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Systems biology

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https://www.readbyqxmd.com/read/28449470/impact-of-cyclooxygenase-2-and-prostaglandin-e2-expression-on-clinical-outcome-after-pulmonary-metastasectomy
#1
Christian Lang, Emilie Hrdliczka, Thomas Schweiger, Olaf Glueck, Gerrit Lewik, Stefan Schwarz, Alberto Benazzo, György Lang, Walter Klepetko, Konrad Hoetzenecker
BACKGROUND: Pulmonary metastasectomy (PM) is a standard procedure in the treatment of stage IV colorectal cancer (CRC). In most centers the indication for PM is solely based on clinical factors without taking the tumor biology into account. This results in diverse outcomes ranging from long-term remission to early recurrence. Inflammation is considered a hallmark of cancer development and progression. On the other hand the accessibility of CRC cells to the immune system reflects the grade of tumor aggressiveness...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28449101/synthetic-biology-approaches-for-the-production-of-plant-metabolites-in-unicellular-organisms
#2
Tessa Moses, Payam Mehrshahi, Alison G Smith, Alain Goossens
Synthetic biology is the repurposing of biological systems for novel objectives and applications. Through the co-ordinated and balanced expression of genes, both native and those introduced from other organisms, resources within an industrial chassis can be siphoned for the commercial production of high-value commodities. This developing interdisciplinary field has the potential to revolutionize natural product discovery from higher plants, by providing a diverse array of tools, technologies, and strategies for exploring the large chemically complex space of plant natural products using unicellular organisms...
April 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28449041/periodontal-disease-tooth-loss-and-cancer-risk
#3
Dominique S Michaud, Zhuxuan Fu, Jian Shi, Mei Chung
Periodontal disease, which includes gingivitis and periodontitis, is highly prevalent in adults and disease severity increases with age. The relationship between periodontal disease and oral cancer has been examined for several decades, but there is increasing interest in the link between periodontal disease and overall cancer risk, with systemic inflammation serving as the main focus for biological plausibility. Numerous case-control studies have addressed the role of oral health in head and neck cancer, and several cohort studies have examined associations with other types of cancers over the past decade...
April 25, 2017: Epidemiologic Reviews
https://www.readbyqxmd.com/read/28448941/geochemistry-and-microbial-diversity-of-cave-waters-in-the-gypsum-karst-aquifers-of-emilia-romagna-region-italy
#4
Ilenia M D'Angeli, Diana I Serrazanetti, Chiara Montanari, Lucia Vannini, Fausto Gardini, Jo De Waele
Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO4, HCO3, Cl, NO3) and some minor constituents (F, Br, NH4 and PO4), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448794/principles-of-systems-biology-no-16
#5
(no author information available yet)
This month: how T cells signal in binary (Vale), advances in interaction mapping (Greenleaf/Sabatini/Ahroni/Bodenmiller), single-cell RNA-seq (Suvà/Ramanathan/Marioni), and more (Hilvert/Wong/Chisholm).
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448624/overexpression-of-the-protein-phosphatase-2a-regulatory-subunit-a-gene-zmpp2aa1-improves-low-phosphate-tolerance-by-remodeling-the-root-system-architecture-of-maize
#6
Jiemin Wang, Laming Pei, Zhe Jin, Kewei Zhang, Juren Zhang
Phosphate (Pi) limitation is a constraint for plant growth and development in many natural and agricultural ecosystems. In this study, a gene encoding Zea mays L. protein phosphatase 2A regulatory subunit A, designated ZmPP2AA1, was induced in roots by low Pi availability. The function of the ZmPP2AA1 gene in maize was analyzed using overexpression and RNA interference. ZmPP2AA1 modulated root gravitropism, negatively regulated primary root (PR) growth, and stimulated the development of lateral roots (LRs)...
2017: PloS One
https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#7
Gabriel N Teku, Mauno Vihinen
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes...
2017: PloS One
https://www.readbyqxmd.com/read/28448263/zinc-and-wound-healing-a-review-of-zinc-physiology-and-clinical-applications
#8
Samuel Kogan, Aditya Sood, Mark S Garnick
Our understanding of the role of zinc in normal human physiology is constantly expanding, yet there are major gaps in our knowledge with regard to the function of zinc in wound healing. This review aims to provide the clinician with sufficient understanding of zinc biology and an up-to-date perspective on the role of zinc in wound healing. Zinc is an essential ion that is crucial for maintenance of normal physiology, and zinc deficiency has many manifestations ranging from delayed wound healing to immune dysfunction and impairment of multiple sensory systems...
