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1601. Chloroformate derivatization for tracing the fate of Amino acids in cells and tissues by multiple stable isotope resolved metabolomics (mSIRM)

Author:
Yang, Ye; Fan, Teresa W-M.; Lane, Andrew N.; Higashi, Richard M.
Source:
Analytica chimica acta 2017
ISSN:
0003-2670
Subject:
amino acid metabolism; amino acids; analytical chemistry; carboxylation; derivatization; humans; liquid diet; lung neoplasms; lungs; mass spectrometry; metabolites; metabolomics; mice; models; patients; protein hydrolysates; pyruvic acid; quantitative analysis; salt content; spectrometers; stable isotopes; tracer techniques; tricarboxylic acid cycle
Abstract:
... Amino acids have crucial roles in central metabolism, both anabolic and catabolic. To elucidate these roles, steady-state concentrations of amino acids alone are insufficient, as each amino acid participates in multiple pathways and functions in a complex network, which can also be compartmentalized. Stable Isotope-Resolved Metabolomics (SIRM) is an approach that uses atom-resolved tracking of met ...
DOI:
10.1016/j.aca.2017.04.014
PubMed:
28576319
PubMed Central:
PMC5638134

1602. Cognitive impacts of ambient air pollution in the National Social Health and Aging Project (NSHAP) cohort

Author:
Tallon, Lindsay A.; Manjourides, Justin; Pun, Vivian C.; Salhi, Carmel; Suh, Helen
Source:
Environment international 2017
ISSN:
0160-4120
Subject:
Americans; air pollution; anxiety; cognition; elderly; geographic information systems; mental health; models; nitrogen dioxide; particulates; regression analysis; stroke
Abstract:
... Pathways through which air pollution may impact cognitive function are poorly understood, particularly with regard to whether and how air pollution interacts with social and emotional factors to influence cognitive health.To examine the association between air pollutant exposures and cognitive outcomes among older adults participating in the National Social Life, Health, and Aging Project (NSHAP) ...
DOI:
10.1016/j.envint.2017.03.019
PubMed:
28392067
PubMed Central:
PMC6022397

1603. Combinatorial optimization of PEG architecture and hydrophobic content improves siRNA polyplex stability, pharmacokinetics, and potency in vivo

Author:
Werfel, Thomas A.; Jackson, Meredith A.; Kavanaugh, Taylor E.; Kirkbride, Kellye C.; Miteva, Martina; Giorgio, Todd D.; Duvall, Craig
Source:
Journal of Controlled Release 2017
ISSN:
0168-3659
Subject:
biocompatibility; blood circulation; chemical bonding; gene silencing; genes; hydrophobicity; intravenous injection; luciferase; models; nanomedicine; pH; pharmacokinetics; polyethylene glycol; renal clearance; small interfering RNA
Abstract:
... A rationally-designed library of ternary siRNA polyplexes was developed and screened for gene silencing efficacy in vitro and in vivo with the goal of overcoming both cell-level and systemic delivery barriers. [2-(dimethylamino)ethyl methacrylate] (DMAEMA) was homopolymerized or colpolymerized (50mol% each) with butyl methacrylate (BMA) from a reversible addition – fragmentation chain transfer (RA ...
DOI:
10.1016/j.jconrel.2017.03.389
PubMed:
28366646
PubMed Central:
PMC5484420

1604. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

Author:
Venko, Katja; Roy Choudhury, A.; Novič, Marjana
Source:
Computational and Structural Biotechnology Journal 2017 v.15 pp. 232-242
ISSN:
2001-0370
Subject:
X-ray diffraction; bilirubin; biotechnology; case studies; chemical structure; drugs; functional properties; models; molecular dynamics; nuclear magnetic resonance spectroscopy; prediction; solubility; tissue distribution; transmembrane proteins; transporters
Abstract:
... The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures o ...
DOI:
10.1016/j.csbj.2017.01.008
PubMed:
28228927
PubMed Central:
PMC5312651

1605. Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease

Author:
Randles, Amanda; Frakes, David H.; Leopold, Jane A.
Source:
Trends in biotechnology 2017
ISSN:
0167-7799
Subject:
cardiovascular diseases; engineering; fluid mechanics; manufacturing; models; planning
Abstract:
... Noninvasive engineering models are now being used for diagnosing and planning the treatment of cardiovascular disease. Techniques in computational modeling and additive manufacturing have matured concurrently, and results from simulations can inform and enable the design and optimization of therapeutic devices and treatment strategies. The emerging synergy between large-scale simulations and 3D pr ...
DOI:
10.1016/j.tibtech.2017.08.008
PubMed:
28942268
PubMed Central:
PMC5651201

1606. COPASI and its Applications in Biotechnology

Author:
Bergmann, Frank T.; Hoops, Stefan; Klahn, Brian; Kummer, Ursula; Mendes, Pedro; Pahle, Jürgen; Sahle, Sven
Source:
Journal of biotechnology 2017
ISSN:
0168-1656
Subject:
biotechnology; computer software; kinetics; models; user interface
Abstract:
... COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introd ...
DOI:
10.1016/j.jbiotec.2017.06.1200
PubMed:
28655634
PubMed Central:
PMC5623632

1607. Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated

Author:
Zhang, Kai; Foster, Helen E.; Rondelet, Arnaud; Lacey, Samuel E.; Bahi-Buisson, Nadia; Bird, Alexander W.; Carter, Andrew P.
Source:
Cell 2017
ISSN:
0092-8674
Subject:
cryo-electron microscopy; dimerization; dynein ATPase; humans; microtubules; models; mutagenesis; proteins
Abstract:
... Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-pa ...
DOI:
10.1016/j.cell.2017.05.025
PubMed:
28602352
PubMed Central:
PMC5473941

