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https://read.qxmd.com/read/30763455/dietary-black-raspberries-impact-the-colonic-microbiome-and-phytochemical-metabolites-in-mice
#1
Junnan Gu, Jennifer M Thomas-Ahner, Kenneth M Riedl, Michael T Bailey, Yael Vodovotz, Steven J Schwartz, Steven K Clinton
SCOPE: Black raspberries (BRB) are a rich source of bioactive phytochemicals, including anthocyanins and ellagitannins. These phytochemicals are poorly absorbed and we hypothesize that upon reaching the colon they may be transformed by gut microbiota into various metabolites that may impact the colonic mucosa or upon absorption have systemic bioactivity. The objective of this study was to define the impact of a BRB-containing diet on the colon microbiome in mice and quantify the phytochemical metabolites in the colon contents and the circulation...
February 14, 2019: Molecular Nutrition & Food Research
https://read.qxmd.com/read/30763315/iris-eda-an-integrated-rna-seq-interpretation-system-for-gene-expression-data-analysis
#2
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies...
February 14, 2019: PLoS Computational Biology
https://read.qxmd.com/read/30763096/the-diverse-nature-of-ion-speciation-at-the-nanoscale-hydrophobic-water-interface
#3
Evangelia Zdrali, Marcel D Baer, Halil I Okur, Christopher Mundy, Sylvie Roke
Many biological systems are composed of nanoscale structures having hydrophobic and hydrophilic groups adjacent to one another and in contact with aqueous electrolyte solution. The interaction of ions with such structures is of fundamental importance. Although many studies have focused on characterizing planar extended (often air/water) interfaces, little is known about ion speciation at complex nanoscale biological systems. To start understanding the complex mechanisms involved, we use a hexadecane nanodroplet system, stabilized with a dilute monolayer of positively charged (DTA+) groups in contact with an electrolyte solution (NaSCN)...
February 14, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30762928/bioinformatic-analysis-of-cacybp-associated-proteins-using-human-glioma-databases
#4
Chengmin Xuan, Yong Gao, Mingwei Jin, Shumei Xu, Lei Wang, Yuan Wang, Rui Han, Kunpeng Shi, Xincheng Chen, Qi An
The ubiquitin-proteasome system is the primary cellular pathway for protein degradation, mediating 80% of intracellular protein degradation. Because of the widespread presence of ubiquitin-modified protein substrates, ubiquitination can regulate a variety of cellular activities including cell proliferation, apoptosis, autophagy, endocytosis, DNA damage repair, and immune responses. With the continuous generation of genomics data in recent years it has become particularly important to analyze these data effectively and reasonably...
February 14, 2019: IUBMB Life
https://read.qxmd.com/read/30761299/hypoxia-modified-cancer-cell-metabolism
#5
REVIEW
Wafaa Al Tameemi, Tina P Dale, Rakad M Kh Al-Jumaily, Nicholas R Forsyth
While oxygen is critical to the continued existence of complex organisms, extreme levels of oxygen within a system, known as hypoxia (low levels of oxygen) and hyperoxia (excessive levels of oxygen), potentially promote stress within a defined biological environment. The consequences of tissue hypoxia, a result of a defective oxygen supply, vary in response to the gravity, extent and environment of the malfunction. Persistent pathological hypoxia is incompatible with normal biological functions, and as a result, multicellular organisms have been compelled to develop both organism-wide and cellular-level hypoxia solutions...
2019: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/30761179/mcimpute-matrix-completion-based-imputation-for-single-cell-rna-seq-data
#6
Aanchal Mongia, Debarka Sengupta, Angshul Majumdar
Motivation: Single-cell RNA sequencing has been proved to be revolutionary for its potential of zooming into complex biological systems. Genome-wide expression analysis at single-cell resolution provides a window into dynamics of cellular phenotypes. This facilitates the characterization of transcriptional heterogeneity in normal and diseased tissues under various conditions. It also sheds light on the development or emergence of specific cell populations and phenotypes. However, owing to the paucity of input RNA, a typical single cell RNA sequencing data features a high number of dropout events where transcripts fail to get amplified...
2019: Frontiers in Genetics
https://read.qxmd.com/read/30761041/disarming-ex-combatants-minds-toward-situated-reintegration-process-in-post-conflict-colombia
#7
Sandra Baez, Hernando Santamaría-García, Agustín Ibáñez
Collective violence in the context of armed conflict impacts the economy, health systems, and social stability of affected countries. This is considered a complex phenomenon with interwoven biological, psychological, social, cultural, and political factors. However, most of the research on this topic still lacks suitable established integrative approaches to assess multilevel perspectives. Social, cognitive and affective mental processes (SCAMP) are critical factors that should be considered in multilevel approaches...
2019: Frontiers in Psychology
https://read.qxmd.com/read/30760983/applications-of-light-sheet-microscopy-in-microdevices
#8
REVIEW
Ignacio Albert-Smet, Asier Marcos-Vidal, Juan José Vaquero, Manuel Desco, Arrate Muñoz-Barrutia, Jorge Ripoll
Light-sheet fluorescence microscopy (LSFM) has been present in cell biology laboratories for quite some time, mainly as custom-made systems, with imaging applications ranging from single cells (in the micrometer scale) to small organisms (in the millimeter scale). Such microscopes distinguish themselves for having very low phototoxicity levels and high spatial and temporal resolution, properties that make them ideal for a large range of applications. These include the study of cellular dynamics, in particular cellular motion which is essential to processes such as tumor metastasis and tissue development...
