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inversion probes

Elżbieta Warchałowska-Śliwa, Beata Grzywacz, Klaus-Gerhard Heller, Dragan P Chobanov
The present study focused on the evolution of the karyotype in four genera of the tribe Pholidopterini: Eupholidoptera Mařan, 1953, Parapholidoptera Mařan, 1953, Pholidoptera Wesmaël, 1838, Uvarovistia Mařan, 1953. Chromosomes were analyzed using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes, and classical techniques, such as C-banding, silver impregnation and fluorochrome DAPI/CMA3 staining. Most species retained the ancestral diploid chromosome number 2n = 31 (male) or 32 (female), while some of the taxa, especially a group of species within genus Pholidoptera, evolved a reduced chromosome number 2n = 29...
2017: Comparative Cytogenetics
Vladimir E Gokhman, Kristen L Kuhn, James B Woolley, Keith R Hopper
Genome sizes were measured and determined for the karyotypes of nine species of aphid parasitoids in the genus Aphelinus Dalman,1820. Large differences in genome size and karyotype were found between Aphelinus species, which is surprising given the similarity in their morphology and life history. Genome sizes estimated from flow cytometry were larger for species in the Aphelinus mali (Haldeman, 1851) complex than those for the species in the Aphelinus daucicola Kurdjumov, 1913 and Aphelinus varipes (Förster,1841) complexes...
2017: Comparative Cytogenetics
Ying-Hua Chu, Yi-Cheng Hsu, Fa-Hsuan Lin
Field probes are miniature receiver coils with localized NMR-active samples inside. They are useful in monitoring magnetic field. This information can be used to improve magnetic resonance image quality. While field probes are coupled to each other marginally in most applications, this coupling can cause incorrect resonance frequency estimates and image reconstruction errors. Here, we propose a method to reduce the coupling between field probes in order to improve the accuracy of magnetic field estimation. An asymmetric sensitivity matrix describing the coupling between channels of field probes and NMR active droplets within field probes was empirically measured...
September 14, 2017: Scientific Reports
K Liu, B Enns, B Evans, N Wang, X Shang, W Sittiwong, P H Dussault, J Guo
We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a cyclobutene-containing amino acid into proteins in response to an amber nonsense codon. Fast and fluorescent labeling of purified proteins and intact proteins in live cells was demonstrated using the inverse electron demand Diels-Alder reaction with a tetrazine.
September 13, 2017: Chemical Communications: Chem Comm
Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman
South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A...
2017: International Journal of Genomics
Tessa de Bitter, Carlijn van de Water, Corina van den Heuvel, Carolien Zeelen, Astrid Eijkelenboom, Bastiaan Tops, Egbert Oosterwijk, Dimitar Kolev, Peter Mulders, Mark Ter Laan, Sanne van Lith, William Leenders
Cancer-specific metabolic alterations are of high interest as therapeutic targets. These alterations vary between tumor types, and to employ metabolic targeting to its fullest potential there is a need for robust methods that identify candidate targetable metabolic pathways in individual cancers. Currently, such methods include (13)C-tracing studies and mass spectrometry/ magnetic resonance spectroscopic imaging. Due to high cost and complexity, such studies are restricted to a research setting. We here present the validation of a novel technique of metabolic profiling, based on multiplex targeted next generation sequencing of RNA with single molecule molecular inversion probes (smMIPs), designed to measure activity of and mutations in genes that encode metabolic enzymes...
September 12, 2017: Scientific Reports
Fang Liu, Yong Liang, K N Houk
Bioorthogonal chemistry has had a major impact on the study of biological processes in vivo. Biomolecules of interest can be tracked by using probes and reporters that do not react with cellular components and do not interfere with metabolic processes in living cells. Much time and effort has been devoted to the screening of potential bioorthogonal reagents experimentally. This Account describes how our groups have performed computational screening of reactivity and mutual orthogonality. Our collaborations with experimentalists have led to the development of new and useful reactions...
