Analysis of Biological Noise in an Organelle Size Control System
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Agarose Gel Electrophoresis
Laboratory for Environmental Pathogen Research Department of Environmental Sciences University of Toledo Agarose gel electrophoresis Background information Agarose gel electrophoresis of DNA is used to determine the presence and distinguish the type of nucleic acids obtained after extraction and to analyze restriction digestion products. Desired DNA fragments can be physically isolated for various purposes such as sequencing, probe preparation, or for cloning fragments into other vectors. Both agarose and polyacrylamide gels are used for DNA analysis. Agarose gels are usually run to size larger fragments (greater than 200 bp) and polyacrylamide gels are run to size fragments less than 200 bp. Typically agarose gels are used for most purposes and polyacrylamide gels are used when small fragments, such as digests of 16S rRNA genes, are being distinguished. There are also specialty agaroses made by FMC (e.g., Metaphor) for separating small fragments. Regular agarose gels may range in concentration from 0.6 to 3.0%. Pouring gels at less or greater than these percentages presents handling problems (e.g., 0.4% agarose for genomic DNA partial digests requires a layer of supporting 0.8% gel). For normal samples make agarose gels at 0.7%. The chart below illustrates the optimal concentrations for fragment size separation. The values listed are approximate and can vary depending on the reference that is used. If you do not know your fragment sizes then the best approach is to start with a 0.7% gel and change subsequently if the desired separation is not achieved. Nucleic acids must be stained prior to visualization. Most laboratories use ethidium bromide but other stains (e.g., SYBR green, GelStar) are available. -
Size Changes in Eukaryotic Ribosomes
Proc. Nat. Acad. Sci. USA Vol. 68, No. 12, pp. 3021-3025, December 1971 Size Changes in Eukaryotic Ribosomes (diffusion constant/sedimentation constant/ribosomal dissociation/chick embryo) JOHN VOURNAKIS AND ALEXANDER RICH Department of Biology, Massachusetts Institute of Technology, Cambridge, Mass. 02139 Contributed by Alexander Rich, September 20, 1971 ABSTRACT Evidence is presented that ribosomes two particles are similar. However, these changes suggest active in protein synthesis and attached to messenger that when the ribosome is attached to messenger RNA it has a RNA on polysomes have a smaller diameter than free cytoplasmic single ribosomes. Measurements have been smaller diameter than is found for the free cytoplastic ribo- made on these two types of ribosomes of differences in some. This more compact form of the ribosome is maintained sedimentation velocity and diffusion constant. Differences even when the nascent polypeptide chain is relased by puro- in these quantities suggest about a 20-A decrease in the mycin. We thus infer that there are substantial differences diameter of the ribosomes from chick embryo muscles in the interactions between the ribosomal subunits when when they are attached to messenger RNA. Similar dif- they ferences are also observed in rabbit reticulocytes and are attached to messenger RNA as compared to the free cyto- mouse ascites tumor cells. These two ribosomal states plasmic single ribosome, which is inactive in protein synthesis. have different sensitivity to Pronase digestion and dis- sociate into ribosomal subunits at different KCI concen- METHODS AND MATERIALS trations. This size difference is not associated with a sig- nificant difference in overall ribosomal mass and appears Preparation of Ribosomes. -
Development and Optimization of Organic Based Monoliths for Use in Affinity Chromatography
