keyword
MENU ▼
Read by QxMD icon Read
search

Molecular markers

keyword
https://www.readbyqxmd.com/read/29452334/seed-2-a-user-friendly-platform-for-amplicon-high-throughput-sequencing-data-analyses
#1
Tomáš Vetrovský, Petr Baldrian, Daniel Morais, Bonnie Berger
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452107/trabecular-meshwork-morphogenesis-a-comparative-analysis-of-wildtype-and-anterior-segment-dysgenesis-mouse-models
#2
Rebecca L Rausch, Richard T Libby, Amy E Kiernan
The trabecular meshwork (TM), a tissue residing in the iridocorneal angle of the eye, is the primary site of aqueous humor outflow and often develops abnormally in children with anterior segment dysgenesis (ASD). However, the cellular mechanisms underlying both normal and pathophysiological TM formation are poorly understood. Here, we improve the characterization of TM development via morphological and molecular analyses. We first assessed the TM of wild-type C57BL/6J mice at multiple time points throughout development (E15...
February 13, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29451745/detection-of-ros1-positive-non-small-cell-lung-cancer-on-cytological-specimens-using-immunocytochemistry
#3
Tatjana Vlajnic, Spasenija Savic, Audrey Barascud, Betty Baschiera, Michel Bihl, Bruno Grilli, Michelle Herzog, Julien Rebetez, Lukas Bubendorf
BACKGROUND: Rearrangements of the ROS1 oncogene are found in 1% to 2% of non-small cell lung cancers (NSCLC) and are regarded as mutually exclusive oncogenic driver mutations. Since the approval of targeted therapy for ROS1-positive NSCLC, ROS1 testing has become a part of the diagnostic routine. Fluorescence in situ hybridization (FISH), optionally selected for by immunohistochemistry on histological material, is a common practice for the detection of ROS1 rearrangements. However, NSCLC often is diagnosed by cytology alone, requiring predictive marker testing on cytological specimens...
February 16, 2018: Cancer Cytopathology
https://www.readbyqxmd.com/read/29451166/molecular-analysis-of-pancreatic-cyst-fluid-changes-clinical-management
#4
David M Arner, Brooke E Corning, Ali M Ahmed, Henry C Ho, Bradley J Weinbaum, Uzma Siddiqui, Harry Aslanian, Reid B Adams, Todd W Bauer, Andrew Y Wang, Vanessa M Shami, Bryan G Sauer
Background and Objectives: DNA molecular analysis has been suggested as a tool to evaluate pancreatic cysts. This study assesses whether the addition of DNA molecular analysis alters clinical management. Methods: This is a retrospective review of 46 consecutive patients who underwent EUS-FNA of pancreatic cysts with DNA molecular analysis at two major academic institutions. Cases were presented to two pancreaticobiliary surgeons first without and then with DNA molecular analysis data...
January 2018: Endoscopic Ultrasound
https://www.readbyqxmd.com/read/29450724/chromaffin-cell-biology-inferences-from-the-cancer-genome-atlas
#5
REVIEW
Lauren Fishbein, Matthew D Wilkerson
Pheochromocytomas and paragangliomas (PCC/PGLs) are rare neuroendocrine tumors that are unusually diverse in metabolic profiles, in classes of molecular alterations and across a large number of altered genes. The Cancer Genome Atlas (TCGA) comprehensively profiled the molecular landscape of PCC/PGLs and identified novel genomic alterations and a new molecular classification of PCC/PGLs. In this review, we discuss the significant clinico-molecular findings of this integrated profiling study. We then review the molecular data of the TCGA cohort centering around known markers of sympathoadrenal cell lineage to better understand chromaffin cell biology...