September 6, 2017: Accounts of Chemical Research
O L Ermolaeva, N S Gusev, E V Skorohodov, Yu V Petrov, M V Sapozhnikov, V L Mironov
We present the results of magnetic force microscopy investigations of domain structures in multilayer [Co (0.5 nm)/Pt (1 nm)]₅ thin film structures (denoted hereafter as Co/Pt) modified by additional Co capping layers and by ion irradiation. It is demonstrated that a Co capping layer essentially changes the domain structure and decreases the threshold of magnetization reversal, due to the formation of noncollinear magnetization in Co/Pt. It is shown that local irradiation with a focused He⁺ ion beam enables the formation of regions with decreased easy-axis anisotropy (magnetic bubbles) that have the inverse magnetization direction in the demagnetized state of Co/Pt...
September 5, 2017: Materials
Dongyeon Kim, Daniel Radin, Donna Leonardi
BACKGROUND/AIM: Extracts of Paeonia suffruticosa are traditionally used in Chinese medicine to increase blood flow. Recently, this extract has been shown to possess anti-tumor and anti-inflammatory properties, though this mechanism remains unknown. In the current work, we prepared extracts of P. suffruticosa and analyzed their effects on MDA-MB-231 triple-negative breast cancer cells. MATERIALS AND METHODS: Varying concentrations of an aqueous extract of P. suffruticosa was administered to MDA-MB-231...
September 2017: Anticancer Research
Svetlana A Romanenko, Natalya A Serdyukova, Polina L Perelman, Svetlana V Pavlova, Nina S Bulatova, Feodor N Golenishchev, Roscoe Stanyon, Alexander S Graphodatsky
It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information...
August 30, 2017: Genes
Michael Rose, Carolin Curtze, Joseph O'Sullivan, Mahmoud El-Gohary, Dennis Crawford, Darin Friess, Jacqueline M Brady
PURPOSE: To develop a model using wearable inertial sensors to assess the performance of orthopaedic residents while performing a diagnostic knee arthroscopy. METHODS: Fourteen subjects performed a diagnostic arthroscopy on a cadaveric right knee. Participants were divided into novices (5 postgraduate year 3 residents), intermediates (5 postgraduate year 4 residents), and experts (4 faculty) based on experience. Arm movement data were collected by inertial measurement units (Opal sensors) by securing 2 sensors to each upper extremity (dorsal forearm and lateral arm) and 2 sensors to the trunk (sternum and lumbar spine)...
August 30, 2017: Arthroscopy: the Journal of Arthroscopic & related Surgery
Manuel Krämer, Christian W Müller, Maike Hermann, Sebastian Decker, André Springer, Ludger Overmeyer, Christof Hurschler, Ronny Pfeifer
Biomechanical stimuli play a major role in fracture healing. Changing the fixation stiffness through the course of healing might accelerate bone healing and prevent healing complications. Shape memory alloy (SMA) based implants were developed to allow for non-invasive stiffness alteration during the fracture healing process. To gain a deeper understanding of the implant functionality based on the alloy characteristics and geometric design, the mechanical properties of different shape memory alloys where mechanically characterized...
August 23, 2017: Journal of the Mechanical Behavior of Biomedical Materials
Fugang Yang, Mehmet S Ozturk, Ruoyang Yao, Xavier Intes
Mesoscopic fluorescence molecular tomography (MFMT) is a novel imaging technique that aims at obtaining the 3-D distribution of molecular probes inside biological tissues at depths of a few millimeters. To achieve high resolution, around 100-150μm scale in turbid samples, dense spatial sampling strategies are required. However, a large number of optodes leads to sizable forward and inverse problems that can be challenging to compute efficiently. In this work, we propose a two-step data reduction strategy to accelerate the inverse problem and improve robustness...
August 1, 2017: Biomedical Optics Express
Roel W Ten Broek, Elise M Bekers, Wendy W J de Leng, Eric Strengman, Bastiaan Bj Tops, Heinz Kutzner, Jan Willem Leeuwis, Joost M van Gorp, David H Creytens, Thomas Mentzel, Paul J van Diest, Astrid Eijkelenboom, Uta Flucke
Spindle cell hemangioma (SCH) is a distinct vascular soft tissue lesion characterized by cavernous blood vessels and a spindle cell component mainly occurring in the distal extremities of young adults. The majority of cases harbor heterozygous mutations in IDH1/2 sporadically or rarely in association with Maffucci syndrome. However, based on mosaicism and accordingly a low percentage of lesional cells harboring a mutant allele, detection can be challenging. We tested 19 sporadic SCHs by Sanger sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), conventional Next Generation Sequencing (NGS) and NGS using a Single Molecule Molecular Inversion Probes (smMIP) based library preparation in order to compare their diagnostic value...