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Student Research Projects, Dissertations, and Theses - Chemistry Department Chemistry, Department of Winter 12-2-2011 Development and Optimization of Organic Based Monoliths for Use in Affinity Chromatography Erika L. Pfaunmiller University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/chemistrydiss Part of the Analytical Chemistry Commons Pfaunmiller, Erika L., "Development and Optimization of Organic Based Monoliths for Use in Affinity Chromatography" (2011). Student Research Projects, Dissertations, and Theses - Chemistry Department. 28. https://digitalcommons.unl.edu/chemistrydiss/28 This Article is brought to you for free and open access by the Chemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Student Research Projects, Dissertations, and Theses - Chemistry Department by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. DEVELOPMENT AND OPTIMIZATION OF ORGANIC BASED MONOLITHS FOR USE IN AFFINITY CHROMATOGRAPHY by Erika L. Pfaunmiller A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfilment of Requirements For the Degree of Master of Science Major: Chemistry Under the Supervision of Professor David S. Hage Lincoln, Nebraska December, 2011 DEVELOPMENT AND OPTIMIZATION OF ORGANIC BASED MONOLITHS FOR USE IN AFFINITY CHROMATOGRAPHY Erika L. Pfaunmiller, M.S. University of Nebraska, 2011 Adviser: David S. Hage Affinity chromatography is an important and useful tool for studying biological interactions, such as the binding of an antibody with an antigen. Monolithic supports offer many advantages over traditional packed bed supports in affinity chromatography, including their ease of preparation, low back pressures and good mass transfer properties. -
Biomems Literature by Year Prof
BioMEMS Literature by Year Prof. Steven S. Saliterman 1. Xu M, Obodo D, Yadavalli VK. The design, fabrication, and applications of flexible bio- sensing devices. Biosensors & Bioelectronics. 2019;124:96-114. 2. Wongkaew N, Simsek M, Griesche C, Baeumner AJ. Functional Nanomaterials and Nanostructures Enhancing Electrochemical Biosensors and Lab-on-a-Chip Performances: Recent Progress, Applications, and Future Perspective. Chemical Reviews. 2019;119(1):120-194. 3. Wang MH, Yin HS, Zhou YL, et al. Photoelectrochemical biosensor for microRNA detec- tion based on a MoS2/g-C3N4/black TiO2 heterojunction with Histostar@AuNPs for signal amplification. Biosensors & Bioelectronics. 2019;128:137-143. 4. Wang JS, Hui N. Electrochemical functionalization of polypyrrole nanowires for the de- velopment of ultrasensitive biosensors for detecting microRNA. Sensors and Actuators B-Chemical. 2019;281:478-485. 5. Sun EWL, Martin AM, Young RL, Keating DJ. The Regulation of Peripheral Metabolism by Gut-Derived Hormones. Frontiers in Endocrinology. 2019;9. 6. Soler M, Huertas CS, Lechuga LM. Label-free plasmonic biosensors for point-of-care di- agnostics: a review. Expert Review of Molecular Diagnostics. 2019;19(1):71-81. 7. Soler M, Huertas CS, Lechuga LM. Label-free plasmonic biosensors for point-of-care di- agnostics: a review. Expert Review of Molecular Diagnostics. 2019;19(1):71-81. 8. Sola L, Damin F, Chiari M. Array of multifunctional polymers for localized immobilization of biomolecules on microarray substrates. Analytica Chimica Acta. 2019;1047:188-196. 9. Seidi S, Ranjbar MH, Baharfar M, Shanehsaz M, Tajik M. A promising design of microflu- idic electromembrane extraction coupled with sensitive colorimetric detection for col- orless compounds based on quantum dots fluorescence. -
A Global Analysis of Enzyme Compartmentalization to Glycosomes
pathogens Article A Global Analysis of Enzyme Compartmentalization to Glycosomes Hina Durrani 1, Marshall Hampton 2 , Jon N. Rumbley 3 and Sara L. Zimmer 1,* 1 Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA; [email protected] 2 Mathematics & Statistics Department, University of Minnesota Duluth, Duluth, MN 55812, USA; [email protected] 3 College of Pharmacy, University of Minnesota, Duluth Campus, Duluth, MN 55812, USA; [email protected] * Correspondence: [email protected] Received: 25 March 2020; Accepted: 9 April 2020; Published: 12 April 2020 Abstract: In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. -
Cilia and Flagella: from Discovery to Disease Dylan J
