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System biology integrative biology

Chao Xiong, Zhiquan Zhang, Gurpreet S Baht, Niccolo Terrando
Surgery is commonly used to improve and maintain quality of life. Unfortunately, in vulnerable patients such as the elderly, complications may occur and significantly diminish the outcome. Indeed, after routine orthopedic surgery to repair a fracture, as many as 50% of elderly patients suffer from neurologic complications like delirium. Also, the capacity to heal and regenerate tissue after surgery decreases with age, and can impact the quality of fracture repair and even osseous integration of implants. Thus, a better understanding of mechanisms that drive these age-dependent changes could provide strategic targets to minimize risk for such complications and optimize outcomes...
February 27, 2018: Journal of Visualized Experiments: JoVE
Joselle M McCracken, Sheng Xu, Adina Badea, Kyung-In Jang, Zheng Yan, David J Wetzel, Kewang Nan, Qing Lin, Mengdi Han, Mikayla A Anderson, Jung Woo Lee, Zijun Wei, Matt Pharr, Renhan Wang, Jessica Su, Stanislav S Rubakhin, Jonathan V Sweedler, John A Rogers, Ralph G Nuzzo
Complex 3D organizations of materials represent ubiquitous structural motifs found in the most sophisticated forms of matter, the most notable of which are in life-sustaining hierarchical structures found in biology, but where simpler examples also exist as dense multilayered constructs in high-performance electronics. Each class of system evinces specific enabling forms of assembly to establish their functional organization at length scales not dissimilar to tissue-level constructs. This study describes materials and means of assembly that extend and join these disparate systems-schemes for the functional integration of soft and biological materials with synthetic 3D microscale, open frameworks that can leverage the most advanced forms of multilayer electronic technologies, including device-grade semiconductors such as monocrystalline silicon...
September 2017: Advanced Biosystems
Shihao Ran, Sebastian Berisha, Rupali Mankar, Wei-Chuan Shih, David Mayerich
Infrared (IR) spectroscopic microscopes provide the potential for label-free quantitative molecular imaging of biological samples, which can be used to aid in histology, forensics, and pharmaceutical analysis. Most IR imaging systems use broadband illumination combined with a spectrometer to separate the signal into spectral components. This technique is currently too slow for many biomedical applications such as clinical diagnosis, primarily due to the availability of bright mid-infrared sources and sensitive MCT detectors...
February 1, 2018: Biomedical Optics Express
Ke Li, Junfang Li, Jin Su, Xuefeng Xiao, Xiujuan Peng, Feng Liu, Defeng Li, Yi Zhang, Tao Chong, Haiyu Xu, Changxiao Liu, Hongjun Yang
BACKGROUND: The quality evaluation of traditional Chinese medicine (TCM) formulations is needed to guarantee the safety and efficacy. In our laboratory, we established interaction rules between chemical quality control and biological activity evaluations to study Yuanhu Zhitong tablets (YZTs). Moreover, a quality marker (Q-marker) has recently been proposed as a new concept in the quality control of TCM. However, no appropriate methods are available for the identification of Q-markers from the complex TCM systems...
March 7, 2018: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Sebastian Kress, Johannes Baur, Christoph Otto, Natalie Burkard, Joris Braspenning, Heike Walles, Joachim Nickel, Marco Metzger
In tissue engineering, the generation and functional maintenance of dense voluminous tissues is mainly restricted due to insufficient nutrient supply. Larger three-dimensional constructs, which exceed the nutrient diffusion limit become necrotic and/or apoptotic in long-term culture if not provided with an appropriate vascularization. Here, we established protocols for the generation of a pre-vascularized biological scaffold with intact arterio-venous capillary loops from rat intestine, which is decellularized under preservation of the feeding and draining vascular tree...
March 16, 2018: Scientific Reports
Elizabeth R Gerstner, Kristian W Pajtler
Ependymoma can arise throughout the whole neuraxis. In children, tumors predominantly occur intracranially, whereas the spine is the most prevalent location in adults. Significant variance in the grade II versus grade III distinction of ependymomas has led to the acknowledgment that the clinical utility of histopathological classification is limited. Epigenomic profiling efforts have identified molecularly distinct groups of ependymomas that adequately reflect the biological, clinical, and histopathological heterogeneities across anatomical compartments, age groups, and grades...
