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# Biased molecules

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#1
Rui Gao, Yi-Lun Ying, Yong-Xu Hu, Yuan-Jie Li, Yi-Tao Long
Solid-state nanopore-based techniques have become a promising strategy for diverse single molecule detections. Owing to the challenge in well and rapid fabrication of solid-state nanopores with the diameter less than 2 nm, small molecule detection is hard to be addressed by existing label-free nanopore methods. In this work, we for the first time propose a metal coated wireless nanopore electrode (WNE) which offers a novel and generally accessible detection method for analyzing small molecules and ions at single molecule/ion level...
June 27, 2017: Analytical Chemistry
#2
Nai-Yong Liu, Jin-Qiang Wang, Zu-Bing Zhang, Jing-Mei Huang, Jia-Ying Zhu
The encyrtid parasitoid, Diversinervus elegans (Hymenoptera: Encyrtidae), is a natural enemy of the notorious scale pests belonging to the family of Coccidae. Venom containing a rich source of bioactive molecules is a key virulent factor used to regulate host physiology by parasitoids. Although knowledge regarding venom constituents accumulated from limited parasitoids has provided insights into their roles in host-parasitoid interaction, toxins involving in manipulating scale physiology remain sparsely documented...
June 23, 2017: Toxicon: Official Journal of the International Society on Toxinology
#3
Jean-Baptiste Ledoux, Agostinho Antunes
Marine natural products (NPs) represent an impressive source of novel bioactive molecules with major biotechnological applications. Nevertheless, the usual chemical and applied perspective leading most of bioprospecting projects come along with various limitations blurring our understanding of the extensive marine chemical diversity. Here, we propose several guidelines: (i) to optimize bioprospecting and (ii) to refine our knowledge on marine chemical ecology focusing on octocorals, one of the most promising sources of marine NPs...
June 26, 2017: Critical Reviews in Biotechnology
#4
Zong-Liang Li, Xiao-Hua Yi, Ran Liu, Jun-Jie Bi, Huan-Yan Fu, Guang-Ping Zhang, Yu-Zhi Song, Chuan-Kui Wang
Large negative differential conductance (NDC) at lower bias regime is a very desirable functional property for single molecular device. Due to the non-conjugated segment separating two conjugated branches, the single thiolated arylethynylene molecule with 9,10-dihydroanthracene core (denoted as TADHA) presents excellent NDC behavior in lower bias regime. Based on the ab initio calculation and non-equilibrium Green's function formalism, the NDC behavior of TADHA molecular device and the H2O-molecule-adsorption effects are studied systematically...
June 23, 2017: Scientific Reports
#5
Saptarshi Roy, Devawati Dutta, Eswara M Satyavarapu, Pawan K Yadav, Chhabinath Mandal, Susanta Kar, Chitra Mandal
Earlier we have established a carbazole alkaloid (mahanine) isolated from an Indian edible medicinal plant as an anticancer agent with minimal effect on normal cells. Here we report for the first time that mahanine-treated drug resistant and sensitive virulent Leishmania donovani promastigotes underwent apoptosis through phosphatidylserine externalization, DNA fragmentation and cell cycle arrest. An early induction of reactive oxygen species (ROS) suggests that the mahanine-induced apoptosis was mediated by oxidative stress...
June 23, 2017: Scientific Reports
#6
Sabrina Marcazzan, Roberto Lodovico Weinstein, Massimo Del Fabbro
In presence of large bone defects, delayed bone union, non-union, fractures, and implant surgery, bone reconstruction may be necessary. Different strategies have been employed to enhance bone healing among which the use of autologous platelet concentrates. Due to the high content of platelets and platelet-derived bioactive molecules (e.g., growth factors, antimicrobial peptides), they are promising candidates to increase bone healing. However, a high heterogeneity of both preclinical and clinical studies resulted in contrasting results...
June 23, 2017: Platelets
#7
Huaming Hou, Xianglei Mao, Vassilia Zorba, Richard E Russo
Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser induced plasma in addition to isotope analysis. LAMIS is powerful tool for tracking the origination of atoms that involved in formation of investigated molecules by labeling atoms with its isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma...
June 22, 2017: Analytical Chemistry
#8
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
#9
Limor Cohen, Mark R Hartman, Aaron Amardey-Wellington, David R Walt
MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification...
June 20, 2017: Nucleic Acids Research
#10
Ville Paakinaho, Diego M Presman, David A Ball, Thomas A Johnson, R Louis Schiltz, Peter Levitt, Davide Mazza, Tatsuya Morisaki, Tatiana S Karpova, Gordon L Hager
Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms of static and sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour of TFs in live cells. Here we analyse the strengths and limitations of in vivo single-molecule tracking and performed a comprehensive analysis on the intranuclear dwell times of four steroid receptors and a number of known cofactors...
June 21, 2017: Nature Communications
#11
Alexander V Rudnev, Veerabhadrarao Kaliginedi, Andrea Droghetti, Hiroaki Ozawa, Akiyoshi Kuzume, Masa-Aki Haga, Peter Broekmann, Ivan Rungger
An open challenge for single-molecule electronics is to find stable contacts at room temperature with a well-defined conductance. Common coinage metal electrodes pose fabrication and operational problems due to the high mobility of the surface atoms. We demonstrate how molecules covalently grafted onto mechanically robust graphite/graphene substrates overcome these limitations. To this aim, we explore the effect of the anchoring group chemistry on the charge transport properties of graphite-molecule contacts by means of the scanning tunneling microscopy break-junction technique and ab initio simulations...
