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https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#1
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28230657/stabilized-hiv-1-envelope-glycoprotein-trimers-for-vaccine-use
#2
Max Medina-Ramírez, Rogier W Sanders, Quentin J Sattentau
PURPOSE OF REVIEW: To provide an update on the latest developments in the field of HIV-1 antibody-based soluble envelope glycoprotein (Env) trimer design for vaccine use. RECENT FINDINGS: The development of soluble native-like HIV-1 Env trimer immunogens has moved the field of antibody-based vaccine design forward dramatically over the past few years with refinement of various stabilizing approaches. However, despite this progress, significant challenges remain...
February 21, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28230557/comparison-of-the-conventional-dresden-protocol-and-accelerated-protocol-with-higher-ultraviolet-intensity-in-corneal-collagen-cross-linking-for-keratoconus
#3
Moonjung Choi, Jiwon Kim, Eung Kweon Kim, Kyoung Yul Seo, Tae-Im Kim
PURPOSE: To compare the accelerated corneal cross-linking (CXL) protocol and the conventional Dresden protocol in patients with keratoconus in terms of visual acuity, keratometric values, and topographic parameters. METHODS: Twenty-eight eyes of 25 patients with primary keratoconus were divided into 2 groups; 15 eyes in group 1 received CXL under the standard Dresden protocol (3 mW/cm for 30 min, dose 5.4 J/cm) and 13 eyes in group 2 were treated with the accelerated protocol (30 mW/cm for 3 min 40 s, dose 6...
February 22, 2017: Cornea
https://www.readbyqxmd.com/read/28228794/prompt-clinical-and-biochemical-response-to-denosumab-in-a-young-adult-patient-with-craniofacial-fibrous-dysplasia
#4
Cristina Eller-Vainicher, Diego Sergio Rossi, Giuseppe Guglielmi, Giada Anna Beltramini, Elisa Cairoli, Antonio Russillo, Giovanna Mantovani, Anna Spada, Iacopo Chiodini
BACKGROUND: We report on the clinical and biochemical outcomes in a 20-year-old male suffering from active craniofacial monostotic fibrous dysplasia (MFD) of the left mandible treated with the RANK-L inhibitor, denosumab, following unsatisfactory responses to prior long-term bisphosphonates therapy. RESULTS: The patient had been treated over 9 years with pamidronate (cumulative dose of 810 mg) with incomplete control of pain. Following initiation of denosumab 60 mg subcutaneously, bone pain and bone turnover markers (osteocalcin, total and bone alkaline phosphatase and carboxy-terminal cross-linking telopeptide of type I collagen) were monitored over a 27 months period...
September 2016: Clinical Cases in Mineral and Bone Metabolism
https://www.readbyqxmd.com/read/28228782/safety-and-effectiveness-of-teriparatide-vs-alendronate-in-postmenopausal-osteoporosis-a-prospective-non-randomized-clinical-study
#5
Gianfilippo Caggiari, Paolo Tranquilli Leali, Giulia Raffaella Mosele, Leonardo Puddu, Francesca Badessi, Carlo Doria
In this work we study the safety and effectiveness of teriparatide and alendronate in patients with postmenopausal osteoporosis at high risk of fracture; it was a double-blinded and it was done by examining the comparisons between teriparatide 20 μg/day and alendronate 10 mg/day. Safety and effectiveness analyses were based on data from 355 woman with a mean age of 68 years. Two groups (A and B) with T-score ≤-2.5 at bone mineral density were analyzed and 3 or more vertebral fractures on radiograph. Group A: was treated with teriparatide 20 μg/day and composed from 182 women, in post-menopausal age, without a history of cancer...
