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https://www.readbyqxmd.com/read/28821194/primary-benign-and-malignant-thyroid-neoplasms-with-signet-ring-cells-cytologic-histologic-and-molecular-features
#1
Nada A Farhat, Ayse M Onenerk, Jeffrey F Krane, Dora Dias-Santagata, Peter M Sadow, William C Faquin
Objectives: Signet ring cells (SRCs) can be seen in a variety of thyroid tumors and can pose a diagnostic pitfall on cytology. This study describes the cytologic, histomorphologic, and molecular aspects of a cohort of primary thyroid tumors with SRCs. Methods: A search was performed of the Massachusetts General Hospital and Brigham and Women's Hospital (Boston, MA) pathology archives for the keywords thyroid, signet, and signet ring features between 2000 and 2014...
September 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28752842/usp6-activation-in-nodular-fasciitis-by-promoter-swapping-gene-fusions
#2
Nimesh R Patel, John S A Chrisinger, Elizabeth G Demicco, Stephen F Sarabia, Jacquelyn Reuther, Erica Kumar, Andre M Oliveira, Steven D Billings, Judith V M G Bovée, Angshumoy Roy, Alexander J Lazar, Dolores H Lopez-Terrada, Wei-Lien Wang
Nodular fasciitis is a self-limited myofibroblastic lesion that can be misdiagnosed as a sarcoma as a result of its rapid growth, cellularity, and sometimes prominent mitotic activity. A recurrent translocation t(17;22) has been identified in nodular fasciitis, fusing the coding region of USP6 to the promoter region of MYH9, and resulting in increased USP6 expression. A subset of cases show USP6 rearrangement without the typical fusion variants by RT-PCR, or any MYH9 rearrangement by FISH. We sought to further characterize such tumors using molecular diagnostic assays...
July 28, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28630090/t-cell-transcriptomes-from-paroxysmal-nocturnal-hemoglobinuria-patients-reveal-novel-signaling-pathways
#3
Kohei Hosokawa, Sachiko Kajigaya, Keyvan Keyvanfar, Wangmin Qiao, Yanling Xie, Danielle M Townsley, Xingmin Feng, Neal S Young
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare acquired disorder originating from hematopoietic stem cells and is a life-threating disease characterized by intravascular hemolysis, bone marrow (BM) failure, and venous thrombosis. The etiology of PNH is a somatic mutation in the phosphatidylinositol glycan class A gene (PIG-A) on the X chromosome, which blocks synthesis of the glycolipid moiety and causes deficiency in GPI-anchored proteins. PNH is closely related to aplastic anemia, in which T cells mediate destruction of BM...
July 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28559291/interaction-of-mycoplasma-hominis-pg21-with-human-dendritic-cells-interleukin-23-inducing-mycoplasmal-lipoproteins-and-inflammasome-activation-of-the-cell
#4
J Goret, L Béven, B Faustin, C Contin-Bordes, C Le Roy, S Claverol, H Renaudin, C Bébéar, S Pereyre
Mycoplasma hominis lacks a cell wall, and lipoproteins anchored to the extracellular side of the plasma membrane are in direct contact with the host components. A Triton X-114 extract of M. hominis enriched with lipoproteins was shown to stimulate the production of interleukin-23 (IL-23) by human dendritic cells (hDCs). The inflammasome activation of the host cell has never been reported upon M. hominis infection. We studied here the interaction between M. hominis PG21 and hDCs by analyzing both the inflammation-inducing mycoplasmal lipoproteins and the inflammasome activation of the host cell...
August 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28536590/miniature-inverted-repeat-transposable-element-insertions-provide-a-source-of-intron-length-polymorphism-markers-in-the-carrot-daucus-carota-l
#5
Katarzyna Stelmach, Alicja Macko-Podgórni, Gabriela Machaj, Dariusz Grzebelus
The prevalence of non-autonomous class II transposable elements (TEs) in plant genomes may serve as a tool for relatively rapid and low-cost development of gene-associated molecular markers. Miniature inverted-repeat transposable element (MITE) copies inserted within introns can be exploited as potential intron length polymorphism (ILP) markers. ILPs can be detected by PCR with primers anchored in exon sequences flanking the target introns. Here, we designed primers for 209 DcSto (Daucus carota Stowaway-like) MITE insertion sites within introns along the carrot genome and validated them as candidate ILP markers in order to develop a set of markers for genotyping the carrot...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28531887/expression-and-characterization-of-membrane-type-4-matrix-metalloproteinase-mt4-mmp-and-its-different-forms-in-melanoma
#6
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...
2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28472459/resolving-rapid-radiations-within-angiosperm-families-using-anchored-phylogenomics
#7
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
#8
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
#9
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/editor-s-highlight-thy1-cd90-expression-is-reduced-by-the-environmental-chemical-tetrabromobisphenol-a-to-promote-adipogenesis-through-induction-of-microrna-103
#10
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-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...
June 1, 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
#11
COMPARATIVE STUDY
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...
May 2017: Cancer
https://www.readbyqxmd.com/read/28192241/molecular-cloning-mrna-expression-and-characterization-of-membrane-bound-hemoglobin-in-oriental-river-prawn-macrobrachium-nipponense
#12
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...
May 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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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...
June 29, 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
#19
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
#20
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...
August 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
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