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https://www.readbyqxmd.com/read/28817827/role-of-next-generation-sequencing-as-a-diagnostic-tool-for-the-evaluation-of-bone-and-soft-tissue-tumors
#1
Kinga Szurian, Karl Kashofer, Bernadette Liegl-Atzwanger
Bone and soft-tissue tumors are in general rare. Diagnosing these tumors is challenging based on the significant number of different tumor entities, the rareness of these tumors, and the considerable morphological heterogeneity which can be found within a single tumor entity. Considering that more than half of the described soft-tissue tumors and approximately 25% of the bone tumors harbor recurrent genetic alterations, the use of auxiliary molecular examinations should be strongly considered. Molecular analyses are important to confirm the diagnosis, to guide treatment, to provide information about prognosis, and to allow patient recruitment for basket trials based on the molecular signature of a tumor...
August 18, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28817824/parametric-linkage-analysis-identifies-five-novel-genome-wide-significant-loci-for-familial-lung-cancer
#2
Anthony M Musolf, Claire L Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y Kupert, Marshall W Anderson, Ann G Schwartz, Susan M Pinney, Christopher I Amos, Joan E Bailey-Wilson
OBJECTIVE: One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS: 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array...
August 18, 2017: Human Heredity
https://www.readbyqxmd.com/read/28817724/from-the-animal-house-to-the-field-are-there-consistent-individual-differences-in-immunological-profile-in-wild-populations-of-field-voles-microtus-agrestis
#3
Elena Arriero, Klara M Wanelik, Richard J Birtles, Janette E Bradley, Joseph A Jackson, Steve Paterson, Mike Begon
Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis, on a range of life history and infection metrics, and on gene expression levels...
2017: PloS One
https://www.readbyqxmd.com/read/28817597/a-unified-censored-normal-regression-model-for-qpcr-differential-gene-expression-analysis
#4
Peter Pipelers, Lieven Clement, Matthijs Vynck, Jan Hellemans, Jo Vandesompele, Olivier Thas
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is considered as the gold standard for accurate, sensitive, and fast measurement of gene expression. Prior to downstream statistical analysis, RT-qPCR fluorescence amplification curves are summarized into one single value, the quantification cycle (Cq). When RT-qPCR does not reach the limit of detection, the Cq is labeled as "undetermined". Current state of the art qPCR data analysis pipelines acknowledge the importance of normalization for removing non-biological sample to sample variation in the Cq values...
2017: PloS One
https://www.readbyqxmd.com/read/28817246/novel-id-gene-csnk2b-the-crossover-from-molecular-diagnosis-to-research-continues
#5
Leanne M Dibbens
No abstract text is available yet for this article.
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28817234/osmium-mediated-4su-to-c-transformation-as-key-to-study-rna-dynamics-by-sequencing-tuc-seq
#6
Christian Riml, Thomas Amort, Dietmar Rieder, Catherina Gasser, Alexandra Lusser, Ronald Micura
To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4-thiouridine (4sU), followed by thio-selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method that eliminates affinity purification and allows for direct assessment of 4sU labeled RNA...
August 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28817151/comprehensive-analysis-of-long-noncoding-rna-mrna-co-expression-patterns-in-thyroid-cancer
#7
Yaying Du, Wenfei Xia, Jinjun Zhang, Dongyi Wan, Zhifang Yang, Xingrui Li
Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas. While aberrations in protein-coding genes are a focus in molecular thyroid cancer medicine, the impact of oncogenes on the expression of long noncoding RNAs (lncRNAs) has been largely uncharacterized. We aimed to identify the expression patterns of lncRNAs and mRNAs in high-throughput molecular profiles of 18 papillary thyroid cancer (PTC) patients. We identified 452 mRNAs and 240 unannotated lncRNAs that were differentially expressed in PTC...
