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https://www.readbyqxmd.com/read/29232711/dependence-of-prevalence-of-contiguous-pathways-in-proteins-on-structural-complexity
#1
Kelly M Thayer, Jesse C Galganov, Avram J Stein
Allostery is a regulatory mechanism in proteins where an effector molecule binds distal from an active site to modulate its activity. Allosteric signaling may occur via a continuous path of residues linking the active and allosteric sites, which has been suggested by large conformational changes evident in crystal structures. An alternate possibility is that the signal occurs in the realm of ensemble dynamics via an energy landscape change. While the latter was first proposed on theoretical grounds, increasing evidence suggests that such a control mechanism is plausible...
2017: PloS One
https://www.readbyqxmd.com/read/29232160/microrna-145-antagonism-reverses-tgf-%C3%AE-inhibition-of-f508del-cftr-correction-in-airway-epithelia
#2
Farruk Lutful Kabir, Namasivayam Ambalavanan, Gang Liu, Peng Li, George M Solomon, Charitharth V Lal, Marina Mazur, Brian Halloran, Tomasz Szul, William T Gerthoffer, Steven M Rowe, William T Harris
INTRODUCTION: microRNAs (miRNAs) destabilize mRNA transcripts and inhibit protein translation. miR-145 is of particular interest in cystic fibrosis (CF) as it has a direct binding site in the 3'-untranslated region of CFTR and is upregulated by the CF genetic modifier TGF-β. HYPOTHESIS: miR-145 mediates TGF-β inhibition of CFTR synthesis and function in airway epithelia. METHODS: Primary human CF (F508del homozygous) and non-CF airway epithelial cells (AECs) were grown to terminal differentiation at air-liquid interface on permeable supports...
December 12, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29232115/arsenobetaine-in-seawater-depth-profiles-from-selected-sites-in-the-north-atlantic
#3
Ronald Alexander Glabonjat, Georg Raber, Benjamin A S Van Mooy, Kevin A Francesconi
Arsenic occurs in marine waters, typically at concentrations of 1-2 μg As kg-1, primarily as the inorganic species arsenate. Marine animals, however, contain extremely high levels of arsenic (typically 2,000-20,000 μg As kg-1 wet mass), most of which is present as arsenobetaine, an organic form of arsenic that has never been found in seawater. We report a method based on ion-exchange pre-concentration and HPLC/mass spectrometry to measure arsenobetaine in seawater, and apply the method to samples of seawater collected at various depths from seven sites in the North Atlantic...
December 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29231859/rational-engineering-of-a-flavoprotein-oxidase-for-improved-direct-oxidation-of-alcohols-to-carboxylic-acids
#4
Mathias Pickl, Christoph K Winkler, Silvia M Glueck, Marco W Fraaije, Kurt Faber
The oxidation of alcohols to the corresponding carbonyl or carboxyl compounds represents a convenient strategy for the selective introduction of electrophilic carbon centres into carbohydrate-based starting materials. The O₂-dependent oxidation of prim-alcohols by flavin-containing alcohol oxidases often yields mixtures of aldehyde and carboxylic acid, which is due to "over-oxidation" of the aldehyde hydrate intermediate. In order to directly convert alcohols into carboxylic acids, rational engineering of 5-(hydroxymethyl)furfural oxidase was performed...
December 12, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29231711/embedding-capture-magneto-catalytic-activity-into-a-nano-catalyst-for-the-determination-of-lipid-kinase
#5
Tao Gao, Chaoli Mu, Hai Shi, Liu Shi, Xiaoxia Mao, Genxi Li
Using emerging nano-catalysts to investigate the activity of bio-catalysts (protein enzymes, catalytic RNAs, ect.) is increasingly receiving attention from material, analytical and biomedical scientists. Here, we have first fabricated a three-in-one nano-catalyst, the nitrilotriacetic acid (NTA)-modified magnetite nanoparticle (NTA-MNPs), to develop an integrated magneto-colorimetric (MagColor) assay for lipid kinase activity, so as to solve the inherent problems in lipid kinase assay. Based on three integrated functions of the NTA-MNPs (capture, magnetic separation and peroxidase activity), catalytic activity of lipid kinase is directly converted to colorimetric signals...
