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https://www.readbyqxmd.com/read/29243094/hierarchical-design-of-artificial-proteins-and-complexes-toward-synthetic-structural-biology
#1
REVIEW
Ryoichi Arai
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field...
December 14, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29242905/the-long-noncoding-rna-landscape-of-the-mouse-eye
#2
Weiwei Chen, Shuai Yang, Zhonglou Zhou, Xiaoting Zhao, Jiayun Zhong, Peter S Reinach, Dongsheng Yan
Purpose: Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Methods: Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29242522/amyloid-%C3%AE-and-tau-complexity-towards-improved-biomarkers-and-targeted-therapies
#3
REVIEW
Juan Carlos Polanco, Chuanzhou Li, Liviu-Gabriel Bodea, Ramon Martinez-Marmol, Frederic A Meunier, Jürgen Götz
Most neurodegenerative diseases are proteinopathies, which are characterized by the aggregation of misfolded proteins. Although many proteins have an intrinsic propensity to aggregate, particularly when cellular clearance systems start to fail in the context of ageing, only a few form fibrillar aggregates. In Alzheimer disease, the peptide amyloid-β (Aβ) and the protein tau aggregate to form plaques and tangles, respectively, which comprise the histopathological hallmarks of this disease. This Review discusses the complexity of Aβ biogenesis, trafficking, post-translational modifications and aggregation states...
December 15, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/29242291/the-x-linked-1-688-satellite-in-drosophilamelanogaster-promotes-specific-targeting-by-painting-of-fourth
#4
Maria Kim, Samaneh Ekhteraei-Tousi, Jacob Lewerentz, Jan Larsson
Repetitive DNA, represented by transposons and satellite DNA, constitutes a large portion of eukaryotic genomes, being the major component of constitutive heterochromatin. There is a growing body of evidence that it regulates several nuclear functions including chromatin state and the proper functioning of centromeres and telomeres. The 1.688 satellite is one of the most abundant repetitive sequences in Drosophilamelanogaster, with the longest array being located in the pericentromeric region of the X-chromosome...
December 13, 2017: Genetics
https://www.readbyqxmd.com/read/29241061/scfv-modified-graphene-coated-ide-arrays-for-label-free-screening-of-cardiovascular-disease-biomarkers-in-physiological-saline
#5
Lotta E Delle, Vivek Pachauri, Shikha Sharma, Olena Shaforost, Hui Ma, Mohammad Adabi, Rainer Lilischkis, Patrick Wagner, Ronald Thoelen, Norbert Klein, Richard O'Kennedy, Sven Ingebrandt
Fatty-acid binding proteins (FABP) and myeloperoxidases (MPO) are associated with many chronic conditions in humans and considered to be important biomarkers for diagnosis of cardiac diseases. Here we assemble a new electrical biosensor platform based on graphene-coated interdigitated electrode arrays (IDE-arrays) towards ultrafast, label-free screening of heart type-FABP and MPO. Arrays of nanoscale (nanoIDE) and microscale (microIDE) electrode-arrays were fabricated on wafer-scale by combining nanoimprint and photolithography processes...
December 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29241030/expression-profiles-of-genes-involved-in-tlrs-and-nlrs-signaling-pathways-of-water-buffaloes-infected-with-fasciola-gigantica
#6
Fu-Kai Zhang, Jun-Ling Hou, Ai-Jiang Guo, Ai-Ling Tian, Zhao-An Sheng, Wen-Bin Zheng, Wei-Yi Huang, Hany M Elsheikha, Xing-Quan Zhu
Infection of ruminants and humans with Fasciola gigantica is attracting increasing attention due to its economic impact and public health significance. However, little is known of innate immune responses during F. gigantica infection. Here, we investigated the expression profiles of genes involved in Toll-like receptors (TLRs) and NOD-like receptors (NLRs) signaling pathways in buffaloes infected with 500F. gigantica metacercariae. Serum, liver and peripheral blood mononuclear cell (PBMC) samples were collected from infected and control buffaloes at 3, 10, 28, and 70days post infection (dpi)...
