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https://www.readbyqxmd.com/read/28531887/expression-and-characterization-of-membrane-type-4-matrix-metalloproteinase-mt4-mmp-and-its-different-forms-in-melanoma
#1
Bettina Hieronimus, Julian Pfohl, Christian Busch, Lutz Graeve
BACKGROUND/AIMS: Membrane-type matrix metalloproteinases (MT-MMPs) are expressed on the cell surface and hydrolyze extracellular matrix components and signaling molecules by which they influence cancer cell migration and metastasis. Two of the six known MT-MMPs are anchored to the plasma membrane via a GPI anchor, one of which is MT4-MMP. Only little is known about MT4-MMP expression, synthesis, regulation and degradation. METHODS: We analyzed several human cancer cell lines as well as tissue homogenates using Western blotting and quantitative PCR for the expression of MT4-MMP...
May 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28472459/resolving-rapid-radiations-within-angiosperm-families-using-anchored-phylogenomics
#2
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford, Emily Moriarty Lemmon, Alan R Lemmon
Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28452858/primary-bone-anaplastic-large-cell-lymphoma-masquerading-as-ewing-sarcoma-diagnosis-by-anchored-multiplex-pcr
#3
Susan Swee-Shan Hue, Prasad Iyer, Luke Han Wei Toh, Sudhanshi Jain, Enrica Ee Kar Tan, Kesavan Sittampalam, Derrick Wen Quan Lian, Kenneth Tou En Chang
A 3-year-old boy presented with pathologic fracture of the left proximal femur. Magnetic resonance imaging revealed an aggressive expansile bony mass associated with cortical destruction and surrounding myositis. Computed tomography-guided biopsy revealed a monomorphic small round blue cell tumor by histology. CD99 immunoreactivity and low-level EWSR1 gene translocation by break-apart fluorescent in situ hybridization initially favored a diagnosis of Ewing sarcoma and chemotherapy commenced. Subsequent molecular evaluation by an anchored multiplex polymerase chain reaction-based assay (Archer FusionPlex Sarcoma Panel) revealed a nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) gene fusion...
April 27, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28442916/expression-and-activity-of-the-urokinase-plasminogen-activator-system-in-canine-primary-brain-tumors
#4
John H Rossmeisl, Kelli Hall-Manning, John L Robertson, Jamie N King, Rafael V Davalos, Waldemar Debinski, Subbiah Elankumaran
BACKGROUND: The expression of the urokinase plasminogen activator receptor (uPAR), a glycosylphosphatidylinositol-anchored protein family member, and the activity of its ligand, urokinase-type plasminogen activator (uPA), have been associated with the invasive and metastatic potentials of a variety of human brain tumors through their regulation of extracellular matrix degradation. Domesticated dogs develop naturally occurring brain tumors that share many clinical, phenotypic, molecular, and genetic features with their human counterparts, which has prompted the use of the dogs with spontaneous brain tumors as models to expedite the translation of novel brain tumor therapeutics to humans...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28329833/thy1-cd90-expression-is-reduced-by-the-environmental-chemical-tetrabromobisphenol-a-to-promote-adipogenesis-through-induction-of-microrna-103
#5
Collynn F Woeller, E'Lissa Flores, Stephen J Pollock, Richard P Phipps
Environmental chemicals termed "obesogens" disrupt the endocrine system to promote adipogenesis and obesity. Tetrabromobisphenol-A (TBBPA) has been reported to increase adipogenesis, however, the mechanism(s) of action are unclear. Thy1 (CD90) is a glycophosphatidylinositol (GPI) -anchored membrane protein that serves as a marker for stem cells and also plays an important role in regulating adipogenesis and obesity. We investigated whether or not TBBPA promotes adipogenesis in human and mouse cells by reducing Thy1 levels...
