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https://www.readbyqxmd.com/read/29156805/circulating-tumor-dna-shows-variable-clonal-response-of-breast-cancer-during-neoadjuvant-chemotherapy
#1
Ji-Yeon Kim, Donghyun Park, Dae-Soon Son, Seok Jin Nam, Seok Won Kim, Hae Hyun Jung, Yeon Jeong Kim, Gahee Park, Woong-Yang Park, Jeong Eon Lee, Yeon Hee Park
Circulating tumor DNA (ctDNA) correlates with tumor burden and provides early detection of treatment response and tumor genetic alterations in breast cancer (BC). In this study, we aimed to identify genetic alterations during the process of tumor clonal evolution and examine if ctDNA level well indicated clinical response to neoadjuvant chemotherapy (NAC) and BC recurrence. We performed targeted ultra-deep sequencing of plasma DNAs, matched germline DNAs and tumor DNAs from locally advanced BC patients. Serial plasma DNAs were collected at diagnosis, after the 1(st) cycle of NAC and after curative surgery...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156716/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#2
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156701/association-of-breast-carcinoma-growth-with-a-non-canonical-axis-of-ifn%C3%AE-ido1-tsp1
#3
Bruno Lopes-Bastos, Liang Jin, Fiona Ruge, Sioned Owen, Andrew Sanders, Christopher Cogle, John Chester, Wen G Jiang, Jun Cai
Reciprocal interactions between cancers and the surrounding microenvironment have an important role in tumour evolution. In this study, our data suggested that through thrombospondin 1 (TSP1), tumour-associated microvessel provides a dormant niche to sustain inactive status of breast invasive ductal carcinoma (IDC) cells. TSP1 levels in the tumour stroma were negatively correlated with vascular indoleamine 2,3-dioxygenase 1 (IDO1) in IDC tissues. IDO1 is an intracellular enzyme initiating the first and rate-limited step of tryptophan breakdown...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156680/vemurafenib-resistance-via-de-novo-rbm-genes-mutations-and-chromosome-5-aberrations-is-overcome-by-combined-therapy-with-palbociclib-in-thyroid-carcinoma-with-braf-v600e
#4
Zeus A Antonello, Nancy Hsu, Manoj Bhasin, Giovanni Roti, Mukta Joshi, Paul Van Hummelen, Emily Ye, Agnes S Lo, S Ananth Karumanchi, Christine R Bryke, Carmelo Nucera
Purpose: Papillary thyroid carcinoma (PTC) is the most frequent endocrine tumor. BRAF(V600E) represents the PTC hallmark and is targeted with selective inhibitors (e.g. vemurafenib). Although there have been promising results in clinical trials using these inhibitors, most patients develop resistance and progress. Tumor clonal diversity is proposed as one mechanism underlying drug resistance. Here we have investigated mechanisms of primary and secondary resistance to vemurafenib in BRAF(WT/V600E)-positive PTC patient-derived cells with P16(-/-) (CDKN2A(-/-))...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156643/melanoma-genetic-abnormalities-tumor-progression-clonal-evolution-and-tumor-initiating-cells
#5
REVIEW
Ugo Testa, Germana Castelli, Elvira Pelosi
Melanoma is an aggressive neoplasia issued from the malignant transformation of melanocytes, the pigment-generating cells of the skin. It is responsible for about 75% of deaths due to skin cancers. Melanoma is a phenotypically and molecularly heterogeneous disease: cutaneous, uveal, acral, and mucosal melanomas have different clinical courses, are associated with different mutational profiles, and possess distinct risk factors. The discovery of the molecular abnormalities underlying melanomas has led to the promising improvement of therapy, and further progress is expected in the near future...
November 20, 2017: Medical Sciences: Open Access Journal
https://www.readbyqxmd.com/read/29156623/omi-and-ground-based-in-situ-tropospheric-nitrogen-dioxide-observations-over-several-important-european-cities-during-2005-2014
#6
Spiru Paraschiv, Daniel-Eduard Constantin, Simona-Lizica Paraschiv, Mirela Voiculescu
In this work we present the evolution of tropospheric nitrogen dioxide (NO₂) content over several important European cities during 2005-2014 using space observations and ground-based in-situ measurements. The NO₂ content was derived using the daily observations provided by the Ozone Monitoring Instrument (OMI), while the NO₂ volume mixing ratio measurements were obtained from the European Environment Agency (EEA) air quality monitoring stations database. The European cities selected are: Athens (37.98° N, 23...