2019: Frontiers in Neuroanatomy
https://read.qxmd.com/read/30760751/the-oxytocinergic-system-mediates-synchronized-interpersonal-movement-during-dance
#9
Liad Josef, Pavel Goldstein, Naama Mayseless, Liat Ayalon, Simone G Shamay-Tsoory
Because the oxytocinergic (OT) system has previously been linked to regulation of complex social cognition and behavior, we examined whether intranasal administration of OT would modulate synchronization during a real-life dance paradigm. The current study examined pairs of friends while dancing after intranasal administration of OT or placebo. Motion tracking software and a computational model were utilized to measure synchrony between the partners as manifested in the velocity of their movements. In line with our predictions, OT increased synchrony between partners...
February 13, 2019: Scientific Reports
https://read.qxmd.com/read/30760596/atomic-level-characterization-of-protein-protein-association
#10
Albert C Pan, Daniel Jacobson, Konstantin Yatsenko, Duluxan Sritharan, Thomas M Weinreich, David E Shaw
Despite the biological importance of protein-protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein-protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)-based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events...
February 13, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30760574/genome-characterization-prevalence-and-transmission-mode-of-a-novel-picornavirus-associated-with-the-threespine-stickleback-fish-gasterosteus-aculeatus
#11
Megan A Hahn, Nolwenn M Dheilly
The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel Picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback Picornavirus (TSPV). Due to their broad geographic distribution throughout the northern hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology...
February 13, 2019: Journal of Virology
https://read.qxmd.com/read/30759996/bola3-deficiency-controls-endothelial-metabolism-and-glycine-homeostasis-in-pulmonary-hypertension
#12
Qiujun Yu, Yi-Yin Tai, Ying Tang, Jingsi Zhao, Vinny Negi, Miranda K Culley, Jyotsna Pilli, Wei Sun, Karin Brugger, Johannes Mayr, Rajeev Saggar, Rajan Saggar, W Dean Wallace, David J Ross, Aaron B Waxman, Stacy G Wendell, Steven J Mullett, John Sembrat, Mauricio Rojas, Omar F Khan, James E Dahlman, Masataka Sugahara, Nobuyuki Kagiyama, Taijyu Satoh, Manling Zhang, Ning Feng, John Gorcsan Iii, Sara O Vargas, Kathleen J Haley, Rahul Kumar, Brian B Graham, Robert Langer, Daniel G Anderson, Bing Wang, Sruti Shiva, Thomas Bertero, Stephen Y Chan
BACKGROUND: Deficiencies of iron-sulfur (Fe-S) clusters, metal complexes that control redox state and mitochondrial metabolism, have been linked to pulmonary hypertension (PH), a deadly vascular disease with poorly defined molecular origins. The BolA Family Member 3 (BOLA3) regulates Fe-S biogenesis, and mutations in BOLA3 result in multiple mitochondrial dysfunction syndrome, a fatal disorder associated with PH. The mechanistic role of BOLA3 in PH remains undefined. METHODS: In vitro assessment of BOLA3 regulation and gain and loss of function assays were performed in human pulmonary artery endothelial cells (PAECs) using siRNA and lentiviral vectors expressing the mitochondrial isoform of BOLA3...
February 14, 2019: Circulation
https://read.qxmd.com/read/30759423/electrobiofabrication-electrically-based-fabrication-with-biologically-derived-materials
#13
Jinyang Li, Si Wu, Eunkyoung Kim, Kun Yan, Huan Liu, Changsheng Liu, Hua Dong, Xue Qu, Xiaowen Shi, Jana Shen, William E Bentley, Gregory F Payne
While conventional materials fabrication methods focus on form and strength to achieve function, the fabrication of materials systems for emerging life science applications will need to satisfy a more subtle set of requirements. A common goal for biofabrication is to recapitulate complex biological contexts (e.g., tissue) for applications that range from animal-on-a-chip to regenerative medicine. In these cases, the materials systems will need to: (i) present appropriate surface functionalities over a hierarchy of length scales (e...
February 13, 2019: Biofabrication
https://read.qxmd.com/read/30759197/gsmodutils-a-python-based-framework-for-test-driven-genome-scale-metabolic-model-development
#14
James Gilbert, Nicole Pearcy, Rupert Norman, Thomas Millat, Klaus Winzer, John King, Charlie Hodgman, Nigel Minton, Jamie Twycross
Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include thousands of reactions and metabolites, with many crucial pathways that only become activated in specific simulation settings. However, despite their widespread use, power and the availability of tools to aid with the construction and analysis of large scale models, little methodology is suggested for their continued management...