August 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28817120/the-erythropoietin-derived-peptide-mk-x-and-erythropoietin-have-neuroprotective-effects-against-ischemic-brain-damage
#8
Seung-Jun Yoo, Bongki Cho, Deokho Lee, Gowoon Son, Yeong-Bae Lee, Hyung Soo Han, Eunjoo Kim, Chanil Moon, Cheil Moon
Erythropoietin (EPO) has been well known as a hematopoietic cytokine over the past decades. However, recent reports have demonstrated that EPO plays a neuroprotective role in the central nervous system, and EPO has been considered as a therapeutic target in neurodegenerative diseases such as ischemic stroke. Despite the neuroprotective effect of EPO, clinical trials have shown its unexpected side effects, including undesirable proliferative effects such as erythropoiesis and tumor growth. Therefore, the development of EPO analogs that would confer neuroprotection without adverse effects has been attempted...
August 17, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28817118/altered-marginal-zone-and-innate-like-b-cells-in-aged-senescence-accelerated-samp8-mice-with-defective-igg1-responses
#9
Isabel Cortegano, Mercedes Rodríguez, Isabel Martín, Maria Carmen Prado, Carolina Ruíz, Rafael Hortigüela, Mario Alía, Marçal Vilar, Helena Mira, Eva Cano, Mercedes Domínguez, Belén de Andrés, María Luisa Gaspar
Aging has a strong impact on the activity of the immune system, enhancing susceptibility to pathogens and provoking a predominant pre-inflammatory status, whereas dampening responses to vaccines in humans and mice. Here, we demonstrate a loss of marginal zone B lymphocytes (MZ, CD19(+)CD45R(+)CD21(++)CD23(lo)) and a decrease of naive B cells (CD19(+)IgD(+)), whereas there is an enhancement of a CD19(+)CD45R(lo) innate-like B cell population (B1REL) and the so-called aged B cell compartment (ABC, CD45R(+)CD21(lo)CD23(lo)CD5(-)CD11b(-)) in aged senescence-accelerated (SAMP8) mice but not in aged senescence-resistant (SAMR1) mice...
August 17, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28817088/the-role-of-neurogenic-inflammation-in-blood-brain-barrier-disruption-and-development-of-cerebral-oedema-following-acute-central-nervous-system-cns-injury
#10
REVIEW
Annabel J Sorby-Adams, Amanda M Marcoionni, Eden R Dempsey, Joshua A Woenig, Renée J Turner
Acute central nervous system (CNS) injury, encompassing traumatic brain injury (TBI) and stroke, accounts for a significant burden of morbidity and mortality worldwide, largely attributable to the development of cerebral oedema and elevated intracranial pressure (ICP). Despite this, clinical treatments are limited and new therapies are urgently required to improve patient outcomes and survival. Originally characterised in peripheral tissues, such as the skin and lungs as a neurally-elicited inflammatory process that contributes to increased microvascular permeability and tissue swelling, neurogenic inflammation has now been described in acute injury to the brain where it may play a key role in the secondary injury cascades that evolve following both TBI and stroke...
August 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28816581/novel-functions-for-chromatin-dynamics-in-mrna-biogenesis-beyond-transcription
#11
Catherine Dargemont, Anna Babour
The first step of gene expression results in the production of mRNA ribonucleoparticles (mRNPs) that are exported to the cytoplasm via the NPC for translation into the cytoplasm. During this process, the mRNA molecule synthesized by RNA polymerase II (Pol II) undergoes extensive maturation, folding and packaging events that are intimately coupled to its synthesis. All these events take place in a chromatin context and it is therefore not surprising that a growing number of studies recently reported specific contributions of chromatin dynamics to various steps of mRNP biogenesis...