February 15, 2018: Cell and Tissue Research
https://www.readbyqxmd.com/read/29450494/comparison-of-the-performance-of-6-prognostic-signatures-for-estrogen-receptor-positive-breast-cancer-a-secondary-analysis-of-a-randomized-clinical-trial
#6
Ivana Sestak, Richard Buus, Jack Cuzick, Peter Dubsky, Ralf Kronenwett, Carsten Denkert, Sean Ferree, Dennis Sgroi, Catherine Schnabel, Frederick L Baehner, Elizabeth Mallon, Mitch Dowsett
Importance: Multiple molecular signatures are available for managing estrogen receptor (ER)-positive breast cancer but with little direct comparative information to guide the patient's choice. Objective: To conduct a within-patient comparison of the prognostic value of 6 multigene signatures in women with early ER-positive breast cancer who received endocrine therapy for 5 years. Design, Setting, and Participants: This retrospective biomarker analysis included 774 postmenopausal women with ER-positive ERBB2 (formerly HER2)-negative breast cancer...
February 15, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/29450137/liver-and-metformin-lessons-of-a-fructose-diet-in-mice
#7
Iara Karise, Fernanda Ornellas, Sandra Barbosa-da-Silva, Cristiane Matsuura, Mariano Del Sol, Marcia Barbosa Aguila, Carlos A Mandarim-de-Lacerda
Studies show that the continuous consumption of fructose can lead to nonalcoholic fatty liver disease (NAFLD) and steatohepatitis. We aimed to investigate the role of Metformin in an animal model of liver injury caused by fructose intake, focusing on the molecular markers of lipogenesis, beta-oxidation, and antioxidant defenses. Male three months old C57BL/6 mice were divided into control group (C) and fructose group (F, 47% fructose), maintained for ten weeks. After, the groups received Metformin or vehicle for a further eight weeks: control (C), control + Metformin (CM), fructose (F), and fructose + Metformin (FM)...
June 2017: Biochimie Open
https://www.readbyqxmd.com/read/29449896/myxofibrosarcoma-primary-cultures-molecular-and-pharmacological-profile
#8
Alessandro De Vita, Federica Recine, Laura Mercatali, Giacomo Miserocchi, Chiara Liverani, Chiara Spadazzi, Roberto Casadei, Alberto Bongiovanni, Federica Pieri, Nada Riva, Dino Amadori, Toni Ibrahim
Background: Myxofibrosarcoma (MFS), formerly considered as a myxoid variant of malignant fibrous histiocytoma, is the most common sarcoma of the extremities in adults and is characterized by a high frequency of local recurrence. The clinical behavior of MFS is unpredictable and the efficacy of chemotherapy is still not well documented. Furthermore, given the relatively recent recognition of MFS as a distinct pathologic entity its cellular and molecular biology has still not been extensively studied in patient-derived preclinical models...
December 2017: Therapeutic Advances in Medical Oncology
https://www.readbyqxmd.com/read/29449635/purkinje-cells-derived-from-tsc-patients-display-hypoexcitability-and-synaptic-deficits-associated-with-reduced-fmrp-levels-and-reversed-by-rapamycin
#9
Maria Sundberg, Ivan Tochitsky, David E Buchholz, Kellen Winden, Ville Kujala, Kush Kapur, Deniz Cataltepe, Daria Turner, Min-Joon Han, Clifford J Woolf, Mary E Hatten, Mustafa Sahin
Accumulating evidence suggests that cerebellar dysfunction early in life is associated with autism spectrum disorder (ASD), but the molecular mechanisms underlying the cerebellar deficits at the cellular level are unclear. Tuberous sclerosis complex (TSC) is a neurocutaneous disorder that often presents with ASD. Here, we developed a cerebellar Purkinje cell (PC) model of TSC with patient-derived human induced pluripotent stem cells (hiPSCs) to characterize the molecular mechanisms underlying cerebellar abnormalities in ASD and TSC...
