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quantitative biology

Laura Mannocci, Jason J Roberts, David L Miller, Patrick N Halpin
As human activities expand beyond national jurisdictions to the high seas, there is increasing need to consider anthropogenic impacts to species that inhabit these waters. The current scarcity of scientific observations of cetaceans in the high seas impedes the assessment of population-level impacts of these activities. This study is directed towards an important management need in the high seas-the development of plausible density estimates to facilitate a quantitative assessment of anthropogenic impacts on cetacean populations in these waters...
October 24, 2016: Conservation Biology: the Journal of the Society for Conservation Biology
Jerome A Staal, Yanxin Pei, Brian R Rood
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease...
October 19, 2016: International Journal of Molecular Sciences
Paolo Cifani, Alex Kentsis
Given superior analytical features, mass spectrometry proteomics is well suited for the basic investigation and clinical diagnosis of human disease. Modern mass spectrometry enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy mass spectrometry in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner...
October 24, 2016: Proteomics
Kyung Suk Lee, Lucy E Lee, Erel Levine
Small animals such as the roundworm C. elegans are excellent models for studying bacterial infection and host response, as well as for genetic and chemical screens. A key methodology is the killing assay, in which the number of surviving animals is tracked as a function of the time post infection. This is a labor-intensive procedure, prone to human error and subjective choices, and often involves undesired perturbation to the animals and their environment. In addition, the survival of animals is just one aspect of a multi-dimensional complex biological process...
October 24, 2016: Scientific Reports
Dengkui DU, Shirong Chen, Gang Yi, Pan Wang, Ying Tang, Liwen Zheng, Junnan Chen
Objective To investigate the effect of low-intensity pulsed ultrasound (LIPUS) on the extracellular matrix synthesis of human osteoarthritis (OA) chondrocytes and explore the underlying mechanism. Methods Human osteoarthritis chondrocytes were collected from abandoned articular cartilage. Then the cells were cultured and identified by toluidine blue staining and immunocytochemical staining of type 2 collagen. The passage 2 cells were randomly divided into 3 groups: control OA group, 30 mW/cm(2) LIPUS-treated OA group, 30 mW/cm(2) LIPUS combined with 5 μmol/L LY294002-treated OA group...
November 2016: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
Daniela Beccati, Miroslaw Lech, Jennifer Ozug, Nur Sibel Gunay, Jing Wang, Elaine Y Sun, Joël R Pradines, Victor Farutin, Zachary Shriver, Ganesh V Kaundinya, Ishan Capila
Heparan sulfate (HS), a glycosaminoglycan present on the surface of cells, has been postulated to have important roles in driving both normal and pathological physiologies. The chemical structure and sulfation pattern (domain structure) of HS is believed to determine its biological function, to vary across tissue types, and to be modified in the context of disease. Characterization of HS requires isolation and purification of cell surface HS as a complex mixture. This process may introduce additional chemical modification of the native residues...
October 22, 2016: Glycoconjugate Journal
Alfredo Ambrosone, Giorgia Batelli, Hamed Bostan, Nunzio D'Agostino, Maria Luisa Chiusano, Gaetano Perrotta, Antonietta Leone, Stefania Grillo, Antonello Costa
Water-limiting conditions affect dramatically plant growth and development and, ultimately, yield of potato plants (Solanum tuberosum L.). Therefore, understanding the mechanisms underlying the response to water deficit is of paramount interest to obtain drought tolerant potato varieties. Herein, potato 10K cDNA array slides were used to profile transcriptomic changes of two potato cell populations under abrupt (shocked cells) or gradual exposure (adapted cells) to polyethylene glycol (PEG)-mediated water stress...
October 19, 2016: Gene
Yun Bai, Jia Wang, Jing Han, Xiao-Li Xie, Cheng-Guang Ji, Jie Yin, Lei Chen, Cun-Kai Wang, Xiao-Yu Jiang, Wei Qi, Hui-Qing Jiang
BACKGROUND AND AIMS: BCL2L10 is an apoptosis-related member of the BCL-2 protein family. The role of BCL2L10 in the pathogenesis of hepatocellular carcinoma (HCC) is poorly understood. This study was aimed to investigate the function and underlying mechanisms of BCL2L10 in HCC. METHODS: BCL2L10 expression in human HCC and corresponding adjacent normal tissues was investigated by quantitative real-time PCR and western blot. The biological functions of BCL2L10 in HCC cell lines were determined by cell viability, colony formation, cell apoptosis, cell cycle and cell metastasis assays, and in vivo by tumorigenicity and lung metastasis assays in nude mice...