September 2016: Clinical Cases in Mineral and Bone Metabolism
https://www.readbyqxmd.com/read/28228013/highly-efficient-and-safe-delivery-of-vegf-sirna-by-bio-reducible-fluorinated-peptide-dendrimers-for-cancer-therapy
#6
Xiaojun Cai, Haofang Zhu, Yanmei Zhang, Zhongwei Gu
RNA interference (RNAi) hold great promise in treating a wide range of diseases. However, it remains highly desirable to develop new delivery systems to circumvent complex extra- and intracellular barriers for successful clinical translation. Here, we report on a versatile polymeric vector, bio-reducible fluorinated peptide dendrimers (BFPD), for highly efficient and safe delivery of siRNA. In virtue of skillfully integrated all of the unique features of reversible cross-linking, fluorination and peptide dendrimers, this novel vector can surmount almost all extra- and intracellular barriers associated with local siRNA delivery through highly improved physiological stability and serum resistance, significantly increased intratumoral enrichment, cellular uptake, as well as successful facilitation of endosomal escape and cytosolic siRNA release...
February 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28226245/subconjunctival-injectable-dendrimer-dexamethasone-gel-for-the-treatment-of-corneal-inflammation
#7
Uri Soiberman, Siva P Kambhampati, Tony Wu, Manoj K Mishra, Yumin Oh, Rishi Sharma, Jiangxia Wang, Abdul Elah Al Towerki, Samuel Yiu, Walter J Stark, Rangaramanujam M Kannan
Corneal inflammation is often encountered as a key pathological event in many corneal diseases. Current treatments involve topical corticosteroids which require frequent instillations due to rapid tear turnover, causing side-effects such as corneal toxicity and elevated intraocular pressure (IOP). Hence, new interventions that can reduce side effects, dosing frequency, and increase patient compliance can be highly beneficial. In this study, we explore a subconjunctival injectable gel based on G4-PAMAM dendrimer and hyaluronic acid, cross-linked using thiol-ene click chemistry, incorporated with dendrimer dexamethasone (D-Dex) conjugates as a potential strategy for sustained delivery and enhanced bioavailability of corticosteroids...
February 16, 2017: Biomaterials
https://www.readbyqxmd.com/read/28225908/intimate-partner-violence-reported-by-female-and-male-users-of-healthcare-units
#8
Claudia Renata Dos Santos Barros, Lilia Blima Schraiber
OBJECTIVE: To analyze nonfatal violence suffered and committed by adult men and women, in an intimate relationship. METHODS: The participants in the research were women aged between 15 and 49 years and men between 18 and 60 years, interviewed by face-to-face questionnaire application. The sample selection was of consecutive type, according to the order of arrival of the users. We conducted temporarily independent investigations and covered different health services to avoid couples and relationships in which the retaliation could be overvalued...
February 16, 2017: Revista de Saúde Pública
https://www.readbyqxmd.com/read/28224892/construction-and-in-vitro-evaluation-of-enzyme-nanoreactors-based-on-carboxymethyl-chitosan-for-arginine-deprivation-in-cancer-therapy
#9
Tian Zeng, Yi Zhang, Qiongjiao Yan, Zhijun Huang, Ling Zhang, Xiaozhe Yi, Junrong Chen, Guanghua He, Yihua Yin
In this study, a pH-induced morphological transition from micelles to vesicles for an amphiphilic photo cross-linkable biocopolymer (Az-NaCMCS), synthesized by mixing azidobenzaldehyde (Az) and an aqueous solution of carboxymethyl chitosan sodium salt (NaCMCS), was used for encapsulation of l-arginine deiminase (ADI). The aqueous solution of enzyme-loaded vesicles obtained was followed by UV-irradiation to result in shell cross-linked enzyme nanoreactors. The nanoreactors were characterized by TEM and DLS. Its encapsulation efficiency and loading capacity were determined...
April 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28224886/alginate-hydrogels-modified-with-low-molecular-weight-hyaluronate-for-cartilage-regeneration
#10
Honghyun Park, Hyun Ji Lee, Hyoseok An, Kuen Yong Lee
Alginate is a typical biomaterial that forms hydrogels in the presence of calcium ions and has often been utilized in tissue engineering approaches. However, it lacks biofunctionality in the form of interactions with cells and proteins. Hyaluronate, a main component of glycosaminoglycans, provides CD44-specific interactions with chondrocytes but typically requires chemical cross-linking agents to fabricate hydrogels, which may cause unexpected side effects in the body. In this study, we propose the design and fabrication of a hybrid structure of alginate and hyaluronate useful for cartilage regeneration...