February 15, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29449608/mapping-molecular-assemblies-with-fluorescence-microscopy-and-object-based-spatial-statistics
#10
Thibault Lagache, Alexandre Grassart, Stéphane Dallongeville, Orestis Faklaris, Nathalie Sauvonnet, Alexandre Dufour, Lydia Danglot, Jean-Christophe Olivo-Marin
Elucidating protein functions and molecular organisation requires to localise precisely single or aggregated molecules and analyse their spatial distributions. We develop a statistical method SODA (Statistical Object Distance Analysis) that uses either micro- or nanoscopy to significantly improve on standard co-localisation techniques. Our method considers cellular geometry and densities of molecules to provide statistical maps of isolated and associated (coupled) molecules. We use SODA with three-colour structured-illumination microscopy (SIM) images of hippocampal neurons, and statistically characterise spatial organisation of thousands of synapses...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29449453/conserved-and-divergent-features-of-human-and-mouse-kidney-organogenesis
#11
Nils O Lindström, Jill A McMahon, Jinjin Guo, Tracy Tran, Qiuyu Guo, Elisabeth Rutledge, Riana K Parvez, Gohar Saribekyan, Robert E Schuler, Christopher Liao, Albert D Kim, Ahmed Abdelhalim, Seth W Ruffins, Matthew E Thornton, Laurence Basking, Brendan Grubbs, Carl Kesselman, Andrew P McMahon
Human kidney function is underpinned by approximately 1,000,000 nephrons, although the number varies substantially, and low nephron number is linked to disease. Human kidney development initiates around 4 weeks of gestation and ends around 34-37 weeks of gestation. Over this period, a reiterative inductive process establishes the nephron complement. Studies have provided insightful anatomic descriptions of human kidney development, but the limited histologic views are not readily accessible to a broad audience...
February 15, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29449451/conserved-and-divergent-molecular-and-anatomic-features-of-human-and-mouse-nephron-patterning
#12
Nils O Lindström, Tracy Tran, Jinjin Guo, Elisabeth Rutledge, Riana K Parvez, Matthew E Thornton, Brendan Grubbs, Jill A McMahon, Andrew P McMahon
The nephron is the functional unit of the kidney, but the mechanism of nephron formation during human development is unclear. We conducted a detailed analysis of nephron development in humans and mice by immunolabeling, and we compared human and mouse nephron patterning to describe conserved and divergent features. We created protein localization maps that highlight the emerging patterns along the proximal-distal axis of the developing nephron and benchmark expectations for localization of functionally important transcription factors, which revealed unanticipated cellular diversity...
February 15, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29449169/interaction-of-the-wnt-%C3%AE-catenin-and-ras-erk-pathways-involving-co-stabilization-of-both-%C3%AE-catenin-and-ras-plays-important-roles-in-the-colorectal-tumorigenesis
#13
REVIEW
Sang-Kyu Lee, Jeong-Ha Hwang, Kang-Yell Choi
Cancer development is usually driven by multiple genetic and molecular alterations rather than by a single defect. In the human colorectal cancer (CRC), series of mutations of genes are involved in the different stages of tumorigenesis. For example, adenomatous polyposis coli (APC) and KRAS mutations have been known to play roles in the initiation and progression of the tumorigenesis, respectively. However, many studies indicate that mutations of these two genes, which play roles in the Wnt/β-catenin and RAS-extra-cellular signal regulated kinase (ERK) pathways, respectively, cooperatively interact in the tumorigenesis in several different cancer types including CRC...
January 10, 2018: Advances in Biological Regulation
https://www.readbyqxmd.com/read/29449053/genetic-and-epigenetic-alterations-in-the-tumour-tumour-margins-and-normal-buccal-mucosa-of-patients-with-oral-cancer
#14
N Eljabo, N Nikolic, J Carkic, D Jelovac, M Lazarevic, N Tanic, J Milasin
Despite adequate surgical resection, oral squamous cell carcinoma (OSCC) shows a high rate of recurrence and metastasis, which could be explained by the presence of molecular alterations in seemingly normal tumour margins and the entire oral mucosa. The aims of this study were (1) to assess the presence of gene amplification (c-Myc and HER2) and promoter methylation (p14 and p16) in the tumours, tumour margins, and unaffected oral mucosa of 40 OSCC patients, and (2) to evaluate the possibility of using these alterations as prognostic markers...