1608. Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies

Author:
AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio; Egea, Pascal F.
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
Animalia; X-radiation; crystal structure; crystals; dimerization; electron microscopy; endoplasmic reticulum; metabolites; mitochondria; models; phospholipids; protein engineering; sequence analysis; yeasts
Abstract:
... Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among th ...
DOI:
10.1016/j.bbrc.2017.05.021
PubMed:
28479252
PubMed Central:
PMC6061939

1609. Cutaneous vaccination with coated microneedles prevents development of airway allergy

Author:
Shakya, Akhilesh Kumar; Lee, Chang Hyun; Gill, Harvinder Singh
Source:
Journal of Controlled Release 2017
ISSN:
0168-3659
Subject:
adjuvants; allergens; bronchioles; children; hypersensitivity; immune response; infants; interferon-gamma; interleukin-10; interleukin-13; interleukin-2; interleukin-4; interleukin-5; mice; models; mucus; oligonucleotides; ovalbumin; patients; protective effect; splenocytes; vaccination; vaccines
Abstract:
... Allergy cases are increasing worldwide. Currently allergies are treated after their appearance in patients. However, now there is effort to make a preventive vaccine against allergies. The rationale is to target patient populations that are already sensitized to allergens but have yet to develop severe forms of the allergic disease, or who are susceptible to allergy development but have not yet de ...
DOI:
10.1016/j.jconrel.2017.08.012
PubMed:
28821461
PubMed Central:
PMC5752139

1610. Cyberinfrastructure for the collaborative development of U2U decision support tools

Author:
Biehl, Larry L.; Zhao, Lan; Song, Carol X.; Panza, Christopher G.
Source:
Climate risk management 2017 v.15 pp. 90-108
ISSN:
2212-0963
Subject:
Internet; algorithms; climate; computer software; data collection; decision support systems; engineering; experts; extension agents; farmers; meteorological data; models; outreach; risk management
Abstract:
... This paper describes the use of cyberinfrastructure to create interactive applications as part of the Useful to Usable (U2U) project. These applications transform historical climate data, knowledge, and models into decision support tools for end users such as crop farmers, university Extension educators, and other agricultural advisors. In creating a cyberinfrastructure to support the U2U project, ...
DOI:
10.1016/j.crm.2016.10.003
Chorus Open Access:
10.1016/j.crm.2016.10.003

1611. Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

Author:
Gaieb, Zied; Morikis, Dimitrios
Source:
Computational and Structural Biotechnology Journal 2017 v.15 pp. 131-137
ISSN:
2001-0370
Subject:
CCR7 receptor; chemokine CCL21; data collection; ligands; mechanics; models; molecular dynamics; protein structure; time series analysis
Abstract:
... Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach desig ...
DOI:
10.1016/j.csbj.2017.01.001
PubMed:
28149485
PubMed Central:
PMC5271675

1612. Determinants of Helix Formation for a Kv1.3 Transmembrane Segment inside the Ribosome Exit Tunnel

Author:
Tu, LiWei; Deutsch, Carol
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
biogenesis; models; mutation; neonates; oligomerization; potassium channels; protein folding; ribosomes
Abstract:
... Proteins begin to fold in the ribosome and misfolding has pathological consequences. Among the earliest folding events in biogenesis is the formation of a helix, an elementary structure that is ubiquitously present and required for correct protein folding in all proteomes. The determinants underlying helix formation in the confined space of the ribosome exit tunnel are relatively unknown. We chose ...
DOI:
10.1016/j.jmb.2017.04.022
PubMed:
28478285
PubMed Central:
PMC5511032

1613. Determining potential adverse effects in marine fish exposed to pharmaceuticals and personal care products with the fish plasma model and whole-body tissue concentrations

Author:
Meador, James P.; Yeh, Andrew; Gallagher, Evan P.
Source:
Environmental pollution 2017
ISSN:
0269-7491
Subject:
Cottidae; adverse effects; bioaccumulation; brackish water; drugs; estuaries; humans; marine fish; mechanism of action; models; personal care products; prediction; toxicity; wastewater treatment
Abstract:
... The Fish Plasma Model (FPM) was applied to water exposure and tissue concentrations in fish collected from two wastewater treatment plant impacted estuarine sites. In this study we compared predicted fish plasma concentrations to Cmax values for humans, which represents the maximum plasma concentration for the minimum therapeutic dose. The results of this study show that predictions of plasma conc ...
DOI:
10.1016/j.envpol.2017.07.047
PubMed:
28764109
PubMed Central:
PMC5595653

1614. Discovery of small molecule inhibitors for the C. elegans caspase CED-3 by high-throughput screening

Author:
Brantley, Scott; Cotten, Steven W.; Lamson, David R.; Smith, Ginger R.; Liu, Rihe; Williams, Kevin P.
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
apoptosis; caspases; chemotypes; inhibitory concentration 50; models; screening
Abstract:
... C.elegans has been widely used as a model organism for programmed cell death and apoptosis. Although, the CED-3 caspase is the primary effector of cell death in C. elegans, no selective inhibitors have been identified. Utilizing high-throughput screening with recombinant C. elegans CED-3 protein, we have discovered and confirmed 21 novel small molecule inhibitors. Six compounds had IC50 values < 1 ...
DOI:
10.1016/j.bbrc.2017.07.100
PubMed:
28733033
PubMed Central:
PMC5590106