November 20, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29156578/pancreatic-cancer-molecular-characterization-clonal-evolution-and-cancer-stem-cells
#7
REVIEW
Elvira Pelosi, Germana Castelli, Ugo Testa
Pancreatic Ductal Adenocarcinoma (PDAC) is the fourth most common cause of cancer-related death and is the most lethal of common malignancies with a five-year survival rate of <10%. PDAC arises from different types of non-invasive precursor lesions: intraductal papillary mucinous neoplasms, mucinous cystic neoplasms and pancreatic intraepithelial neoplasia. The genetic landscape of PDAC is characterized by the presence of four frequently-mutated genes: KRAS, CDKN2A, TP53 and SMAD4. The development of mouse models of PDAC has greatly contributed to the understanding of the molecular and cellular mechanisms through which driver genes contribute to pancreatic cancer development...
November 18, 2017: Biomedicines
https://www.readbyqxmd.com/read/29156487/evolution-and-molecular-mechanism-of-four-electron-reducing-ferredoxin-dependent-bilin-reductases-from-oceanic-phages
#8
Benjamin Ledermann, Meike Schwan, Johannes A Sommerkamp, Eckhard Hofmann, Oded Béjà, Nicole Frankenberg-Dinkel
Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalyzing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalyzing the reduction of BV to phycocyanobilin...
November 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29156423/under-pressure-evolutionary-engineering-of-yeast-strains-for-improved-performance-in-fuels-and-chemicals-production
#9
REVIEW
Robert Mans, Jean-Marc G Daran, Jack T Pronk
Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci...
November 17, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29156347/creation-of-a-3mn-1fe-cluster-in-the-oxygen-evolving-complex-of-photosystem-ii-and-investigation-of-its-functional-activity
#10
B К Semin, L N Davletshina, M Seibert, A B Rubin
Extraction of Mn cations from the oxygen-evolving complex (OEC) of Ca-depleted PSII membranes (PSII[-Ca,4Mn]) by reductants like hydroquinone (H2Q) occurs with lower efficiency at acidic pH (2Mn/reaction center [RC] are extracted at pH5.7) than at neutral pH (3Mn/RC are extracted at pH6.5) [Semin et al. Photosynth. Res. 125 (2015) 95]. Fe(II) also extracts Mn cations from PSII(-Ca,4Mn), but only 2Mn/RC at pH6.5, forming a heteronuclear 2Mn/2Fe cluster [Semin and Seibert, J. Bioenerg. Biomembr. 48 (2016) 227]...
November 11, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29156162/the-evolution-of-limb-deformity-what-has-changed-over-the-past-ten-years
#11
REVIEW
Jessica L Wilczek, Guido A LaPorta
Limb deformity correction has been widely discussed in orthopedic literature with an increasing interest in technologically based surgical strategies. However, principles described by Ilizarov and Paley still form the basis of these newly developing surgical systems. The recent advances and increased use of computers and mobile devices in the medical arena, along with the application of dynamic hexapod external fixation, have allowed for easier and more convenient strategies, leading to a greater outreach and more confidence in the newer surgeon when faced with addressing a patient with a limb deformity...
January 2018: Clinics in Podiatric Medicine and Surgery
https://www.readbyqxmd.com/read/29155921/aridification-as-a-driver-of-biodiversity-a-case-study-for-the-cycad-genus-dioon-zamiaceae
#12
José Said Gutiérrez-Ortega, Takashi Yamamoto, Andrew P Vovides, Miguel Angel Pérez-Farrera, José F Martínez, Francisco Molina-Freaner, Yasuyuki Watano, Tadashi Kajita
Background and Aims: Aridification is considered a selective pressure that might have influenced plant diversification. It is suggested that plants adapted to aridity diversified during the Miocene, an epoch of global aridification (≈15 million years ago). However, evidence supporting diversification being a direct response to aridity is scarce, and multidisciplinary evidence, besides just phylogenetic estimations, is necessary to support the idea that aridification has driven diversification...
November 16, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29155894/estimating-virus-effective-population-size-and-selection-without-neutral-markers
#13
Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Sophie Valière, Frédéric Grognard, Frédéric Fabre
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers...
November 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29155880/molecular-characterization-of-novel-mosquito-borne-rickettsia-spp-from-mosquitoes-collected-at-the-demilitarized-zone-of-the-republic-of-korea
#14
Alice N Maina, Terry A Klein, Heung-Chul Kim, Sung-Tae Chong, Yu Yang, Kristin Mullins, Ju Jiang, Heidi St John, Richard G Jarman, Jun Hang, Allen L Richards
Rickettsiae are associated with a diverse range of invertebrate hosts. Of these, mosquitoes could emerge as one of the most important vectors because of their ability to transmit significant numbers of pathogens and parasites throughout the world. Recent studies have implicated Anopheles gambiae as a potential vector of Rickettsia felis. Herein we report that a metagenome sequencing study identified rickettsial sequence reads in culicine mosquitoes from the Republic of Korea. The detected rickettsiae were characterized by a genus-specific quantitative real-time PCR assay and sequencing of rrs, gltA, 17kDa, ompB, and sca4 genes...