December 12, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29231705/a-simple-and-convenient-aptasensor-for-protein-using-electronic-balance-as-readout
#6
Alian Wang, Xiaoming Ma, Yanzhu Ye, Fang Luo, Longhua Guo, Bin Qiu, Zhenyu Lin, Guonan Chen
Electronic balance, one of the most common equipments in the laboratory, is normally adopted to directly measure the weight of the target with high accuracy, however little attention has been paid on the extension of its application. In this study, electronic balance was used as readout to develop a novel aptasensor for protein quantification for the first time. Thrombin was selected as a model target and its two aptamers recognizing different sites of the protein were used (one aptamer was immobilized on the surface of magnetic microparticles and the other aptamer was functionalized with platinum nanoparticles)...
December 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29231704/site-specific-glycan-heterogeneity-characterization-by-hilic-solid-phase-extraction-rplc-fractionation-and-capillary-zone-electrophoresis-electrospray-ionization-tandem-mass-spectrometry
#7
Yanyan Qu, Liangliang Sun, Zhenbin Zhang, Norman J Dovichi
Reversed-phase chromatographic separation of glycopeptides tends to be dominated by the peptide composition. In contrast, capillary zone electrophoresis separation of glycopeptides is particularly sensitive to the sialic acid composition of the glycan. In this paper, we combine the two techniques to achieve superior N-glycopeptide analysis. Glycopeptides were first isolated from a tryptic digest using HILIC solid-phase extraction. The glycopeptides were separated using reversed-phase UHPLC to generate four fractions corresponding to different peptide backbones...
December 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29231258/retrospective-review-of-immunocompromised-children-undergoing-skin-biopsy-for-suspected-invasive-infection-analysis-of-factors-predictive-of-invasive-mold
#8
Robert J Smith, Sarah B Klieger, Salwa E Sulieman, Emily Berger, James R Treat, Brian T Fisher
OBJECTIVES: Cutaneous lesions are often the first marker of invasive mold infection, which can cause substantial morbidity in immunocompromised children. The purpose of this study was to describe the evaluation and outcomes of immunocompromised children who presented with findings requiring skin biopsy because of concern about invasive infection. In children who were biopsied, we sought to determine the factors predictive of invasive mold infection. METHODS: A retrospective review was conducted at the Children's Hospital of Philadelphia...
December 12, 2017: Pediatric Dermatology
https://www.readbyqxmd.com/read/29231248/slurp-1-is-mutated-in-mal-de-meleda-a-potential-molecular-signature-for-melanoma-and-a-putative-squamous-lineage-tumor-suppressor-gene
#9
Christina Bergqvist, Humam Kadara, Lamiaa Hamie, Georges Nemer, Remi Safi, Mirna Karouni, Nadine Marrouche, Ossama Abbas, Divina J Hasbani, Abdul G Kibbi, Dany Nassar, Yutaka Shimomura, Mazen Kurban
BACKGROUND: Mal de Meleda (MDM) is a rare inherited autosomal recessive genodermatosis characterized by palmoplantar keratoderma (PPK) with transgrediens and caused by mutations in the SLURP1 gene. Uncommonly, cutaneous tumors have been found at PPK sites in MDM patients. OBJECTIVE: To study a Middle Eastern family with MDM with both PPK and skin tumors. METHODS: We studied a Middle Eastern (Palestinian) family with clinical features of MDM and cutaneous tumors...
December 12, 2017: International Journal of Dermatology
https://www.readbyqxmd.com/read/29231014/-correlation-between-genetic-variants-and-polymorphism-of-caveolin-and-sudden-unexplained-death
#10
F Y Wu, X H Tang, L L Gai, X P Kong, B Hao, E W Huang, H Shi, L H Sheng, L Quan, S P Liu, B Luo
OBJECTIVES: To explore the genetic variation sites of caveolin (CAV) and their correlation with sudden unexplained death (SUD). METHODS: The blood samples were collected from SUD group (71 cases), coronary artery disease (CAD) group (62 cases) and control group (60 cases), respectively. The genome DNA were extracted and sequencing was performed directly by amplifying gene coding region and exon-intron splicing region of CAV1 and CAV3 using PCR...