December 11, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29240228/chromatographic-methods-in-hiv-medicine-application-to-therapeutic-drug-monitoring
#7
REVIEW
Timothy L Archibald, Derek E Murrell, Stacy D Brown
HIV antiretroviral therapy spans several different drug classes, meant to combat various aspects of viral infection and replication. Many authors have argued the benefits of therapeutic drug monitoring (TDM) for the HIV-patient including compliance assurance and assessment of appropriate drug concentrations; however, the array of drug chemistries and combinations makes TDM an arduous task. HPLC-UV and LC-MS/MS are both frequent instruments for the quantification of HIV drugs in biological matrices with investigators striving to balance sensitivity and affordability...
December 14, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29239171/thermoresponsive-arrays-patterned-via-photo-click-chemistry-smart-maldi-plate-for-protein-digest-enrichment-desalting-and-direct-ms-analysis
#8
Xiao Meng, Junjie Hu, Zhicong Chao, Ying Liu, Huangxian Ju, Quan Cheng
Sample desalting and concentrating is a crucial step prior to MALDI-MS analysis. Current sample pretreatment approaches require tedious fabrication and operation procedures, which are unamenable to high-throughput analysis and also result in sample loss. Here we report the development of a smart MALDI substrate for on-plate desalting, enrichment, and direct MS analysis of protein digests based on thermo-responsive, hydrophilic/hydrophobic transition of surface grafted poly(N-isopropylacrylamide) (PNIPAM) microarrays...
December 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29238345/f-type-lectins-a-highly-diversified-family-of-fucose-binding-proteins-with-a-unique-sequence-motif-and-structural-fold-involved-in-self-non-self-recognition
#9
REVIEW
Gerardo R Vasta, L Mario Amzel, Mario A Bianchet, Matteo Cammarata, Chiguang Feng, Keiko Saito
The F-type lectin (FTL) family is one of the most recent to be identified and structurally characterized. Members of the FTL family are characterized by a fucose recognition domain [F-type lectin domain (FTLD)] that displays a novel jellyroll fold ("F-type" fold) and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed proteins exhibiting single, double, or greater multiples of the FTLD, either tandemly arrayed or combined with other structurally and functionally distinct domains, yielding lectin subunits of pleiotropic properties even within a single species...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29237756/the-prokaryotic-na-ca2-exchanger-ncx_mj-transports-na-and-ca2-in-a-3-1-stoichiometry
#10
Irina Shlosman, Fabrizio Marinelli, José D Faraldo-Gómez, Joseph A Mindell
Intracellular Ca2+ signals control a wide array of cellular processes. These signals require spatial and temporal regulation of the intracellular Ca2+ concentration, which is achieved in part by a class of ubiquitous membrane proteins known as sodium-calcium exchangers (NCXs). NCXs are secondary-active antiporters that power the translocation of Ca2+ across the cell membrane by coupling it to the flux of Na+ in the opposite direction, down an electrochemical gradient. Na+ and Ca2+ are translocated in separate steps of the antiport cycle, each of which is thought to entail a mechanism whereby ion-binding sites within the protein become alternately exposed to either side of the membrane...
December 13, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/29237407/identification-and-in-silico-characterization-of-a-novel-p-p208pfsx1-mutation-in-v-atpase-a3-subunit-associated-with-autosomal-recessive-osteopetrosis-in-a-pakistani-family
#11
Muhammad Ajmal, Asif Mir, Sughra Wahid, Chiea Chuen Khor, Jia Nee Foo, Saima Siddiqi, Mehran Kauser, Salman Akbar Malik, Muhammad Nasir
BACKGROUND: Osteopetrosis is a rare inherited bone disorder mainly described as an increased bone density caused by defective osteoclastic bone resorption. To date, genetic variants of eleven genes have been reported so far to be associated with different types of osteopetrosis. However, malignant infantile osteopetrosis, a lethal form of the disease, is mostly (50%) caused by mutation(s) in TCIRG1 gene. In this study, we investigated a consanguineous Pakistani family clinically and genetically to elucidate underlying molecular basis of the infantile osteopetrosis...