August 17, 2017: Nucleus
https://www.readbyqxmd.com/read/28816551/1%C3%AE-25-dihydroxyvitamin-d3-up-regulates-il-34-expression-in-sh-sy5y-neural-cells
#12
Dong Zhang, Miaomiao Li, Yang Dong, Xinhui Zhang, Xingyun Liu, Zhangming Chen, Yongji Zhu, Huiming Wang, Xuwen Liu, Jialiang Zhu, Yujun Shen, Heinrich Korner, Songcheng Ying, Shengyun Fang, Yuxian Shen
Vitamin D supplementation is regarded as a novel approach to treat Alzheimer's disease, but the underlying mechanism remains elusive. The cytokine IL-34 provides strong neuroprotective and survival signals in brain injury and neurodegeneration and could be an immunological mediator for the vitamin D-induced protection. The aim of this study was to investigate whether human IL-34 is up-regulated in neuronal cells by the hormonally active form of vitamin D, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3]. We found that IL-34 was detectable in a variety of cell lines and its expression was strongly induced in SH-SY5Y neural cells in a dose- and time-dependent manner by 1α,25(OH)2D3 through the vitamin D receptor (VDR)...
January 1, 2017: Innate Immunity
https://www.readbyqxmd.com/read/28816422/dolichol-kinase-deficiency-dolk-cdg-two-new-cases-and-expansion-of-phenotype
#13
Eric T Rush, Craig V Baker, William B Rizzo
Congenital disorders of glycosylation (CDGs) are a group of genetic diseases caused by mutations in genes that are necessary for the addition of oligosaccharides to acceptor proteins or lipids. An early step in this process requires dolichol kinase (DK) to catalyze the formation of dolichyl phosphate, which acts as a membrane anchor for initial attachment of sugar residues that are subsequently built up to oligosaccharides and transferred to acceptor proteins and lipids for further processing. Biallelic mutations in DOLK, the gene for DK, result in human in a CDG with variable symptoms, ranging from nonsyndromic dilated cardiomypopathy to severe multiorgan involvement...
September 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28816414/accuracy-and-utility-of-an-epigenetic-biomarker-for-smoking-in-populations-with-varying-rates-of-false-self-report
#14
Allan M Andersen, Robert A Philibert, Fredrick X Gibbons, Ronald L Simons, Jeffrey Long
Better biomarkers to detect smoking are needed given the tremendous public health burden caused by smoking. Current biomarkers to detect smoking have significant limitations, notably a short half-life for detection and lack of sensitivity for light smokers. These limitations may be particularly problematic in populations with less accurate self-reporting. Prior epigenome-wide association studies indicate that methylation status at cg05575921, a CpG residue located in the aryl hydrocarbon receptor repressor (AHRR) gene, may be a robust indicator of smoking status in individuals with as little as half of a pack-year of smoking...
September 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28816413/porcine-spermatogonial-stem-cells-self-renew-effectively-in-a-three-dimensional-culture-microenvironment
#15
Ji Eun Park, Min Hee Park, Min Seong Kim, Yeo Reum Park, Jung Im Yun, Hee Tae Cheong, Minseok Kim, Jung Hoon Choi, Eunsong Lee, Seung Tae Lee
Generally, self-renewal of spermatogonial stem cells (SSCs) is maintained in vivo in a three-dimensional (3D) microenvironment consisting of the seminiferous tubule basement membrane, indicating the importance of the 3D microenvironment for in vitro culture of SSCs. Here, we report a 3D culture microenvironment that effectively maintains porcine SSC self-renewal during culture. Porcine SSCs were cultured in an agarose-based 3D hydrogel and in 2D culture plates either with or without feeder cells. Subsequently, the effects of 3D culture on the maintenance of undifferentiated SSCs were identified by analyzing cell colony formation and morphology, AP activity, and transcriptional and translational regulation of self-renewal-related genes and the effects on proliferation by analyzing cell viability and single cell-derived colony number...
August 17, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28816234/novel-mutations-of-tcirg1-cause-a-malignant-and-mild-phenotype-of-autosomal-recessive-osteopetrosis-aro-in-four-chinese-families
#16
Xiao-Ya Zhang, Jin-Wei He, Wen-Zhen Fu, Chun Wang, Zhen-Lin Zhang
Human autosomal recessive osteopetrosis (ARO), also known as infantile malignant osteopetrosis, is a rare genetic bone disorder that often causes death. Mutations in T-cell immune regulator 1 (TCIRG1) are a frequent cause of human ARO. Six additional genes (TNFSF11, TNFRSF11A, CLCN7, OSTM1, SNX10, PLEKHM1) were also found to be associated with human ARO. In order to expand the mutation spectrum and clinical diversity for a better understanding of the ARO phenotype and to further investigate the clinical characteristics of benign subjects with ARO, we here report five individuals with ARO from four unrelated Chinese families...