April 2017: Wounds: a Compendium of Clinical Research and Practice
https://www.readbyqxmd.com/read/28448135/total-synthesis-of-%C3%A2-lycojaponicumin-d-and-lycodoline-type-lycopodium-alkaloids
#9
Xian-He Zhao, Qing Zhang, Ji-Yuan Du, Xin-Yun Lu, Ye-Xing Cao, Yu-Hua Deng, Chun-An Fan
Lycopodium alkaloids with structural diversity and biological significance have been stimulating an increasing interest in synthetic and medicinal communities, in which inspiration and exploration of their related biogenetic relationship generally comprises one of the major concerns. Driven by the plausible biogenetic entry to lycojaponicumin D as the first member of Lycopodium alkaloids having structurally unusual C(3)-C(13) linked scaffold, a new connection with lycodoline has been proposed and discovered on the basis of the design of an unprecedented bioinspired tandem fragmentation/Mannich reaction...
April 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28448069/systems-biology-guided-by-xcms-online-metabolomics
#10
Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson, Julijana Ivanisevic, H Paul Benton, Mingliang Fang, Aries Aisporna, Brian Hilmers, Farris L Poole, Michael P Thorgersen, Michael W W Adams, Gregory Krantz, Matthew W Fields, Paul D Robbins, Laura J Niedernhofer, Trey Ideker, Erica L Majumder, Judy D Wall, Nicholas J W Rattray, Royston Goodacre, Luke L Lairson, Gary Siuzdak
No abstract text is available yet for this article.
April 27, 2017: Nature Methods
https://www.readbyqxmd.com/read/28448027/dry-powder-and-nebulized-aerosol-inhalation-of-pharmaceuticals-delivered-to-mice-using-a-nose-only-exposure-system
#11
Jonathan E Phillips, Xuxia Zhang, James A Johnston
Obstructive respiratory diseases like asthma and chronic obstructive pulmonary disease (COPD) are currently treated by inhaled anti-inflammatory and bronchodilator drugs. Despite the availability of multiple treatments, both diseases are growing public health concerns. The majority of asthma patients are well controlled on current inhaled therapies but a substantial number of patients with severe asthma are not. Asthma affects an estimated 300 million people worldwide and approximately 20 percent have a severe form of the disease...
April 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447989/fabrication-of-extracellular-matrix-derived-foams-and-microcarriers-as-tissue-specific-cell-culture-and-delivery-platforms
#12
Anna Kornmuller, Cody F C Brown, Claire Yu, Lauren E Flynn
Cell function is mediated by interactions with the extracellular matrix (ECM), which has complex tissue-specific composition and architecture. The focus of this article is on the methods for fabricating ECM-derived porous foams and microcarriers for use as biologically-relevant substrates in advanced 3D in vitro cell culture models or as pro-regenerative scaffolds and cell delivery systems for tissue engineering and regenerative medicine. Using decellularized tissues or purified insoluble collagen as a starting material, the techniques can be applied to synthesize a broad array of tissue-specific bioscaffolds with customizable geometries...
April 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447485/empirical-estimation-of-under-reporting-in-the-u-s-food-and-drug-administration-adverse-event-reporting-system-faers
#13
Yasser M Alatawi, Richard A Hansen
OBJECTIVE: To examine how closely reporting rates in the FDA Adverse Event Reporting System (FAERS) reflect expected rates of known adverse drug events (ADEs). METHODS: We selected three groups of drugs to reflect hypothesized variation in sensitivity to reporting, including statins, biologics, and narrow therapeutics index drugs (NTI). The numbers of ADEs in FAERS were divided by utilization estimates from ambulatory health care data (NAMCS/NHAMCS) to calculate a reported proportion...
April 27, 2017: Expert Opinion on Drug Safety
https://www.readbyqxmd.com/read/28447364/the-ja-and-aba-signaling-pathways-crosstalk-during-one-but-not-repeated-dehydration-stresses-a-non-specific-panicky-or-a-meaningful-response
#14
Zoya Avramova
Experiencing diverse and recurring biotic and abiotic stresses throughout life, plants have evolved mechanisms to respond, survive and, eventually, adapt to changing habitats. The initial response to drought involves a large number of genes that are involved also in response to other stresses. According to current models, this initial response is non-specific, becoming stress-specific only at later time points. The question, then, is whether non-specific activation of various stress-signaling systems leading to the expression of numerous stresses-regulated genes is a false-alarm ('panicky') response or whether it has biologically relevant consequences for the plant...