1615. Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade

Author:
Wei, Spencer C.; Levine, Jacob H.; Cogdill, Alexandria P.; Zhao, Yang; Anang, Nana-Ama A.S.; Andrews, Miles C.; Sharma, Padmanee; Wang, Jing; Wargo, Jennifer A.; Pe’er, Dana; Allison, James P.
Source:
Cell 2017
ISSN:
0092-8674
Subject:
CD8-positive T-lymphocytes; humans; immune response; melanoma; mice; models; patients
Abstract:
... Immune-checkpoint blockade is able to achieve durable responses in a subset of patients; however, we lack a satisfying comprehension of the underlying mechanisms of anti-CTLA-4- and anti-PD-1-induced tumor rejection. To address these issues, we utilized mass cytometry to comprehensively profile the effects of checkpoint blockade on tumor immune infiltrates in human melanoma and murine tumor models ...
DOI:
10.1016/j.cell.2017.07.024
PubMed:
28803728
PubMed Central:
PMC5591072

1616. Efficient synthesis of CN2097 using in situ activation of sulfhydryl group

Author:
Darwish, Shaban; Parang, Keykavous; Marshall, John; Goebel, Dennis J.; Tiwari, Rakesh
Source:
Tetrahedron letters 2017
ISSN:
0040-4039
Subject:
arginine; brain; chemical reactions; chemical structure; humans; models; nervous system diseases; organic compounds; stroke
Abstract:
... CN2097 (R7Cs-sCYK[KTE(β-Ala)]V) is a rationally designed peptidomimetic that shows effectiveness in preclinical models for the treatment of neurological disorders, such as Angelman syndrome, traumatic brain injury (TBI) and stroke. Because of its therapeutic activity for the treatment of human CNS disorders, there was an urgent need to develop an efficient strategy for large-scale synthesis of CN2 ...
DOI:
10.1016/j.tetlet.2017.06.066
PubMed:
28824209
PubMed Central:
PMC5557301

1617. Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline

Author:
Rodriguez, Roberto A.; Chen, Liao Y.; Plascencia-Villa, Germán; Perry, George
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
Alzheimer disease; cerebrospinal fluid; heparan sulfate; models; neurotoxicity; peptides; proteoglycans; thermodynamics
Abstract:
... Amyloid-beta (Aβ) peptides, Aβ40 and the more neurotoxic Aβ42, have been the subject of many research efforts for Alzheimer's disease. In two recent independent investigations, the atomistic structure of Aβ42 fibril has been clearly established in the S-shaped conformation consisting of three β-sheets stabilized by salt bridges formed between the Lys28 sidechain and the C-terminus of Ala42. This s ...
DOI:
10.1016/j.bbrc.2017.04.084
PubMed:
28427941
PubMed Central:
PMC5489073

1618. Engineering Epithelial-Stromal Interactions In Vitro for Toxicology Assessment

Author:
Belair, David G.; Abbott, Barbara D.
Source:
Toxicology 2017
ISSN:
0300-483X
Subject:
adults; coculture; epithelium; homeostasis; humans; in vitro studies; models; morphogenesis; phenotype; screening; stem cells; stromal cells; toxicology
Abstract:
... Crosstalk between epithelial and stromal cells drives the morphogenesis of ectodermal organs during development and promotes normal mature adult epithelial tissue homeostasis. Epithelial-stromal interactions (ESIs) have historically been examined using mammalian models and ex vivo tissue recombination. Although these approaches have elucidated signaling mechanisms underlying embryonic morphogenesi ...
DOI:
10.1016/j.tox.2017.03.007
PubMed:
28285100
PubMed Central:
PMC5985517

1619. Enhanced forest cover mapping using spectral unmixing and object-based classification of multi-temporal Landsat imagery

Author:
Gudex-Cross, David; Pontius, Jennifer; Adams, Alison
Source:
Remote sensing of environment 2017
ISSN:
0034-4257
Subject:
image analysis; forest types; species diversity; models; climate change; trees; natural resource management; pests; forest inventory; land cover; Landsat; remote sensing; Populus; Acer saccharum; stand basal area; forest resources; databases; biogeography; New York; Vermont
Abstract:
... Spatially-explicit tree species distribution maps are increasingly valuable to forest managers and researchers in light of the effects of climate change and invasive pests on forest resources. Traditional forest classifications are limited to broad classes of forest types with variable accuracy. Advanced remote sensing techniques, such as spectral unmixing and object-based image analysis, offer no ...
DOI:
10.1016/j.rse.2017.05.006
Chorus Open Access:
10.1016/j.rse.2017.05.006

1620. Enhancing tissue permeability with MRI guided preclinical focused ultrasound system in rabbit muscle: From normal tissue to VX2 tumor

Author:
Sun, Yao; Xiong, Xiaobing; Pandya, Darpan; Jung, Youngkyoo; Mintz, Akiva; Hayasaka, Satoru; Wadas, Thaddeus J.; Li, King C.P.
Source:
Journal of Controlled Release 2017
ISSN:
0168-3659
Subject:
antagonists; drugs; energy; genes; hindlimbs; integrins; magnetic resonance imaging; mice; models; muscle tissues; muscles; neoplasms; permeability; rabbits; radiolabeling; statistical analysis; therapeutics; thermal properties; tomography
Abstract:
... High Intensity Focused Ultrasound (HIFU) is an emerging noninvasive, nonionizing physical energy based modality to ablate solid tumors with high power, or increase local permeability in tissues/tumors in pulsed mode with relatively low power. Compared with traditional ablative HIFU, nondestructive pulsed HIFU (pHIFU) is present in the majority of novel applications recently developed for enhancing ...
DOI:
10.1016/j.jconrel.2017.04.017
PubMed:
28412225
PubMed Central:
PMC6047512