April 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29230389/cyclic-tensile-strain-can-play-a-role-in-directing-both-intramembranous-and-endochondral-ossification-of-mesenchymal-stem-cells
#11
Simon F Carroll, Conor T Buckley, Daniel J Kelly
Successfully regenerating damaged or diseased bone and other joint tissues will require a detailed understanding of how joint specific environmental cues regulate the fate of progenitor cells that are recruited or delivered to the site of injury. The goal of this study was to explore the role of cyclic tensile strain (CTS) in regulating the initiation of mesenchymal stem cell/multipotent stromal cell (MSC) differentiation, and specifically their progression along the endochondral pathway. To this end, we first explored the influence of CTS on the differentiation of MSCs in the absence of any specific growth factor, and secondly, we examined the influence of the long-term application of this mechanical stimulus on markers of endochondral ossification in MSCs maintained in chondrogenic culture conditions...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/29230236/post-transcriptional-regulation-of-pcsk9-by-mir-191-mir-222-and-mir-224
#12
Parisa Naeli, Fatemeh Mirzadeh Azad, Mahshid Malakootian, Nabil G Seidah, Seyed J Mowla
Since proprotein convertase subtilisin kexin 9 (PCSK9) discovery, a gene involved in LDL metabolism regulation and cardiovascular diseases (CVD), many therapeutic strategies have been introduced for direct targeting of PCSK9. The main goal of these strategies has been to reduce PCSK9 protein level either by application of antibodies or inhibition of its production. In this study, we have tried to discover microRNAs (miRNAs) which can target, and hence regulate, PCSK9 expression. Using bioinformatics tools, we selected three microRNAs with binding sites on 3'-UTR of PCSK9...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29230152/development-of-a-mixed-methods-investigation-of-process-and-outcomes-of-community-based-participatory-research
#13
Julie Lucero, Nina Wallerstein, Bonnie Duran, Margarita Alegria, Ella Greene-Moton, Barbara Israel, Sarah Kastelic, Maya Magarati, John Oetzel, Cynthia Pearson, Amy Schulz, Malia Villegas, Emily R White Hat
This article describes a mixed methods study of community-based participatory research (CBPR) partnership practices and the links between these practices and changes in health status and disparities outcomes. Directed by a CBPR conceptual model and grounded in indigenous-transformative theory, our nation-wide, cross-site study showcases the value of a mixed methods approach for better understanding the complexity of CBPR partnerships across diverse community and research contexts. The article then provides examples of how an iterative, integrated approach to our mixed methods analysis yielded enriched understandings of two key constructs of the model: trust and governance...
January 2018: Journal of Mixed Methods Research
https://www.readbyqxmd.com/read/29229779/subtle-changes-at-the-variable-domain-interface-of-the-t-cell-receptor-can-strongly-increase-affinity
#14
Preeti Sharma, David M Kranz
Most affinity maturation campaigns for antibodies and T cell receptors (TCRs) operate on the residues at the binding site, located within the loops known as complementarity determining regions (CDRs). Accordingly, mutations in contact residues or so-called second shell residues that increase affinity are typically identified by directed evolution using combinatorial libraries. Here we used single codon libraries of both CDR and non-CDR residues to generate a deep mutational scan of a human TCR against the cancer antigen MART-1/HLA-A2...
December 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29229775/molecular-characterization-of-dxcf-cyanobacteriochromes-from-the-cyanobacterium-acaryochloris-marina-identifies-a-blue-light-power-sensor
#15
Masumi Hasegawa, Keiji Fushimi, Keita Miyake, Takahiro Nakajima, Yuki Oikawa, Gen Enomoto, Moritoshi Sato, Masahiko Ikeuchi, Rei Narikawa
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole-binding photoreceptors that sense a wide range of wavelengths from ultraviolet to far-red. The primary photoreaction in these reactions is a Z/E isomerization of the double bond between rings C and D. After this isomerization, various color-tuning events establish distinct spectral properties of the CBCRs. Among the various CBCRs, the DXCF CBCR lineage is widely distributed among cyanobacteria. Because the DXCF CBCRs from the cyanobacterium Acaryochloris marina vary widely in sequence, we focused on these CBCRs in this study...