Dartmouth Undergraduate Journal of Science Volume 20 Article 2 Number 1 Assembly 2017 Cilia and Flagella: From Discovery to Disease Dylan J. Cahill Dylan Cahill, [email protected] Follow this and additional works at: https://digitalcommons.dartmouth.edu/dujs Part of the Engineering Commons, Life Sciences Commons, Medicine and Health Sciences Commons, Physical Sciences and Mathematics Commons, and the Social and Behavioral Sciences Commons Recommended Citation Cahill, Dylan J. (2017) "Cilia and Flagella: From Discovery to Disease," Dartmouth Undergraduate Journal of Science: Vol. 20 : No. 1 , Article 2. Available at: https://digitalcommons.dartmouth.edu/dujs/vol20/iss1/2 This Research Article is brought to you for free and open access by the Student-led Journals and Magazines at Dartmouth Digital Commons. It has been accepted for inclusion in Dartmouth Undergraduate Journal of Science by an authorized editor of Dartmouth Digital Commons. For more information, please contact [email protected]. BIOLOGY Cilia and Flagella: FromCilia and Discovery Flagella: to Disease From Discovery to Disease BY DYLAN CAHILL ‘18 Introduction certain insect sperm fagella (3, 5, 6). A unique Figure 1: Chlamydomonas intracellular transport mechanism known as reinhardtii, a single-celled, bi- In 1674, peering through the lens of a crude flagellate green alga, viewed intrafagellar transport is responsible for the light microscope, Antoni van Leeuwenhoek with a scanning electron assembly and maintenance of these organelles Chlamydomonas observed individual living cells for the frst time microscope. is (3, 6). Cilia and fagella are primarily composed a model organism in flagellar in history (1). He noted long, thin appendages of the protein tubulin, which polymerizes into dynamics and motility studies. -
Product Specifications Agarose Hires Molecular Biology Grade
Product Specifications Electrophoresis Reagents, Buffers, Agarose, Polymerase Chain Reaction Custom Primers and Probes Hybridization and Detection Reagents Agarose HiRes Molecular Biology Grade Store at Room Temperature Catalog Number Description Size 40-3015-10 Agarose HiRes Ultra Pure Molecular Biology Grade 100 gms 40-3015-50 Agarose HiRes Ultra Pure Molecular Biology Grade 500 gms 40-3015-01 Agarose HiRes Ultra Pure Molecular Biology Grade 1 KG Product Description & Application Agarose HiRes is certified Ultra Pure molecular biology grade DNase and RNase-free agarose powder. It is specifically recommended for resolution of short fragments ranging in size between 20 bp and 800 bp and is an excellent substitute for polyacrylamide electrophoresis for resolution of short DNA fragments. HiRes Agarose is commonly used for electrophoretic resolution of fragments obtained from amplification of short tandem repeats (STR’s), di, tri and tetra-nucleotide repeats, and other polymorphic loci. Specifications Appearance White homegeous powder Gel strength of 1.5 % (w/v) gel >1680g / cm 2 Gel strength of 3 % (w/v) gel >3290g / cm 2 Gelling temperature 33-34°C Melting temperature 74°C EEO: 0.1-0.2 Moisture: <4% DNase and RNase None detected High Resolution Gel Electrophoresis of DNA Gene Link HiRes agarose is an intermediate melting temperature agarose (~74°C) that provides one of the finest resolutions for DNA fragments from STR, tri and tetra-nucleotide repeat amplification and other length based polymorphisms. Using a 2 – 4% gel (made in either TAE or TBE) it is possible to resolve fragments that are anywhere from 20 – 800 bp in length. A 4% HiRes agarose gel can differentiate a 99bp fragment from a 110 bp fragment running the gels at 45 mAmps at room temperature. -
The Flagellum and Flagellar Pocket of Trypanosomatids