1621. Evaluating the impact of soil conservation measures on soil organic carbon at the farm scale

Author:
Pezzuolo, Andrea; Dumont, Benjamin; Sartori, Luigi; Marinello, Francesco; De Antoni Migliorati, Massimiliano; Basso, Bruno
Source:
Computers and electronics in agriculture 2017
ISSN:
0168-1699
Subject:
agricultural soils; autumn; carbon dioxide; carbon sequestration; carbon sinks; climate; crop residues; crops; data collection; direct seeding; farmers; farms; greenhouse gas emissions; issues and policy; models; no-tillage; oxidation; soil conservation; soil fertility; soil organic carbon; subsidies; Italy
Abstract:
... No-tillage (NT) is considered the least invasive conservation agriculture technique and has shown to be the effective in increasing soil C stocks, and reducing losses compared to others tillage systems. In Italy, the Veneto Region was the first to establish a subsidies scheme aimed at promoting the adoption of NT practices. This program encourages farmers to perform direct seeding, alternate autum ...
DOI:
10.1016/j.compag.2017.02.004
Chorus Open Access:
10.1016/j.compag.2017.02.004

1622. Expression and purification of functional insulin and insulin-like growth factor 1 holoreceptors from mammalian cells

Author:
Delle Bovi, Richard J.; Miller, W. Todd
Source:
Analytical biochemistry 2017
ISSN:
0003-2697
Subject:
affinity chromatography; detergents; insulin; insulin receptors; insulin-like growth factor I; insulin-like growth factor I receptor; ligands; mammals; membrane proteins; models; protein phosphorylation; resins; solubilization; tyrosine
Abstract:
... The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are receptor tyrosine kinases (RTKs) involved in the regulation of many important cellular processes. The current proposed models of activation are derived from structural studies using soluble extracellular domains and cytoplasmic tyrosine kinase domains. Preparations of full length IR and IGF1R have been hampered by the ...
DOI:
10.1016/j.ab.2017.08.011
PubMed:
28830678
PubMed Central:
PMC5701837

1623. Extended-spectrum antiprotozoal bumped kinase inhibitors: A review

Author:
Van Voorhis, Wesley C.; Doggett, J. Stone; Parsons, Marilyn; Hulverson, Matthew A.; Choi, Ryan; Arnold, Samuel L.M.; Riggs, Michael W.; Hemphill, Andrew; Howe, Daniel K.; Mealey, Robert H.; Lau, Audrey O.T.; Merritt, Ethan A.; Maly, Dustin J.; Fan, Erkang; Ojo, Kayode K.
Source:
Experimental parasitology 2017
ISSN:
0014-4894
Subject:
Miozoa; animals; models; parasites; parasitoses; pharmacokinetics; protein kinases; protein phosphorylation; therapeutics
Abstract:
... Many life-cycle processes in parasites are regulated by protein phosphorylation. Hence, disruption of essential protein kinase function has been explored for therapy of parasitic diseases. However, the difficulty of inhibiting parasite protein kinases to the exclusion of host orthologues poses a practical challenge. A possible path around this difficulty is the use of bumped kinase inhibitors for ...
DOI:
10.1016/j.exppara.2017.01.001
PubMed:
28065755
PubMed Central:
PMC5498274
CHORUS:
10.1016/j.exppara.2017.01.001

1624. Facilitating trypanosome imaging

Author:
Glogger, Marius; Subota, Ines; Pezzarossa, Anna; Denecke, Anna-Lena; Carrington, Mark; Fenz, Susanne F.; Engstler, Markus
Source:
Experimental parasitology 2017
ISSN:
0014-4894
Subject:
cell viability; crosslinking; cytoskeleton; ethylene glycol; fluorescence; hydrogels; image analysis; microscopy; models; plasma membrane; polyethylene glycol; thiols
Abstract:
... Research on trypanosomes as a model organism has provided a substantial contribution to a detailed understanding of basic cellular processes within the last few years. At the same time, major advances in super-resolution microscopy have been achieved, facilitating the resolution of biological structures in living cells at a scale of a few nm. However, the motility of trypanosomes has prevented acc ...
DOI:
10.1016/j.exppara.2017.03.010
PubMed:
28363776
PubMed Central:
PMC5540225

1625. Fish consumption in relation to myocardial infarction, stroke and mortality among women and men with type 2 diabetes: A prospective cohort study

Author:
Wallin, Alice; Orsini, Nicola; Forouhi, Nita G.; Wolk, Alicja
Source:
Clinical nutrition 2017
ISSN:
0261-5614
Subject:
cohort studies; confidence interval; coronary disease; fish consumption; men; models; mortality; myocardial infarction; noninsulin-dependent diabetes mellitus; patients; risk; stroke; women
Abstract:
... The accumulated evidence supports an inverse association of fish consumption with cardiovascular disease and mortality, but data among patients with type 2 diabetes are sparse. We aimed to assess fish consumption in relation to myocardial infarction (MI), stroke and mortality among individuals with type 2 diabetes.Women and men with diagnosed type 2 diabetes (n = 2225; aged 45–84 years) within two ...
DOI:
10.1016/j.clnu.2017.01.012
PubMed:
28185684
PubMed Central:
PMC5851676

