Experimental Estimation of the Bisulfite Isomer Quotient As a Function of Temperature: Implications for Sulfur Isotope Fractionations in Aqueous Sulfite Solutions

Total Page:16

File Type:pdf, Size:1020Kb

Experimental Estimation of the Bisulfite Isomer Quotient As a Function of Temperature: Implications for Sulfur Isotope Fractionations in Aqueous Sulfite Solutions Lawrence Berkeley National Laboratory Recent Work Title Experimental estimation of the bisulfite isomer quotient as a function of temperature: Implications for sulfur isotope fractionations in aqueous sulfite solutions Permalink https://escholarship.org/uc/item/7bb6q2wt Authors Eldridge, DL Mysen, BO Cody, GD Publication Date 2018 DOI 10.1016/j.gca.2017.10.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Geochimica et Cosmochimica Acta 220 (2018) 309–328 www.elsevier.com/locate/gca Experimental estimation of the bisulfite isomer quotient as a function of temperature: Implications for sulfur isotope fractionations in aqueous sulfite solutions Daniel L. Eldridge ⇑, Bjorn O. Mysen, George D. Cody Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Road NW, Washington, DC 20015, United States Received 1 June 2017; accepted in revised form 6 October 2017; available online 16 October 2017 Abstract À 2À Bisulfite (HSO3 ) and sulfite (SO3 ) compounds play key roles in numerous geochemical and biochemical processes extend- ing from the atmosphere to the subseafloor biosphere. Despite decades of spectroscopic investigations, the molecular compo- À sition of HSO3 in solution remains uncertain and, thus, the role of bisulfite in (bio)chemical and isotope fractionation À À processes is unclear. We report new experimental estimates for the bisulfite isomer quotient (Qi = [(HO)SO2 ]/[(HS)O3 ]; [] = concentration) as a function of temperature from the interpretation of Raman spectra collected from aqueous NaHSO3 + À solutions contained in fused silica capsules. In pure NaHSO3 solutions (1Na :1HSO3 , stoichiometric) over [NaHSO3]= 0.2–0.4 m (moles/kg H2O), the following relationship is obtained: : ð : Þ ðQ Þ¼878 59 32 98 À : ð : Þ; ln i T 1 9642 0 1081 where T = 278–358 K (5–85 °C) (based on 50 determinations; additional significant figures are provided to avoid rounding À À errors). This relationship suggests that the minor isomer, (HS)O3 , may comprise 23–38% (±3%) of the mole fraction of HSO3 over 5–85 °C, respectively, which is higher in relative abundance than has generally been understood previously. We addition- ally provide estimates for Qi in NaHSO3 solutions containing a total ionic strength of m = 1.0 m (0.2 m NaHSO3 + 0.8 m NaCl) and different pH (3.3–4.5), but do not appear to resolve any significant differences in Qi as a function of these additional variables. These new values of Qi are employed to re-assess the bulk sulfur isotope fractionations among bisulfite and other S À (IV) compounds as a function of temperature, which appear to be highly dependent on the amount of (HS)O3 present. Our new constraints on the bisulfite isomer quotient may allow for a detailed assessment of the molecular composition and isotope À mass balance of S(IV) solutions containing HSO3 , and may be useful in the further investigation of the mechanisms and iso- tope fractionations associated with a number of processes that involve bisulfite compounds. These may include the intracel- lular enzymatic transformations of sulfite and bisulfite compounds that occur as part of dissimilatory sulfate reduction, which is a major and geologically important form of anaerobic respiration. Ó 2017 Elsevier Ltd. All rights reserved. Keywords: Sulfite; Bisulfite; Raman spectroscopy; Isotope effects; Dissimilatory sulfate reduction 1. INTRODUCTION Aqueous sulfite compounds (overall oxidation state: S4+, or S(IV)) are produced and consumed by a variety of ⇑ Corresponding author. chemical and biological processes in natural environments E-mail address: [email protected] (D.L. Eldridge). https://doi.org/10.1016/j.gca.2017.10.005 0016-7037/Ó 2017 Elsevier Ltd. All rights reserved. 