#12
Joana Dias, Edwin Leeansyah, Johan K Sandberg
Mucosa-associated invariant T (MAIT) cells are a large innate-like T-cell subset in humans defined by invariant TCR Vα7.2 use and expression of CD161. MAIT cells recognize microbial riboflavin metabolites of bacterial or fungal origin presented by the monomorphic MR1 molecule. The extraordinary level of evolutionary conservation of MR1 and the limited known diversity of riboflavin metabolite antigens have suggested that MAIT cells are relatively homogeneous and uniform in responses against diverse microbes carrying the riboflavin biosynthesis pathway...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
#13
REVIEW
Kherim Willems, Veerle Van Meervelt, Carsten Wloka, Giovanni Maglia
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
#14
Salvador Cardona Serra, Alejandro Gaita-Ariño, Maria Stamenova, Stefano Sanvito
In a straightforward application of molecular nanospintronics to quantum computing, single-molecule spin transistors can be used to measure and control nuclear spin qubits. A jump in the conductance occurs when the electronic spin inverts its polarization, and this happens at a so-called anticrossing between energy levels, which in turn only takes place at a specific magnetic field determined by the nuclear spin state. So far, this procedure has only been implemented for the terbium(III) bis(phthalocyaninato) complex...
June 16, 2017: Journal of Physical Chemistry Letters
#15
Massimo Mella, Emanuele Curotto
Despite the fact that the \emph{para}--hydrogen molecule ($p$--H$_2$) and its isotopomers ($o$--D$_2$ and $p$--T$_2$) are commonly modelled as spherical objects due to the large separation between rotational states, there may be situations (\emph{e.g.} adsorption in pores and on surfaces) in which such an approximation neglects important degrees of freedom (\emph{i.e.} the rotational ones) and introduces uncontrolled biases in the predicted properties. To better understand when approximating such molecules as spheres introduces shortcomings in their representation, we employed diffusion Monte Carlo to simulate small/medium--sized molecular aggregates, either isolated in space or experiencing external model potentials, to compute energetic quantities and distribution functions...
June 15, 2017: Journal of Physical Chemistry. A
#16
Sean E DeWolf, Alana A Shigeoka, Andrew Scheinok, Sashi G Kasimsetty, Alexander K Welch, Dianne B McKay
BACKGROUND: Gender-biased outcomes are associated with acute kidney injury (AKI) and human and animal studies have shown that females are preferentially protected from renal ischemia. However, the reason for this is not known. One clue might lie with pattern recognition receptors (PRRs), which are triggers of ischemic injury when ligated by molecules in the ischemic milieu. Several PRR families are expressed by renal tubular epithelial cells (RTEs) and incite cell death signaling and production of pro-inflammatory molecules...
June 15, 2017: Nephron
#17
Yan Xu, Biao Liu, Fengan Ding, Xiaodie Zhou, Pin Tu, Bo Yu, Yan He, Peilin Huang
Circulating tumor cells (CTCs), isolated as a 'liquid biopsy', may provide important diagnostic and prognostic information. Therefore, rapid, reliable and unbiased detection of CTCs are required for routine clinical analyses. It was demonstrated that negative enrichment, an epithelial marker-independent technique for isolating CTCs, exhibits a better efficiency in the detection of CTCs compared with positive enrichment techniques that only use specific anti-epithelial cell adhesion molecules. However, negative enrichment techniques incur significant cell loss during the isolation procedure, and as it is a method that uses only one type of antibody, it is inherently biased...
June 2017: Oncology Letters
#18
Martina Kocan, Mohsin Sarwar, Sheng Y Ang, Jingbo Xiao, Juan J Marugan, Mohammed A Hossain, Chao Wang, Dana S Hutchinson, Chrishan S Samuel, Alexander I Agoulnik, Ross A D Bathgate, Roger J Summers
Activation of the relaxin receptor RXFP1 has been associated with improved survival in acute heart failure. ML290 is a small molecule RXFP1 agonist with simple structure, long half-life and high stability. Here we demonstrate that ML290 is a biased agonist in human cells expressing RXFP1 with long-term beneficial actions on markers of fibrosis in human cardiac fibroblasts (HCFs). ML290 did not directly compete with orthosteric relaxin binding and did not affect binding kinetics, but did increase binding to RXFP1...
June 7, 2017: Scientific Reports
#19
Khalid Abd-Elaziz, Ingrid Duijkers, Lars Stöckl, Bruno Dietrich, Christine Klipping, Kelvin Eckert, Steffen Goletz
STUDY QUESTION: What are the differences and similarities of pharmacokinetic (PK) and pharmacodynamic (PD) characteristics of the novel recombinant human FSH follitropin epsilon expressed in the human cell line GlycoExpress compared with a Chinese hamster ovary (CHO) derived compound and a urinary derived product? SUMMARY ANSWER: Overall follitropin epsilon, with a fully human glycosylation, shows a comparable PK profile at single-dose as well as multiple-dose administration compared to recombinant CHO-derived FSH as well as urinary derived FSH, whereas the PD properties differ from product to product with follitropin epsilon being most active in PD parameters...
June 7, 2017: Human Reproduction
#20
Martin Winkler, Michael Niemeyer, Antje Hellmuth, Philipp Janitza, Gideon Christ, Sophia L Samodelov, Verona Wilde, Petra Majovsky, Marco Trujillo, Matias D Zurbriggen, Wolfgang Hoehenwarter, Marcel Quint, Luz Irina A Calderón Villalobos
Auxin is a small molecule morphogen that bridges SCF(TIR1/AFB)-AUX/IAA co-receptor interactions leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors. Here, we systematically dissect auxin sensing by SCF(TIR1)-IAA6 and SCF(TIR1)-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. We show that TIR1-IAA19 and TIR1-IAA6 have distinct auxin affinities that correlate with ubiquitylation and turnover dynamics of the AUX/IAA...
June 7, 2017: Nature Communications
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