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https://www.readbyqxmd.com/read/28424207/a-distributed-solute-model-an-extended-two-pore-model-with-application-to-the-glomerular-sieving-of-ficoll
#1
Carl M Öberg, Joseph J Groszek, Shuvo Roy, William H Fissell, Bengt Rippe
One of the many unresolved questions regarding the permeability of the glomerular filtration barrier is the reason behind the marked difference in permeability between albumin and polysaccharide probe molecules such as Ficoll and dextran of the same molecular size. Although the differences in permeability have been mainly attributed to charge effects, we have previously shown that this would require a highly charged filtration barrier, having a charge density that is ~10 times more than that on the albumin molecule...
April 19, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28406749/nucleosome-repositioning-during-differentiation-of-a-human-myeloid-leukemia-cell-line
#2
Vladimir B Teif, Jan-Philipp Mallm, Tanvi Sharma, David B Mark Welch, Karsten Rippe, Roland Eils, Jörg Langowski, Ada L Olins, Donald E Olins
Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope)...
March 4, 2017: Nucleus
https://www.readbyqxmd.com/read/28402732/different-methods-for-inlay-production-effect-on-internal-and-marginal-adaptation-adjustment-time-and-contact-point
#3
M P Rippe, C Monaco, L Volpe, M A Bottino, R Scotti, L F Valandro
The aim of this study was to evaluate the effect of different production methods of resin and ceramic inlays on marginal and internal adaptation, adjustment time, and proximal contacts. Forty premolars were selected, embedded (their roots), and prepared to receive inlays that were made as follows (n=10): LaRe-digital impression with a Lava C.O.S. scanner, followed by milling of Lava Ultimate block (composite resin) in a milling center; CeRe-digital impression with a Cerec 3D Bluecam scanner, followed by milling of Lava Ultimate block in Cerec; CeDis-digital impression with a Cerec 3D Bluecam scanner, followed by milling of IPS e...
April 12, 2017: Operative Dentistry
https://www.readbyqxmd.com/read/28399420/dietary-rose-hip-exerts-antiatherosclerotic-effects-and-increases-nitric-oxide-mediated-dilation-in-apoe-null-mice
#4
Michele Cavalera, Ulrika Axling, Catarina Rippe, Karl Swärd, Cecilia Holm
Atherosclerosis is a disease in which atheromatous plaques develop inside arteries, leading to reduced or obstructed blood flow that in turn may cause stroke and heart attack. Rose hip is the fruit of plants of the genus Rosa, belonging to the Rosaceae family, and it is rich in antioxidants with high amounts of ascorbic acid and phenolic compounds. Several studies have shown that fruits, seeds and roots of these plants exert antidiabetic, antiobesity and cholesterol-lowering effects in rodents as well as humans...
March 21, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28358161/post-translational-modifications-involved-in-the-biosynthesis-of-thiopeptide-antibiotics
#5
REVIEW
Qingfei Zheng, Hui Fang, Wen Liu
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins...
April 18, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28348006/gabab-receptor-attenuation-of-gabaa-currents-in-neurons-of-the-mammalian-central-nervous-system
#6
Wen Shen, Changlong Nan, Peter T Nelson, Harris Ripps, Malcolm M Slaughter
Ionotropic receptors are tightly regulated by second messenger systems and are often present along with their metabotropic counterparts on a neuron's plasma membrane. This leads to the hypothesis that the two receptor subtypes can interact, and indeed this has been observed in excitatory glutamate and inhibitory GABA receptors. In both systems the metabotropic pathway augments the ionotropic receptor response. However, we have found that the metabotropic GABAB receptor can suppress the ionotropic GABAA receptor current, in both the in vitro mouse retina and in human amygdala membrane fractions...