February 2018: Seminars in Neurology
Timothy F Vandervoet, Peter C Ellsworth, Yves Carrière, Steven E Naranjo
Conservation biological control can be an effective tactic for minimizing insect-induced damage to agricultural production. In the Arizona cotton system, a suite of generalist arthropod predators provides critical regulation of Bemisia tabaci Gennadius (MEAM1) (Hemiptera: Aleyrodidae) and other pests. Arthropod predator and B. tabaci populations were manipulated with a range of broad-spectrum and selective insecticide exclusions to vary predator to prey interactions in a 2-yr field study. Predator to prey ratios associated with B...
March 13, 2018: Journal of Economic Entomology
Guillermo de Anda-Jáuregui, Kai Guo, Brett A McGregor, Junguk Hur
The quintessential biological response to disease is inflammation. It is a driver and an important element in a wide range of pathological states. Pharmacological management of inflammation is therefore central in the clinical setting. Anti-inflammatory drugs modulate specific molecules involved in the inflammatory response; these drugs are traditionally classified as steroidal and non-steroidal drugs. However, the effects of these drugs are rarely limited to their canonical targets, affecting other molecules and altering biological functions with system-wide effects that can lead to the emergence of secondary therapeutic applications or adverse drug reactions (ADRs)...
2018: Frontiers in Physiology
Joseph Páez Chávez, Dirk Jungmann, Stefan Siegmund
The paper presents a comprehensive numerical study of mathematical models used to describe complex biological systems in the framework of integrated pest management. Our study considers two specific ecosystems that describe the application of control mechanisms based on pesticides and natural enemies, implemented in an impulsive and periodic manner, due to which the considered models belong to the class of impulsive differential equations. The present work proposes a numerical approach to study such type of models in detail, via the application of path-following (continuation) techniques for nonsmooth dynamical systems, via the novel continuation platform COCO (Dankowicz and Schilder)...
December 2018: Journal of Biological Dynamics
Guo-Ying Sun, Hui-Hui Yang, Xin-Xin Guan, Wen-Jing Zhong, Yong-Ping Liu, Ming-Yuan Du, Xiao-Qin Luo, Yong Zhou, Cha-Xiang Guan
Vasoactive intestinal peptide (VIP) is one of the most abundant neuropeptides in the lungs with various biological characters. We have reported that VIP inhibited the expressions of TREM-1 and IL-17A, which are involved in the initiation and amplification of inflammation in acute lung injury (ALI). However, the overall effect of VIP on ALI remains unknown. The aim of this study is to investigate the therapeutic effect of VIP mediated by lentivirus (Lenti-VIP) on lipopolysaccharide (LPS)-induced murine ALI. We found that the expression of intrapulmonary VIP peaked at day7 after the intratracheal injection of Lenti-VIP...
March 12, 2018: Molecular Immunology
Margarita Villar, Lourdes Mateos-Hernandez, Jose de la Fuente
BACKGROUND: Why an autoimmune disease that is the main cause of the acute neuromuscular paralysis worldwide has not yet a well-characterized cause or an effective treatment? The existence of different clinical variants for the Guillain-Barré syndrome (GBS) coupled with the fact that a high number of pathogens can cause an infection that sometimes, but not always, precedes the development of the syndrome, confers a high degree of uncertainty for both prognosis and treatment. In the post-genomic era, the development of omics technologies for the high-throughput analysis of biological molecules is allowing the characterization of biological systems in a degree of depth unimaginable before...
March 14, 2018: Current Medicinal Chemistry
Aleta Pupovac, Berna Senturk, Chiara Griffoni, Katharina Maniura-Weber, Markus Rottmar, Sally L McArthur
3D human skin models provide a platform for toxicity testing, biomaterials evaluation, and investigation of fundamental biological processes. However, the majority of current in vitro models lack an inflammatory system, vasculature, and other characteristics of native skin, indicating scope for more physiologically complex models. Looking at the immune system, there are a variety of cells that could be integrated to create novel skin models, but to do this effectively it is also necessary to understand the interface between skin biology and tissue engineering as well as the different roles the immune system plays in specific health and disease states...