February 22, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28192645/cytological-molecular-and-clinical-features-of-noninvasive-follicular-thyroid-neoplasm-with-papillary-like-nuclear-features-versus-invasive-forms-of-follicular-variant-of-papillary-thyroid-carcinoma
#6
Liena Zhao, Dora Dias-Santagata, Peter M Sadow, William C Faquin
BACKGROUND: The noninvasive follicular variant of papillary thyroid carcinoma (PTC) has an indolent clinical behavior in comparison with other PTCs, including the invasive follicular variant of papillary thyroid carcinoma (IFVPTC). Recently, the term noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) was introduced to emphasize the low biological potential of these tumors. This study compares clinical, cytological, and molecular features of NIFTP and IFVPTC...
February 13, 2017: Cancer
https://www.readbyqxmd.com/read/28192241/molecular-cloning-mrna-expression-and-characterization-of-membrane-bound-hemoglobin-in-oriental-river-prawn-macrobrachium-nipponense
#7
Shengming Sun, Fujun Xuan, Hongtuo Fu, Jian Zhu, Xianping Ge, Xugan Wu
Most hemoglobins are respiratory proteins and are ubiquitous in animals, bacteria, fungi, protists, and plants. In this study, we describe a membrane-bound hemoglobin in the oriental river prawn Macrobrachium nipponense (MnHb), which also expresses hemocyanin. MnHb cDNA was cloned using the rapid amplification of cDNA ends (RACE) approach, which afforded a 1201bp gene encoding a 193 amino acid polypeptide. Bioinformatic evaluation suggested MnHb is membrane anchored by N-myristoylation, and immunofluorescence confirmed its location in the membrane of chief cells in the gill...
February 10, 2017: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/28032541/molecular-characteristics-of-streptococcus-agalactiae-strains-deficient-in-alpha-like-protein-encoding-genes
#8
Christina Gabrielsen, Johan A Mæland, Randi Valsø Lyng, Andreas Radtke, Jan Egil Afset
Streptococcus agalactiae (group B streptococci, GBS) are important human and animal pathogens, which can be subdivided based on different capsular polysaccharides and surface-anchored alpha-like proteins (Alps), as well as other proteins. Nearly all GBS strains possess an Alp (Alp GBS), although Alp-negative GBS (non-Alp GBS) do occur. In this study, 10 (1.1 %) of 932 clinical human GBS tested lacked an Alp encoding gene. All 10 strains were from patients with bloodstream infection, confirming that non-Alp GBS can be highly virulent...
January 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27783658/complementary-primer-asymmetric-pcr-compas-pcr-applied-to-the-identification-of-salmo-salar-salmo-trutta-and-their-hybrids
#9
Marc B Anglès d'Auriac
Avoiding complementarity between primers when designing a PCR assay constitutes a central rule strongly anchored in the mind of the molecular scientist. 3'-complementarity will extend the primers during PCR elongation using one another as template, consequently disabling further possible involvement in traditional target amplification. However, a 5'-complementarity will leave the primers unchanged during PCR cycles, albeit sequestered to one another, therefore also suppressing target amplification. We show that 5'-complementarity between primers may be exploited in a new PCR method called COMplementary-Primer-Asymmetric (COMPAS)-PCR, using asymmetric primer concentrations to achieve target PCR amplification...
2016: PloS One
https://www.readbyqxmd.com/read/27730518/molecular-and-bioinformatic-characterization-of-the-rice-root-uv-b-sensitive-gene-family
#10
Ning Yu, Yaping Liang, Xinxiang Peng, Xuewen Hou
BACKGROUND: ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. FINDINGS: In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases...
December 2016: Rice
https://www.readbyqxmd.com/read/27647802/next-generation-sequencing-adds-value-to-the-preoperative-diagnosis-of-pancreatic-cysts
#11
Matthew W Rosenbaum, Martin Jones, Jonathan C Dudley, Long P Le, A John Iafrate, Martha B Pitman
BACKGROUND: The diagnosis of a pancreatic cyst as mucinous or high-risk dictates the need for follow-up or surgery. Molecular analysis of aspirated pancreatic cyst fluid (PCF) can provide valuable information not obtained by carcinoembryonic antigen (CEA) analysis or cytology. METHODS: All patients who underwent molecular analysis of PCF between March 2013 and June 2015 were reviewed, including pathology, imaging, and follow-up. Molecular testing was performed using a patented, anchored multiplex polymerase chain reaction next-generation sequencing (NGS) platform, which sequenced numerous hotspots in 39 genes linked with malignancy...