2017: PloS One
https://www.readbyqxmd.com/read/29155692/mass-transport-modeling-for-the-electroreduction-of-co-sub-2-sub-on-cu-nanowires
#15
David Raciti, Mark Mao, Chao Wang
Mass transport plays an important role in the CO<sub>2</sub> reduction electrocatalysis. Albeit being more pronounced on nanostructured electrodes, the studies of mass transport for CO<sub>2</sub> reduction have yet been limited to planar electrodes. We report here the development of a mass transport model for the electroreduction of CO<sub>2</sub> on Cu nanowire electrodes. Fed with the experimental data from electrocatalytic studies, the local concentrations of CO<sub>2</sub>, HCO<sub>3</sub><sup>-</sup>, CO<sub>3</sub><sup>2-</sup> and OH<sup>-</sup> on the nanostructured electrodes are calculated by solving the diffusion equations with spatially distributed electrochemical reaction terms incorporated...
November 20, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29155593/dynamical-density-functional-theory-for-the-evaporation-of-droplets-of-nanoparticle-suspension
#16
Christopher Chalmers, Roger Smith, Andrew J Archer
We develop a lattice gas model for the drying of droplets of a nanoparticle suspension on a planar surface, using dynamical density functional theory (DDFT) to describe the time evolution of the solvent and nanoparticle density profiles. The DDFT assumes a diffusive dynamics but does not include the advective hydrodynamics of the solvent, so the model is relevant to highly viscous or near to equilibrium systems. Nonetheless, we see an equivalent of the coffee-ring stain effect, but in the present model it occurs for thermodynamic rather the fluid-mechanical reasons...
November 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29155487/novel-cyp6d1-and-voltage-gated-sodium-channel-alleles-of-the-house-fly-musca-domestica-and-their-roles-in-pyrethroid-resistance
#17
Jing Pan, Chan Yang, Yan Liu, Qi Gao, Mei Li, Xinghui Qiu
BACKGROUND: The house fly Musca domestica is an important disease vector. Point mutation mediated target-site insensitivity of the voltage gated sodium channel (VSSC) and increased detoxification mediated by CYP6D1 overexpression have been characterized to be two major mechanisms of pyrethroid resistance. In this study, genetic mutations in Vssc and CYP6D1 genes and their contribution to pyrethroid resistance were investigated. RESULTS: Twelve lines of house flies homozygous for four genotypes were established...
November 20, 2017: Pest Management Science
https://www.readbyqxmd.com/read/29155461/nanoscale-trimetallic-metal-organic-frameworks-enable-efficient-oxygen-evolution-electrocatalysis
#18
Xiaoqing Huang
Metal-organic frameworks (MOFs) are a class of promising materials for diverse catalysis, but they are usually not directly employed for oxygen evolution electrocatalysis. Most reports focus on using MOFs as templates to in-situ create efficient electrocatalysts via annealing. Herein, we prepared a series of Fe/Ni/-based trimetallic MOFs (Fe/Ni/Co(Mn)-Material of Institute Lavoisier (MIL-53)) by solvothermal synthesis, which can be directly adopted as electrocatalysts. It was revealed that the Fe/Ni/Co(Mn)-MIL-53 exhibited volcano-type oxygen evolution reaction (OER) activity as a function of compositions...
November 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29155415/phase-diagrams-of-ferroelectric-nanocrystals-strained-by-an-elastic-matrix
#19
Andrei Nikitchenko, Andrei V Azovtsev, Nikolay A Pertsev
Ferroelectric crystallites embedded into a dielectric matrix experience temperature-dependent elastic strains caused by differences in the thermal expansion of the crystallites and the matrix. Owing to the electrostriction, these lattice strains may affect polarization states of ferroelectric inclusions significantly, making them different from those of a stress-free bulk crystal. Here, using a nonlinear thermodynamic theory, we study the mechanical effect of elastic matrix on the phase states of embedded single-domain ferroelectric nanocrystals...
November 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29155385/local-low-dose-urokinase-thrombolysis-for-the-management-of-hemodynamically-stable-pulmonary-embolism-with-right-ventricular-dysfunction
#20
Sara Alcántara Carmona, Marina Pérez Redondo, Luis Nombela Franco, Rocío González Costero, Bárbara Balandín Moreno, Miguel Valdivia de la Fuente, Santiago Méndez Alonso, Agustín García Suárez, Ana Royuela
AIMS: To evaluate the effectiveness of local low-dose urokinase thrombolysis (LLDUT) in hemodynamically stable pulmonary embolism with right ventricular dysfunction (RVD). METHODS AND RESULTS: Prospective study. LLDUT with a 200,000 IU bolus followed by a 100,000 IU/h infusion. Treatment duration was determined through radiological control performed 48-72h into treatment. Follow-up echocardiogram was performed within seven days after LLDUT completion. Evolution of thrombus burden, pulmonary artery pressures (PAP) and RVD were studied, and hemorrhagic complications and mortality were recorded...
November 21, 2017: EuroIntervention
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