February 13, 2019: Bioinformatics
https://read.qxmd.com/read/30758008/encapsulation-of-inuloxin-a-a-plant-germacrane-sesquiterpene-with-potential-herbicidal-activity-in-%C3%AE-cyclodextrins
#15
Arash Moeini, Marco Masi, Maria C Zonno, Angela Boari, Alessio Cimmino, Oreste Tarallo, Maurizio Vurro, Antonio Evidente
Inuloxin A is a promising plant phytotoxic sesquiterpene that deserves further studies to evaluate its potential as a bioherbicide. However, its low solubility in water and its bioavailability could hamper its practical applications. For this reason, inuloxin A was complexed with β-cyclodextrins by using three different methods, i.e., kneading, co-precipitation and grinding. The resulted complexes were fully characterized by different techniques such as 1H NMR, UV-vis, XRD, DSC and SEM, and they were biologically assayed in comparison with the pure compound in several biological systems...
February 13, 2019: Organic & Biomolecular Chemistry
https://read.qxmd.com/read/30756125/proteomics-and-metabolomics-in-pregnancy-an-overview
#16
Niraj Vora, Ram Kalagiri, Lea H Mallett, Jin Ho Oh, Umaima Wajid, Saef Munir, Natalie Colon, Venkata Nakta Raju, Madhava R Beeram, M Nasir Uddin
Importance: Pregnancy is getting more and more complex due to increasing number of complications that may affect fetal outcomes. The introduction of newer "proteomics and metabolomics" technologies in the field of obstetrics and gynecology may allow physicians to identify possible associated etiologies that affect the mother during pregnancy and lead to associated complications affecting the offspring. Objective: The principal objective of this review article is to provide a comprehensive evaluation of the use of proteomics and metabolomics in complicated pregnancies...
February 2019: Obstetrical & Gynecological Survey
https://read.qxmd.com/read/30755112/trabecular-titanium-acetabular-cups-in-hip-revision-surgery-mid-term-clinical-and-radiological-outcomes
#17
Federico De Meo, Giorgio Cacciola, Vittorio Bellotti, Antongiolio Bruschetta, Pietro Cavaliere
INTRODUCTION: Severe acetabular bone loss during revision hip arthroplasty can be restored with different surgical techniques. Best results have been observed using porous tantalum cementless cups. Trabecular Titanium (TT) cups were designed to reproduce the structure, mechanical and biological characteristics of trabecular bone. Few clinical studies have been published with these cups. The aim of this study is to evaluate the clinical and radiological outcome of patients with large acetabular defects (Paprosky IIb or higher) revised using TT cups...
November 2018: Hip International: the Journal of Clinical and Experimental Research on Hip Pathology and Therapy
https://read.qxmd.com/read/30753736/how-complex-should-an-in-vitro-model-be-evaluation-of-complex-3d-alveolar-model-with-transcriptomic-data-and-computational-biological-network-models
#18
Diego Marescotti, Tommaso Serchi, Karsta Luettich, Yang Xiang, Elisa Moschini, Marja Talikka, Florian Martin, Karine Baumer, Remi Dulize, Dariusz Peric, David Bornand, Emmanuel Guedj, Alain Sewer, Sebastian Cambier, Servane Contal, Aline Chary, Arno C Gutleb, Stefan Frentzel, Nikoloai V Ivanov, Manuel C Peitsch, Julia Hoeng
To more accurately model inhalation toxicity in vitro, we developed a tetra-culture system that combines lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation. We characterized the influence of the added complexity using network perturbation analysis and gene expression data. This will allow us to gain insight into the steady-state profile of the assembled, complete three-dimensional model using all four cell types and of simpler models of one, two, or three cell types...
February 12, 2019: ALTEX
https://read.qxmd.com/read/30747098/fibromyalgia-and-the-concept-of-resilience
#19
REVIEW
Roberto Casale, Piercarlo Sarzi-Puttini, Rossana Botto, Alessandra Alciati, Alberto Batticciotto, Daniela Marotto, Riccardo Torta
The concept of resilience varies according to the context in which it is used. Resilience is broadly defined as a protective factor that makes people less vulnerable to future adverse life events, in this implying the previous occurrence of an adverse event that has to be confronted before individual equilibrium can be restored. This definition can be applied to fibromyalgia and other chronic pain situations. Resilience is profoundly related to reaction to acute or chronic stress, and is therefore involved in the stress response system...
January 2019: Clinical and Experimental Rheumatology
https://read.qxmd.com/read/30746493/metabolic-responses-to-polymyxin-treatment-in-acinetobacter-baumannii-atcc-19606-integrating-transcriptomics-and-metabolomics-with-genome-scale-metabolic-modeling
#20
Yan Zhu, Jinxin Zhao, Mohd Hafidz Mahamad Maifiah, Tony Velkov, Falk Schreiber, Jian Li
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic pathogen over the past decades, with a high incidence in nosocomial infections. Discovered in the late 1940s but abandoned in the 1970s, polymyxins (i.e., polymyxin B and colistin) have been revived as the last-line therapy against Gram-negative "superbugs," including MDR A. baumannii. Worryingly, resistance to polymyxins in A. baumannii has been increasingly reported, urging the development of novel antimicrobial therapies to rescue this last-line class of antibiotics...
January 2019: MSystems
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