April 26, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28447347/abundance-of-the-benign-melanocytic-universe-dermoscopic-histopathological-correlation-in-nevi
#15
REVIEW
Nora Woltsche, Karin Schmid-Zalaudek, Teresa Deinlein, Katrin Rammel, Rainer Hofmann-Wellenhof, Iris Zalaudek
The broad universe of "melanocytic nevi" includes a variety of different subtypes, which can be classified either due to their morphology, epidemiology, genetic alterations or risk for developing melanoma. Regarding morphology, on the one hand macroscopic/clinical and on the other hand histopathological appearance were used to subdivide in the past, often resulting in confusion and poor interobserver agreement, while nowadays dermoscopy presents the clinician's precious bridge between naked-eye examination and histopathological diagnostics, allowing prediction of the lesions' histopathology, follow up and monitoring over time without need of excision...
May 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28447192/rescue-of-a-wild-type-rabies-virus-from-cloned-cdna-and-assessment-of-the-proliferative-capacity-of-recombinant-viruses
#16
Qin Tian, Yifei Wang, Qiong Zhang, Jun Luo, Mingzhu Mei, Yongwen Luo, Xiaofeng Guo
Reverse genetic systems (RGS) have been widely used for fixed rabies virus (RABV) strains. However, RGS, for wild-type (wt) strains, have been seldom reported despite the value of this approach in defining the biological characteristics of these strains. In this work, we developed a wt RGS using a swine-origin RABV strain (GD-SH-01) for the first time. In order to have a better understanding of the contribution and function of individual gene on viral proliferation for wt RABV isolates, we constructed a full-length cDNA clone of GD-SH-01 and exchanged the single genes encoding RABV protein of a highly attenuated RABV strain HEP-Flury with those of the virulent strain...
April 26, 2017: Virus Genes
https://www.readbyqxmd.com/read/28447151/rhythms-in-the-endocrine-system-of-fish-a-review
#17
REVIEW
Mairi Cowan, Clara Azpeleta, Jose Fernando López-Olmeda
The environment which living organisms inhabit is not constant and many factors, such as light, temperature, and food availability, display cyclic and predictable variations. To adapt to these cyclic changes, animals present biological rhythms in many of their physiological variables, timing their functions to occur when the possibility of success is greatest. Among these variables, many endocrine factors have been described as displaying rhythms in vertebrates. The aim of the present review is to provide a thorough review of the existing knowledge on the rhythms of the endocrine system of fish by examining the hormones that show rhythmicity, how environmental factors control these rhythms and the variation in the responses of the endocrine system depending on the time of the day...
April 26, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28446878/computational-model-predicts-the-effects-of-targeting-cellular-metabolism-in-pancreatic-cancer
#18
Mahua Roy, Stacey D Finley
Reprogramming of energy metabolism is a hallmark of cancer that enables the cancer cells to meet the increased energetic requirements due to uncontrolled proliferation. One prominent example is pancreatic ductal adenocarcinoma, an aggressive form of cancer with an overall 5-year survival rate of 5%. The reprogramming mechanism in pancreatic cancer involves deregulated uptake of glucose and glutamine and other opportunistic modes of satisfying energetic demands in a hypoxic and nutrient-poor environment. In the current study, we apply systems biology approaches to enable a better understanding of the dynamics of the distinct metabolic alterations in KRAS-mediated pancreatic cancer, with the goal of impeding early cell proliferation by identifying the optimal metabolic enzymes to target...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28446726/low-concentration-of-bpa-induces-mice-spermatocytes-apoptosis-via-gpr30
#19
Chaoliang Wang, Jianxiang Zhang, Qi Li, Tianbiao Zhang, Zishi Deng, Jing Lian, Donghui Jia, Rui Li, Tao Zheng, Xiaoju Ding, Fan Yang, Chao Ma, Rui Wang, Weixing Zhang, Jian Guo Wen
Bisphenol A (BPA) acts as xenoestrogen and has a great impact on disorders of human reproductive system. However, the mechanism through which BPA can affect human testicular function remains to be indentified. GPR30 is a novel membrane estrogen receptor with high-affinity and low-capacity binding to estrogens. We demonstrated that estrogen receptor α (ERα), estrogen receptor β (ERβ) as well as GPR30 are expressed in mouse spermatocyte-derived GC-2 cells using Real-time PCR. We treated the cells with different doses of BPA and found that even low doses of BPA can inhibit GC-2 cell growth using MTT assay...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28446711/chemical-roots-of-biological-evolution-the-origins-of-life-as-a-process-of-development-of-autonomous-functional-systems
#20
REVIEW
Kepa Ruiz-Mirazo, Carlos Briones, Andrés de la Escosura
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals...
April 2017: Open Biology
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