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https://www.readbyqxmd.com/read/28343097/strait-razor-v2s-advancing-sequence-based-str-allele-reporting-and-beyond-to-other-marker-systems
#1
Jonathan L King, Frank R Wendt, Jie Sun, Bruce Budowle
STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28342984/hdac4-and-hdac6-sustain-dna-double-strand-break-repair-and-stem-like-phenotype-by-promoting-radioresistance-in-glioblastoma-cells
#2
Francesco Marampon, Francesca Megiorni, Simona Camero, Clara Crescioli, Heather P McDowell, Roberta Sferra, Antonella Vetuschi, Simona Pompili, Luca Ventura, Francesca De Felice, Vincenzo Tombolini, Carlo Dominici, Roberto Maggio, Claudio Festuccia, Giovanni Luca Gravina
The role of histone deacetylase (HDAC) 4 and 6 in glioblastoma (GBM) radioresistance was investigated. We found that tumor samples from 31 GBM patients, who underwent temozolomide and radiotherapy combined treatment, showed HDAC4 and HDAC6 expression in 93.5% and 96.7% of cases, respectively. Retrospective clinical data analysis demonstrated that high-intensity HDAC4 and/or HDAC6 immunostaining was predictive of poor clinical outcome. In vitro experiments revealed that short hairpin RNA-mediated silencing of HDAC4 or HDAC6 radiosensitized U87MG and U251MG GBM cell lines by promoting DNA double-strand break (DSBs) accumulation and by affecting DSBs repair molecular machinery...
March 22, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28342807/myocardin-inhibited-the-gap-protein-connexin-43-via-promoted-mir-206-to-regulate-vascular-smooth-muscle-cell-phenotypic-switch
#3
Hui Li, Yuan Xiang, Li-Juan Fan, Xiao-Yu Zhang, Jia-Peng Li, Cheng-Xi Yu, Le-Yuan Bao, Dong-Sun Cao, Wei-Bing Xing, Xing-Hua Liao, Tong-Cun Zhang
Myocardin is regarded as a key mediator for the change of smooth muscle phenotype. The gap junction protein connexin 43 (Cx43) has been shown to be involved in vascular smooth muscle cells (VSMCs) proliferation and the development of atherosclerosis. However, the role of myocardin on gap junction of cell communication and the relation between myocardin and Cx43 in VSMC phenotypic switch has not been investigated. The goal of the present study is to investigate the molecular mechanism by which myocardin affects Cx43-regulated VSMC proliferation...
March 22, 2017: Gene
https://www.readbyqxmd.com/read/28342763/serotonin-and-neuroplasticity-links-between-molecular-functional-and-structural-pathophysiology-in-depression
#4
REVIEW
Christoph Kraus, Eero Castrén, Siegfried Kasper, Rupert Lanzenberger
Serotonin modulates neuroplasticity, especially during early life, and dysfunctions in both systems likewise contribute to pathophysiology of depression. Recent findings demonstrate that serotonin reuptake inhibitors trigger reactivation of juvenile-like neuroplasticity. How these findings translate to clinical antidepressant treatment in major depressive disorder remains unclear. With this review, we link preclinical with clinical work on serotonin and neuroplasticity to bring two pathophysiologic models in clinical depression closer together...
March 22, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28342541/continuous-gradient-temperature-raman-spectroscopy-and-differential-scanning-calorimetry-of-n-3dpa-and-dha-from-100-to-10%C3%A2-c
#5
C Leigh Broadhurst, Walter F Schmidt, Julie K Nguyen, Jianwei Qin, Kuanglin Chao, Steven R Aubuchon, Moon S Kim
Docosahexaenoic acid (DHA, 22:6n-3) is exclusively utilized in fast signal processing tissues such as retinal, neural and cardiac. N-3 docosapentaenoic acid (n-3DPA, 22:5n-3), with just one less double bond, is also found in the marine food chain yet cannot substitute for DHA. Gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near and at phase transitions...