February 12, 2018: International Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/29447932/determining-the-venous-oxygen-reservoir-a-novel-hypothetical-approach-to-titration-of-supplemental-oxygen-in-preterm-newborns
#15
Chad C Andersen, Nicolette A Hodyl, Nina M Ziegler, Michael J Stark
While normal oxygen saturation is commonly thought to be a marker of normal oxygenation, cutaneous saturation does not account for the sufficiency of oxygen within each cell or that of the system overall. Rather, cutaneous oximetry simply defines the saturation of haemoglobin (Hb) with oxygen in a pulsatile vessel. Assessment of sufficiency is best determined by measurement of the amount of oxygen left over following aerobic respiration. This left over oxygen is 'stored' on Hb in the venous compartment and can be calculated as the venous oxygen content...
March 2018: Medical Hypotheses
https://www.readbyqxmd.com/read/29447461/genetic-ablation-of-p16-ink4a-does-not-protect-against-cellular-senescence-in-mouse-models-of-copd-emphysema
#16
Isaac K Sundar, Kahkashan Rashid, Janice Gerloff, Dongmei Li, Irfan Rahman
Cigarette smoke (CS) affects DNA damage and cellular senescence signaling pathways in the pathogenesis of chronic obstructive pulmonary disease (COPD). p16(INK4a) (p16: a cyclin-dependent kinase inhibitor) is a key marker of cellular senescence, which is induced by CS in lung cells. It is thought that removal of p16 attenuates premature aging by removing senesced cells. However, the role of p16 in CS-induced stress induce premature senescence (SIPS) and senescence-associated secretory phenotype (SASP during the development of COPD/emphysema is not known...
February 15, 2018: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/29447366/parent-of-origin-dependent-gene-expression-in-male-and-female-schistosome-parasites
#17
Julien Kincaid-Smith, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, Eve Toulza
Schistosomes are the causative agents of schistosomiasis, a Neglected Tropical Disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called « evolutionary scandal » displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism...
February 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29447168/quantitative-proteome-profile-of-water-deficit-stress-responses-in-eastern-cottonwood-populus-deltoides-leaves
#18
Paul E Abraham, Benjamin J Garcia, Lee E Gunter, Sara S Jawdy, Nancy Engle, Xiaohan Yang, Daniel A Jacobson, Robert L Hettich, Gerald A Tuskan, Timothy J Tschaplinski
Drought stress is a recurring feature of world climate and the single most important factor influencing agricultural yield worldwide. Plants display highly variable, species-specific responses to drought and these responses are multifaceted, requiring physiological and morphological changes influenced by genetic and molecular mechanisms. Moreover, the reproducibility of water deficit studies is very cumbersome, which significantly impedes research on drought tolerance, because how a plant responds is highly influenced by the timing, duration, and intensity of the water deficit...
2018: PloS One
https://www.readbyqxmd.com/read/29447134/histone-deacetylase-5-hdac5-regulates-neuropathic-pain-through-sry-related-hmg-box-10-sox10-dependent-mechanism-in-mice
#19
Pan Gu, Zhiqiang Pan, Xiao-Min Wang, Liting Sun, Lydia Wai Tai, Chi Wai Cheung
A strong link between histone deacetylases (HDACs) and nociceptive hypersensitivity has been indicated in different pain models. However, the underlying molecular and cellular mechanisms remain elusive. Here, we discovered that partial sciatic nerve ligation-induced mechanical allodynia and thermal hyperalgesia in mice were associated with increased mRNA and protein expressions of HDAC5 (a member of class IIa HDACs) and SRY-related HMG-box 10 (SOX10) in the ipsilateral lumbar dorsal horn. Gene knockdown of spinal HDAC5 or SOX10 attenuated partial sciatic nerve ligation-induced nociceptive hypersensitivity, companied with decrease of spinal neuronal sensitization markers, namely phosphorylated-Erk, phosphorylated-GluN1 (ser896), and c-Fos...
March 2018: Pain
https://www.readbyqxmd.com/read/29446543/cyclin-dependent-kinase-inhibitor-2a-b-gene-deletions-are-markers-of-poor-prognosis-in-indian-children-with-acute-lymphoblastic-leukemia
#20
Manisha Agarwal, Sameer Bakhshi, Sadanand N Dwivedi, Madhulika Kabra, Rashmi Shukla, Rachna Seth
BACKGROUND: Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. PROCEDURE: Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study...
February 15, 2018: Pediatric Blood & Cancer
keyword
keyword
15358
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"