the NsoA2 leader. Tryptic peptides observed by LC-MS/MS covered the complete sequence of preNsoA1-3 and part of the leader sequence of preNsoA4 and confirmed the expression and the predicted sequences of the preNsoA peptides. Further, the data revealed that the preNsoA1-3 peptides were partly modified with dehydrations and formation of lanthionine rings. A certain amount of fully modified preNsoA1-3 was observed. Details of modifications of the core peptide and the C-terminal tryptic peptide TATCGCHITGK covering rings D and E indicated that 22% of these preNsoA1-3 peptides were completely modified. A lower amount of ring formation is estimated for rings A-C. Intact masses of immunoprecipitation-derived peptides determined by LC-MS accurately matched the expected preNsoA precursor peptides. The most abundant peptides detected were preNsoA2-3-8H2O followed by preNsoA1-8H2O and other states of dehydration. The results confirm incomplete processing of preNsoA peptides in the heterologous system, with the formation of a certain amount of fully modified peptides.
Combing signal processing methods with algorithm priori information to produce synergetic improvements on continuous imaging of brain electrical impedance tomography
Authors: Li Haoting , Chen Rongqing , Xu Canhua , Liu Benyuan , Dong Xiuzhen , Fu Feng 
Published: June 2018

AbstractDynamic electrical impedance tomography (EIT) promises to be a valuable technique for monitoring the development of brain injury. But in practical long-term monitoring, noise and interferences may cause insufficient image quality. To help unveil intracranial conductivity changes, signal processing methods were introduced to improve EIT data quality and algorithms were optimized to be more robust. However, gains for EIT image reconstruction can be significantly increased if we combine the two techniques properly. The basic idea is to apply the priori information in algorithm to help de-noise EIT data and use signal processing to optimize algorithm. First, we process EIT data with principal component analysis (PCA) and reconstruct an initial CT-EIT image. Then, as the priori that changes in scalp and skull domains are unwanted, we eliminate their corresponding boundary voltages from data sets. After the two-step denoising process, we finally re-select a local optimal regularization parameter and accomplish the reconstruction. To evaluate performances of the signal processing-priori information based reconstruction (SPR) method, we conducted simulation and in-vivo experiments. The results showed SPR could improve brain EIT image quality and recover the intracranial perturbations from certain bad measurements, while for some measurement data the generic reconstruction method failed.
Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils
Authors: Kaur Gundeep , Kaundal Soni , Kapoor Srajan , Grimes Jonathan M. , Huiskonen Juha T. , Thakur Krishan Gopal 
Published: June 2018

AbstractCarD is an essential global transcription regulator from Mycobacterium tuberculosis (Mtb) that binds RNA polymerase and activates transcription by stabilizing the transcription initiation complex. Available crystal structures have captured two distinct, monomeric and domain-swapped homodimeric, oligomeric states of CarD. However, the actual oligomeric state of CarD in solution and its biological relevance has remained unclear. Here, we confirm the presence of the homodimeric state of CarD in solution by using synchrotron-based small-angle X-ray scattering. Furthermore, by using biochemical and biophysical experiments, in addition to mass-spectrometry, transmission electron microscopy, and confocal imaging, we show that CarD is the first soluble cytosolic protein in Mtb which displays the tendency to form amyloid-like fibrils both in vitro as well as in vivo. We demonstrate that the deletion of the fourteen N-terminal residues involved in domain-swapping hampers amyloid formation, thus, suggesting that domain-swapping is crucial in amyloidogenesis. The discovery of the amyloidogenic property of an essential cytosolic global transcription regulator, CarD, in a pathogenic bacteria will further open up new frontiers in research.
Across-subject offline decoding of motor imagery from MEG and EEG
Authors: Halme Hanna-Leena , Parkkonen Lauri 
Published: June 2018