October 22, 2016: Molecular Carcinogenesis
Stefan Grob, Ueli Grossniklaus
Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues...
2017: Methods in Molecular Biology
Duthika M Mallawaaratchy, Susannah Hallal, Ben Russell, Linda Ly, Saeideh Ebrahimkhani, Heng Wei, Richard I Christopherson, Michael E Buckland, Kimberley L Kaufman
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM) biology and represent novel sources of biomarkers that are detectable in the peripheral circulation. Despite this notionally non-invasive approach to assess GBM tumours in situ, a comprehensive GBM EV protein signature has not been described. Here, EVs secreted by six GBM cell lines were isolated and analysed by quantitative high-resolution mass spectrometry. Overall, 844 proteins were identified in the GBM EV proteome, of which 145 proteins were common to EVs secreted by all cell lines examined; included in the curated EV compendium (Vesiclepedia_559; http://microvesicles...
October 21, 2016: Journal of Neuro-oncology
Bassem Refaat, Jawwad Ahmad, Shakir Idris, Fadi Fayez Kamfar, Ahmed Mohamed Ashshi, Sarah Abdullah Batwa, Faizah Ahmed Malibary
This is a prospective observational study that measures the expression of vitamin D (VD) metabolising and signalling molecules and Ca(2+) sensing receptor (CaSR) in human Fallopian tube (FT) during the menstrual cycle and ectopic pregnancy (EP). Fresh FTs were obtained during total abdominal hysterectomy at the follicular (n = 16) and midluteal (n = 16) phases. Specimens from remote and implantation sites as well as trophoblastic tissues were also freshly collected from each FT with EP (n = 10)...
October 22, 2016: Cell and Tissue Research
Florian Graef, Branko Vukosavljevic, Jean-Philippe Michel, Marius Wirth, Oliver Ries, Chiara De Rossi, Maike Windbergs, Véronique Rosilio, Christian Ducho, Sarah Gordon, Claus-Michael Lehr
Gram-negative bacteria possess a unique and complex cell envelope, composed of an inner and outer membrane separated by an intermediate cell wall-containing periplasm. This tripartite structure acts intrinsically as a significant biological barrier, often limiting the permeation of anti-infectives, and so preventing such drugs from reaching their target. Furthermore, identification of the specific permeation-limiting envelope component proves difficult in the case of many anti-infectives, due to the challenges associated with isolation of individual cell envelope structures in bacterial culture...
October 18, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
Paramee Kumkrong, Benjaporn Thiensong, Phuong Mai Le, Garnet McRae, Anthony Windust, Suladda Deawtong, Juris Meija, Paulette Maxwell, Lu Yang, Zoltán Mester
Methods based on species specific isotope dilution were developed for the accurate and SI traceable determination of arsenobetaine (AsBet) and methylmercury (MeHg) in prawn and cuttlefish tissues by LC-MS/MS and SPME GC-ICPMS. Quantitation of AsBet and MeHg were achieved by using a (13)C-enriched AsBet spike (NRC CRM CBET-1) and an enriched spike of Me(198)Hg (NRC CRM EMMS-1), respectively, wherein analyte mass fractions in enriched spikes were determined by reverse isotope dilution using natural abundance AsBet and MeHg primary standards...
November 2, 2016: Analytica Chimica Acta
Bowen Niu, Bo Li, Chongyang Wu, Jiang Wu, Yuan Yan, Rui Shang, Chunling Bai, Guangpeng Li, Jinlian Hua
Melatonin has been reported to be an important endogenous hormone for regulating neurogenesis, immunityand the biological clock. Recently, the effects of melatonin on neural stem cells (NSCs), mesenchymal stem cells(MSCs), and induced pluripotent stem cells(iPSCs) have been reported; however, the effects of melatonin on spermatogonia stem cells (SSCs) are not clear. Here, 1μM and 1nM melatonin was added to medium when goat SSCs were cultured in vitro, the results showed that melatonin could increase the formation and size of SSC colonies...