310 D.L. Eldridge et al. / Geochimica et Cosmochimica Acta 220 (2018) 309–328 that span conditions from those of the atmosphere to the and consumption of sulfite compounds (Parey et al., 2013; subseafloor biosphere. Sulfite compounds can be produced Wing and Halevy, 2014; Leavitt et al., 2015). Our under- in the atmosphere by the hydrolysis of volcanogenic or standing of the precise mechanisms and isotope effects asso- anthropogenic SO2(g) emissions during the overall genera- ciated with the enzyme-mediated transformation of sulfite tion of acid rain and sulfate aerosols (e.g., Brandt and compounds within sulfate reducing microorganisms will van Eldik, 1995). In low-temperature aqueous environ- require a detailed understanding of the molecular composi- À ments where aqueous sulfide (H2S/HS ) is continuously tion of sulfite compounds in aqueous solution. generated by anaerobic respiration (dissimilatory sulfate Sulfite compounds exhibit a complex speciation in aque- reduction), redox interfaces are often established based on ous solution that is often ignored in many models and con- opposing sulfide and oxygen concentration gradients where siderations of the general DSR metabolism. This speciation sulfite compounds can persist at relatively low concentra- alone may result in complex chemical and isotope fraction- tions due to their continuous production and consumption ation behavior (Eldridge et al., 2016). A basic understand- by chemical and biological oxidation processes (e.g., eux- ing of the molecular composition of S(IV) solutions is inic basins and organic-rich marine sediments: Millero, based on the relative stabilities of sulfite compounds via 1991; Zhang and Millero, 1993; Zopfi et al., 2001, 2004; the following equilibrium reactions: Li et al., 2010). As part of this cycling, sulfite compounds SO ð Þ $ SO ð Þ ð1Þ can be additionally utilized by some microorganisms for 2 g 2 aq þ $ À þ þ ð Þ sulfite compound disproportionation (e.g., Bak and SO2ðaqÞ H2O HSO3 H 2 Pfennig, 1987), an intriguing metabolism whose influence HSOÀ $ SO2À þ Hþ ð3Þ on global and environmental-scale sulfur cycling is still 3 3 uncertain (Johnston, 2011). At the intracellular level, sulfite The relative distribution of S(IV) species therefore compounds are key intermediate substrates produced and depends principally on the pH of the aqueous solution, consumed by enzyme-mediated reactions within microor- and also on temperature and other variables such as ionic ganisms (bacteria and archaea) that carry out dissimilatory strength (m). The equilibrium constants and other thermody- sulfate reduction (e.g., Ishimoto and Fujimoto, 1961; Peck, namic data (e.g., DH°rxn) for these overall reactions are gen- 1962; Kobayashi et al., 1974; Oliveira et al., 2008; Parey erally well-constrained (Goldberg and Parker, 1985; Millero et al., 2010, 2013), and assimilatory sulfate reduction in et al., 1989). For example, at 25 °C and infinite dilution (low bacteria, archaea, and plants that yields reduced sulfur ionic strength), SO2(aq) dominates in solutions where pH < À 2À for building principle amino acids (cysteine and methion- 1.9, HSO3 dominates over pH = 1.9–7.2, and SO3 at pH ine) and other functions (e.g., Canfield, 2001). > 7.2 (‘‘dominates” means comprises 50% relative molar À Of the many natural processes involving S(IV) com- fraction). This indicates that HSO3 is an abundant if not pounds, dissimilatory sulfate reduction (DSR) is worthy dominant form of S(IV) over a wide range of solution con- of special consideration because it serves as a ubiquitous ditions relevant to many natural systems including the intra- and influential pathway of anaerobic respiration that oper- cellular environment of sulfate reducing organisms. ates globally in organic-rich seafloor sediments (e.g., This simple picture is complicated by the more nuanced Jørgensen, 1982; Bowles et al., 2014), and has had a pro- and somewhat uncertain molecular composition of bisulfite À found impact in the surficial