December 13, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/29235974/processing-fixed-and-stored-adipose-derived-stem-cells-for-quantitative-protein-array-assays
#12
Jessica S Sadick, Eric M Darling
Accurately characterizing cellular subpopulations is essential for elucidating the mechanisms underlying normal and pathological biology. Isolation of specific cell types can be accomplished by labeling unique cell-associated proteins with fluorescent antibodies. Cell fixation is commonly used to prepare these samples and allow for long-term storage, but this poses challenges for subsequent protein analysis. We previously established the FITSAR (formaldehyde-fixed intracellular target-sorted antigen retrieval) method, in which protein can be isolated and characterized from fixed, enriched cell subpopulations...
December 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/29235973/linear-array-of-multi-substrate-tracts-for-simultaneous-assessment-of-cell-adhesion-migration-and-differentiation
#13
Ricardo A Moreno-Rodriguez, Edward L Krug, Leticia Reyes, Roger R Markwald
Cell migration, which is central to a wide variety of life processes, involves integration of the extracellular matrix (ECM) with the internal cytoskeleton and motor proteins via receptors spanning the plasma membrane. Cell migration can be induced by a variety of signals, including gradients of external soluble molecules, differences in ECM composition, or electrical gradients. Current in vitro methods to study cell migration only test one substrate at a time. Here, we present a method for assessing cell adhesion, migration, and differentiation in up to 20 different test conditions simultaneously, using only minute amounts of target substrate...
December 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/29235416/skeletal-muscle-cell-contraction-reduces-a-novel-myokine-chemokine-c-x-c-motif-ligand-10-cxcl10-potential-roles-in-exercise-regulated-angiogenesis
#14
Yuri Ishiuchi, Hitoshi Sato, Kazuki Tsujimura, Hideo Kawaguchi, Takashi Matsuwaki, Keitaro Yamanouchi, Masugi Nishihara, Taku Nedachi
Accumulating evidence indicates that skeletal muscle secrets proteins referred to as myokines and that exercise contributes to their regulation. In this study, we propose that chemokine (C-X-C motif) ligand 10 (CXCL10) functions as a novel myokine. Initially, we stimulated differentiated C2C12 myotubes with or without electrical pulse stimulation (EPS) to identify novel myokines. Cytokine array analysis revealed that CXCL10 secretion was significantly reduced by EPS, which was further confirmed by enzyme-linked immunosorbent assay and quantitative polymerase chain reaction analysis...
December 13, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29234488/sirt6-histone-deacetylase-functions-as-a-potential-oncogene-in-human-melanoma
#15
Liz Mariely Garcia-Peterson, Mary Ann Ndiaye, Chandra K Singh, Gagan Chhabra, Wei Huang, Nihal Ahmad
Melanoma is an aggressive skin cancer that can rapidly metastasize to become fatal, if not diagnosed early. Despite recent therapeutic advances, management of melanoma remains difficult. Therefore, novel molecular targets and strategies are required to manage this neoplasm. This study was undertaken to determine the role of the sirtuin SIRT6 in melanoma. Employing a panel of human melanoma cells and normal human melanocytes, we found significant SIRT6 mRNA and protein upregulation in melanoma cells. Further, using a tissue microarray coupled with quantitative Vectra analysis, we demonstrated significant SIRT6 overexpression in human melanoma tissues...