1626. Flexible connectors between capsomer subunits that regulate capsid assembly

Author:
Hasek, Mary L.; Maurer, Joshua B.; Hendrix, Roger W.; Duda, Robert L.
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
Escherichia coli; X-radiation; arginine; bacteriophages; capsid; glutamic acid; models; mutants; mutation; phenotype; proteins
Abstract:
... Viruses build icosahedral capsids of specific size and shape by regulating the spatial arrangement of the hexameric and pentameric protein capsomers in the growing shell during assembly. In the T=7 capsids of E. coli bacteriophage HK97 and other phages, sixty capsomers are hexons, while the rest are pentons that are correctly positioned during assembly. Assembly of the HK97 capsid to the correct s ...
DOI:
10.1016/j.jmb.2017.07.002
PubMed:
28705762
PubMed Central:
PMC5555079

1627. Functional analyses of putative PalS (Palindromic Self-recognition) motifs in bacterial Hfq

Author:
Jackson, Tommie C.; Sukhodolets, Maxim V.
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
Escherichia coli; adenosine diphosphate; amino acids; bacterial proteins; carcinogenesis; chimerism; genetic engineering; histones; humans; metabolism; models; nucleic acids; stress response
Abstract:
... The bacterial protein Hfq has been linked to nucleic acid metabolism and signaling, however its explicit role has been elusive. Recently it was proposed that the C-termini of Hfq subunits in Hfq6 complexes could be involved in functional interactions with other Hfq hexamers and/or nucleic acids. To test the proposed model of the native Hfq complex experimentally, we genetically engineered chimeric ...
DOI:
10.1016/j.bbrc.2017.03.160
PubMed:
28366634
PubMed Central:
PMC5606250

1628. Functional contacts between MPER and the anti-HIV-1 broadly neutralizing antibody 4E10 extend into the core of the membrane

Author:
Rujas, Edurne; Insausti, Sara; García-Porras, Miguel; Sánchez-Eugenia, Rubén; Tsumoto, Kouhei; Nieva, José L.; Caaveiro, Jose M.M.
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
Human immunodeficiency virus; epitopes; hydrophobicity; lipids; models; mutation; neutralization; neutralizing antibodies; ontogeny; researchers; transmembrane proteins; vaccine development; vaccines; viruses
Abstract:
... The exceptional breadth of broadly neutralizing antibodies (bNAbs) against the membrane-proximal external region (MPER) of the transmembrane protein gp41 makes this class of antibodies an ideal model to design HIV vaccines. From a practical point of view, however, the preparation of vaccines eliciting bNAbs is still a major roadblock that limits their clinical application. Fresh mechanistic insigh ...
DOI:
10.1016/j.jmb.2017.03.008
PubMed:
28300601
PubMed Central:
PMC5479317

1629. Gender-specific expression of ATP-binding cassette (Abc) transporters and cytoprotective genes in mouse choroid plexus

Author:
Flores, Katiria; Manautou, José E.; Renfro, J. Larry
Source:
Toxicology 2017
ISSN:
0300-483X
Subject:
blood-brain barrier; brain; choroid plexus; epithelium; females; gender differences; genes; kidneys; liver; males; methotrexate; mice; models; multiple drug resistance; quantitative polymerase chain reaction; transcription factors; transporters
Abstract:
... The choroid plexus (CP) and blood-brain barrier (BBB) control the movement of several drugs and endogenous compounds between the brain and systemic circulation. The multidrug resistance associated protein (Mrp) efflux transporters form part of these barriers. Several Mrp transporters are positively regulated by the transcription factor nuclear factor erythroid-2-related factor (Nrf2) in liver. The ...
DOI:
10.1016/j.tox.2017.05.019
PubMed:
28587784
PubMed Central:
PMC5865591

1630. Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Author:
Almazan, Eugene Matthew P.; Lesko, Sydney L.; Markey, Michael P.; Rouhana, Labib
Source:
Developmental biology 2017
ISSN:
0012-1606
Subject:
Platyhelminthes; RNA; cell differentiation; chromosome number; epithelial cells; evolution; genes; genetic markers; karyotyping; models; nucleotide sequences; pandemic; progeny; proteins; stem cells; transcriptome; North America
Abstract:
... Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North ...
DOI:
10.1016/j.ydbio.2017.07.022
PubMed:
28774726
PubMed Central:
PMC5750089

1631. Gβ1 is required for neutrophil migration in zebrafish

Author:
Ke, Wenfan; Ye, Ding; Mersch, Kacey; Xu, Hui; Chen, Songhai; Lin, Fang
Source:
Developmental biology 2017
ISSN:
0012-1606
Subject:
Danio rerio; G-protein coupled receptors; actin; chemoattractants; chemotaxis; image analysis; larvae; models; neutrophils; phosphatidylinositol 3-kinase; protein subunits; tissues
Abstract:
... Signaling mediated by G protein-coupled receptors (GPCRs) is essential for the migration of cells toward chemoattractants. The recruitment of neutrophils to injured tissues in zebrafish larvae is a useful model for studying neutrophil migration and trafficking in vivo. Indeed, the study of this process led to the discovery that PI3Kγ is required for the polarity and motility of neutrophils, featur ...
DOI:
10.1016/j.ydbio.2017.05.024
PubMed:
28554852
PubMed Central:
PMC5799152