October 18, 2016: Oncotarget
Yan Zhao, Pengcheng Liu, Junyong Wang, Xirong Xiao, Xiangzhou Meng, Yunhui Zhang
BACKGROUND: In utero polybrominated diphenyl ethers (PBDEs) exposure has been associated with adverse fetal growth. Alterations in placental DNA methylation might mediate those adverse effects. OBJECTIVES: To examine the associations between in utero PBDEs exposure and DNA methylation in human placenta. METHODS: Eighty apparently healthy mother-newborn pairs delivering at the Second Affiliated Hospital of Wenzhou Medical College were enrolled in this study...
October 18, 2016: Environment International
Bin Tang, Yanmei Huang, Hongqin Yang, Peixiao Tang, Hui Li
As a natural dietary polyphenol, 3,4,5-tri-O-caffeoylquinic acid (3,4,5-triCQA) exhibits numerous stronger pharmacological activities than that of its analogues. Studies on interaction between 3,4,5-triCQA and protein are very helpful for understanding the mechanism of these enhanced biological functions. In this study, (1)H saturation transfer difference NMR ((1)H STD-NMR) combined with multi-spectroscopy were used to probe the interaction of 3,4,5-triCQA with human serum albumin (HSA). Both qualitative and quantitative (1)H STD-NMR indicated that 3,4,5-triCQA can specifically bind to HSA at the favored Sudlow's site II with caffeoyl groups as the main recognizable moiety...
October 17, 2016: Journal of Photochemistry and Photobiology. B, Biology
Ana Rita Araujo, Lendert Gelens, Rahuman S M Sheriff, Silvia D M Santos
Cell division is characterized by a sequence of events by which a cell gives rise to two daughter cells. Quantitative measurements of cell-cycle dynamics in single cells showed that despite variability in G1-, S-, and G2 phases, duration of mitosis is short and remarkably constant. Surprisingly, there is no correlation between cell-cycle length and mitotic duration, suggesting that mitosis is temporally insulated from variability in earlier cell-cycle phases. By combining live cell imaging and computational modeling, we showed that positive feedback is the molecular mechanism underlying the temporal insulation of mitosis...
October 20, 2016: Molecular Cell
Sachin Kumar, Marie-Dominique Filippi
Transmission electron microscopy (TEM) provides details of the cellular organization and ultrastructure. However, TEM analysis of rare cell populations, especially cells in suspension such as hematopoietic stem cells (HSCs), remains limited due to the requirement of a high cell number during sample preparation. There are a few cytospin or monolayer approaches for TEM analysis from scarce samples, but these approaches fail to get significant quantitative data from the limited number of cells. Here, an alternative and novel approach for sample preparation in TEM studies is described for rare cell populations that enables quantitative analysis...
October 12, 2016: Journal of Visualized Experiments: JoVE
Maryam Jamshidi-Aidji, Gertrud Elisabeth Morlock
Phytochemicals are promising agents in the development of new antibiotics. A streamlined strategy for rapid screening and reliable characterization of antibiotics in botanicals was demonstrated in contrast to the commonly applied chromatographic column fractionation followed by microtiter plate assay. Modern direct bioautography hyphenated to structure elucidation techniques is a straightforward bioanalytical tool, especially if microbiological assays were taken into account. At one go, lipophilic antimicrobials in Salvia miltiorrhiza root samples were analyzed using high-performance thin-layer chromatography (HPTLC) in direct combination with Aliivibrio fischeri and Bacillus subtilis bioassays...
October 21, 2016: Analytical Chemistry
Adam Pap, Katalin F Medzihradszky, Zsuzsanna Darula
Growing evidence on the diverse biological roles of extracellular glycosylation as well as the need for quality control of protein pharmaceuticals make glycopeptide analysis both exciting and important again after a long hiatus. High-throughput O-glycosylation studies have to tackle the complexity of glycosylation as well as technical difficulties and, up to now, have yielded only limited results mostly from single enrichment experiments. In this study, we address the technical reproducibility of the characterization of the most prevalent O-glycosylation (mucin-type core 1 structures) in human serum, using a two-step lectin affinity-based workflow...
October 20, 2016: Analytical and Bioanalytical Chemistry
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