March 2017: Physiological Reports
https://www.readbyqxmd.com/read/28316106/chironomus-riparius-diptera-genome-sequencing-reveals-the-impact-of-minisatellite-transposable-elements-on-population-divergence
#7
Ann-Marie Oppold, Hanno Schmidt, Marcel Rose, Sören Lukas Hellmann, Florian Dolze, Fabian Ripp, Bettina Weich, Urs Schmidt-Ott, Erwin Schmidt, Robert Kofler, Thomas Hankeln, Markus Pfenninger
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28295227/mild-perinatal-adversities-moderate-the-association-between-maternal-harsh-parenting-and-hair-cortisol-evidence-for-differential-susceptibility
#8
Dafna A Windhorst, Ralph C A Rippe, Viara R Mileva-Seitz, Frank C Verhulst, Vincent W V Jaddoe, Gerard Noppe, Elisabeth F C van Rossum, Erica L T van den Akker, Henning Tiemeier, Marinus H van IJzendoorn, Marian J Bakermans-Kranenburg
It has been shown that following exposure to mild perinatal adversity, children have greater susceptibility to both the negative and positive aspects of their subsequent environment. In a large population-based cohort study (N = 1,776), we investigated whether mild perinatal adversity moderated the association between maternal harsh parenting and children's hair cortisol levels, a biomarker of chronic stress. Mild perinatal adversity was defined as late preterm birth (gestational age at birth of 34-37 weeks, 6 days) or small for gestational age (birth weight between the 2...
April 2017: Developmental Psychobiology
https://www.readbyqxmd.com/read/28285351/cavin-3-prkcdbp-deficiency-reduces-the-density-of-caveolae-in-smooth-muscle
#9
Baoyi Zhu, Karl Swärd, Mari Ekman, Bengt Uvelius, Catarina Rippe
Cavins belong to a family of proteins that contribute to the formation of caveolae, which are membrane organelles with functional roles in muscle and fat. Here, we investigate the effect of cavin-3 ablation on vascular and urinary bladder structure and function. Arteries and urinary bladders from mice lacking cavin-3 (knockout: KO) and from controls (wild type: WT) were examined. Our studies revealed that the loss of cavin-3 resulted in ∼40% reduction of the caveolae protein cavin-1 in vascular and bladder smooth muscle...
March 11, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28278164/rosiglitazone-drives-cavin-2-sdpr-expression-in-adipocytes-in-a-cebp%C3%AE-dependent-manner
#10
Björn Hansson, Catarina Rippe, Dorota Kotowska, Sebastian Wasserstrom, Johanna Säll, Olga Göransson, Karl Swärd, Karin G Stenkula
Caveolae are abundant adipocyte surface domains involved in insulin signaling, membrane trafficking and lipid homeostasis. Transcriptional control mechanisms for caveolins and cavins, the building blocks of caveolae, are thus arguably important for adipocyte biology and studies in this area may give insight into insulin resistance and diabetes. Here we addressed the hypothesis that one of the less characterized caveolar components, cavin-2 (SDPR), is controlled by CCAAT/Enhancer Binding Protein (CEBPα) and Peroxisome Proliferator-Activated Receptor Gamma (PPARG)...
2017: PloS One
https://www.readbyqxmd.com/read/28260651/ribosomally-synthesized-and-post-translationally-modified-peptide-natural-product-discovery-in-the-genomic-era
#11
REVIEW
Kenton J Hetrick, Wilfred A van der Donk
In the past 15 years, the cost of sequencing a genome has plummeted. Consequently, the number of sequenced bacterial genomes has exponentially increased, and methods for natural product discovery have evolved rapidly to take advantage of the wealth of genomic data. This review highlights applications of genome mining software to compare and organize large-scale data sets and methods for identifying unique biosynthetic pathways amongst the thousands of ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters...
March 2, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28256131/ycao-dependent-posttranslational-amide-activation-biosynthesis-structure-and-function
#12
Brandon J Burkhart, Christopher J Schwalen, Greg Mann, James H Naismith, Douglas A Mitchell
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products...