December 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29229759/jmjd6-induces-hotair-an-oncogenic-lincrna-by-physically-interacting-with-its-proximal-promoter
#16
Antara Biswas, Abhijith Shettar, Geetashree Mukherjee, Paturu Kondaiah, Kartiki V Desai
<span style="color: black;">Using microarray analysis we found that HOX transcript antisense intergenic RNA (HOTAIR) is upregulated by Jumonji domain containing-6 (JMJD6), a bifunctional lysyl hydroxylase and arginine demethylase. In breast cancer, JMJD6 and HOTAIR RNAs increase tumor growth and associate with poor prognosis but no molecular relationship between them is known. We show that overexpression of JMJD6 increased HOTAIR expression and JMJD6 siRNAs suppressed it in ER+ MCF-7, triple negative MDA-MB-231 and non-breast cancer HEK 293 cells...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29229737/the-superantigen-toxic-shock-syndrome-toxin-1-alters-human-aortic-endothelial-cell-function
#17
Katarina Kulhankova, Kyle J Kinney, Jessica M Stach, Françoise A Gourronc, Isabella M Grumbach, Aloysius J Klingelhutz, Wilmara Salgado-Pabón
Staphylococcus aureus infective endocarditis (IE) is a fast-progressing and tissue destructive infection of the cardiac endothelium. The superantigens (SAgs) toxic shock syndrome toxin-1 (TSST-1), staphylococcal enterotoxin C (SEC), and the enterotoxin gene cluster (egc) play a novel and essential role in the etiology of S. aureus IE. Recent studies indicate that SAgs act at the infection site to cause tissue pathology and promote vegetation growth. The underlying mechanism of SAg involvement has not been clearly defined...
December 11, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29229706/causal-evidence-for-learning-dependent-frontal-lobe-contributions-to-cognitive-control
#18
Paul S Muhle-Karbe, Jiefeng Jiang, Tobias Egner
The lateral prefrontal cortex (LPFC) plays a central role in the prioritization of sensory input based on task-relevance. Such top-down control of perception is of fundamental importance in goal-directed behavior, but can also be costly when deployed excessively, necessitating a mechanism that regulates control engagement to align it with changing environmental demands. We have recently introduced the "flexible control model," which explains this regulation as resulting from a self-adjusting reinforcement-learning mechanism that infers latent statistical structure in dynamic task environments to predict forthcoming states...
December 11, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29229705/proteolytic-processing-of-neurexins-by-presenilins-sustains-synaptic-vesicle-release
#19
Emilia Servián-Morilla, Estefanía Robles-Lanuza, Ana C Sánchez-Hidalgo, Rafael J Camacho-Garcia, Juan A Paez-Gomez, Fabiola Mavillard, Carlos A Saura, Amalia Martinez-Mir, Francisco G Scholl
Proteolytic processing of synaptic adhesion components can accommodate the function of synapses to activity-dependent changes. The adhesion system formed by Neurexins (Nrxns) and Neuroligins (Nlgns) bi-directionally orchestrate the function of pre- and postsynaptic terminals. Previous studies have shown that Presenilins (PS), components of the gamma-secretase complex frequently mutated in familial Alzheimer's disease, clear from glutamatergic terminals the accumulation of Neurexin C-terminal fragments (Nrxn-CTF) generated by ectodomain shedding...
December 11, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29229665/ras-and-the-plasma-membrane-a-complicated-relationship
#20
Yong Zhou, Priyanka Prakash, Alemayehu A Gorfe, John F Hancock
The primary site of Ras signal transduction is the plasma membrane (PM). On the PM, the ubiquitously expressed Ras isoforms, H-, N-, and K-Ras, spatially segregate to nonoverlapping nanometer-sized domains, called nanoclusters, with further lateral segregation into nonoverlapping guanosine triphosphate (GTP)-bound and guanosine diphosphate (GDP)-bound nanoclusters. Effector binding and activation is restricted to GTP nanoclusters, rendering the underlying assembly mechanism essential to Ras signaling. Ras nanoclusters have distinct lipid compositions as a result of lipid-sorting specificity encoded in each Ras carboxy-terminal membrane anchor...
December 11, 2017: Cold Spring Harbor Perspectives in Medicine
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