geochemistry of the Earth (HSO3 ), which may be comprised of two distinct isomers throughout geologic history as inferred from the rock (Golding, 1960; Connick et al., 1982; Horner and record (e.g., Canfield, 2001, 2004; Farquhar et al., 2010; Connick, 1986; Littlejohn et al., 1992; Risberg et al., Rickard, 2014). In addition to stimulating a global oxida- 2007). Bisulfite compounds can also undergo reactions with 2À À tive sulfur cycle (Jørgensen, 1977, 1982; Jørgensen et al., each other to form a dimer (S2O5 ,HS2O5 ) when the over- À 1990; Canfield and Teske, 1996; Jørgensen and Nelson, all HSO3 concentration is relatively high (Golding, 1960; À 2004), aqueous sulfide (H2S/HS ) produced by DSR pro- Connick et al., 1982; Beyad et al., 2014). The two isomers À vides a primary source of reduced sulfur for authigenic pyr- of HSO3 differ in the structural site of protonation. One ite (FeS2) formation in marine sedimentary environments isomer contains a proton bound to an oxygen atom that À (e.g., Rickard, 2014). DSR has long been known to produce can be represented as (HO)SO2 , and the other isomer con- relatively large and variable sulfur isotope fractionations tains a proton bound to the sulfur atom represented as (HS) À between extracellular sulfate and sulfide (e.g., Kaplan and O3 . An overall equilibrium for isomerization can be written Rittenberg, 1964; Sim et al., 2011a, 2011b; Leavitt et al., as: 2013, 2015) that can exert primary controls on the sulfur ðHSÞOÀ $ðHOÞSOÀ ð4Þ isotopic composition of geologically-preserved sulfur min- 3 2 erals such as authigenic pyrite and sulfate minerals, which A corresponding equilibrium quotient (Qi) can be writ- in turn have been used to search for the earliest signs of ten to represent their relative concentrations in solution the metabolism in the ancient rock record (e.g., Shen ([] = concentration): et al., 2001, 2009; Shen and Buick, 2004; Ueno et al., ½ðHOÞSOÀ Q ¼ 2 ð5Þ 2008; Wacey et al., 2011; see also Johnston, 2011). Such i ½ðHSÞOÀ variability is generally understood to arise from factors that 3 affect the overall expression of step-wise isotope fractiona- Experimental studies have investigated values for Qi by tions associated with a series of intracellular enzyme- means of 17O-NMR, Raman, and sulfur K-edge XANES mediated reactions that centrally involve the production spectroscopies (Horner and Connick, 1986; Littlejohn D.L.
Recommended publications
  • DNA Methylation Analysis: Choosing the Right Method
    biology Review DNA Methylation Analysis: Choosing the Right Method Sergey Kurdyukov 1,* and Martyn Bullock 2 Received: 8 July 2015; Accepted: 22 December 2015; Published: 6 January 2016 Academic Editor: Melanie Ehrlich 1 Genomics Core facility, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia 2 Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia; [email protected] * Correspondence: [email protected]; Tel.: +61-299-264-756 Abstract: In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims to provide biologists, particularly those new to the field of epigenetics, with a simple algorithm to help guide them in the selection of the most appropriate assay to meet their research needs. First of all, we have separated all methods into two categories: those that are used for: (1) the discovery of unknown epigenetic changes; and (2) the assessment of DNA methylation within particular regulatory regions/genes of interest. The techniques are then scrutinized and ranked according to their robustness, high throughput capabilities and cost. This review includes the majority of methods available to date, but with a particular focus on commercially available kits or other simple and straightforward solutions that have proven to be useful. Keywords: DNA methylation; 5-methylcytosine; CpG islands; epigenetics; next generation sequencing 1. Introduction DNA methylation in vertebrates is characterized by the addition of a methyl or hydroxymethyl group to the C5 position of cytosine, which occurs mainly in the context of CG dinucleotides.
