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quantitative biology

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https://www.readbyqxmd.com/read/29346517/does-telomere-length-indicate-biological-physical-and-cognitive-health-among-older-adults-evidence-from-the-health-and-retirement-study
#1
Lauren Brown, Yuan Zhang, Colter Mitchel, Jennifer Ailshire
Telomere length (TL) has been suggested as a biomarker that can indicate individual variability in the rate of aging. Yet, it remains unclear whether TL is related to recognized indicators of health in an aging, older nationally representative sample. We examine whether TL is associated with 15 biological, physical and cognitive markers of health among older adults ages 54+. TL was assayed from saliva using quantitative PCR (T/S ratio) in the 2008 Health and Retirement Study (n=4,074). We estimated probability of high risk levels across indictors of health by TL and age-singly and jointly...
January 16, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29346099/cell-membrane-tracking-in-living-brain-tissue-using-differential-interference-contrast-microscopy
#2
John Lee, Ilya Kolb, Craig R Forest, Christopher J Rozell
Differential interference contrast (DIC) microscopy is widely used for observing unstained biological samples that are otherwise optically transparent. Combining this optical technique with machine vision could enable the automation of many life science experiments; however, identifying relevant features under DIC is challenging. In particular, precise tracking of cell boundaries in a thick ( ) slice of tissue has not previously been accomplished. We present a novel deconvolution algorithm that achieves the state-of-the-art performance at identifying and tracking these membrane locations...
April 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29345443/suv-calculation-in-breast-cancer-which-normalization-should-be-applied-when-using-18f-fdg-pet
#3
Olivier Humbert, Jean-Marc Riedinger, David Chardin, Isabelle Desmoulins, François Brunotte, Alexandre Cochet
BACKGROUND: When using 18F-FDG PET, glucose metabolism quantification is affected by various factors. We aimed to investigate the benefit of different SUV normalizations to improve the accuracy of 18F-FDG uptake to predict breast cancer aggressiveness and response to treatment. METHODS: Two hundred fifty-two women with locally advanced breast cancer treated with neoadjuvant chemotherapy (NAC) were included. Women underwent 18F-FDG PET before and after the first course of NAC...
January 17, 2018: Quarterly Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/29345189/microrna-19-contributes-to-the-malignant-phenotypes-of-osteosarcoma-in-vitro-by-targeting-pax6
#4
Qingbing Meng, Ming Dai, Xuejun Nie, Wensheng Zhang, Xingli Xu, Jian Li, Hongxin Mu, Xiaolan Liu, Ling Qin, Xiaoqi Zhu, Jun Yan, Minqian Zheng
This study was conducted to detect the expression of miR-19 and Pax6 (Paired box protein 6) in human osteosarcoma cells and the effects on biological characteristics of osteosarcoma cells. Quantitative real-time polymerase chain reaction was used to detect the expression of Pax6 and miR-19 in normal human osteoblasts (hFOB 1.19) and osteosarcoma cell lines (U2OS, Saos-2, and MG-63). Results showed that miR-19 was significantly upregulated in osteosarcoma cell lines compared with that in hFOB 1.19 cells, while the expression of Pax6 messenger RNA was significantly downregulated...
January 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#5
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344642/microarray-analysis-reveals-tmub1-as-a-cell-cycle-associated-protein-in-rat-hepatocytes
#6
Hangwei Fu, Jianhua Xu, Jian Chen, Guangyao Li, Xiaobiao Zhao, Ping Chen
Transmembrane and ubiquitin-like domain containing protein 1 (Tmub1), formerly known as hepatocyte odd protein shuttling (HOPS) has been recognized as a ubiquitously expressed shuttling protein that moves between the nucleus and cytoplasm in hepatocytes. Tmub1 is involved in liver regeneration and functions as a bridging protein in tumor cell proliferation. To investigate the transcriptional profile and potential biological processes affected by Tmub1 expression in normal rat hepatocytes, microarray and bioinformatics experiments were used to identify 127 mRNAs differentially expressed between Tmub1‑overexpression, Tmub1‑knockdown and normal BRL‑3A cells (fold‑change ≥2...