January 2017: Cancer
https://www.readbyqxmd.com/read/27571201/development-of-2-7-diamino-1-8-naphthyridine-danp-anchored-hairpin-primers-for-rt-pcr-detection-of-chikungunya-virus-infection
#12
Huixin Chen, Mariya Parimelalagan, Fumie Takei, Hapuarachchige Chanditha Hapuarachchi, Evelyn Siew-Chuan Koay, Lee Ching Ng, Phui San Ho, Kazuhiko Nakatani, Justin Jang Hann Chu
A molecular diagnostic platform with DANP-anchored hairpin primer was developed and evaluated for the rapid and cost-effective detection of Chikungunya virus (CHIKV) with high sensitivity and specificity. The molecule 2, 7-diamino-1, 8-naphthyridine (DANP) binds to a cytosine-bulge and emits fluorescence at 450 nm when it is excited by 400 nm light. Thus, by measuring the decline in fluorescence emitted from DANP-primer complexes after PCR reaction, we could monitor the PCR progress. By adapting this property of DANP, we have previously developed the first generation DANP-coupled hairpin RT-PCR assay...
August 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27357120/anchored-enrichment-dataset-for-true-flies-order-diptera-reveals-insights-into-the-phylogeny-of-flower-flies-family-syrphidae
#13
Andrew Donovan Young, Alan R Lemmon, Jeffrey H Skevington, Ximo Mengual, Gunilla Ståhls, Menno Reemer, Kurt Jordaens, Scott Kelso, Emily Moriarty Lemmon, Martin Hauser, Marc De Meyer, Bernhard Misof, Brian M Wiegmann
BACKGROUND: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies...
2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27244445/multiplex-real-time-pcr-assays-that-measure-the-abundance-of-extremely-rare-mutations-associated-with-cancer
#14
Diana Y Vargas, Fred Russell Kramer, Sanjay Tyagi, Salvatore A E Marras
We describe the use of "SuperSelective" primers that enable the detection and quantitation of somatic mutations whose presence relates to cancer diagnosis, prognosis, and therapy, in real-time PCR assays that can potentially analyze rare DNA fragments present in blood samples (liquid biopsies). The design of these deoxyribonucleotide primers incorporates both a relatively long "5' anchor sequence" that hybridizes strongly to target DNA fragments, and a very short, physically and functionally separate, "3' foot sequence" that is perfectly complementary to the mutant target sequence, but mismatches the wild-type sequence...
2016: PloS One
https://www.readbyqxmd.com/read/27028240/detecting-gene-rearrangements-in-patient-populations-through-a-2-step-diagnostic-test-comprised-of-rapid-ihc-enrichment-followed-by-sensitive-next-generation-sequencing
#15
Danielle A Murphy, Heather A Ely, Robert Shoemaker, Aaron Boomer, Brady P Culver, Ian Hoskins, Josh D Haimes, Ryan D Walters, Diane Fernandez, Joshua A Stahl, Jeeyun Lee, Kyoung-Mee Kim, Jennifer Lamoureux, Jason Christiansen
Targeted therapy combined with companion diagnostics has led to the advancement of next-generation sequencing (NGS) for detection of molecular alterations. However, using a diagnostic test to identify patient populations with low prevalence molecular alterations, such as gene rearrangements, poses efficiency, and cost challenges. To address this, we have developed a 2-step diagnostic test to identify NTRK1, NTRK2, NTRK3, ROS1, and ALK rearrangements in formalin-fixed paraffin-embedded clinical specimens. This test is comprised of immunohistochemistry screening using a pan-receptor tyrosine kinase cocktail of antibodies to identify samples expressing TrkA (encoded by NTRK1), TrkB (encoded by NTRK2), TrkC (encoded by NTRK3), ROS1, and ALK followed by an RNA-based anchored multiplex polymerase chain reaction NGS assay...
