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https://www.readbyqxmd.com/read/27903834/saliva-diagnostics-current-views-and-directions
#1
Karolina Elżbieta Kaczor-Urbanowicz, Carmen Martin Carreras-Presas, Katri Aro, Michael Tu, Franklin Garcia-Godoy, David Tw Wong
In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a "mirror of the body," can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term "Salivaomics" aimed to highlight the rapid development of knowledge about various "omics" constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome...
November 29, 2016: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/27901108/survey-of-the-green-picoalga-bathycoccus-genomes-in-the-global-ocean
#2
Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27894410/association-of-hfe-gene-mutations-with-nonalcoholic-fatty-liver-disease-in-the-iranian-population
#3
L Saremi, S Lotfipanah, M Mohammadi, H Hosseinzadeh, A Sayad, Z Saltanatpour
To determine whether the HFE gene variants H63D and C282Y are associated with NAFLD in persons with type 2 diabetes, we conducted a case-control study including 145 case of NAFLD patients with a history of type 2 diabetes and 145 matching control. The genomic DNA was extracted from the peripheral venous blood and the genotyping of HFE gene mutations was analyzed using the PCR-RFLP technique. Statistical analysis was performed using SPSS 12.0 software by χ2 test, t test and ANOVA (P<0.05). Data showed no increased frequency of HFE mutations in persons with type 2 diabetes and no association between H63D mutation and NAFLD in the study population...
October 31, 2016: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/27884753/cell-free-dna-induced-apoptosis-of-granulosa-cells-by-oxidative-stress
#4
Yichun Guan, Wenjuan Zhang, Xingling Wang, Pengfei Cai, Qi Jia, Wenjie Zhao
BACKGROUND: Cell-free DNA is a DNA fragment that is produced by cell apoptosis which can affect the micro-environment of cell apoptosis. The levels of Cell-free DNA have been associated with successful rate of in vitro fertilization-embryo transfer (IVF-ET) and embryonic development. Our aim is to determine the relationship between cell-free DNA and embryo quality. The mechanisms of cell-free DNA in granulose and the apoptosis will be determined also. METHODS: The study enrolled patients who were undergone IVF for the first time and grouped the patients as pregnant (n=130) and non-pregnant (n=59)...
November 21, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27884161/hpv16-integration-probably-contributes-to-cervical-oncogenesis-through-interrupting-tumor-suppressor-genes-and-inducing-chromosome-instability
#5
Jun-Wei Zhao, Fang Fang, Yi Guo, Tai-Lin Zhu, Yun-Yun Yu, Fan-Fei Kong, Ling-Fei Han, Dong-Sheng Chen, Fang Li
BACKGROUND: The integration of human papilloma virus (HPV) into host genome is one of the critical steps that lead to the progression of precancerous lesion into cancer. However, the mechanisms and consequences of such integration events are poorly understood. This study aims to explore those questions by studying high risk HPV16 integration in women with cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (SCC). METHODS: Specifically, HPV integration status of 13 HPV16-infected patients were investigated by ligation-mediated PCR (DIPS-PCR) followed by DNA sequencing...
November 25, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27867769/comparative-analysis-of-the-complete-chloroplast-genome-sequences-in-psammophytic-haloxylon-species-amaranthaceae
#6
Wenpan Dong, Chao Xu, Delu Li, Xiaobai Jin, Ruili Li, Qi Lu, Zhili Suo
The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species...
2016: PeerJ
https://www.readbyqxmd.com/read/27862402/a-simple-thermoplastic-substrate-containing-hierarchical-silica-lamellae-for-high-molecular-weight-dna-extraction
#7
Ye Zhang, Yi Zhang, Jeffrey M Burke, Kristin Gleitsman, Sarah M Friedrich, Kelvin J Liu, Tza-Huei Wang
An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles.
November 8, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27857867/dna-methylation-signature-of-post-injury-neointimal-cells-during-vascular-remodeling-in-the-rat-balloon-injury-model
#8
Jendai Richards, Henry Ato Ogoe, Wenzhi Li, Oguljahan Babayewa, Wei Xu, Tameka Bythwood, Minerva Garcia-Barrios, Li Ma, Qing Song
Vascular smooth muscle cell (VSMC) accumulation in the neointimal is a common feature in vascular diseases such as atherosclerosis, transplant arteriosclerosis and restenosis. In this study, we isolated the neointimal cells and uninjured residential vascular smooth muscle cells by laser micro dissection and carried out single-cell whole-genome methylation sequencing. We also sequenced the bisulfite converted genome of circulating bone-marrow-derived cells such as peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC)...