1632. Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability

Author:
Ring, Caroline L.; Pearce, Robert G.; Woodrow Setzer, R.; Wetmore, Barbara A.; Wambaugh, John F.
Source:
Environment international 2017
ISSN:
0160-4120
Subject:
Centers for Disease Control and Prevention; Europeans; National Health and Nutrition Examination Survey; adults; chemical structure; environmental monitoring; human health; models; prioritization; risk; screening; tissues; toxicity; United States
Abstract:
... The thousands of chemicals present in the environment (USGAO, 2013) must be triaged to identify priority chemicals for human health risk research. Most chemicals have little of the toxicokinetic (TK) data that are necessary for relating exposures to tissue concentrations that are believed to be toxic. Ongoing efforts have collected limited, in vitro TK data for a few hundred chemicals. These data ...
DOI:
10.1016/j.envint.2017.06.004
PubMed:
28628784
PubMed Central:
PMC6116525

1633. Improving in vivo outcomes of decellularized vascular grafts via incorporation of a novel extracellular matrix

Author:
Kristofik, Nina J.; Qin, Lingfeng; Calabro, Nicole E.; Dimitrievska, Sashka; Li, Guangxin; Tellides, George; Niklason, Laura E.; Kyriakides, Themis R.
Source:
Biomaterials 2017
ISSN:
0142-9612
Subject:
cell culture; extracellular matrix; mice; models; modulus of elasticity; rats; tensile strength; United States
Abstract:
... Each year, hundreds of thousands coronary bypass procedures are performed in the US, yet there currently exists no off-the-shelf alternative to autologous vessel transplant. In the present study, we investigated the use of mouse thrombospondin-2 knockout (TSP2 KO) cells, which secrete a non-thrombogenic and pro-migratory extracellular matrix (TSP2 KO ECM), to modify small diameter vascular grafts. ...
DOI:
10.1016/j.biomaterials.2017.06.025
PubMed:
28667900
PubMed Central:
PMC5918415

1634. Interpretation of field potentials measured on a multi electrode array in pharmacological toxicity screening on primary and human pluripotent stem cell-derived cardiomyocytes

Author:
Tertoolen, L.G.J.; Braam, S.R.; van Meer, B.J.; Passier, R.; Mummery, C.L.
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
action potentials; cardiomyocytes; drug toxicity; drugs; electrodes; humans; models; pharmacology; risk; screening; stem cells
Abstract:
... Multi electrode arrays (MEAs) are increasingly used to detect external field potentials in electrically active cells. Recently, in combination with cardiomyocytes derived from human (induced) pluripotent stem cells they have started to become a preferred tool to examine newly developed drugs for potential cardiac toxicity in pre-clinical safety pharmacology. The most important risk parameter is pr ...
DOI:
10.1016/j.bbrc.2017.01.151
PubMed:
28153730
PubMed Central:
PMC5854265

1635. Inverse relationship between urban green space and childhood autism in California elementary school districts

Author:
Wu, Jianyong; Jackson, Laura
Source:
Environment international 2017
ISSN:
0160-4120
Subject:
air pollution; autism; canopy; childhood; children; confidence interval; elementary students; forests; grasslands; models; regression analysis; trees; urban areas; California
Abstract:
... Green space has a variety of health benefits. However, little is known about its impact on autism, the fastest-growing neurodevelopmental disorder in children. This study examined the relationship between green space and childhood autism prevalence. Autism count data in 2010 were obtained for 543 of ~560 public elementary school districts in California. Multiple types of green space were measured ...
DOI:
10.1016/j.envint.2017.07.010
PubMed:
28735150
PubMed Central:
PMC6104398

1636. John Saunders' ZPA, Sonic hedgehog and digit identity – How does it really all work?

Author:
Zhu, Jianjian; Mackem, Susan
Source:
Developmental biology 2017
ISSN:
0012-1606
Subject:
animal development; legs; models; molecular genetics; signal transduction
Abstract:
... Among John Saunders' many seminal contributions to developmental biology, his discovery of the limb ‘zone of polarizing activity’ (ZPA) is arguably one of the most memorable and ground-breaking. This discovery introduced the limb as a premier model for understanding developmental patterning and promoted the concept of patterning by a morphogen gradient. In the 50 years since the discovery of the Z ...
DOI:
10.1016/j.ydbio.2017.02.001
PubMed:
28161524
PubMed Central:
PMC5540801

1637. Logistic regression analysis of populations of electrophysiological models to assess proarrythmic risk

Author:
Morotti, Stefano; Grandi, Eleonora
Source:
MethodsX 2017 v.4 pp. 25-34
ISSN:
2215-0161
Subject:
arrhythmia; calcium; drugs; electrophysiology; models; potassium channels; protocols; regression analysis; risk; sodium; stochastic processes
Abstract:
... Population-based computational approaches have been developed in recent years and helped to gain insight into arrhythmia mechanisms, and intra- and inter-patient variability (e.g., in drug responses). Here, we illustrate the use of multivariable logistic regression to analyze the factors that enhance or reduce the susceptibility to cellular arrhythmogenic events. As an example, we generate 1000 mo ...
DOI:
10.1016/j.mex.2016.12.002
PubMed:
28116246
PubMed Central:
PMC5225282

1638. Measurement and modeling of particulate matter concentrations: Applying spatial analysis and regression techniques to assess air quality