AbstractLong calibration time hinders the feasibility of brain-computer interfaces (BCI). If other subjects’ data were used for training the classifier, BCI-based neurofeedback practice could start without the initial calibration. Here, we compare methods for inter-subject decoding of left- vs. right-hand motor imagery (MI) from MEG and EEG. Six methods were tested on data involving MEG and EEG measurements of healthy participants. Inter-subject decoders were trained on subjects showing good within-subject accuracy, and tested on all subjects, including poor performers. Three methods were based on Common Spatial Patterns (CSP), and three others on logistic regression with l1- or l2,1-norm regularization. The decoding accuracy was evaluated using (1) MI and (2) passive movements (PM) for training, separately for MEG and EEG. With MI training, the best accuracies across subjects (mean 70.6% for MEG, 67.7% for EEG) were obtained using multi-task learning (MTL) with logistic regression and l2,1-norm regularization. MEG yielded slightly better average accuracies than EEG. With PM training, none of the inter-subject methods yielded above chance level (58.7%) accuracy. In conclusion, MTL and training with other subject’s MI is efficient for inter-subject decoding of MI. Passive movements of other subjects are likely suboptimal for training the MI classifiers.
MicroRNA expression analysis identifies a subset of downregulated miRNAs in ALS motor neuron progenitors
Authors: Rizzuti Mafalda , Filosa Giuseppe , Melzi Valentina , Calandriello Luca , Dioni Laura , Bollati Valentina , Bresolin Nereo , Comi Giacomo Pietro , Barabino Silvia , Nizzardo Monica , Corti Stefania 
Published: June 2018

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurological disorder that is characterized by a progressive degeneration of motor neurons (MNs). The pathomechanism underlying the disease is largely unknown, even though increasing evidence suggests that RNA metabolism, including microRNAs (miRNAs) may play an important role. In this study, human ALS induced pluripotent stem cells were differentiated into MN progenitors and their miRNA expression profiles were compared to those of healthy control cells. We identified 15 downregulated miRNAs in patients’ cells. Gene ontology and molecular pathway enrichment analysis indicated that the predicted target genes of the differentially expressed miRNAs were involved in neurodegeneration-related pathways. Among the 15 examined miRNAs, miR-34a and miR504 appeared particularly relevant due to their involvement in the p53 pathway, synaptic vesicle regulation and general involvement in neurodegenerative diseases. Taken together our results demonstrate that the neurodegenerative phenotype in ALS can be associated with a dysregulation of miRNAs involved in the control of disease-relevant genetic pathways, suggesting that targeting entire gene networks can be a potential strategy to treat complex diseases such as ALS.
Reversible mislocalization of a disease-associated MRE11 splice variant product
Authors: Hartlerode Andrea J. , Regal Joshua A. , Ferguson David O. 
Published: June 2018

AbstractAtaxia-telangiectasia (AT) and related disorders feature cancer predisposition, neurodegeneration, and immunodeficiency resulting from failure to respond to DNA damage. Hypomorphic mutations in MRE11 cause an AT-like disorder (ATLD) with variable clinical presentation. We have sought to understand how diverse MRE11 mutations may provide unique therapeutic opportunities, and potentially correlate with clinical variability. Here we have undertaken studies of an MRE11 splice site mutation that was found in two ATLD siblings that died of pulmonary adenocarcinoma at the young ages of 9 and 16. The mutation, termed MRE11 alternative splice mutation (MRE11ASM), causes skipping of a highly conserved exon while preserving the protein’s open reading frame. A new mouse model expressing Mre11ASM from the endogenous locus demonstrates that the protein is present at very low levels, a feature in common with the MRE11ATLD1 mutant found in other patients. However, the mechanisms causing low protein levels are distinct. MRE11ASM is mislocalized to the cytoplasm, in contrast to MRE11ATLD1, which remains nuclear. Strikingly, MRE11ASM mislocalization is corrected by inhibition of the proteasome, implying that the protein undergoes strict protein quality control in the nucleus. These findings raise the prospect that inhibition of poorly understood nuclear protein quality control mechanisms might have therapeutic benefit in genetic disorders causing cytoplasmic mislocalization.
Fungi in perennial ice from Scărișoara Ice Cave (Romania)
Authors: Brad Traian , Itcus Corina , Pascu Madalina-Denisa , Perșoiu Aurel , Hillebrand-Voiculescu Alexandra , Iancu Lavinia , Purcarea Cristina 
Published: June 2018