    [Show full text]
  • Sulfur Dioxide and Some Sulfites, Bisulfites and Metabisulfites
    SULFUR DIOXIDE AND SOME SULFITES, BISULFITES AND METABISULFITES 1. Exposure Data 1.1 Chemical and physical data 1.1.1 Synonyms and structural and molecular data Sulfr dioxi Chem. Abstr. Serv Reg. No.: 7446-09-5 Replaced CAS Nos.: 8014-94-6; 12396-99-5; 83008-56-4; 89125-89-3 Chem. Abstr. Name; Sulfur dioxide IUPAC Systematic Name: Sulfur dioxide Synonyms: Sulfurous acid anhydride; sulfurous anhydride; sulfurous oxide; sulfur oxide (S02); sulfur superoxide; sulphur dioxide 0=8=0 S02 MoL. wt: 64.07 Sodium sulfte Chem. Abstr. Serv Reg. No.: 7757-83-7 Altemate CAS No.: 10579-83-6 Replaced CAS No.: 68135-69-3 Chem. Abstr. Name: Sulfurous acid, di sodium salt IUPAC Systematic Name: Sulfurous acid, disodium salt Synonyms: Anhydrous sodium sulfite; disodium sulfite; sodium sulphite o 1/ Na · 0 - 8 - 0 · Na Na2S0J MoL. wt: 126.04 Sodium bisulfe Chem. Abstr. Serv Reg. No.: 7631-90-5 Replaced CAS Nos.: 57414-01-4; 69098-86-8; 89830-27-3; 91829-63-9 Chem. Abstr. Name: Sulfurous acid, monosodium salt IUPAC Systematic Name: Sulfurous acid, monosodium salt -131- 132 lARe MONOGRAPHS VOLUME 54 Synonyms: Hydrogen sulfite sodium; monosodium sulfite; sodium acid sulfite; sodium bisulphite; sodium hydrogen sulfite; sodium sulfite (NaHS03) o Il HO - S - a · Na NaHS03 MoL. wt: 104.06 Sodium metabisulfte Chem. Abstr. Serv Reg. No.: 7681-57-4 Altemate CAS No.: 7757-74-6 Replaced CAS No.: 15771-29-6 Chem. Abstr. Name: Disulfurous acid, disodium salt IUPAC Systematic Name: Pyrosulfurous acid, disodium salt Synonyms: Disodium disulfite; disodium metabisulfite; disodium pyrosulfite; sodium disulfite; sodium metabisulphite; sodium pyrosulfite oIl Il0 Na · 0- S - a - S - a · Na .Na2S20S MoL.
    [Show full text]
  • In Bisulfite/Permanganate for Organic Compounds Oxidation
    Water Research 148 (2019) 198e207 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres New insight into the reactivity of Mn(III) in bisulfite/permanganate for organic compounds oxidation: The catalytic role of bisulfite and oxygen * Shifa Zhong, Huichun Zhang Department of Civil Engineering, Case Western Reserve University, 2104 Adelbert Road, Cleveland, OH, 44106-7201, USA article info abstract À À Article history: A recently discovered bisulfite(HSO3 )/permanganate(MnO4 ) system was reported to produce highly Received 24 June 2018 reactive free Mn(III) that can oxidize organic compounds in milliseconds. However, this characteristic Received in revised form reactivity was not found in all other known reaction systems that can also produce free Mn(III). Why can 18 September 2018 Mn(III) in NaHSO /KMnO be so active? Here, we found NaHSO and O acted as catalysts for the reaction Accepted 12 October 2018 3 4 3 2 between Mn(III) and organic compounds. Without O , 0% of organic compounds were oxidized in Available online 23 October 2018 2 NaHSO3/KMnO4, indicating the absence of O2 inactivated Mn(III) reactivity. When the reaction between NaHSO and KMnO was monitored in air, Mn(III) catalyzed rapid oxidation of NaHSO by O . Then, the Keywords: 3 4 3 2 Bisulfite and permanganate Mn(III) that could oxidize organic compounds was found to be the ones involved in the catalytic reaction Bisulfite/oxygen reaction between NaHSO3 and O2, thus the link between O2 and Mn(III) reactivity was established. Finally, Disproportionation NaHSO3/O2 can be viewed as catalysts for the reaction between Mn(III) and organic compounds because Mn(III) catalyst 1) when Mn(III) was involved in oxidizing organic compounds, it stopped being the catalyst for the Mn(III) oxidant reaction between NaHSO3 and O2 so that they were consumed to a much smaller extent; and 2) without Water treatment NaHSO3 and O2, Mn(III) lost its oxidation ability.
