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Systems biology

Mariella G Filbin, Dominik Sturm
Gliomas are the most common primary central nervous system (CNS) neoplasms in children and adolescents and are thought to arise from their glial progenitors or stem cells. Although the exact cells of origin for most pediatric gliomas remain to be identified, our current understanding is that specific cell populations during CNS development are susceptible to particular oncogenic events during certain time windows and thus give rise to pediatric gliomas with distinct histological, molecular, and clinical features...
February 2018: Seminars in Neurology
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
Zachary J Reitman, Frank Winkler, Andrew E H Elia
Glioblastoma (GBM) is the most common primary malignant tumor of the central nervous system. The current standard of care for GBM is maximal resection followed by postoperative radiation with concomitant and adjuvant temozolomide. Despite this multimodality treatment, the median survival for GBM remains marginally better than 1 year. In the past decade, genome-wide analyses have uncovered new molecular features of GBM that have refined its classification and provided new insights into the molecular basis for GBM pathogenesis...
February 2018: Seminars in Neurology
Teresa Morales-Ruiz, Álvaro C Romero-Valenzuela, Vanessa M Vázquez-Grande, Teresa Roldán-Arjona, Rafael R Ariza, Dolores Córdoba-Cañero
Base excision repair (BER) is a major defense pathway against spontaneous DNA damage. This multistep process is initiated by DNA glycosylases that recognise and excise the damaged base, and proceeds by the concerted action of additional proteins that perform incision of the abasic site, gap filling and ligation. BER has been extensively studied in bacteria, yeasts and animals. Although knowledge of this pathway in land plants is increasing, there are no reports detecting BER in algae. We describe here an experimental in vitro system allowing the specific analysis of BER in the model alga Chlamydomonas reinhardtii...
March 5, 2018: DNA Repair
Shushan He, Lutz Maibaum
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use coarse-grained molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol. This mixture is known to exhibit both uniform and coexisting phases. We compare and combine different statistical measures of membrane structure to identify the onset of phase coexistence in composition space...
March 16, 2018: Journal of Physical Chemistry. B
Yimin Wang, Fang Ye, Chanyan Huang, Faling Xue, Yingyuan Li, Shaowei Gao, Zeting Qiu, Si Li, Qinchang Chen, Huaqiang Zhou, Yiyan Song, Wenqi Huang, Wulin Tan, Zhongxing Wang
BACKGROUND: Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. METHODS: Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected...
March 15, 2018: Clinical Journal of Pain
Caleb J Bashor, James J Collins
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function...
March 16, 2018: Annual Review of Biophysics
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Qingwang Xue, Chunxue Liu, Xia Li, Li Dai, Huaisheng Wang
Various fluorescent sensing systems for miRNAs detection have been developed. But they mostly contain enzymatic amplification reactions and label procedures. The strict reaction conditions of tool enzymes and the high cost of labeling limit their potential applications, especially in complex biological matrix. Here we have addressed the difficult problems and report a strategy for label-free fluorescent DNA dendrimers based on enzyme-free nonlinear hybridization chain reaction (HCR)-mediated multiple G-quadruplex for simple, sensitive and selective detection of miRNAs with low-background signal...
March 16, 2018: Bioconjugate Chemistry
Ming Xiao, Daozhi Shen, Kevin P Musselman, Walter W Duley, Y Norman Zhou
Neuromorphic computational systems that emulate biological synapses in the human brain are fundamental in the development of artificial intelligence protocols beyond the standard von Neumann architecture. Such systems require new types of building blocks, such as memristors that access a quasi-continuous and wide range of conductive states, which is still an obstacle for the realization of high-efficiency and large-capacity learning in neuromorphoric simulation. Here, we introduce hydrogen and sodium titanate nanobelts, the intermediate products of hydrothermal synthesis of TiO2 nanobelts, to emulate the synaptic behavior...
March 16, 2018: Nanoscale
Michael B Ranke, Jan M Wit
Growth hormone (GH) research and its clinical application for the treatment of growth disorders span more than a century. During the first half of the 20th century, clinical observations and anatomical and biochemical studies formed the basis of the understanding of the structure of GH and its various metabolic effects in animals. The following period (1958-1985), during which pituitary-derived human GH was used, generated a wealth of information on the regulation and physiological role of GH - in conjunction with insulin-like growth factors (IGFs) - and its use in children with GH deficiency (GHD)...
March 16, 2018: Nature Reviews. Endocrinology
Keiko Fujita, Yoshinao Aoki, Shunji Suzuki
Vitis vinifera cv. Koshu is an indigenous cultivar in Japan and has several characteristics that distinguish it from European V. vinifera. In Japan, Koshu is the most popular cultivar for wine making. We report herein a cell culture established from Koshu for use as a system for the production of resveratrol and its derivatives. Grape cell culture YU-1 was developed from the apex tissues of Koshu. YU-1 growth was favorably compared with BY-2 growth, a standard cell line in plant cell biology. Stilbene production and stilbene synthesis gene expression in YU-1 were upregulated by UV-C irradiation...