January 17, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29344252/itraq-based-quantitative-proteomic-analysis-and-bioinformatics-study-of-proteins-in-retinoblastoma
#7
Yong Cheng, Qingyu Meng, Lvzhen Huang, Xuan Shi, Jing Hou, Xiaoxin Li, Jianhong Liang
The aim of the present study was to analyze proteins in the aqueous humor (AH) of patients' retinoblastoma (RB), and investigate their potential role in RB using the comparative proteomic technique of isobaric tags for relative and absolute quantitation (iTRAQ) coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 0.1 ml AH was collected from 10 children with RB (mean age, 3.8 years; range, 2-5 years) and patients with senile cataracts (mean age, 70.4 years; range, 65-79 years), which was used as the control...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343841/microdosimetric-modeling-of-biological-effectiveness-for-boron-neutron-capture-therapy-considering-intra-and-intercellular-heterogeneity-in-10b-distribution
#8
Tatsuhiko Sato, Shin-Ichiro Masunaga, Hiroaki Kumada, Nobuyuki Hamada
We here propose a new model for estimating the biological effectiveness for boron neutron capture therapy (BNCT) considering intra- and intercellular heterogeneity in 10B distribution. The new model was developed from our previously established stochastic microdosimetric kinetic model that determines the surviving fraction of cells irradiated with any radiations. In the model, the probability density of the absorbed doses in microscopic scales is the fundamental physical index for characterizing the radiation fields...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343499/a-population-phylogenetic-view-of-mitochondrial-heteroplasmy
#9
Peter R Wilton, Arslan Zaidi, Kateryna Makova, Rasmus Nielsen
The mitochondrion has recently emerged as an active player in a myriad of cellular processes. Additionally, it was recently shown that more than 200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model...
January 17, 2018: Genetics
https://www.readbyqxmd.com/read/29342982/detection-of-zro%C3%A2-nanoparticles-in-lung-tissue-sections-by-time-of-flight-secondary-ion-mass-spectrometry-and-ion-beam-microscopy
#10
Lothar Veith, Julia Böttner, Antje Vennemann, Daniel Breitenstein, Carsten Engelhard, Jan Meijer, Irina Estrela-Lopis, Martin Wiemann, Birgit Hagenhoff
The increasing use of nanoparticles (NP) in commercial products requires elaborated techniques to detect NP in the tissue of exposed organisms. However, due to the low amount of material, the detection and exact localization of NP within tissue sections is demanding. In this respect, Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) and Ion Beam Microscopy (IBM) are promising techniques, because they both offer sub-micron lateral resolutions along with high sensitivities. Here, we compare the performance of the non-material-consumptive IBM and material-consumptive ToF-SIMS for the detection of ZrO₂ NP (primary size 9-10 nm) in rat lung tissue...
January 15, 2018: Nanomaterials
https://www.readbyqxmd.com/read/29342931/transcriptome-analysis-based-on-rna-seq-in-understanding-pathogenic-mechanisms-of-diseases-and-the-immune-system-of-fish-a-comprehensive-review
#11
REVIEW
Arun Sudhagar, Gokhlesh Kumar, Mansour El-Matbouli
In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection...
January 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29341315/use-of-quantitative-real-time-pcr-to-determine-viability-of-streptococcus-equi-subspecies-equi-in-respiratory-secretions-from-horses-with-strangles
#12
N Pusterla, C M Leutenegger, S M Barnum, B A Byrne
BACKGROUND: In recent years, molecular approaches have been able to characterise the viability of equine upper respiratory tract pathogens using absolute molecular quantitation as well as detection of transcripts for virulence genes. OBJECTIVES: The objective this study was to investigate molecular surrogates for S. equi subspecies equi (S. equi) viability in biological samples from horses with strangles. STUDY DESIGN: Retrospective cross-sectional study...
January 17, 2018: Equine Veterinary Journal
https://www.readbyqxmd.com/read/29341016/oxygenation-imaging-by-nuclear-magnetic-resonance-methods
#13
Heling Zhou, Nuria Arias-Ramos, Pilar López-Larrubia, Ralph P Mason, Sebastián Cerdán, Jesús Pacheco-Torres
Oxygen monitoring is a topic of exhaustive research due to its central role in many biological processes, from energy metabolism to gene regulation. The ability to monitor in vivo the physiological distribution and the dynamics of oxygen from subcellular to macroscopic levels is a prerequisite to better understand the mechanisms associated with both normal and disease states (cancer, neurodegeneration, stroke, etc.). This chapter focuses on magnetic resonance imaging (MRI) based techniques to assess oxygenation in vivo...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340790/an-automated-framework-for-qsar-model-building
#14
Samina Kausar, Andre O Falcao
BACKGROUND: In-silico quantitative structure-activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules based on their chemical structure. With the passage of time, the exponentially growing amount of synthesized and known chemicals data demands computationally efficient automated QSAR modeling tools, available to researchers that may lack extensive knowledge of machine learning modeling...
