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https://www.readbyqxmd.com/read/28316106/chironomus-riparius-diptera-genome-sequencing-reveals-the-impact-of-minisatellite-transposable-elements-on-population-divergence
#1
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
#2
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...
March 13, 2017: Developmental Psychobiology
https://www.readbyqxmd.com/read/28285351/cavin-3-prkcdbp-deficiency-reduces-the-density-of-caveolae-in-smooth-muscle
#3
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
#4
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
#5
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
#6
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
#7
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...
February 28, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/28131315/retrieving-chromatin-patterns-from-deep-sequencing-data-using-correlation-functions
#15
Jana Molitor, Jan-Philipp Mallm, Karsten Rippe, Fabian Erdel
Epigenetic modifications and other chromatin features partition the genome on multiple length scales. They define chromatin domains with distinct biological functions that come in sizes ranging from single modified DNA bases to several megabases in the case of heterochromatic histone modifications. Due to chromatin folding, domains that are well separated along the linear nucleosome chain can form long-range interactions in three-dimensional space. It has now become a routine task to map epigenetic marks and chromatin structure by deep sequencing methods...
February 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28117558/microstructured-blood-vessel-surrogates-reveal-structural-tropism-of-motile-malaria-parasites
#16
Mendi J Muthinja, Johanna Ripp, Janina K Hellmann, Tamas Haraszti, Noa Dahan, Leandro Lemgruber, Anna Battista, Lucas Schütz, Oliver T Fackler, Ulrich S Schwarz, Joachim P Spatz, Friedrich Frischknecht
Plasmodium sporozoites, the highly motile forms of the malaria parasite, are transmitted naturally by mosquitoes and traverse the skin to find, associate with, and enter blood capillaries. Research aimed at understanding how sporozoites select blood vessels is hampered by the lack of a suitable experimental system. Arrays of uniform cylindrical pillars can be used to study small cells moving in controlled environments. Here, an array system displaying a variety of pillars with different diameters and shapes is developed in order to investigate how Plasmodium sporozoites associate to the pillars as blood vessel surrogates...
January 24, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28077628/the-creatininase-homolog-mfte-from-mycobacterium-smegmatis-catalyzes-a-peptide-cleavage-reaction-in-the-biosynthesis-of-a-novel-ribosomally-synthesized-post-translationally-modified-peptide-ripp
#17
Nathan A Bruender, Vahe Bandarian
Most ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are processed by tailoring enzymes to create complex natural products that are still recognizably peptide-based. However, some tailoring enzymes dismantle the peptide en route to synthesis of small molecules. A small molecule natural product of as yet unknown structure, mycofactocin, is thought to be synthesized in this way via the mft gene cluster found in many strains of mycobacteria. This cluster harbors at least six genes, which appear to be conserved across species...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28059275/development-and-characterization-of-high-suppression-and-high-%C3%A3-tendue-narrowband-spectral-filters
#18
Adam Kinos, Qian Li, Lars Rippe, Stefan Kröll
The present work addresses critical issues in constructing high suppression, narrowband spectral filters in rare-earth-ion-doped crystals, mainly targeting the application of ultrasound optical tomography but is also applicable for areas such as quantum memories, self-filtering of laser frequencies, and other applications relying on high absorption in rare-earth-ion-doped crystals. The polarization of light transmitted through a highly absorbing crystal is experimentally analyzed. Additionally, an existing wave propagation method is used to simulate beam propagation through a spectral hole to study the high étendue requirements of ultrasound optical tomography...
December 20, 2016: Applied Optics
https://www.readbyqxmd.com/read/28057678/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#19
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28051889/race-ethnicity-in-medical-education-an-analysis-of-a-question-bank-for-step-1-of-the-united-states-medical-licensing-examination
#20
Kelsey Ripp, Lundy Braun
Phenomenon: There is growing concern over racial/ethnic bias in clinical care, yet how best to reduce bias remains challenging, in part because the sources of bias in medical education are poorly understood. One possible source is the routinized use of race/ethnicity in lectures, assessment, and preparatory materials, including question banks for licensing examinations. Because students worldwide use question banks to prepare for the United States Medical Licensing Examination, we examined how race/ethnicity was used in one of the most commonly recommended question banks...
January 4, 2017: Teaching and Learning in Medicine
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