August 17, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28816065/improved-hematopoietic-gene-therapy-in-a-mouse-model-of-fanconi-anemia-mediated-by-mesenchymal-stromal-cells
#17
Maria Fernandez-Garcia, Maria Lamana Luzuriaga, Miriam Hernando-Rodriguez, Rebeca Sanchez-Dominguez, Juan Bueren, Rosa Yañez
In this study we propose a novel approach based on the use of mesenchymal stromal cells (MSC) aiming at limiting risks of graft failure in gene therapy protocols associated with low conditioning regimens. Because the engraftment of corrected hematopoietic stem cells (HSCs) is particularly challenging in Fanconi anemia (FA), we have investigated the relevance of MSCs in an experimental model of FA gene therapy. Our results firstly showed that risks of graft failure in recipients conditioned with a moderate dose of 5Gy and infused with limited numbers of WT HSCs are significantly higher in Fanca-/- recipients as compared to WT recipients...
August 17, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28816060/the-broad-spectrum-antimicrobial-potential-of-mn-co-4-s2cnme-ch2co2h-a-water-soluble-co-releasing-molecule-corm-401-intracellular-accumulation-transcriptomic-and-statistical-analyses-and-membrane-polarization
#18
Lauren Katie Wareham, Samantha McLean, Ronald Begg, Namrata Rana, Salar Ali, John J Kendall, Guido Sanguinetti, Brian E Mann, Robert K Poole
AIMS: Carbon monoxide (CO)-releasing molecules (CORMs) are candidates for animal and antimicrobial therapeutics. We aimed to probe the antimicrobial potential of a novel manganese CORM. RESULTS: [Mn(CO)4S2CNMe(CH2CO2H)], CORM-401, inhibits growth of Escherichia coli and several antibiotic-resistant clinical pathogens. CORM-401 releases CO that binds oxidases in vivo but is an ineffective respiratory inhibitor. Extensive CORM accumulation (assayed as intracellular manganese) accompanies antimicrobial activity...
August 17, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28815995/progressive-macrothrombocytopenia-and-hearing-loss-in-a-large-family-with-diaph1-related-disease
#19
Akira Ganaha, Tadashi Kaname, Ayano Shinjou, Yasutsugu Chinen, Kumiko Yanagi, Teruyuki Higa, Shunsuke Kondo, Mikio Suzuki
In this study, we describe a Japanese family with progressive hearing loss and macrothrombocytopenia. Using next-generation and Sanger sequencing analyses, we identified a heterozygous variant in exon 27 of the DIAPH1 gene (NM_005219), c.3637C>T, p.R1213X. All patients in the family had sensorineural hearing loss and macrothrombocytopenia. None of the patients exhibited a tendency to bleed. No pathogenic variants were found in the MYH9 gene. Hearing loss began with high-frequency loss during early childhood and progressed to severe hearing loss involving all frequencies...
August 16, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815877/new-intragenic-rearrangements-in-non-finnish-mulibrey-nanism
#20
Florence Jobic, Gilles Morin, Catherine Vincent-Delorme, Estelle Cadet, Rosalie Cabry, Michèle Mathieu-Dramard, Henri Copin, Jacques Rochette, Guillaume Jedraszak
Prenatal growth is a complex dynamic process controlled by various genetic and environmental factors. Among genetic syndromes characterized by growth restriction, MULIBREY nanism represents a rare autosomal recessive condition presenting with severe pre- and post-natal growth failure, characteristic dysmorphic features but normal neurological development. The phenotype of MULIBREY nanism is variable and overlaps with others such as the Silver-Russell syndrome. We report here three patients in two distinct non-Finnish families from North France who were first suspected to have Silver-Russell syndrome which failed to be confirmed on molecular analyses...
August 17, 2017: American Journal of Medical Genetics. Part A
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