April 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28224499/finding-rna-protein-interaction-sites-using-hmms
#11
Tao Wang, Jonghyun Yun, Yang Xie, Guanghua Xiao
RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Several Hidden Markov model-based (HMM) approaches have been suggested to identify protein-RNA binding sites from CLIP-Seq datasets. In this chapter, we describe how HMM can be applied to analyze CLIP-Seq datasets, including the bioinformatics preprocessing steps to extract count information from the sequencing data before HMM and the downstream analysis steps following peak-calling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224220/calcium-intake-in-winter-pregnancy-attenuates-impact-of-vitamin-d-inadequacy-on-urine-ntx-a-marker-of-bone-resorption
#12
Eileen C O'Brien, Mark T Kilbane, Malachi J McKenna, Ricardo Segurado, Aisling A Geraghty, Fionnuala M McAuliffe
PURPOSE: Pregnancy is characterised by increased bone turnover, but high bone turnover with resorption exceeding formation may lead to negative maternal bone remodelling. Recent studies are conflicting regarding the effect of calcium on skeletal health in pregnancy. The aim of this study was to examine the seasonal effect of serum 25-hydroxyvitamin D (25OHD) and dietary calcium on a marker of bone resorption. METHODS: This was prospective study of 205 pregnant women [two cohorts; early pregnancy at 13 weeks (n = 96), and late pregnancy at 28 weeks (n = 109)]...
February 21, 2017: European Journal of Nutrition
https://www.readbyqxmd.com/read/28224143/ara-h-2-cross-linking-catalyzed-by-mtgase-decreases-its-allergenicity
#13
Zhihua Wu, Jun Lian, Ruifang Zhao, Kun Li, Xin Li, Anshu Yang, Ping Tong, Hongbing Chen
Peanuts, whose major allergen is Ara h 2, are included among the eight major food allergens. After reduction using dithiothreitol (DTT), cross-linking of Ara h 2 could be catalyzed by microbial transglutaminase (MTGase), a widely used enzyme in the food industry. In this study, Ara h 2 cross-linking was catalyzed by MTGase after it was reduced by DTT. Using mass spectrometry and PLINK software, five cross-linkers were identified, and five linear allergen epitopes were found to be involved in the reactions. The IgE binding capacity of cross-linked Ara h 2 was found to be significantly lower compared to that of native and reduced Ara h 2...
February 22, 2017: Food & Function
https://www.readbyqxmd.com/read/28223526/hypermutation-signature-reveals-a-slippage-and-realignment-model-of-translesion-synthesis-by-rev3-polymerase-in-cisplatin-treated-yeast
#14
Romulo Segovia, Yaoqing Shen, Scott A Lujan, Steven J M Jones, Peter C Stirling
Gene-gene or gene-drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. Using Saccharomyces cerevisiae and focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223511/a-signal-sequence-suppressor-mutant-that-stabilizes-an-assembled-state-of-the-twin-arginine-translocase
#15
Qi Huang, Felicity Alcock, Holger Kneuper, Justin C Deme, Sarah E Rollauer, Susan M Lea, Ben C Berks, Tracy Palmer
The twin-arginine protein translocation (Tat) system mediates transport of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of chloroplasts. The Tat system of Escherichia coli is made up of TatA, TatB, and TatC components. TatBC comprise the substrate receptor complex, and active Tat translocases are formed by the substrate-induced association of TatA oligomers with this receptor. Proteins are targeted to TatBC by signal peptides containing an essential pair of arginine residues...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223504/transcriptome-wide-microrna-and-target-dynamics-in-the-fat-body-during-the-gonadotrophic-cycle-of-aedes-aegypti
#16
Xiufeng Zhang, Emre Aksoy, Thomas Girke, Alexander S Raikhel, Fedor V Karginov