    [Show full text]
  • Winemaking Basics-Bruce Hagen.Pdf
    Winemaking Basics Bruce Hagen Sourcing grapes: good wine starts with good grapes Ripeness: is generally expressed as percent sugar or °Brix (°B). The normal range is 22 – 26°B (17.5 to 19 for sparkling and 21 for some ‘crisp’ and austere whites). Use a hydrometer or a refractometer to check it. If you harvest much above 26, you should consider diluting the juice (must) with water to adjust it to downward a bit, depending on the alcohol level you are comfortable with. The problem with making wines from high °Brix grapes is that the resulting alcohol level will be high. The fermentation may stop (stick) and the wine may taste hot. Therefore, you should consider diluting the must or juice, if the sugar level is much above 26 (see adjusting the °Brix below). The alcohol conversion factor for most yeasts is about .57, but ranges from .55 to as high as .64. Multiply the °B by the conversion factor to determine the probable alcohol level: ex 26°B x .57 = 14.8%. If the °B level is 27, the resulting alcohol level will be 15.4 —very hot! If you dilute to 25, the alcohol will be 14.25%. If you dilute it to 24ºB, the alcohol will be 13.7% —quite acceptable. Whites vs. reds: § White grapes are de-stemmed, crushed, and pressed before fermentation. § Skin contact is relatively short. § Red grapes are typically de-stemmed, crushed, cold-soaked (optional), and he wine pressed off the skins and seeds after fermentation. Skin contact is lengthy, so color and tannins are more intense.
    [Show full text]
  • Website Exposure May Cause Bronchitis to Develop with Coughing, ( Or in Your Facility’S RTK Phlegm, And/Or Shortness of Breath
    Right to Know Hazardous Substance Fact Sheet Common Name: SODIUM BISULFITE Synonym: Sodium Hydrogen Sulfite CAS Number: 7631-90-5 Chemical Name: Sulfurous Acid, Monosodium Salt RTK Substance Number: 1685 Date: August 1998 Revision: April 2008 DOT Number: UN 2693 (Solution) Description and Use EMERGENCY RESPONDERS >>>> SEE BACK PAGE Sodium Bisulfite is a white, crystalline solid with a slight odor Hazard Summary of rotten eggs. It is often in a liquid solution. It is used in Hazard Rating NJDOH NFPA making paper and leather, as a food preservative and in dye HEALTH 2 - and chemical production. FLAMMABILITY 0 - REACTIVITY 0 - CORROSIVE POISONOUS GASES ARE PRODUCED IN FIRE Reasons for Citation f Sodium Bisulfite is on the Right to Know Hazardous Substance List because it is cited by ACGIH, DOT, NIOSH, Hazard Rating Key: 0=minimal; 1=slight; 2=moderate; 3=serious; 4=severe IARC and EPA. f This chemical is on the Special Health Hazard Substance List. f Sodium Bisulfite can affect you when inhaled. f Contact can severely irritate and burn the skin and eyes. f Inhaling Sodium Bisulfite can irritate the nose, throat and lungs. f Sodium Bisulfite may cause a skin allergy and an asthma- like allergy. SEE GLOSSARY ON PAGE 5. f Sodium Bisulfite is CORROSIVE when in a liquid solution with water. FIRST AID Eye Contact f Quickly brush off excess chemical from the face. Immediately flush with large amounts of water for at least 60 Workplace Exposure Limits minutes, lifting upper and lower lids. Remove contact NIOSH: The recommended airborne exposure limit (REL) is lenses, if worn, while flushing.