August 28, 2017: Genes, Chromosomes & Cancer
Michael Sennert, Christian Happel, Yücel Korkusuz, Frank Grünwald, Björn Polenz, Daniel Gröner
RATIONALE AND OBJECTIVES: Several minimally invasive thermal techniques have been developed for the treatment of benign thyroid nodules. A new technique for this indication is high-intensity focused ultrasound (HIFU). The aim of this study was to assess effectiveness in varying preablative nodule volumes and whether outcome patterns that were reported during studies with other thermal ablative procedures for thyroid nodule ablation would also apply to HIFU. MATERIALS AND METHODS: Over the last 2 years, 19 nodules in 15 patients (12 women) whose average age was 58...
August 23, 2017: Academic Radiology
Calvin A Mok, Vinci Au, Owen A Thompson, Mark L Edgley, Louis Gevirtzman, John Yochem, Joshua Lowry, Nadin Memar, Matthew R Wallenfang, Dominique Rasoloson, Bruce Bowerman, Ralf Schnabel, Geraldine Seydoux, Donald G Moerman, Robert H Waterston
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS)...
August 21, 2017: Genetics
Christopher Dacosta, Yongping Bao
Colorectal cancer is an increasingly significant cause of mortality whose risk is linked to diet and inversely correlated with cruciferous vegetable consumption. This is likely to be partly attributable to the isothiocyanates derived from eating these vegetables, such as sulforaphane, which is extensively characterised for cytoprotective and tumour-suppressing activities. However, its bioactivities are likely to extend in complexity beyond those currently known; further insight into these bioactivities could aid the development of sulforaphane-based chemopreventive or chemotherapeutic strategies...
August 19, 2017: Nutrients
Mark D Ericson, Katie T Freeman, Sathya M Schnell, Katlyn A Fleming, Carrie Haskell-Luevano
The melanocortin system consists of five reported receptors, agonists from the proopiomelanocortin gene transcript, and two antagonists, agouti-signaling protein (ASP) and agouti-related protein (AGRP). For both ASP and AGRP, the hypothesized Arg-Phe-Phe pharmacophores are on exposed β-hairpin loops. In this study, the Asn and Ala positions of a reported AGRP macrocyclic scaffold (c[Pro-Arg-Phe-Phe-Asn-Ala-Phe-DPro]) were explored with 14-compound and 8-compound libraries, respectively, to generate more potent, selective melanocortin receptor antagonists...
August 16, 2017: Journal of Medicinal Chemistry
Richard N Collins, Kevin M Rosso
Molecular-level pathways in the aqueous redox transformation of uranium by iron remain unclear, despite the importance of this knowledge for predicting uranium transport and distribution in natural and engineered environments. As the relative importance of homogeneous versus heterogeneous pathways is difficult to probe experimentally, here we apply computational molecular simulation to isolate rates of key one electron transfer reactions in the homogeneous pathway. By comparison to experimental observations the role of the heterogeneous pathway also becomes clear...
August 25, 2017: Journal of Physical Chemistry. A
Manon S Oud, Liliana Ramos, Moira K O'Bryan, Robert I McLachlan, Özlem Okutman, Stephane Viville, Petra F de Vries, Dominique F C M Smeets, Dorien Lugtenberg, Jayne Y Hehir-Kwa, Christian Gilissen, Maartje van de Vorst, Lisenka E L M Vissers, Alexander Hoischen, Aukje M Meijerink, Kathrin Fleischer, Joris A Veltman, Michiel J Noordam
Microdeletions of the Y chromosome (YCMs), Klinefelter syndrome (47,XXY), and CFTR mutations are known genetic causes of severe male infertility, but the majority of cases remain idiopathic. Here, we describe a novel method using single molecule Molecular Inversion Probes (smMIPs), to screen infertile men for mutations and copy number variations affecting known disease genes. We designed a set of 4,525 smMIPs targeting the coding regions of causal (n = 6) and candidate (n = 101) male infertility genes. After extensive validation, we screened 1,112 idiopathic infertile men with non-obstructive azoospermia or severe oligozoospermia...
August 11, 2017: Human Mutation
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