March 22, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/28340249/orthodontic-strain-affects-the-hippo-pathway-effector-yap-concomitant-with-proliferation-in-human-periodontal-ligament-fibroblasts
#6
Diana Huelter-Hassler, Pascal Tomakidi, Thorsten Steinberg, Britta A Jung
Objectives: During orthodontic tooth movement (OTM), human periodontal ligament fibroblasts (hPDLFs) sense, and respond to mechanical forces. Since the molecular constituents involved in these processes are not fully elucidated, the objective of the present study was to identify further key molecules of the cellular strain response. Materials and Methods: Primary hPDLFs were strained with a static equiaxial strain of 2.5 per cent for 15 minutes, 1 hour, 6 hours, and 24 hours...
March 17, 2017: European Journal of Orthodontics
https://www.readbyqxmd.com/read/28339768/the-transcription-factor-olig2-is-important-for-the-biology-of-diffuse-intrinsic-pontine-gliomas
#7
Jane L Anderson, Ranjithmenon Muraleedharan, Nicole Oatman, Amanda Klotter, Satarupa Sengupta, Ronald R Waclaw, Jianqiang Wu, Rachid Drissi, Lili Miles, Eric H Raabe, Matthew L Weirauch, Maryam Fouladi, Lionel M Chow, Lindsey Hoffman, Mariko DeWire, Biplab Dasgupta
Background.: Diffuse intrinsic pontine glioma (DIPG) is a high-grade brainstem glioma of children with dismal prognosis. There is no single unifying model about the cell of origin of DIPGs. Proliferating cells in the developing human and mouse pons, the site of DIPGs, express neural stem/progenitor cell (NPC) markers, including Sox2, nestin, vimentin, Olig2, and glial fibrillary acidic protein, in an overlapping and non-overlapping manner, suggesting progenitor cell heterogeneity in the pons...
February 23, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339700/a-clinical-perspective-on-the-2016-who-brain-tumor-classification-and-routine-molecular-diagnostics
#8
Martin J van den Bent, Michael Weller, Patrick Y Wen, Johan M Kros, Ken Aldape, Susan Chang
The 2007 World Health Organization (WHO) classification of brain tumors did not use molecular abnormalities as diagnostic criteria. Studies have shown that genotyping allows a better prognostic classification of diffuse glioma with improved treatment selection. This has resulted in a major revision of the WHO classification, which is now for adult diffuse glioma centered around isocitrate dehydrogenase (IDH) and 1p/19q diagnostics. This revised classification is reviewed with a focus on adult brain tumors, and includes a recommendation of genes of which routine testing is clinically useful...
February 21, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339660/eculizumab-in-secondary-atypical-haemolytic-uraemic-syndrome
#9
Teresa Cavero, Cristina Rabasco, Antía López, Elena Román, Ana Ávila, Ángel Sevillano, Ana Huerta, Jorge Rojas-Rivera, Carolina Fuentes, Miquel Blasco, Ana Jarque, Alba García, Santiago Mendizabal, Eva Gavela, Manuel Macía, Luis F Quintana, Ana María Romera, Josefa Borrego, Emi Arjona, Mario Espinosa, José Portolés, Carolina Gracia-Iguacel, Emilio González-Parra, Pedro Aljama, Enrique Morales, Mercedes Cao, Santiago Rodríguez de Córdoba, Manuel Praga
Background.: Complement dysregulation occurs in thrombotic microangiopathies (TMAs) other than primary atypical haemolytic uraemic syndrome (aHUS). A few of these patients have been reported previously to be successfully treated with eculizumab. Methods.: We identified 29 patients with so-called secondary aHUS who had received eculizumab at 11 Spanish nephrology centres. Primary outcome was TMA resolution, defined by a normalization of platelet count (>150 × 10 9 /L) and haemoglobin, disappearance of all the markers of microangiopathic haemolytic anaemia (MAHA), and improvement of renal function, with a ≥25% reduction of serum creatinine from the onset of eculizumab administration...
February 20, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28339588/mri-features-predict-survival-and-molecular-markers-in-diffuse-lower-grade-gliomas
#10
Hao Zhou, Martin Vallières, Harrison X Bai, Chang Su, Haiyun Tang, Derek Oldridge, Zishu Zhang, Bo Xiao, Weihua Liao, Yongguang Tao, Jianhua Zhou, Paul Zhang, Li Yang
Background.: Previous studies have shown that MR imaging features can be used to predict survival and molecular profile of glioblastoma. However, no study of a similar type has been performed on lower-grade gliomas (LGGs). Methods.: Presurgical MRIs of 165 patients with diffuse low- and intermediate-grade gliomas (histological grades II and III) were scored according to the Visually Accessible Rembrandt Images (VASARI) annotations. Radiomic models using automated texture analysis and VASARI features were built to predict isocitrate dehydrogenase 1 (IDH1) mutation, 1p/19q codeletion status, histological grade, and tumor progression...