    [Show full text]
  • Safety Data Sheet SODIUM BISULFITE
    Safety Data Sheet SODIUM BISULFITE Section 1 - Product and Company Identification Product Name: Sodium Bisulfite Chemical Formula: NaHSO3 CAS Number: 007631-90-5 Other Designations: Sodium Bisulfite Solution, Sodium Hydrogen Sulfite Solution. General Use: Food and pharmaceutical preservative, waste water dechlorination agent, laboratory reagent, reducing agent, dietary supplement, and color preservative. Manufacturer: INEOS Calabrian Corporation 5500 Hwy. 366 Port Neches, Texas77651 Telephone: 409-727-1471 Fax: 409-727-5803 Emergency Contact: CHEMTREC 800-424-9300 Section 2 - Hazards Identification Emergency Overview Target Organs: Respiratory system, eyes, skin GHS Classification: Acute Toxicity, Oral (Category 4) Acute Toxicity, Dermal (Category 5) Serious Eye Irritant (Category 2A) GHS Label Elements: Signal Word – Warning Pictogram Corrosive Irritant Hazard Statements: H302 – Harmful if swallowed H313 – May be harmful to skin H319 – Causes serious eye irritation Precautionary P280 – Wear protective equipment for hands, eyes, face and respiratory tract Statements: P305, P351 and P338 – IF IN EYES: Rinse with water for several minutes. Remove contact lenses if present and continue rinsing. Other Hazards: Contact with acids liberates toxic sulfur dioxide gas. HMIS Classification: Health Hazard 2 Flammability 0 Physical 0 1 Safety Data Sheet SODIUM BISULFITE NFPA Rating: Health Hazard 2 Fire 0 Reactivity 0 Potential Health Inhalation: Irritant to respiratory tract Effects: Eye: Irritant Skin: Irritant Ingestion: Harmful if swallowed Aggravated Medical Condition: Capable of provoking bronchospasm in sulfite sensitive individuals with asthma. Section 3 - Composition / Information on Ingredients Composition CAS Number % Wt Water - 50 – 70 Sodium bisulfite 007631-90-5 30 – 50 Sodium Sulfite 007757-83-7 < 1.0 Sodium Sulfate 007757-82-6 < 3.5 Section 4 - First Aid Measures Exposure Route Symptom Treatment Inhalation: Sore throat, shortness of Remove from exposure to fresh air.
    [Show full text]
  • The Bispcr2 Method for Targeted Bisulfite Sequencing Diana L Bernstein, Vasumathi Kameswaran, John E Le Lay, Karyn L Sheaffer and Klaus H Kaestner*
    Bernstein et al. Epigenetics & Chromatin (2015) 8:27 DOI 10.1186/s13072-015-0020-x METHODOLOGY Open Access The BisPCR2 method for targeted bisulfite sequencing Diana L Bernstein, Vasumathi Kameswaran, John E Le Lay, Karyn L Sheaffer and Klaus H Kaestner* Abstract Background: DNA methylation has emerged as an important regulator of development and disease, necessitating the design of more efficient and cost-effective methods for detecting and quantifying this epigenetic modification. Next-generation sequencing (NGS) techniques offer single base resolution of CpG methylation levels with high statis- tical significance, but are also high cost if performed genome-wide. Here, we describe a simplified targeted bisulfite sequencing approach in which DNA sequencing libraries are prepared following sodium bisulfite conversion and two rounds of PCR for target enrichment and sample barcoding, termed BisPCR2. Results: We have applied the BisPCR2 technique to validate differential methylation at several type 2 diabetes risk loci identified in genome-wide studies of human islets. We confirmed some previous findings while not others, in addi- tion to identifying novel differentially methylated CpGs at these genes of interest, due to the much higher depth of sequencing coverage in BisPCR2 compared to prior array-based approaches. Conclusion: This study presents a robust, efficient, and cost-effective technique for targeted bisulfite NGS, and illus- trates its utility by reanalysis of prior findings from genome-wide studies. Keywords: Targeted bisulfite sequencing, DNA methylation, Next-generation sequencing Background disorders, and cardiovascular disease [9–11]. Many of the DNA methylation refers to the addition of a methyl studies linking DNA methylation to disease have been group to the 5-carbon position of cytosine residues, and prompted by the observation that only a small fraction in mammalian genomes occurs most commonly in the of the inherited risk of these complex disorders can be context of CpG dinucleotides.
