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https://www.readbyqxmd.com/read/29344904/mgmt-assessment-in-pituitary-adenomas-comparison-of-different-immunohistochemistry-fixation-chemicals
#1
Alexander S G Micko, Romana Höftberger, Adelheid Wöhrer, Matthias Millesi, Engelbert Knosp, Stefan Wolfsberger
PURPOSE: Despite the established role of O6-methyl-guanine-DNA methyltransferase (MGMT) as a marker for temozolomide response, consensus of the most reliable method to assess MGMT expression in pituitary adenomas is still missing. Currently, immunohistochemistry (IHC) assessment of formaldehyde fixed tissue samples is most widely used in a semiquantitative description. As formaldehyde fails to completely preserve nucleic acids, RCL2, an alcohol-based formaldehyde-free fixative, has been proposed as a more reliable alternative in terms of cell stability...
January 17, 2018: Pituitary
https://www.readbyqxmd.com/read/29343995/humanmethylation450k-array-identified-biomarkers-predict-tumour-recurrence-progression-at-initial-diagnosis-of-high-risk-non-muscle-invasive-bladder-cancer
#2
Mark O Kitchen, Richard T Bryan, Richard D Emes, Christopher J Luscombe, K K Cheng, Maurice P Zeegers, Nicholas D James, Lyndon M Gommersall, Anthony A Fryer
Background: High-risk non-muscle invasive bladder cancer (HR-NMIBC) is a clinically unpredictable disease. Despite clinical risk estimation tools, many patients are undertreated with intra-vesical therapies alone, whereas others may be over-treated with early radical surgery. Molecular biomarkers, particularly DNA methylation, have been reported as predictive of tumour/patient outcomes in numerous solid organ and haematologic malignancies; however, there are few reports in HR-NMIBC and none using genome-wide array assessment...
2018: Biomarkers in Cancer
https://www.readbyqxmd.com/read/29341428/epigenetic-silencing-of-tap1-in-aldefluor-breast-cancer-stem-cells-contributes-to-their-enhanced-immune-evasion
#3
Mohammad Sultan, Dejan Vidovic, Arianne S Paine, Thomas T Huynh, Krysta M Coyle, Margaret L Thomas, Brianne M Cruickshank, Cheryl A Dean, Derek R Clements, Youra Kim, Kristin Lee, Shashi A Gujar, Ian C Weaver, Paola Marcato
Avoiding detection and destruction by immune cells is key for tumor initiation and progression. The important role of cancer stem cells (CSC) in tumor initiation has been well established, yet their ability to evade immune detection and targeting is only partly understood. To investigate the ability of breast CSCs to evade immune detection we identified a highly tumorigenic population in a spontaneous murine mammary tumor based on increased aldehyde dehydrogenase (ALDH) activity. We performed tumor growth studies in immunocompetent and immunocompromised mice...
January 17, 2018: Stem Cells
https://www.readbyqxmd.com/read/29340947/the-impact-of-depuration-on-mussel-hepatopancreas-bacteriome-composition-and-predicted-metagenome
#4
J A Rubiolo, A Lozano-Leon, R Rodriguez-Souto, N Fol Rodríguez, M R Vieytes, L M Botana
Due to the rapid elimination of bacteria through normal behaviour of filter feeding and excretion, the decontamination of hazardous contaminating bacteria from shellfish is performed by depuration. This process, under conditions that maximize shellfish filtering activity, is a useful method to eliminate microorganisms from bivalves. The microbiota composition in bivalves reflects that of the environment of harvesting waters, so quite different bacteriomes would be expected in shellfish collected in different locations...
January 17, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29339259/perturbations-of-the-gut-microbiome-genes-in-infants-with-atopic-dermatitis-according-to-feeding-type
#5
Min-Jung Lee, Mi-Jin Kang, So-Yeon Lee, Eun Lee, Kangjin Kim, Sungho Won, Dong In Suh, Kyung Won Kim, Youn Ho Sheen, Kangmo Ahn, Bong-Soo Kim, Soo-Jong Hong
BACKGROUND: Perturbations of the infant gut microbiota can shape the development of the immune system and link to the risk of allergic diseases. OBJECTIVE: To understand the role of the gut microbiome in atopic dermatitis, the metagenome of the infant gut microbiome was analyzed according to feeding types. METHODS: The composition of gut microbiota was analyzed in fecal samples from 129 infants (6-month-old) by pyrosequencing, including 66 healthy infants and 63 infants with atopic dermatitis...
January 12, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29339171/dna-methylation-level-of-the-neprilysin-promoter-in-alzheimer-s-disease-brains
#6
Kenichi Nagata, Tatsuo Mano, Shigeo Murayama, Takaomi C Saido, Atsushi Iwata
Neprilysin (NEP), a membrane-bound metalloprotease, has been shown to play an essential role in the clearance of amyloid beta (Aβ) peptides. Previous studies have reported that NEP expression is downregulated in the normal aging brain as well as in the Alzheimer's disease (AD) brain, providing evidence that the downregulation of NEP expression contributes to the age-dependent deposition of Aβ-containing plaques, a pathological hallmark of AD. However, the mechanisms underlying the downregulation remain unclear...