The mosquito Aedes aegypti is a major vector of numerous viral diseases, because it requires a blood meal to facilitate egg development. The fat body, a counterpart of mammalian liver and adipose tissues, is the metabolic center, playing a key role in reproduction. Therefore, understanding of regulatory networks controlling its functions is critical, and the role of microRNAs (miRNAs) in the process is largely unknown. We aimed to explore miRNA expression and potential targets in the female fat body of Ae. aegypti, as well as their changes postblood meal (PBM)...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223211/sensitizing-exposure-to-amphetamine-increases-ampa-receptor-phosphorylation-without-increasing-cell-surface-expression-in-the-rat-nucleus-accumbens
#17
Qiang Wang, Dongdong Li, Nancy Bubula, Matthew R Campioni, Daniel S McGehee, Paul Vezina
Exposure to psychostimulants like cocaine or amphetamine leads to long-lasting sensitization of their behavioral and neurochemical effects. Here we characterized changes in AMPA receptor distribution and phosphorylation state in the rat nucleus accumbens (NAcc) weeks after amphetamine exposure to assess their potential contribution to sensitization by this drug. Using protein cross-linking, biochemical, subcellular fractionation, and slice electrophysiological approaches in the NAcc, we found that, unlike cocaine, previous exposure to amphetamine did not increase cell surface levels of either GluA1 or GluA2 AMPA receptor subunits, redistribution of these subunits to the synaptic or perisynaptic cellular membrane domains, protein-protein associations required to support the accumulation and retention of AMPA receptors in the PSD, or the peak amplitude of AMPA receptor mediated mEPSCs recorded in NAcc slices...
February 18, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28222617/presynaptic-calmodulin-targets-lessons-from-structural-proteomics
#18
Noa Lipstein, Melanie Göth, Christine Piotrowski, Kevin Pagel, Andrea Sinz, Olaf Jahn
Calmodulin (CaM) is a highly conserved Ca(2+)-binding protein that is exceptionally abundant in the brain. In the presynaptic compartment of neurons, CaM transduces changes in Ca(2+) concentration into the regulation of synaptic transmission dynamics. Areas covered: We review selected literature including published CaM interactor screens and outline established and candidate presynaptic CaM targets. We present a workflow of biochemical and structural proteomic methods that were used to identify and characterize the interactions between CaM and Munc13 proteins...
March 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28221772/desleucyl-oritavancin-with-a-damaged-d-ala-d-ala-binding-site-inhibits-the-transpeptidation-step-of-cell-wall-biosynthesis-in-whole-cells-of-staphylococcus-aureus
#19
Sung Joon Kim, Manmilan Singh, Shasad Sharif, Jacob Schaefer
We have used solid-state NMR to characterize the exact nature of the dual mode of action of oritavancin in preventing cell-wall assembly in Staphylococcus aureu. Measurements performed on whole cells labeled selectively in vivo have established that des-N-methylleucyl-N-4-(4-fluorophenyl)benzyl-chloroeremomycin, an Edman degradation product of [19F]oritavancin, which has a damaged D-Ala-D-Ala binding aglycon, is a potent inhibitor of the transpeptidase activity of cell-wall biosynthesis. The desleucyl-drug binds to partially cross-linked peptidoglycan by a cleft formed between the drug aglycon and its biphenyl hydrophobic sidechain...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28220890/clinical-investigation-of-the-posterior-scleral-contraction-to-treat-macular-traction-maculopathy-in-highly-myopic-eyes
#20
An-Peng Pan, Ting Wan, Shuang-Qian Zhu, Liang Dong, An-Quan Xue
Myopic traction maculopathy (MTM) can cause vision disabilities in highly myopic eyes. This retrospective case series investigated the clinical outcomes of posterior scleral contraction (PSC) using genipin-cross-linked sclera as the material to treat MTM in highly myopic eyes. In total, 32 eyes from 29 highly myopic patients who underwent PSC for MTM were recruited. The changes in best-corrected visual acuity (BCVA) and axial length were evaluated, macular reattachment and macular hole (MH) closure was assessed by optical coherence tomography, and complications were evaluated...
February 21, 2017: Scientific Reports
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