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quantitative biology

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https://www.readbyqxmd.com/read/27911038/quantitating-the-cell-turning-images-into-numbers-with-imagej
#1
REVIEW
Ellen T Arena, Curtis T Rueden, Mark C Hiner, Shulei Wang, Ming Yuan, Kevin W Eliceiri
Modern biological research particularly in the fields of developmental and cell biology has been transformed by the rapid evolution of the light microscope. The light microscope, long a mainstay of the experimental biologist, is now used for a wide array of biological experimental scenarios and sample types. Much of the great developments in advanced biological imaging have been driven by the digital imaging revolution with powerful processors and algorithms. In particular, this combination of advanced imaging and computational analysis has resulted in the drive of the modern biologist to not only visually inspect dynamic phenomena, but to quantify the involved processes...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27910940/supportive-angiogenic-and-osteogenic-differentiation-of-mesenchymal-stromal-cells-and-endothelial-cells-in-monolayer-and-co-cultures
#2
Florian Böhrnsen, Henning Schliephake
Sites of implantation with compromised biology may be unable to achieve the required level of angiogenic and osteogenic regeneration. The specific function and contribution of different cell types to the formation of prevascularized, osteogenic networks in co-culture remains unclear. To determine how bone marrow-derived mesenchymal stromal cells (BMSCs) and endothelial cells (ECs) contribute to cellular proangiogenic differentiation, we analysed the differentiation of BMSCs and ECs in standardized monolayer, Transwell and co-cultures...
December 2, 2016: International Journal of Oral Science
https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#3
Paul Villoutreix, Julien Delile, Barbara Rizzi, Louise Duloquin, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras
We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910868/relationship-between-nanotopographical-alignment-and-stem-cell-fate-with-live-imaging-and-shape-analysis
#4
Peter Newman, Jorge Luis Galenano-Niño, Pamela Graney, Joselito M Razal, Andrew I Minett, João Ribas, Raquel Ovalle-Robles, Maté Biro, Hala Zreiqat
The topography of a biomaterial regulates cellular interactions and determine stem cell fate. A complete understanding of how topographical properties affect cell behavior will allow the rational design of material surfaces that elicit specified biological functions once placed in the body. To this end, we fabricate substrates with aligned or randomly organized fibrous nanostructured topographies. Culturing adipose-derived stem cells (ASCs), we explore the dynamic relationship between the alignment of topography, cell shape and cell differentiation to osteogenic and myogenic lineages...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909956/docking-and-three-dimensional-quantitative-structure-activity-relationship-analyses-of-imidazole-and-thiazolidine-derivatives-as-aurora-a-kinase-inhibitors
#5
Chaeuk Im
Aurora A kinase is involved in the inactivation of apoptosis leading to ovarian, breast, colon, and pancreatic cancers. Inhibitors of Aurora A kinase promote aberrant mitosis resulting in arrest at a pseudo G1 state to induce mitotic catastrophe, ultimately leading to apoptosis. In this study, ligand-based and docking-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of imidazole and thiazolidine derivatives as potential Aurora A kinase inhibitors were performed. The results provided highly reliable and predictive 3D-QSAR comparative molecular similarity index analysis (CoMSIA) models with a cross-validated q(2) value of 0...
December 1, 2016: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/27909745/dechlorination-of-three-tetrachlorobenzene-isomers-by-contaminated-harbor-sludge-derived-enrichment-cultures-follows-thermodynamically-favorable-reactions
#6
Yue Lu, Javier Ramiro-Garcia, Pieter Vandermeeren, Steffi Herrmann, Danuta Cichocka, Dirk Springael, Siavash Atashgahi, Hauke Smidt
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers...
December 1, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27908684/identification-and-profiling-of-mirnas-in-overwintering-lissorhoptrus-oryzophilus-via-next-generation-sequencing
#7
Yang Shuang, Zhang Juhong, Wang Shang, Zhang Xinxin, Liu Yan, Xi Jinghui
MicroRNAs (miRNAs) are important regulators of various biological processes in organisms. Insects subjected to abiotic stress can regulate gene expression post-transcriptionally through the use of microRNAs. However, the role of miRNAs in response to cold stress in Lissorhoptrus oryzophilus Kuschel remains unknown. The rice water weevil, L. oryzophilus, is an invasive insect that is able to survive cold winters. To characterize changes in miRNAs in response to overwintering in L. oryzophilus, a comprehensive comparative analysis of microRNAs was performed involving an overwintering and a normal adult...