Molecular & Biochemical Parasitology 115 (2001) 1–17 www.parasitology-online.com. Reviews: Parasite cell Biology: 1 The flagellum and flagellar pocket of trypanosomatids Scott M. Landfear *, Marina Ignatushchenko Department of Molecular Microbiology and Immunology, Oregon Health Sciences Uni6ersity, Portland, OR 97201, USA Received 9 November 2000; received in revised form 26 January 2001; accepted 5 March 2001 Abstract The flagellum and flagellar pocket are distinctive organelles present among all of the trypanosomatid protozoa. Currently, recognized functions for these organelles include generation of motility for the flagellum and dedicated secretory and endocytic activities for the flagellar pocket. The flagellar and flagellar pocket membranes have long been recognized as morphologically separate domains that are component parts of the plasma membrane that surrounds the entire cell. The structural and functional specialization of these two membranes has now been underscored by the identification of multiple proteins that are targeted selectively to each of these domains, and non-membrane proteins have also been identified that are targeted to the internal lumina of these organelles. Investigations on the functions of these organelle-specific proteins should continue to shed light on the unique biological activities of the flagellum and flagellar pocket. In addition, work has begun on identifying signals or modifications of these proteins that direct their targeting to the correct subcellular location. Future endeavors should further refine our knowledge of targeting signals and begin to dissect the molecular machinery involved in transporting and retaining each polypeptide at its designated cellular address. © 2001 Elsevier Science B.V. All rights reserved. Keywords: Trypanosomatid protozoa; Flagellum; Flagellar Pocket; Organelle-specific proteins; Review 1. -
Agarose Gels (Horizontal Gel Electrophoresis)
TECHNIQUES IN MOLECULAR BIOLOGY – AGAROSE GELS (HORIZONTAL GEL ELECTROPHORESIS) DNA gels are used to separate fragments of DNA and RNA. Unlike most protein separations which use acrylamide polymers, use agarose in a submerged horizontal orientation, and at time called horizontal gel electrophoresis. This handout will cover the details of agarose gels, the theory of separation by agarose gel electrophoresis and tips for conducting successful gel electrophoresis. The basic principle of separation for all electrophoresis is the movement of a charged molecule in a medium subjected to an electric field. v=Eq/f V is the velocity of the molecule subjected to electrophoresis. E is the electrical field in volts/cm, q is the net charge on the molecule and f is the frictional coefficient. The impact of f depends on the mass and shape of the molecule. This equation simply explains that the rate (v) of a particle depends on the electrical field and charge but inversely impacted by the counteracting force generated by the viscous drag. Factors influencing F is of course the size and shape of the molecule. Think of a short linear oligonucleotide vs a large supercoiled plasmid vs long chromosomal DNA. Adding a value to f is the media through which the molecules migrate. Agarose is a seaweed extract (red algae agar) and is a long polymer of D and L galactose and derivatives in a linear polymer bonded by two different glycosidic bonds. Once hydrated and formed into a gel, the carbohydrate will form helical Repeating pattern of agarose fibers and aggregates creating channels of 50 to more than 200 nm in diameter. -
GENERAL BIOLOGY LABORATORY II Bioassays of Major Biomolecules: Nucleic Acids
Weeks 9-10: Bioassays of major biomolecules: Nucleic acids GENERAL BIOLOGY LABORATORY II Canbolat Gürses, Hongling Yuan, Samet Kocabay, Hikmet Geckil Department of Molecular Biology and Genetics Inonu University Weeks 9-10 Bioassays of major biomolecules: Nucleic acids DNA is the genetic material in all organisms. Scientists work with DNA for a variety of reasons, such as cloning, amplification, sequencing, and other genetic manipulations. In general, the first steps in DNA (or RNA) studies involve DNA isolation and their qualitative, and quantitative determination. DNA or RNA concentration in solution can be determined through the optic properties (max. absorbance) of nucleotides at 260 nm. Once their concentration and purity are determined, nucleic acids can be investigated with more specific and sensitive methods (e.g., agarose gel electrophoresis, etc.). 