January 12, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29332190/transcriptomic-profiling-of-developing-fiber-in-levant-cotton-gossypium-herbaceum-l
#7
Mithil J Parekh, Sushil Kumar, Ranbir S Fougat, Harshvardhan N Zala, Ramesh J Pandit
Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G...
January 13, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29330119/temporal-changes-of-the-bacterial-community-colonizing-wheat-straw-in-the-cow-rumen
#8
Wei Jin, Ying Wang, Yuanfei Li, Yanfen Cheng, Weiyun Zhu
This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time...
January 9, 2018: Anaerobe
https://www.readbyqxmd.com/read/29329142/whole-genome-methylation-profiling-of-peripheral-blood-mononuclear-cell-for-acute-exacerbations-of-chronic-obstructive-pulmonary-disease-treated-with-corticosteroid
#9
Shih-Wei Lee, Julia Tzu-Ya Weng, Paul Wei-Che Hsu, Tzu-Yi Chuang, Chih-Wei Liu, Chung-Hsuan Chen, Lawrence Shih-Hsin Wu
OBJECTIVE: Although association studies in the general population may be relevant for determining susceptibility to chronic obstructive pulmonary disease (COPD), they may be less applicable for pharmacogenetics research in participants who have already acquired the disease. PATIENTS AND METHODS: A genome-wide methylation profiling (generated by HumanMethylation450 BeadChips study was performed on peripheral blood mononuclear cells of 24 patients with AECOPD (acute exacerbation COPD), with good and poor responsiveness to standard corticosteroid treatment...
January 10, 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29318930/effect-of-genetic-polymorphisms-in-srebf-scap-pathway-on-therapeutic-response-to-rosuvastatin-in-saudi-metabolic-syndrome-patients
#10
Misbahuddin Mohd Rafeeq, Hamed Said Habib, Hussam Aly Sayed Murad, Mamdouh Abdullah Gari, Zohair Jamil Gazzaz
AIM: Genetic variants contribute to statins' therapeutic variability. SREBF-SCAP pathway is a key player in lipid homeostasis. Hence, effect of SREBF-SCAP polymorphisms on therapeutic response was studied. PATIENTS & METHODS: Metabolic syndrome patients of either sex were prescribed rosuvastatin 10 mg for 24 weeks. Clinical, anthropometric and lipid measurements were done before and after treatment. Genotyping was done by pyrosequencing. RESULTS & CONCLUSION: No associations of SCAP and SREBF-1a genotypes with baseline lipids but significant associations with lipid reductions were observed...
January 10, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29317789/aspergillus-subgenus-polypaecilum-from-the-built-environment
#11
J B Tanney, C M Visagie, N Yilmaz, K A Seifert
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29316256/immunosuppressive-effect-of-the-gut-microbiome-altered-by-high-dose-tacrolimus-in-mice
#12
Z Zhang, L Liu, H Tang, W Jiao, S Zeng, Y Xu, Q Zhang, Z Sun, A Mukherjee, X Zhang, X Hu
The alterations induced in gut microbiota by tacrolimus may affect immune function and organ transplantation. Mice were treated with a high-dose of tacrolimus for 14 days. The fecal microbiota were analyzed by pyrosequencing the 16S rRNA genes, and the effect on metabolism was predicted using the sequence data. The subgroups of T cells in the serum, gut-associated lymphoid tissue and draining lymph nodes were determined by flow cytometry. Tacrolimus treatment significantly altered the relative abundance of Allobaculum, Bacteroides and Lactobacillus and CD4+ CD25hi FoxP3+ regulatory T-cells in the colonic mucosa and the circulation...
January 9, 2018: American Journal of Transplantation
https://www.readbyqxmd.com/read/29315254/prognostic-significance-of-activated-leukocyte-cell-adhesion-molecule-alcam-in-association-with-promoter-methylation-of-the-alcam-gene-in-breast-cancer
#13
Young Ju Jeong, Hoon Kyu Oh, Sung Hwan Park, Jin Gu Bong
Activated leukocyte cell adhesion molecule (ALCAM) has been implicated in tumorigenesis. In this study, we studied DNA methylation status of the ALCAM gene using pyrosequencing in breast cancer tissues. We analyzed the association between the methylation status of the ALCAM gene and its expression. Also, the effects of inflammation on the ALCAM gene methylation and its expression were investigated. The ALCAM gene methylation was associated with the ALCAM transcripts in tumor tissues. The methylation status of the ALCAM gene was not significantly different between tumor and normal tissues...
January 9, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29313157/microbial-community-response-reveals-underlying-mechanism-of-industrial-scale-manganese-sand-biofilters-used-for-the-simultaneous-removal-of-iron-manganese-and-ammonia-from-groundwater
#14
Yu Zhang, Rui Sun, Aijuan Zhou, Jiaguang Zhang, Yunbo Luan, Jianna Jia, Xiuping Yue, Jie Zhang
Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied...