Author:
Sajjadi, Seyed Ali; Zolfaghari, Ghasem; Adab, Hamed; Allahabadi, Ahmad; Delsouz, Mehri
Source:
MethodsX 2017 v.4 pp. 372-390
ISSN:
2215-0161
Subject:
air pollution; air quality; dust; kriging; models; monitoring; particulates; Iran; United Kingdom
Abstract:
... This paper presented the levels of PM2.5 and PM10 in different stations at the city of Sabzevar, Iran. Furthermore, this study was an attempt to evaluate spatial interpolation methods for determining the PM2.5 and PM10 concentrations in the city of Sabzevar. Particulate matters were measured by Haz-Dust EPAM at 48 stations. Then, four interpolating models, including Radial Basis Functions (RBF), I ...
DOI:
10.1016/j.mex.2017.09.006
PubMed:
29085784
PubMed Central:
PMC5655390

1639. Meddling with Fate: The Proteasomal Deubiquitinating Enzymes

Author:
de Poot, Stefanie A.H.; Tian, Geng; Finley, Daniel
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
active sites; dissociation; models; proteasome endopeptidase complex; ubiquitin
Abstract:
... Three deubiquitinating enzymes—Rpn11, Usp14, and Uch37—are associated with the proteasome regulatory particle. These enzymes allow proteasomes to remove ubiquitin from substrates before they are translocated into the core particle to be degraded. Although the translocation channel is too narrow for folded proteins, the force of translocation unfolds them mechanically. As translocation proceeds, ub ...
DOI:
10.1016/j.jmb.2017.09.015
PubMed:
28988953
PubMed Central:
PMC5675770

1640. Modeling downdraft biomass gasification process by restricting chemical reaction equilibrium with Aspen Plus

Author:
Han, Jun; Liang, Yan; Hu, Jin; Qin, Linbo; Street, Jason; Lu, Yongwu; Yu, Fei
Source:
Energy conversion and management 2017
ISSN:
0196-8904
Subject:
Gibbs free energy; biofuels; biomass; chemical reactions; gasification; hardwood; liquids; models; temperature; transportation; water content
Abstract:
... Thermo-chemical conversion of biomass has been regarded as one of attractive routes of producing the clean and environmental friendly bio-fuels. Downdraft biomass gasification process has been served as a key technology to provide the bio-syngas with high quality, which can be used to produce the renewable liquid transportation fuels through Fischer Tropsch Synthesis in Mississippi State Universit ...
DOI:
10.1016/j.enconman.2017.10.030
Chorus Open Access:
10.1016/j.enconman.2017.10.030

1641. Modeling of variability and uncertainty in human health risk assessment

Author:
Dutta, Palash
Source:
MethodsX 2017 v.4 pp. 76-85
ISSN:
2215-0161
Subject:
algorithms; health effects assessments; human health; models; risk; risk assessment; toxicity; uncertainty
Abstract:
... Health risk assessments have been carried out worldwide to examine potential health risk due to exposure to toxic contaminants in various environments. In risk assessment, it is most important to know the nature of all available information, data or model parameters. It is observed that available information/data are tainted with uncertainty and variability in the same time, i.e., uncertainty and ...
DOI:
10.1016/j.mex.2017.01.005
PubMed:
28239562
PubMed Central:
PMC5318352

1642. Models of toxicity of diacetyl and alternative diones

Author:
Brass, David M.; Palmer, Scott M.
Source:
Toxicology 2017
ISSN:
0300-483X
Subject:
GRAS substances; color; diacetyl; flavor; ingredients; lung function; models; odors; toxicity; vapors; volatile organic compounds; working conditions
Abstract:
... Diacetyl (DA; 2,3-butanedione), with the chemical formula (CH3CO)2 is a volatile organic compound with a deep yellow color and a strong buttery flavor and aroma. These properties have made DA a particularly useful and common food flavoring ingredient. However, because of this increased occupational use, workers can be exposed to high vapor concentrations in the workplace. Despite being listed by t ...
DOI:
10.1016/j.tox.2017.02.011
PubMed:
28232124
PubMed Central:
PMC5540796

1643. Molecular Regulation of Alternative Polyadenylation (APA) within the Drosophila Nervous System

Author:
Baier, Raul Vallejos; Picao-Osorio, Joao; Alonso, Claudio R.
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
3' untranslated regions; Drosophila; RNA-binding proteins; central nervous system; embryogenesis; genes; mammals; microRNA; models; neurodevelopment; tissues
Abstract:
... Alternative polyadenylation (APA) is a widespread gene regulatory mechanism that generates mRNAs with different 3′-ends, allowing them to interact with different sets of RNA regulators such as microRNAs and RNA-binding proteins. Recent studies have shown that during development, neural tissues produce mRNAs with particularly long 3′UTRs, suggesting that such extensions might be important for neura ...
DOI:
10.1016/j.jmb.2017.03.028
PubMed:
28366829
PubMed Central:
PMC5656104

1644. MR image-guided delivery of cisplatin-loaded brain-penetrating nanoparticles to invasive glioma with focused ultrasound

Author:
Timbie, Kelsie F; Afzal, Umara; Date, Abhijit; Zhang, Clark; Song, Ji; Wilson Miller, G.; Suk, Jung Soo; Hanes, Justin; Price, Richard J
Source:
Journal of Controlled Release 2017
ISSN:
0168-3659
Subject:
animals; blood-brain barrier; brain neoplasms; cisplatin; coatings; drug therapy; extracellular matrix; fluorescence; models; nanoparticles; neoplasm cells; polyethylene glycol
Abstract:
... Systemically administered chemotherapeutic drugs are often ineffective in the treatment of invasive brain tumors due to poor therapeutic index. Within gliomas, despite the presence of heterogeneously leaky microvessels, dense extracellular matrix and high interstitial pressure generate a “blood-tumor barrier” (BTB), which inhibits drug delivery and distribution. Meanwhile, beyond the contrast MRI- ...
DOI:
10.1016/j.jconrel.2017.03.017
PubMed:
28288892
PubMed Central:
PMC5593770