AbstractScreening of 1,000-years old ice layers from the perennial ice block of Scărișoara Ice Cave (NW Romania) revealed the presence of fungal communities. Using culture-dependent methods and molecular techniques based on DGGE fingerprinting of 18S rRNA gene fragments and sequencing, we identified 50 cultured and 14 uncultured fungi in presently-forming, 400 and 900 years old ice layers, corresponding to 28 distinct operational taxonomic units (OTUs). The dominant ice-contained fungal OTUs were related to Ascomycota, Basidiomycota and Cryptomycota phyla. Representatives of Mucoromycota and Chytridiomycota were also isolated from recent and 400 years old ice samples. The cryophilic Mrakia stokesii was the most abundant fungal species found in the cave ice samples of all prospected ages, alongside other cryophilic fungi also identified in various glacial environments. Ice deposits formed during the Little Ice Age (dated between AD 1,250 and 1,850) appeared to have a higher fungal diversity than the ice layer formed during the Medieval Warm Period (prior to AD 1,250). A more complex fungal community adapted to low temperatures was obtained from all analyzed ice layers when cultivated at 4 °C as compared to 15 °C, suggesting the dominance of cold-adapted fungi in this glacial habitat. The fungal distribution in the analyzed cave ice layers revealed the presence of unique OTUs in different aged-formed ice deposits, as a first hint for putative further identification of fungal biomarkers for climate variations in this icy habitat. This is the first report on fungi from a rock-hosted cave ice block.
Dual role of SND1 facilitates efficient communication between abiotic stress signalling and normal growth in Arabidopsis
Authors: Jeong Chan Young , Lee Won Je , Truong Hai An , Trịnh Cao Sơn , Jin Joo Yeon , Kim Sulhee , Hwang Kwang Yeon , Kang Chon-Sik , Moon Joon-Kwan , Hong Suk-Whan , Lee Hojoung 
Published: June 2018

AbstractCertain plant cells synthesize secondary cell walls besides primary cell walls. This biosynthesis is strictly controlled by an array of transcription factors. Here, we show that SND1, a regulator of cell-wall biosynthesis, regulates abscisic acid (ABA) biosynthesis to ensure optimal plant growth. In Arabidopsis, the lack of SND1 and its homolog NST1 leads to the deficiency of secondary cell walls, preventing snd1nst1 double mutant seedlings from growing upright. Compared to wild type seedlings, the snd1 knockout mutant seedlings accumulated less anthocyanin and exhibited low tolerance to salt stress. Compared to wild type seedlings, the snd1 knockout seedlings were more sensitive to salt stress. Although SND1 can bind to the promoter of Myb46, we observed that SND1 binds directly to the promoter of the ABI4 gene, thereby reducing ABA levels under normal growth conditions. Thus, plants adjust secondary cell wall thickening and growth via SND1. SND1 has a dual function: it activates the Myb46 pathway, fostering lignin biosynthesis to produce sufficient cell wall components for growth, while maintaining a low ABA concentration, as it inhibits growth. This dual function of SND1 may help plants modulate their growth efficiently.
Role of neuritin in retinal ganglion cell death in adult mice following optic nerve injury
Authors: Azuchi Yuriko , Namekata Kazuhiko , Shimada Tadayuki , Guo Xiaoli , Kimura Atsuko , Harada Chikako , Saito Atsuko , Yamagata Kanato , Harada Takayuki 
Published: June 2018

AbstractNeuritin is a small extracellular protein that plays important roles in the process of neural development, synaptic plasticity, and neural cell survival. Here we investigated the function of neuritin in a mouse model of optic nerve injury (ONI). ONI induced upregulation of neuritin mRNA in the retina of WT mice. The retinal structure and the number of retinal ganglion cells (RGCs) were normal in adult neuritin knockout (KO) mice. In vivo retinal imaging and histopathological analyses demonstrated that RGC death and inner retinal degeneration following ONI were more severe in neuritin KO mice. Immunoblot analyses revealed that ONI-induced phosphorylation of Akt and ERK were suppressed in neuritin KO mice. Our findings suggest that neuritin has neuroprotective effects following ONI and may be useful for treatment of posttraumatic complication.