March 3, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28244986/a-new-genome-mining-tool-redefines-the-lasso-peptide-biosynthetic-landscape
#13
Jonathan I Tietz, Christopher J Schwalen, Parth S Patel, Tucker Maxson, Patricia M Blair, Hua-Chia Tai, Uzma I Zakai, Douglas A Mitchell
Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides...
May 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#14
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#15
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196481/nuctools-analysis-of-chromatin-feature-occupancy-profiles-from-high-throughput-sequencing-data
#16
Yevhen Vainshtein, Karsten Rippe, Vladimir B Teif
BACKGROUND: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28195477/enzymatic-n-and-c-protection-in-cyanobactin-ripp-natural-products
#17
Debosmita Sardar, Yue Hao, Zhenjian Lin, Maho Morita, Satish K Nair, Eric W Schmidt
Recent innovations in peptide natural product biosynthesis reveal a surprising wealth of previously uncharacterized biochemical reactions that have potential applications in synthetic biology. Among these, the cyanobactins are noteworthy because these peptides are protected at their N- and C-termini by macrocyclization. Here, we use a novel bifunctional enzyme AgeMTPT to protect linear peptides by attaching prenyl and methyl groups at their free N- and C-termini. Using this peptide protectase in combination with other modular biosynthetic enzymes, we describe the total synthesis of the natural product aeruginosamide B and the biosynthesis of linear cyanobactin natural products...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28165449/dissection-of-goadsporin-biosynthesis-by-in-vitro-reconstitution-leading-to-designer-analogues-expressed-in-vivo
#18
Taro Ozaki, Kona Yamashita, Yuki Goto, Morito Shimomura, Shohei Hayashi, Shumpei Asamizu, Yoshinori Sugai, Haruo Ikeda, Hiroaki Suga, Hiroyasu Onaka
Goadsporin (GS) is a member of ribosomally synthesized and post-translationally modified peptides (RiPPs), containing an N-terminal acetyl moiety, six azoles and two dehydroalanines in the peptidic main chain. Although the enzymes involved in GS biosynthesis have been defined, the principle of how the respective enzymes control the specific modifications remains elusive. Here we report a one-pot synthesis of GS using the enzymes reconstituted in the 'flexible' in vitro translation system, referred to as the FIT-GS system...
February 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28165313/colonoscopic-and-histologic-features-of-rectal-masses-in-dogs-82-cases-1995-2012
#19
Krista N Adamovich-Rippe, Philipp D Mayhew, Stanley L Marks, Laura E Selmic, William T N Culp, Angela M Youello, Jeffrey J Runge, David E Holt, Philip H Kass, John R Peauroi
OBJECTIVE To evaluate colonoscopic and histologic features of rectal masses in dogs. DESIGN Retrospective case series. ANIMALS 82 client-owned dogs with rectal masses that underwent colonoscopy. PROCEDURES Medical records of dogs with rectal masses that underwent colonoscopy were reviewed. History, signalment, clinical signs, results of physical examination, diagnostic imaging findings, and results of colonoscopy (including complications) were recorded. When available, tissue samples obtained during colonoscopy and by means of surgical biopsy were reviewed by a single board-certified pathologist...
February 15, 2017: Journal of the American Veterinary Medical Association
https://www.readbyqxmd.com/read/28135077/mechanistic-understanding-of-lanthipeptide-biosynthetic-enzymes
#20
Lindsay M Repka, Jonathan R Chekan, Satish K Nair, Wilfred A van der Donk
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that display a wide variety of biological activities, from antimicrobial to antiallodynic. Lanthipeptides that display antimicrobial activity are called lantibiotics. The post-translational modification reactions of lanthipeptides include dehydration of Ser and Thr residues to dehydroalanine and dehydrobutyrine, a transformation that is carried out in three unique ways in different classes of lanthipeptides. In a cyclization process, Cys residues then attack the dehydrated residues to generate the lanthionine and methyllanthionine thioether cross-linked amino acids from which lanthipeptides derive their name...
January 30, 2017: Chemical Reviews
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