1 DNA can be extracted and isolated from any cell, tissue, or organ using a variety of methods such as alkali lysis, enzymatic lysis and boiling methods and it can be precipitated from the rest of cell components by ethanol, isopropanol precipitation. As we have seen for proteins which have specific absorbance maxima at 280 nm, nucleic acids absorb light maximally at 260 nm. However, while one unit A at 280 nm is equal to one unit of protein (as mg ml-1), for DNA and RNA 1 A unit at 260 nm is equal to about 50 and 40 µg ml-1, respectively. The cell extract is a mixture of all cell components and organelles. Once large particles (e.g., organelles, membrane fragments, etc) are removed by a low speed centrifugation, the solution part (i.e., supernatant) contains cell components such as proteins and nucleic acids dissolved in an aqueous environment. -
Driving Nucleolar Assembly
Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press PERSPECTIVE Driving nucleolar assembly Kathleen L. McCann,1 and Susan J. Baserga1,2,3,4 1Department of Genetics, 2Department of Molecular Biophysics and Biochemistry, 3Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA In this issue of Genes & Development,Grobandcol- breaks down (open mitosis), transcription of the ribosomal leagues (pp. 220–230) identify the minimal molecular re- RNA (rRNA) is inhibited, and the nucleolus disassem- quirements to assemble a fully functional nucleolus in bles. Upon completion of mitosis, rRNA transcription human cells and demonstrate the importance of the is reinitiated within the NOR, ribosome biogenesis fac- nucleolar transcription factor upstream binding factor tors are recruited, and the nucleolus is assembled. Only (UBF) as a mitotic bookmark at the ribosomal DNA NORs that are actively engaged in transcription can (rDNA). direct nucleolar assembly (Hernandez-Verdun 2011). Consequently, the nucleolus truly appears to be ‘‘an organelle formed by the act of building a ribosome’’ (Melese and Xue 1995). In all eukaryotes, the nucleolus is an essential, non- To begin to reveal the molecular mechanisms of nucle- membrane-bound organelle within the nucleus. Assem- olar formation, McStay’s laboratory (Mais et al. 2005; Grob bled around the ribosomal DNA (rDNA), the nucleolus et al. 2014) has applied synthetic biology. In an earlier is the site of ribosome biogenesis. In addition to its role report, they introduced 6.4 kb of DNA repeat sequences in making ribosomes, the nucleolus functions in other from the intergenic spacer of the Xenopus ribosomal gene important cellular processes, including stress sensing, into a noncanonical site in the human genome. -
Plastid in Human Parasites
SCIENTIFIC CORRESPONDENCE being otherwise homo Plastid in human geneous. The 35-kb genome-containing organ parasites elle identified here did not escape the attention of early Sm - The discovery in malarial and toxo electron microscopists who plasmodial parasites of genes normally - not expecting the pres occurring in the photosynthetic organelle ence of a plastid in a proto of plants and algae has prompted specula zoan parasite like tion that these protozoans might harbour Toxoplasma - ascribed to it a vestigial plastid1• The plastid-like para various names, including site genes occur on an extrachromosomal, 'Hohlzylinder' (hollow cylin maternally inherited2, 35-kilobase DNA der), 'Golgi adjunct' and circle with an architecture reminiscent of 'grof3e Tilkuole mit kriiftiger that of plastid genomes3•4• Although the Wandung' (large vacuole 35-kb genome is distinct from the 6-7-kb with stout surrounds) ( see linear mitochondrial genome3-6, it is not refs cited in ref. 9). Our pre known where in the parasite cells the plas liminary experiments with tid-like genome resides. Plasmodium falciparum, the To determine whether a plastid is pre causative agent of the most sent, we used high-resolution in situ lethal form of malaria, hybridization7 to localize transcripts of a identify an organelle (not plastid-like 16S ribosomal RNA gene shown) which appears sim from Toxoplasma gondii8, the causative ilar to the T. gondii plastid. agent of toxoplasmosis. Transcripts accu The number of surrounding mulate in a small, ovoid organelle located membranes in the P. anterior to the nucleus in the mid-region falciparum plastid, and its of the cell (a, b in the figure).