March 15, 2018: Cytotechnology
Hironori Aoki, Eiichiro Yamamoto, Hiro-O Yamano, Tamotsu Sugai, Tomoaki Kimura, Yoshihito Tanaka, Hiro-O Matsushita, Kenjiro Yoshikawa, Ryo Takagi, Eiji Harada, Michiko Nakaoka, Yuko Yoshida, Taku Harada, Gota Sudo, Makoto Eizuka, Akira Yorozu, Hiroshi Kitajima, Takeshi Niinuma, Masahiro Kai, Masanori Nojima, Hiromu Suzuki, Hiroshi Nakase
BACKGROUND: Colorectal serrated lesions (SLs) are important premalignant lesions whose clinical and biological features are not fully understood. AIMS: We aimed to establish accurate colonoscopic diagnosis and treatment of SLs through evaluation of associations among the morphological, pathological, and molecular characteristics of SLs. METHODS: A total of 388 premalignant and 18 malignant colorectal lesions were studied. Using magnifying colonoscopy, microsurface structures were assessed based on Kudo's pit pattern classification system, and the Type II pit pattern was subcategorized into classical Type II, Type II-Open (Type II-O) and Type II-Long (Type II-L)...
March 15, 2018: Digestive Diseases and Sciences
Kyle I Mentkowski, Jonathan D Snitzer, Sarah Rusnak, Jennifer K Lang
Extracellular vesicles (EVs) comprise a heterogeneous group of small membrane vesicles, including exosomes, which play a critical role in intracellular communication and regulation of numerous physiological processes in health and disease. Naturally released from virtually all cells, these vesicles contain an array of nucleic acids, lipids and proteins which they transfer to target cells within their local milieu and systemically. They have been proposed as a means of "cell-free, cell therapy" for cancer, immune disorders, and more recently cardiovascular disease...
March 15, 2018: AAPS Journal
Young Woong Jang, DoHyung Lim, Hansol Seo, Myung Chul Lee, O-Sung Lee, Yong Seuk Lee
INTRODUCTION: Open-wedge high tibial osteotomy (OWHTO) is a well-established surgical option for medial compartment osteoarthritis of the varus knee. The initial strength of the fixation plate is critical for successful correction maintenance and healing of the osteotomy site. This study was conducted to verify if a newly designed anatomical plate (LCfit) improves the stability of both the medial implant and lateral hinge area, as well as to evaluate how the metal block contributes to both medial and lateral stability...
March 15, 2018: Archives of Orthopaedic and Trauma Surgery
Haseeb Khaliq, Zhong Juming, Peng Ke-Mei
Boron is an essential mineral that plays an important role in several biological processes. Boron is required for growth of plants, animals, and humans. There are increasing evidences of this nutrient showing a variety of pleiotropic effects, ranging from anti-inflammatory and antioxidant effects to the modulation of different body systems. In the past few years, the trials showed disease-related polymorphisms of boron in different species, which has drawn attention of scientists to the significance of boron to health...
March 15, 2018: Biological Trace Element Research
Ana P F Santos, Bianca M Souza, Tânia F C V Silva, Rodrigo P Cavalcante, Silvio C Oliveira, Amílcar Machulek, Rui A R Boaventura, Vítor J P Vilar
The mineralization of bio-recalcitrant humic acids (HAs) by a solar photo-Fenton (SPF) process was investigated in aqueous system, in order to understand its abatement in real high-HA content matrices, such as sanitary landfill leachates. SPF reactions were performed in tubular photoreactors with CPCs at lab-scale (simulated solar light) and pilot-scale (natural sunlight). Considering the experimental conditions selected for this work, the formation of insoluble HA-Fe3+ complexes was observed. Thus, to avoid HA precipitation, oxalic acid (Ox) was added, since Fe3+ -Ox complexes present a higher stability constant...
March 15, 2018: Environmental Science and Pollution Research International
Laura Colino, Javier Herranz-Herrer, Elena Gil-Benito, Teresa Ponte-Lopez, Pablo Del Sol-Calderon, Maria Rodrigo-Yanguas, María Gil-Ligero, Antonio J Sánchez-López, Jose de Leon, Hilario Blasco-Fontecilla
PURPOSE OF REVIEW: The current serotonin-based biological model of suicidal behavior (SB) may be too simplistic. There is emerging evidence that other biomarkers and biological systems may be involved in SB pathophysiology. The literature on the endocannabinoid (EC) systems and SB is limited. The objective of the present article is to review all available information on the relationship between cannabinoid receptors (CB1 and CB2 receptors), and SB and/or psychological pain. RECENT FINDINGS: Our review is limited by the small number and heterogeneity of studies identified: (1) an autopsy study describing elevated levels of CB1 receptor activity in the prefrontal cortex and suicide in both depression and alcoholism and (2) studies supporting the involvement of both CB1 and CB2 receptors in the regulation of neuropathic pain and stress-induced analgesia...
March 15, 2018: Current Psychiatry Reports
Ke Xie, Suowei Wu, Ziwen Li, Yan Zhou, Danfeng Zhang, Zhenying Dong, Xueli An, Taotao Zhu, Simiao Zhang, Shuangshuang Liu, Jinping Li, Xiangyuan Wan
Map-based cloning of maize ms33 gene showed that ZmMs33 encodes a sn-2 glycerol-3-phosphate acyltransferase, the ortholog of rice OsGPAT3, and it is essential for male fertility in maize. Genetic male sterility has been widely studied for its biological significance and commercial value in hybrid seed production. Although many male-sterile mutants have been identified in maize (Zea mays L.), it is likely that most genes that cause male sterility are unknown. Here, we report a recessive genetic male-sterile mutant, male sterility33 (ms33), which displays small, pale yellow anthers, and complete male sterility...
March 15, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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
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