March 29, 2016: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/26990025/the-application-of-next-generation-sequencing-based-molecular-diagnostics-in-endometrial-stromal-sarcoma
#16
Xiaodong Li, Mona Anand, Josh D Haimes, Namitha Manoj, Aaron M Berlin, Brian A Kudlow, Marisa R Nucci, Tony L Ng, Colin J R Stewart, Cheng-Han Lee
AIMS: Endometrial stromal sarcomas (ESSs) are divided into low-grade and high-grade subtypes, with the latter showing more aggressive clinical behaviour. Although histology and immunophenotype can aid in the diagnosis of these tumours, genetic studies can provide additional diagnostic insights, as low-grade ESSs frequently harbour fusions involving JAZF1/SUZ12 and/or JAZF1/PHF1, whereas high-grade ESSs are defined by YWHAE-NUTM2A/B fusions. The aim of this study was to evaluate the utility of a next-generation sequencing (NGS)-based assay in identifying ESS fusions in archival formalin-fixed paraffin-embedded tumour samples...
October 2016: Histopathology
https://www.readbyqxmd.com/read/26985951/molecular-characterization-tissue-expression-profile-and-single-nucleotide-polymorphism-analysis-of-the-periostin-gene-in-swine
#17
D Xu, H M Ma, D F Xiao
Periostin, also called osteoblast-specific factor 2, is an important regulator of bone, cardiac development, and wound healing. A recent study revealed that periostin plays an important role in tumor development and is upregulated in a wide variety of cancers. However, little is known about periostin in swine. Therefore, the cDNA sequence of the porcine periostin gene was obtained by rapid amplification of cDNA ends (RACE). One C/T single nucleotide polymorphism anchored in intron 9 was identified and genotyped by PCR-RFLP-HaeIII...
March 11, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/26845560/a-new-glabrous-gene-csgl3-identified-in-trichome-development-in-cucumber-cucumis-sativus-l
#18
Jin-Ying Cui, Han Miao, Li-Hong Ding, Todd C Wehner, Pan-Na Liu, Ye Wang, Sheng-Ping Zhang, Xing-Fang Gu
Spines or trichomes on the fruit of cucumbers enhance their commercial value in China. In addition, glabrous mutants exhibit resistance to aphids and therefore their use by growers can reduce pesticide residues. Previous studies have reported two glabrous mutant plants containing the genes, csgl1 and csgl2. In the present study, a new glabrous mutant, NCG157, was identified showing a gene interaction effect with csgl1 and csgl2. This mutant showed the glabrous character on stems, leaves, tendrils, receptacles and ovaries, and there were no spines or tumors on the fruit surface...
2016: PloS One
https://www.readbyqxmd.com/read/26821654/knockdown-of-nadph-cytochrome-p450-reductase-results-in-reduced-resistance-to-buprofezin-in-the-small-brown-planthopper-laodelphax-striatellus-fall%C3%A3-n
#19
Yueliang Zhang, Yaming Wang, Lihua Wang, Jing Yao, Huifang Guo, Jichao Fang
NADPH-cytochrome P450 reductase (CPR) plays an important role in cytochrome P450 function, and CPR knockdown in several insects leads to increased susceptibility to insecticides. However, a putative CPR gene has not yet been fully characterized in the small brown planthopper Laodelphax striatellus, a notorious agricultural pest in rice that causes serious damage by transmitting rice stripe and rice black-streaked dwarf viruses. The objective of this study was to clone the cDNA and to knock down the expression of the gene that encodes L...
February 2016: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/26779187/genome-wide-analysis-of-the-fasciclin-like-arabinogalactan-protein-gene-family-reveals-differential-expression-patterns-localization-and-salt-stress-response-in-populus
#20
Lina Zang, Tangchun Zheng, Yanguang Chu, Changjun Ding, Weixi Zhang, Qinjun Huang, Xiaohua Su
Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) involved in plant growth, development and response to abiotic stress. Although many studies have been performed to identify molecular functions of individual family members, little information is available on genome-wide identification and characterization of FLAs in the genus Populus. Based on genome-wide analysis, we have identified 35 Populus FLAs which were distributed on 16 chromosomes and phylogenetically clustered into four major groups...
2015: Frontiers in Plant Science
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