1645. Multi-level and hybrid modelling approaches for systems biology

Author:
Bardini, R.; Politano, G.; Benso, A.; Di Carlo, S.
Source:
Computational and Structural Biotechnology Journal 2017 v.15 pp. 396-402
ISSN:
2001-0370
Subject:
assets; biotechnology; models; ontogeny; phenotype; space and time
Abstract:
... During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in ...
DOI:
10.1016/j.csbj.2017.07.005
PubMed:
28855977
PubMed Central:
PMC5565741

1646. Netrin1 establishes multiple boundaries for axon growth in the developing spinal cord

Author:
Varadarajan, Supraja G.; Butler, Samantha J.
Source:
Developmental biology 2017
ISSN:
0012-1606
Subject:
axons; innervation; mice; models; spinal cord; stem cells
Abstract:
... The canonical model for netrin1 function proposed that it acted as a long-range chemotropic axon guidance cue. In the developing spinal cord, floor-plate (FP)-derived netrin1 was thought to act as a diffusible attractant to draw commissural axons to the ventral midline. However, our recent studies have shown that netrin1 is dispensable in the FP for axon guidance. We have rather found that netrin1 ...
DOI:
10.1016/j.ydbio.2017.08.001
PubMed:
28780049
PubMed Central:
PMC5786155

1647. Neutron reflectivity measurement of protein A—antibody complex at the solid-liquid interface

Author:
Mazzer, Alice R.; Clifton, Luke A.; Perevozchikova, Tatiana; Butler, Paul D.; Roberts, Christopher J.; Bracewell, Daniel G.
Source:
Journal of chromatography 2017
ISSN:
0021-9673
Subject:
adsorption; affinity chromatography; antibodies; biopharmaceuticals; buffers; desorption; glass; immunoglobulin G; ligands; models; pH; silica
Abstract:
... Chromatography is a ubiquitous unit operation in the purification of biopharmaceuticals yet few studies have addressed the biophysical characterisation of proteins at the solution-resin interface. Chromatography and other adsorption and desorption processes have been shown to induce protein aggregation which is undesirable in biopharmaceutical products. In order to advance understanding of how ads ...
DOI:
10.1016/j.chroma.2017.03.084
PubMed:
28410804
PubMed Central:
PMC5408906

1648. Notch and Fgf signaling during electrosensory versus mechanosensory lateral line organ development in a non-teleost ray-finned fish

Author:
Modrell, Melinda S.; Tidswell, Olivia R.A.; Baker, Clare V.H.
Source:
Developmental biology 2017
ISSN:
0012-1606
Subject:
Danio rerio; Polyodon spathula; catfish; epithelium; fibroblast growth factors; ganglia; head; models; neuromasts; sensory neurons; signal transduction
Abstract:
... The lateral line system is a useful model for studying the embryonic and evolutionary diversification of different organs and cell types. In jawed vertebrates, this ancestrally comprises lines of mechanosensory neuromasts over the head and trunk, flanked on the head by fields of electrosensory ampullary organs, all innervated by lateral line neurons in cranial lateral line ganglia. Both types of s ...
DOI:
10.1016/j.ydbio.2017.08.017
PubMed:
28818669
PubMed Central:
PMC5650464

1649. OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing

Author:
Xu, Gang; Ma, Tianqi; Zang, Tianwu; Sun, Weitao; Wang, Qinghua; Ma, Jianpeng
Source:
Journal of Molecular Biology 2017
ISSN:
0022-2836
Subject:
energy; models; protein structure
Abstract:
... We report a new distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing, named OPUS-DOSP, for protein structure modeling. The framework of OPUS-DOSP is based on OPUS-PSP, previously developed by us (JMB (2008) 376, 288–301), with refinement and new features. In particular, distance or orientation contribution is considered depending on the range of conta ...
DOI:
10.1016/j.jmb.2017.08.013
PubMed:
28864201
PubMed Central:
PMC6193766

1650. Paxillin and embryonic PolyAdenylation Binding Protein (ePABP) engage to regulate androgen-dependent Xenopus laevis oocyte maturation - A model of kinase-dependent regulation of protein expression

Author:
Miedlich, Susanne U.; Taya, Manisha; Young, Melissa Rasar; Hammes, Stephen R.
Source:
Molecular and Cellular Endocrinology 2017
ISSN:
0303-7207
Subject:
Xenopus laevis; binding proteins; mammals; meiosis; messenger RNA; models; oocytes; phosphorylation; protein synthesis; serine; testosterone; translation (genetics)
Abstract:
... Steroid-triggered Xenopus laevis oocyte maturation is an elegant physiologic model of nongenomic steroid signaling, as it proceeds completely independent of transcription. We previously demonstrated that androgens are the main physiologic stimulator of oocyte maturation in Xenopus oocytes, and that the adaptor protein paxillin plays a crucial role in mediating this process through a positive feedb ...
DOI:
10.1016/j.mce.2017.03.028
PubMed:
28359799
PubMed Central:
PMC5500300