November 28, 2016: Cryobiology
https://www.readbyqxmd.com/read/27908666/molecular-cloning-and-expression-analysis-of-five-heat-shock-protein-70-hsp70-family-members-in-lateolabrax-maculatus-with-vibrio-harveyi-infection
#8
Ying-Li Han, Cong-Cong Hou, Chen Du, Jun-Quan Zhu
Heat shock proteins 70 (HSP70s) are molecular chaperones that aid in protection against environmental stress. In this study, we cloned and characterized five members of the HSP70 family (designated as HSPa1a, HSC70-1, HSC70-2, HSPa4 and HSPa14) from Lateolabrax maculatus using rapid amplification cDNA ends (RACE). Multiple sequence alignment and structural analysis revealed that all members of the HSP70 family had a conserved domain architecture, with some distinguishing features unique to each HSP70. Quantitative real-time (qPCR) analysis revealed that all members of the HSP70 family were ubiquitously and differentially expressed in all major types of tissues, including testicular tissue...
November 28, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27908295/dopamine-2-receptor-extracellular-n-terminus-regulates-receptor-surface-availability-and-is-the-target-of-human-pathogenic-antibodies-from-children-with-movement-and-psychiatric-disorders
#9
Nese Sinmaz, Fiona Tea, Deepti Pilli, Alicia Zou, Mazen Amatoury, Tina Nguyen, Vera Merheb, Sudarshini Ramanathan, Sandra T Cooper, Russell C Dale, Fabienne Brilot
Anti-Dopamine-2 receptor (D2R) antibodies have been recently identified in a subgroup of children with autoimmune movement and psychiatric disorders, however the epitope(s) and mechanism of pathogenicity remain unknown. Here we report a major biological role for D2R extracellular N-terminus as a regulator of receptor surface availability, and as a major epitope targeted and impaired in brain autoimmunity. In transfected human cells, purified anti-D2R antibody from patients specifically and significantly reduced human D2R surface levels...
December 1, 2016: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/27908111/nuclear-quantum-effects-in-a-hiv-cancer-inhibitor-the-case-of-ellipticine
#10
Subrahmanyam Sappati, Ali Hassanali, Ralph Gebauer, Prasenjit Ghosh
Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27907870/immunochromatographic-determination-of-bacopaside-i-in-biological-samples
#11
Sontaya Sookying, Dumrongsak Pekthong, Sarawut Oo-Puthinan, Watoo Phrompittayarat, Waraporn Putalun, Hiroyuki Tanaka, Jie Xing, Zhaoqi Zhan, Nantaka Khorana, Nitra Nuengchamnong, Kornkanok Ingkaninan
We describe a novel immunochromatographic method for qualitative and quantitative analyses of bacopaside I, a bioactive constituent in Bacopa monnieri (L.) Wettst in biological samples. The assay was performed on polyethersulfone membrane using a polyclonal antibody raised against bacopaside I. The finalised method could quantitatively determine bacopaside I in the range of 31.3-1000.0ng and the detection and quantification limits were 1.0 and 31.3ng, respectively. The percentage recoveries of bacopaside I in blood and urine were nearly 100% indicating the accuracy of the extraction...
November 23, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/27907861/in-situ-time-lapse-study-of-extracellular-polymeric-substance-discharge-in-streptococcus-mutans-biofilm
#12
Bernard Haochih Liu, Li-Chieh Yu
Streptococcus mutans is one of the main pathogens that cause tooth decay. By metabolizing carbohydrates, S. mutans emits extracellular polymeric substance (EPS) that adheres to the tooth surface and forms layers of biofilm. Periodontal disease occurs due to the low pH environment created by S. mutans biofilm, and such an acidic environment gradually erodes tooth enamel. Since the existence of EPS is essential in the formation of biofilm, the in-situ investigation of its generation and distribution in real time is the key to the control and suppression of S...
November 24, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27907853/sewall-wright-shifting-balance-theory-and-the-hardening-of-the-modern-synthesis
#13
Yoichi Ishida
The period between the 1940s and 1960s saw the hardening of the modern synthesis in evolutionary biology. Gould and Provine argue that Wright's shifting balance theory of evolution hardened during this period. But their account does not do justice to Wright, who always regarded selection as acting together with drift. This paper presents a more adequate account of the development of Wright's shifting balance theory, paying particular attention to his application of the theory to the geographical distribution of flower color dimorphism in Linanthus parryae...