January 24, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339043/high-atp2a2-expression-correlates-with-better-prognosis-of-diffuse-astrocytic-tumor-patients
#11
Wei-Qing Li, Nan-Zhe Zhong, Jin He, Yi-Ming Li, Li-Jun Hou, Hui-Min Liu, Chun-Yan Xia, Liang-Zhe Wang, Yi-Cheng Lu
Novel molecular markers are required for defining subsets of diffuse astrocytic tumor patients with differing prognoses. Here, we examined ATP2A2 expression in 109 human diffuse astrocytic tumor samples (39 grade II diffuse astrocytoma (DA), 19 grade III anaplastic astrocytoma (AA), 51 grade IV glioblastoma) and its correlation with patient clinicopathologic characteristics. ATP2A2 expression significantly correlated with tumor grade and survival (P<0.05). High ATP2A2 expression was detected in 35.3% (18/51) of glioblastoma patients, compared to 61...
March 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28338728/characterising-root-trait-variability-in-chickpea-cicer-arietinum-l-germplasm
#12
Yinglong Chen, Michel Edmond Ghanem, Kadambot Hm Siddique
Chickpea (Cicer arietinum L.) is an important grain legume crop but its sustainable production is challenged by predicted climate changes, which are likely to increase production limitations and uncertainty in yields. Characterising the variability in root architectural traits in a core collection of chickpea germplasm will provide the basis for breeding new germplasm with suitable root traits for the efficient acquisition of soil resources and adaptation to drought and other abiotic stresses. This study used a semi-hydroponic phenotyping system for assessing root trait variability across 270 chickpea genotypes...
October 6, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338645/development-of-44-novel-polymorphic-ssr-markers-for-determination-of-shiitake-mushroom-lentinula-edodes-cultivars
#13
Hwa-Yong Lee, Suyun Moon, Donghwan Shim, Chang Pyo Hong, Yi Lee, Chang-Duck Koo, Jong-Wook Chung, Hojin Ryu
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms...
March 24, 2017: Genes
https://www.readbyqxmd.com/read/28338114/molecular-analysis-of-vascular-endothelial-growth-factor-vegf-receptors-in-eus-guided-samples-obtained-from-patients-with-pancreatic-adenocarcinoma
#14
Madalin Ionut Costache, Sevastita Iordache, Cornelia Alexandra Costache, Ene Dragos, Alexandru Dragos, Adrian Saftoiu
BACKGROUND AND AIMS: Vascular endothelial growth factor (VEGF) and its receptors (VEGF-R1 and VEGF-R2) are the most important angiogenesis stimulating factors in pancreatic cancer. This study aims to assess VEGF-R1 and VEGF-R2 gene expression in EUS-FNA samples and identify prognostic markers in pancreatic adenocarcinoma. METHODS: This was a retrospective study of prospectively collected data of 88 consecutive patients, with clinical and imaging suspicion of pancreatic neoplasms, based on samples obtained through endoscopic ultrasound-guided fine needle aspiration (EUS-FNA)...
March 2017: Journal of Gastrointestinal and Liver Diseases: JGLD
https://www.readbyqxmd.com/read/28337966/acid-fast-positive-and-acid-fast-negative-mycobacterium-tuberculosis-the-koch-paradox
#15
Catherine Vilchèze, Laurent Kremer
Acid-fast (AF) staining, also known as Ziehl-Neelsen stain microscopic detection, developed over a century ago, is even today the most widely used diagnostic method for tuberculosis. Herein we present a short historical review of the evolution of AF staining methods and discuss Koch's paradox, in which non-AF tubercle bacilli can be detected in tuberculosis patients or in experimentally infected animals. The conversion of Mycobacterium tuberculosis from an actively growing, AF-positive form to a nonreplicating, AF-negative form during the course of infection is now well documented...