July 2016: Molecular Biology (Los Angeles, Calif.)
https://www.readbyqxmd.com/read/27854212/non-random-distribution-of-dmd-deletion-breakpoints-and-implication-of-double-strand-breaks-repair-and-replication-error-repair-mechanisms
#9
Isabelle Marey, Rabah Ben Yaou, Nathalie Deburgrave, Aurélie Vasson, Juliette Nectoux, France Leturcq, Bruno Eymard, Pascal Laforet, Anthony Behin, Tanya Stojkovic, Michèle Mayer, Vincent Tiffreau, Isabelle Desguerre, François Constant Boyer, Aleksandra Nadaj-Pakleza, Xavier Ferrer, Karim Wahbi, Henri-Marc Becane, Mireille Claustres, Jamel Chelly, Mireille Cossee
BACKGROUND: Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). OBJECTIVE: Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair...
May 27, 2016: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/27847329/the-genetic-profile-of-susceptibility-to-infectious-diseases-in-roman-period-populations-from-central-poland
#10
Magda Lewandowska, Krystyna Jędrychowska-Dańska, Alicja Zamerska, Tomasz Płoszaj, Henryk W Witas
For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 -196 to -174 ins/del) related to susceptibility to infections in humans...
November 12, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27824579/investigation-into-the-effects-of-nucleotide-content-on-the-electrical-characteristics-of-dna-plasmid-molecular-wires
#11
Noah Goshi, Alaleh Narenji, Chris Bui, John L Mokili, Sam Kassegne
In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between [Formula: see text] in length (>6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods...
September 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27822563/development-of-an-immunofet-biosensor-for-the-detection-of-biotinylated-pcr-product
#12
Wannaporn Muangsuwan, Chamras Promptmas, Wutthinan Jeamsaksiri, Win Bunjongpru, Awirut Srisuwan, Charndet Hruanun, Amporn Poyai, Prapimpun Wongchitrat, Montri Yasawong
ImmunoFET (IMFET) biosensor is a simple platform for the detection of biotinylated products of polymerase chain reaction (PCR). Construction of the IMFET biosensor started with adsorption of 1.5 mg/mL of protein A (PA) onto the insulated gate surface of ISFET for 90 min. Next, the immobilized 1/500 dilution of anti-biotin antibody was adsorbed onto the PA layer for 60 min. The IMFET biosensor was subsequently ready for detection of the biotinylated amplicon. The IMFET biosensor showed highly specific binding to the biotinylated PCR product of the phaE gene of Haloquadratum walsbyi DSM 16854...
October 2016: Heliyon
https://www.readbyqxmd.com/read/27819325/automatic-detection-and-measurement-of-viral-replication-compartments-by-ellipse-adjustment
#13
Yasel Garcés, Adán Guerrero, Paloma Hidalgo, Raul Eduardo López, Christopher D Wood, Ramón A Gonzalez, Juan Manuel Rendón-Mancha
Viruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses...
November 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27817745/cell-free-circulating-epigenomic-signatures-non-invasive-biomarker-for-cardiovascular-and-other-age-related-chronic-diseases
#14
Arpit Bhargava, Naveen Kumar Khare, Neha Bunkar, Koel Chaudhury, Kailash Chand Pandey, Subodh Kumar Jain, Pradyumna Kumar Mishra
The burden of cardio-vascular and other age-related non-communicable diseases are rapidly increasing worldwide. Majority of these chronic ailments are curable, if diagnosed at early stages. Candidate biomarkers of early detection are therefore essential for identification of high-risk individuals, prompt and accurate disease diagnosis, and to monitor therapeutic response. The functional significance of circulating nucleic acids that recapitulate specific disease profiles is now well established. But subtle changes in DNA sequence may not solely reflect the differentiation of gene expression patterns observed in diverse set of diseases as epigenetic phenomena play a larger role in aetiology and patho-physiology...