January 16, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29340699/long-term-expression-of-glomerular-genes-in-diabetic-nephropathy
#15
Dominik Chittka, Bernhard Banas, Laura Lennartz, Franz Josef Putz, Kathrin Eidenschink, Sebastian Beck, Thomas Stempfl, Christoph Moehle, Simone Reichelt-Wurm, Miriam C Banas
Background: Although diabetic nephropathy (DN) is the most common cause for end-stage renal disease in western societies, its pathogenesis still remains largely unclear. A different gene pattern of diabetic and healthy kidney cells is one of the probable explanations. Numerous signalling pathways have emerged as important pathophysiological mechanisms for diabetes-induced renal injury. Methods: Glomerular cells, as podocytes or mesangial cells, are predominantly involved in the development of diabetic renal lesions...
January 11, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29340519/evaluating-the-current-state-of-the-art-of-huntington-disease-research-a-scientometric-analysis
#16
L A Barboza, N C Ghisi
Huntington disease (HD) is an incurable neurodegenerative disorder caused by a dominant mutation on the 4th chromosome. We aim to present a scientometric analysis of the extant scientific undertakings devoted to better understanding HD. Therefore, a quantitative study was performed to examine the current state-of-the-art approaches that foster researchers' understandings of the current knowledge, research trends, and research gaps regarding this disorder. We performed literature searches of articles that were published up to September 2016 in the "ISI Web of Science™" (http://apps...
January 11, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#17
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29340386/on-chip-functional-neuroimaging-with-mechanical-stimulation-in-caenorhabditis-elegans-larvae-for-studying-development-and-neural-circuits
#18
Yongmin Cho, David N Oakland, Sol Ah Lee, William R Schafer, Hang Lu
Mechanosensation is fundamentally important for the abilities of an organism to experience touch, hear sounds, and maintain balance. Caenorhabditis elegans is a powerful system for studying mechanosensation as this worm is well suited for in vivo functional imaging of neurons. Many years of research using labor-intensive methods have generated a wealth of knowledge about mechanosensation in C. elegans, and the recent microfluidic-based platforms continue to push the boundary for this field. However, developmental aspects of sensory biology, including mechanosensation, are still not fully understood...
January 17, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29340250/integrated-genomic-analyses-of-lung-squamous-cell-carcinoma-for-identification-of-a-possible-competitive-endogenous-rna-network-by-means-of-tcga-datasets
#19
Pengbo Ning, Zhongxing Wu, Aoxue Hu, Xuepeng Li, Jun He, Xiaocheng Gong, Yuqiong Xia, Yukui Shang, Huijie Bian
The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play important roles in the initiation, progression, and metastasis of human cancers. Nonetheless, a mechanistic understanding of noncoding RNA functions in lung squamous cell carcinoma (LUSC) is lacking. To fill this critical gap in knowledge, we obtained mRNA, miRNA, and lncRNA expression data on patients with LUSC from the updated Cancer Genome Atlas (TCGA) database (2016)...
2018: PeerJ
https://www.readbyqxmd.com/read/29340096/crispr-cas9-mediated-reversibly-immortalized-mouse-bone-marrow-stromal-stem-cells-bmscs-retain-multipotent-features-of-mesenchymal-stem-cells-mscs
#20
Xue Hu, Li Li, Xinyi Yu, Ruyi Zhang, Shujuan Yan, Zongyue Zeng, Yi Shu, Chen Zhao, Xingye Wu, Jiayan Lei, Yasha Li, Wenwen Zhang, Chao Yang, Ke Wu, Ying Wu, Liping An, Shifeng Huang, Xiaojuan Ji, Cheng Gong, Chengfu Yuan, Linghuan Zhang, Wei Liu, Bo Huang, Yixiao Feng, Bo Zhang, Rex C Haydon, Hue H Luu, Russell R Reid, Michael J Lee, Jennifer Moriatis Wolf, Zebo Yu, Tong-Chuan He
Mesenchymal stem cells (MSCs) are multipotent non-hematopoietic progenitor cells that can undergo self-renewal and differentiate into multi-lineages. Bone marrow stromal stem cells (BMSCs) represent one of the most commonly-used MSCs. In order to overcome the technical challenge of maintaining primary BMSCs in long-term culture, here we seek to establish reversibly immortalized mouse BMSCs (imBMSCs). By exploiting CRISPR/Cas9-based homology-directed-repair (HDR) mechanism, we target SV40T to mouse Rosa26 locus and efficiently immortalize mouse BMSCs (i...
December 19, 2017: Oncotarget
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