January 8, 2018: AMB Express
https://www.readbyqxmd.com/read/29312770/development-of-pulmonary-langerhans-cell-histiocytosis-in-a-patient-with-established-adenocarcinoma-of-the-lung
#15
Or Kalchiem-Dekel, Adina Paulk, Seth J Kligerman, Allen P Burke, Nirav G Shah, Renee K Dixon
Newly-appearing lung nodules on surveillance imaging in patients with pre-existing lung cancer can present a diagnostic dilemma when attempting to differentiate between metastatic disease, infection, and other inflammatory conditions. Here we report a case of an EGFR-/ALK-/BRAF+ metastatic adenocarcinoma patient who underwent lung biopsy for evaluation of upper-lobe predominant lung nodules revealed to represent pulmonary Langerhans cell histiocytosis (PLCH). The patient was a heavy smoker and admitted to increase her smoking habit after initially learning about her diagnosis with lung cancer...
December 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29310734/differential-methylation-of-insulin-like-growth-factor-2-in-offspring-of-physically-active-pregnant-women
#16
M R Marshall, N Paneth, J A Gerlach, L M Mudd, L Biery, D P Ferguson, J M Pivarnik
Several studies have suggested that maternal lifestyle during pregnancy may influence long-term health of offspring by altering the offspring epigenome. Whether maternal leisure-time physical activity (LTPA) during pregnancy might have this effect is unknown. The purpose of this study was to determine the relationship between maternal LTPA during pregnancy and offspring DNA methylation. Participants were recruited from the Archive for Research on Child Health study. At enrollment, participants' demographic information and self-reported LTPA during pregnancy were determined...
January 9, 2018: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/29306533/microbial-analysis-of-endodontic-infections-in-root-filled-teeth-with-apical-periodontitis-before-and-after-irrigation-using-pyrosequencing
#17
Homan Zandi, Anne K Kristoffersen, Dag Ørstavik, Isabela N Rôças, José F Siqueira, Morten Enersen
INTRODUCTION: The root canal microbiota in root-filled teeth with post-treatment apical periodontitis before and after chemomechanical instrumentation and irrigation with either 1% sodium hypochlorite (NaOCl) or 2% chlorhexidine digluconate were analyzed by using the pyrosequencing method. METHODS: Samples from 10 root-filled teeth with apical periodontitis undergoing retreatment were taken before (S1) and after (S2) preparation using irrigation with either NaOCl (n = 5) or 2% chlorhexidine digluconate (n = 5)...
January 3, 2018: Journal of Endodontics
https://www.readbyqxmd.com/read/29305225/droplet-digital-pcr-for-mutation-detection-in-formalin-fixed-paraffin-embedded-melanoma-tissues-a-comparison-with-sanger-sequencing-and-pyrosequencing
#18
Ashleigh C McEvoy, Benjamin A Wood, Nima M Ardakani, Michelle Pereira, Robert Pearce, Lester Cowell, Cleo Robinson, Fabienne Grieu-Iacopetta, Alexander J Spicer, Benhur Amanuel, Melanie Ziman, Elin S Gray
Identification of somatic mutations is crucial to guide therapeutic decisions for personalized melanoma treatment. However, genetic analysis of the tumor is usually performed on limited and often low-quality DNA, from tumors with low tumor cellularity and high tumor heterogeneity. Different mutation detection platforms exist with varying analytical sensitivities. Here we evaluated the detection of common mutations in BRAF, NRAS, and TERT-promoter in 40 melanoma formalin-fixed, paraffin-embedded tissues using droplet digital PCR (ddPCR), and compared the results to the detection rate obtained by Sanger sequencing and pyrosequencing...
January 2, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29303410/relationship-of-nutrient-dynamics-and-bacterial-community-structure-at-the-water-sediment-interface-using-a-benthic-chamber-experiment
#19
Bo-Min Ki, In Ae Huh, Jung-Hyun Choi, Kyung-Suk Cho
The relationships between nutrient dynamics and the bacterial community at the water-sediment interface were investigated using the results of nutrient release fluxes, bacterial communities examined by 16S rRNA pyrosequencing and canonical correlation analysis (CCA) accompanied by lab-scale benthic chamber experiment. The nutrient release fluxes from the sediments into the water were as follows: -3.832 to 12.157 mg m-2 d-1 for total phosphorus, 0.049 to 9.993 mg m-2 d-1 for PO4-P, -2.011 to 41.699 mg m-2 d-1 for total nitrogen, -7...
January 5, 2018: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/29302586/erratum-analysis-of-gastric-body-microbiota-by-pyrosequencing-possible-role-of-bacteria-other-than-helicobacter-pylori-in-the-gastric-carcinogenesis
#20
Sung-Hwa Sohn, Nayoung Kim, Hyun Jin Jo, Jaeyeon Kim, Ji Hyun Park, Ryoung Hee Nam, Yeong-Jae Seok, Yeon-Ran Kim, Dong Ho Lee
[This corrects the article on p. 115 in vol. 22, PMID: 28698866.].
December 2017: Journal of Cancer Prevention
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