October 27, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27816361/genetic-variants-in-cd44-and-mat1a-confer-susceptibility-to-acute-skin-reaction-in-breast-cancer-patients-undergoing-radiation-therapy
#15
Kamalesh Dattaram Mumbrekar, Satish Rao Bola Sadashiva, Shama Prasada Kabekkodu, Donald Jerard Fernandes, Bejadi Manjunath Vadhiraja, Tomo Suga, Yoshimi Shoji, Fumiaki Nakayama, Takashi Imai, Kapaettu Satyamoorthy
PURPOSE: Heterogeneity in radiation therapy (RT)-induced normal tissue toxicity is observed in 10% of cancer patients, limiting the therapeutic outcomes. In addition to treatment-related factors, normal tissue adverse reactions also manifest from genetic alterations in distinct pathways majorly involving DNA damage-repair genes, inflammatory cytokine genes, cell cycle regulation, and antioxidant response. Therefore, the common sequence variants in these radioresponsive genes might modify the severity of normal tissue toxicity, and the identification of the same could have clinical relevance as a predictive biomarker...
September 20, 2016: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/27807740/reduced-risk-of-apoptosis-mechanisms-of-stress-responses
#16
Irina Milisav, Borut Poljšak, Samo Ribarič
Apoptosis signaling pathways are integrated into a wider network of interconnected apoptotic and anti-apoptotic pathways that regulate a broad range of cell responses from cell death to growth, development and stress responses. An important trigger for anti- or pro-apoptotic cell responses are different forms of stress including hypoxia, energy deprivation, DNA damage or inflammation. Stress duration and intensity determine whether the cell's response will be improved cell survival, due to stress adaptation, or cell death by apoptosis, necrosis or autophagy...
November 2, 2016: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/27793845/enhanced-detection-of-cancer-biomarkers-in-blood-borne-extracellular-vesicles-using-nanodroplets-and-focused-ultrasound
#17
Robert J Paproski, Juan Jovel, Gane Ka-Shu Wong, John D Lewis, Roger J Zemp
The feasibility of personalized medicine approaches will be greatly improved by the development of non-invasive methods to interrogate tumor biology. Extracellular vesicles shed by solid tumors into the bloodstream have been under recent investigation as a source of tumor-derived biomarkers such as proteins and nucleic acids. We report here an approach using sub-micrometer perfluorobutane nanodroplets and focused ultrasound to enhance the release of extracellular vesicles from specific locations in tumors into the blood...
October 28, 2016: Cancer Research
https://www.readbyqxmd.com/read/27789654/titanium-dioxide-food-additive-e171-induces-ros-formation-and-genotoxicity-contribution-of-micro-and-nano-sized-fractions
#18
Héloïse Proquin, Carolina Rodríguez-Ibarra, Carolyn G J Moonen, Ismael M Urrutia Ortega, Jacob J Briedé, Theo M de Kok, Henk van Loveren, Yolanda I Chirino
Since 1969, the European Union approves food-grade titanium dioxide (TiO2), also known as E171 colouring food additive. E171 is a mixture of micro-sized particles (MPs) and nano-sized particles (NPs). Previous studies have indicated adverse effects of oral exposure to E171, i.e. facilitation of colon tumour growth. This could potentially be partially mediated by the capacity to induce reactive oxygen species (ROS). The aim of the present study is to determine whether E171 exposure induces ROS formation and DNA damage in an in vitro model using human Caco-2 and HCT116 cells and to investigate the contribution of the separate MPs and NPs TiO2 fractions to these effects...
October 27, 2016: Mutagenesis
https://www.readbyqxmd.com/read/27788272/a-viral-immunity-chromosome-in-the-marine-picoeukaryote-ostreococcus-tauri
#19
Sheree Yau, Claire Hemon, Evelyne Derelle, Hervé Moreau, Gwenaël Piganeau, Nigel Grimsley
Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27788210/nuclear-commd1-is-associated-with-cisplatin-sensitivity-in-ovarian-cancer
#20
Alina Fedoseienko, Hylke W Wieringa, G Bea A Wisman, Evelien Duiker, Anna K L Reyners, Marten H Hofker, Ate G J van der Zee, Bart van de Sluis, Marcel A T M van Vugt
Copper metabolism MURR1 domain 1 (COMMD1) protein is a multifunctional protein, and its expression has been correlated with patients' survival in different types of cancer. In vitro studies revealed that COMMD1 plays a role in sensitizing cancer cell lines to cisplatin, however, the mechanism and its role in platinum sensitivity in cancer has yet to be established. We evaluated the role of COMMD1 in cisplatin sensitivity in A2780 ovarian cancer cells and the relation between COMMD1 expression and response to platinum-based therapy in advanced stage high-grade serous ovarian cancer (HGSOC) patients...
2016: PloS One
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