March 15, 2018: Advanced Healthcare Materials
Laurent Schwartz, Olivier Lafitte, Jorgelindo da Veiga Moreira
Background: Diseases and health conditions have been classified according to anatomical site, etiological, and clinical criteria. Physico-chemical mechanisms underlying the biology of diseases, such as the flow of energy through cells and tissues, have been often overlooked in classification systems. Objective: We propose a conceptual framework toward the development of an energy-oriented classification of diseases, based on the principles of physical chemistry. Methods: A review of literature on the physical chemistry of biological interactions in a number of diseases is traced from the point of view of the fluid and solid mechanics, electricity, and chemistry...
2018: Frontiers in Physiology
Tatsuya Yamada, Makoto Nishiyama, Shigeyuki Oba, Henri Claver Jimbo, Kazushi Ikeda, Shin Ishii, Kyonsoo Hong, Yuichi Sakumura
Biological cells express intracellular biomolecular information to the extracellular environment as various physical responses. We show a novel computational approach to estimate intracellular biomolecular pathways from growth cone electrophysiological responses. Previously, it was shown that cGMP signaling regulates membrane potential (MP) shifts that control the growth cone turning direction during neuronal development. We present here an integrated deterministic mathematical model and Bayesian reversed-engineering framework that enables estimation of the molecular signaling pathway from electrical recordings and considers both the system uncertainty and cell-to-cell variability...
March 14, 2018: Scientific Reports
Lorenzo Vannozzi, Immihan Ceren Yasa, Hakan Ceylan, Arianna Menciassi, Leonardo Ricotti, Metin Sitti
Programming materials with tunable physical and chemical interactions among its components pave the way of generating 3D functional active microsystems with various potential applications in tissue engineering, drug delivery, and soft robotics. Here, the development of a recapitulated fascicle-like implantable muscle construct by programmed self-folding of poly(ethylene glycol) diacrylate hydrogels is reported. The system comprises two stacked layers, each with differential swelling degrees, stiffnesses, and thicknesses in 2D, which folds into a 3D tube together...
March 14, 2018: Macromolecular Bioscience
Kumar Parijat Tripathi, Marina Piccirillo, Mario Rosario Guarracino
BACKGROUND: The endomembrane system, known as secretory pathway, is responsible for the synthesis and transport of protein molecules in cells. Therefore, genes involved in the secretory pathway are essential for the cellular development and function. Recent scientific investigations show that ER and Golgi apparatus may provide a convenient drug target for cancer therapy. On the other hand, it is known that abundantly expressed genes in different cellular organelles share interconnected pathways and co-regulate each other activities...
March 8, 2018: BMC Bioinformatics
Xiang-Tian Yu, Tao Zeng
The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations...
2018: Methods in Molecular Biology
Junu Bae, Zijian Zhou, Thomas Theis, Warren S Warren, Qiu Wang
Hyperpolarized magnetic resonance (HP-MR) is a powerful, sensitive, and noninvasive approach to visualize molecular structure, function, and dynamics in vitro and in vivo. Current applications of HP-MR mostly rely on hyperpolarization of target compounds in dedicated hyperpolarizers because biomolecules can typically not be hyperpolarized directly in vivo. The injected hyperpolarized probes often undergo multiple metabolic pathways in living systems, and it remains challenging to localize and identify specific targets with high chemical selectivity...
March 2018: Science Advances
Azam Peyvandipour, Nafiseh Saberian, Adib Shafi, Michele Donato, Sorin Draghici
Motivation: Identification of novel therapeutic effects for existing U.S. Food and Drug Administration (FDA)-approved drugs, drug repurposing, is an approach aimed to dramatically shorten the drug discovery process, which is costly, slow and risky. Several computational approaches use transcriptional data to find potential repurposing candidates. The main hypothesis of such approaches is that if gene expression signature of a particular drug is opposite to the gene expression signature of a disease, that drug may have a potential therapeutic effect on the disease...
March 9, 2018: Bioinformatics
Lauren K Lucas, Chris C Nice, Zachariah Gompert
Patterns of phenotypic variation within and among species can be shaped and constrained by trait genetic architecture. This is particularly true for complex traits, such as butterfly wing patterns, that consist of multiple elements. Understanding the genetics of complex trait variation across species boundaries is difficult, as it necessitates mapping in structured populations and can involve many loci with small or variable phenotypic effects. Here, we investigate the genetic architecture of complex wing pattern variation in Lycaeides butterflies as a case study of mapping multivariate traits in wild populations that include multiple nominal species or groups...
March 13, 2018: Molecular Ecology Resources
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