September 2017: Genes & Cancer
https://www.readbyqxmd.com/read/29234486/jnk-signaling-a-multiplexing-hub-in-programmed-cell-death
#16
REVIEW
Danny N Dhanasekaran, E Premkumar Reddy
Jun N-terminal kinases or JNKs have been shown to be involved in a wide array of signaling events underlying tumorigenesis and tumor progression. Through its interaction with a diverse set of signaling proteins and adaptors, JNKs regulate cell proliferation, invasive migration, therapy resistance, and programmed cell death. JNKs have been shown to play a role in apoptotic as well as non-apoptotic programmed cell death mechanisms including those of necroptosis, ferroptosis, pyroptosis, and autophagy. Most of the tumorigenic regulatory functions of JNKs can be related to their ability to module cell death via these programmed cell death mechanisms...
September 2017: Genes & Cancer
https://www.readbyqxmd.com/read/29234067/the-human-blood-nerve-barrier-transcriptome
#17
Steven P Palladino, E Scott Helton, Preti Jain, Chaoling Dong, Michael R Crowley, David K Crossman, Eroboghene E Ubogu
The blood-nerve barrier (BNB), formed by tight junction-forming microvessels within peripheral nerve endoneurium, exists to regulate its internal microenvironment essential for effective axonal signal transduction. Relatively little is known about the unique human BNB molecular composition. Such knowledge is crucial to comprehend the relationships between the systemic circulation and peripheral nerves in health, adaptations to intrinsic or extrinsic perturbations and alterations that may result in disease. We performed RNA-sequencing on cultured early- and late-passage adult primary human endoneurial endothelial cells and laser-capture microdissected endoneurial microvessels from four cryopreserved normal adult human sural nerves referenced to the Genome Reference Consortium Human Reference 37 genome browser, using predefined criteria guided by known transcript or protein expression in vitro and in situ...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233753/targeting-the-26s-proteasome-to-protect-against-proteotoxic-diseases
#18
REVIEW
Natura Myeku, Karen E Duff
Aggregates of misfolded proteins can compromise the function of the 26S proteasome complex, leaving neurons susceptible to accelerated and impaired protein homeostasis, thereby contributing to the pathogenesis of neurodegeneration. Strategies aimed at enhancing the function of the 26S proteasome via phosphorylation of key subunit epitopes have been effective in reducing protein aggregates in mouse models of disease. We discuss how phosphodiesterase (PDE) inhibitors and G protein-coupled receptor (GPCR)-targeted drugs might be considered as candidate therapeutics, acting on second messenger signal transduction...
December 9, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/29232935/extraction-optimization-of-flavonoids-from-hypericum-formosanum-and-matrix-metalloproteinase-1-inhibitory-activity
#19
Ho-Shin Huang, Ean-Tun Liaw
Hypericum formosanum is a valuable herb in Taiwan. In this study, response surface methodology was employed to optimize the ultrasound-assisted extraction of flavonoids from Hypericum formosanum. A central composite design with three variables (ethanol concentration, extraction time, and extraction temperature) was applied. Experimental results were fitted to the second order polynomial model and one-way analysis of variance was used to determine the goodness of fit of the model and the optimal conditions for responses...
December 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29232015/constant-vigilance-plant-functions-guarded-by-resistance-proteins
#20
Jianbin Su, Benjamin J Spears, Sang Hee Kim, Walter Gassmann
Unlike animals, plants do not have an adaptive immune system and have instead evolved sophisticated and multi-layered innate immune mechanisms. To overcome plant immunity, pathogens secrete a diverse array of effectors into the apoplast and virtually all cellular compartments in order to dampen immune signaling and interfere with plant functions. Here we describe the scope of the arms race throughout the cell and summarize various strategies used by both plants and pathogens. Through studying the ongoing evolutionary battle between plants and key pathogens, we may yet uncover potential ways to achieve the ultimate goal of engineering broad-spectrum resistant crops without affecting food quality or productivity...
December 12, 2017: Plant Journal: for Cell and Molecular Biology
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