March 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28337772/anti-fatigue-activity-of-sea-cucumber-peptides-prepared-from-stichopus-japonicas-in-an-endurance-swimming-rat-model
#16
Jing Ye, Shen Caihong, Huang Yayan, Xueqin Zhang, Xiao Meitian
BACKGROUND: Sea cucumber (Stichopus japonicus) is a well-known nutritious and luxurious seafood in Asia which has attracted increasing attention because of its nutrition and bioactivities in recent years. In this study, the anti-fatigue activity of sea cucumber peptides (SCP) prepared from Stichopus japonicas was evaluated in a load-induced endurance swimming model. RESULTS: The SCP prepared in this study was mainly made up of low-molecular-weight peptides (<2 kDa)...
March 23, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28337643/recombinant-heat-shock-protein-27-hsp27-hspb1-protects-against-cadmium-induced-oxidative-stress-and-toxicity-in-human-cervical-cancer-cells
#17
Daiana G Alvarez-Olmedo, Veronica S Biaggio, Geremy A Koumbadinga, Nidia N Gómez, Chunhua Shi, Daniel R Ciocca, Zarah Batulan, Mariel A Fanelli, Edward R O'Brien
Cadmium (Cd) is a carcinogen with several well-described toxicological effects in humans, but its molecular mechanisms are still not fully understood. Overexpression of heat shock protein 27 (HSP27/HSPB1)-a multifunctional protein chaperone-has been shown to protect cells from oxidative damage and apoptosis triggered by Cd exposure. The aims of this work were to investigate the potential use of extracellular recombinant HSP27 to prevent/counteract Cd-induced cellular toxicity and to evaluate if peroxynitrite was involved in the development of Cd-induced toxicity...
March 24, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28337538/prevalence-and-genetic-characterization-of-toxoplasma-gondii-in-free-range-chickens-from-grocery-stores-and-farms-in-maryland-ohio-and-massachusetts-usa
#18
Yuqing Ying, Shiv K Verma, Oliver C H Kwok, Fatima Alibana, Rima Mcleod, Chunlei Su, Jitender P Dubey, Abani K Pradhan
Chickens are considered important in the epidemiology of Toxoplasma gondii. Chicken hearts (n = 1185) obtained from grocery stores were tested for T. gondii infection. Antibodies to T. gondii were assayed in fluid removed from the heart cavity using the modified agglutination test (MAT) at 1:5, 1:25, and 1:100 dilutions. MAT antibodies were detected in 222 hearts at 1:5 dilution and 8 hearts at 1:25 dilution, but none were positive at 1:100 dilution. Seropositive (n = 230, 19.4%) chicken hearts were bioassayed in mice and seronegative (n = 157) chickens were bioassayed in cats...
March 24, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28337522/pre-symptomatic-autoimmunity-in-rheumatoid-arthritis-when-does-the-disease-start
#19
REVIEW
Alexander Tracy, Christopher D Buckley, Karim Raza
It is well recognised that a state of autoimmunity, in which immunological tolerance is broken, precedes the development of symptoms in the majority of patients with rheumatoid arthritis (RA). For individuals who will later develop seropositive disease, this manifests as autoantibodies directed against proteins that have undergone specific post-translational modifications. There is evidence that the induction of this autoantibody response occurs at peripheral extra-articular mucosal sites, such as the periodontium and lung...
March 23, 2017: Seminars in Immunopathology
https://www.readbyqxmd.com/read/28337426/pathogen-identification-in-suspected-cases-of-pyogenic-spondylodiscitis
#20
Ahmad Farajzadeh Sheikh, Azar D Khosravi, Hamed Goodarzi, Roohangiz Nashibi, Alireaza Teimouri, Azim Motamedfar, Reza Ranjbar, Sara Afzalzadeh, Mehrandokht Cyrus, Mohammad Hashemzadeh
Pyogenic spinal infection continues to represent a worldwide problem. In approximately one-third of patients with pyogenic spondylodiscitis, the infectious agent is never identified. Of the cases that lead to organismal identification, bacteria are more commonly isolated from the spine rather than fungi and parasites. This study applied universal prokaryotic 16S rRNA PCR as a rapid diagnostic tool for the detection of bacterial agents in specimens from patients suspected of pyogenic spondylodiscitis. Gram and Ziehl-Neelsen staining were used as a preliminary screening measure for microbiologic evaluation of patient samples...
2017: Frontiers in Cellular and Infection Microbiology
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