November 28, 2016: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/27906190/robust-high-throughput-kinetic-analysis-of-apoptosis-with-real-time-high-content-live-cell-imaging
#14
Jesse D Gelles, Jerry Edward Chipuk
Quantitative and kinetic analyses of apoptotic cell death are integral components of exploring cell biology, measuring cellular stress responses, and performing high-throughput genomic/RNAi/drug screens. Here, we present a detailed method that integrates robust kinetic real-time high-content imaging with Annexin V labelling to provide a highly sensitive, accurate, simple and zero-handling approach to quantify extrinsic and intrinsic inducers of apoptosis. The sensitivity of this non-toxic method outperforms previous high-throughput methodologies using viability dyes or caspase-activation reporters...
December 1, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27906059/a-mitochondrial-hsp70-hspa9b-is-linked-to-miltefosine-resistance-and-stress-response-in-leishmania-donovani
#15
P Vacchina, B Norris-Mullins, E S Carlson, M A Morales
BACKGROUND: Protozoan parasites of the genus Leishmania are responsible for leishmaniasis, a neglected tropical disease affecting millions worldwide. Visceral leishmaniasis (VL), caused by Leishmania donovani, is the most severe form of leishmaniasis with high rates of mortality if left untreated. Current treatments include pentavalent antimonials and amphotericin B. However, high toxicity and emergence of resistance hinder the success of these options. Miltefosine (HePC) is the first oral treatment available for leishmaniasis...
December 1, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27904704/lncrna-sox2ot-overexpression-serves-as-a-poor-prognostic-biomarker-in-gastric-cancer
#16
Yuanyuan Zhang, Rui Yang, Jianchun Lian, Haiyan Xu
Sox2 overlapping transcript (Sox2ot) serves as an unfavorable prognostic factor in lung cancer and hepatocellular carcinoma, but the clinical significance and biological function of Sox2ot in gastric cancer is still unknown. The objective of our research is to explore the significance of Sox2ot in gastric cancer. Quantitative real-time polymerase chain reaction was performed to determine Sox2ot in gastric cancer tissues and cell lines. Furthermore, the Sox2ot status in one hundred and thirty two gastric cancer samples was detected to analyzed correlations between Sox2ot and clinicopathological features...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27904695/overexpression-of-akip1-predicts-poor-prognosis-of-patients-with-breast-carcinoma-and-promotes-cancer-metastasis-through-akt-gsk-3%C3%AE-snail-pathway
#17
Dan Mo, Xinning Li, Chunhong Li, Junrong Liang, Tian Zeng, Naiwei Su, Qipei Jiang, Jingjing Huang
Recent evidence has demonstrated that A kinase interacting protein 1 (AKIP1), a molecular regulator of protein kinase A, was overexpressed in breast cancer. However, the prognostic and biological role of AKIP1 in breast cancer is still elusive. The purpose of our study was to elucidate the role and molecular mechanism of AKIP1 in breast cancer development. The mRNA levels of AKIP1 in breast cancer and paired normal breast tissues were examined by quantitative real-time PCR. The relationship of AKIP1 expression with clinicopathological characteristics and clinical prognosis of breast cancer patients was investigated...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27904675/expression-of-long-non-coding-rna-hotair-in-oral-squamous-cell-carcinoma-tca8113-cells-and-its-associated-biological-behavior
#18
Huawei Liu, Zhiyong Li, Chao Wang, Lin Feng, Haitao Huang, Changkui Liu, Fengxia Li
As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#19
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903429/polyhydroxyalkanoate-as-a-slow-release-carbon-source-for-in-situ-bioremediation-of-contaminated-aquifers-from-laboratory-investigation-to-pilot-scale-testing-in-the-field
#20
Lucia Pierro, Bruna Matturro, Simona Rossetti, Marco Sagliaschi, Salvatore Sucato, Eduard Alesi, Ernst Bartsch, Firoozeh Arjmand, Marco Petrangeli Papini
A pilot-scale study aiming to evaluate the potential use of poly-3-hydroxy-butyrate (PHB) as an electron donor source for in situ bioremediation of chlorinated hydrocarbons in groundwater was conducted. Compared with commercially available electron donors, PHB offers a restricted fermentation pathway (i.e., through acetic acid and molecular hydrogen) by avoiding the formation of any residual carbon that could potentially spoil groundwater quality. The pilot study was carried out at an industrial site in Italy, heavily contaminated by different chlorinated aliphatic hydrocarbons (CAHs)...
November 26, 2016: New Biotechnology
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