    [Show full text]
  • Methylated DNA Immunoprecipitation and High-Throughput Sequencing (Medip-Seq) Using Low Amounts of Genomic DNA
    CELLULAR REPROGRAMMING Volume 16, Number 3, 2014 Original Article ª Mary Ann Liebert, Inc. DOI: 10.1089/cell.2014.0002 Methylated DNA Immunoprecipitation and High-Throughput Sequencing (MeDIP-seq) Using Low Amounts of Genomic DNA Ming-Tao Zhao,1 Jeffrey J. Whyte,1 Garrett M. Hopkins,2 Mark D. Kirk,2 and Randall S. Prather1 Abstract DNA modifications, such as methylation and hydroxymethylation, are pivotal players in modulating gene ex- pression, genomic imprinting, X-chromosome inactivation, and silencing repetitive sequences during embryonic development. Aberrant DNA modifications lead to embryonic and postnatal abnormalities and serious human diseases, such as cancer. Comprehensive genome-wide DNA methylation and hydroxymethylation studies provide a way to thoroughly understand normal development and to identify potential epigenetic mutations in human diseases. Here we established a working protocol for methylated DNA immunoprecipitation combined with next-generation sequencing [methylated DNA immunoprecipitation (MeDIP)-seq] for low starting amounts of genomic DNA. By using spike-in control DNA sets with standard cytosine, 5-methylcytosine (5mC), and 5- hydroxymethylcytosine (5hmC), we demonstrate the preferential binding of antibodies to 5mC and 5hmC, respectively. MeDIP-PCRs successfully targeted highly methylated genomic loci with starting genomic DNA as low as 1 ng. The enrichment efficiency declined for constant spiked-in controls but increased for endogenous methylated regions. A MeDIP-seq library was constructed starting with 1 ng of DNA, with the majority of fragments between 250 bp and 600 bp. The MeDIP-seq reads showed higher quality than the Input control. However, after being preprocessed by Cutadapt, MeDIP (97.53%) and Input (94.98%) reads showed comparable alignment rates.
    [Show full text]
  • The Chemical and Preservative Properties of Sulfur Dioxide Solution for Brining Fruit
    The Chemical and Preservative Properties of Sulfur Dioxide Solution for Brining Fruit Circular of Information 629 June 1969 Agricultural Experiment Station, Oregon State University, Corvallis The Chemical and Preservative Properties of Sulfur Dioxide Solution for Brining Fruit C. H. PAYNE, D. V. BEAVERS, and R. F. CAIN Department of Food Science and Technology Sweet cherries and other fruits are preserved in sul- control are given in papers by Waiters et al. (1963) and fur dioxide solutions for manufacture into maraschino, Yang et al. (1966). cocktail, and glace fruit. The sulfur dioxide solution, Sulfur dioxide and calcium are directly related to commonly called brine, may be prepared from liquid brined cherry quality. Improper use of these chemicals sulfur dioxide, sodium bisulfite, or sodium metabisulfite may result in cherries that are soft, poorly bleached, or using alkali or acid to control pH. Calcium salts such as spoiled due to fermentation. It is the purpose of this calcium hydroxide, calcium carbonate, and calcium chlo- circular to show how the basic chemical and preservative ride are added to the brine to prevent cracking and pro- components of brine solutions are afifected during prep- mote firming of the fruit tissue through interaction with aration, storage, and use. pectic materials. Directions for brine preparation and Chemical Properties of Sulfur Dioxide Solutions When sulfur dioxide or materials containing sulfur range of sulfur dioxide concentrations, the relative dis- dioxide (bisulfite or metabisulfite) are dissolved in tribution of the sulfur dioxide ionic forms is constant. water, three types of chemical substances are formed: Within the initial pH range used for brining cher- sulfurous acid (H2SO3),1 bisulfite (HSO3"), and sulfite ries, there is a predominance of calcium bisulfite (SO~).
    [Show full text]
  • Optimizing the DNA Methylation Analysis Workflow Karen Reece, Ph.D
    Optimizing the DNA Methylation Analysis Workflow Karen Reece, Ph.D. Senior Research Scientist ©2013 Promega Corporation. 1 Understanding the Challenges of DNA Methylation Analysis and Possible Solutions Agenda Introduction to epigenetics • Overview • Mechanisms • Why study? Challenges/solutions at each step of DNA methylation analysis • gDNA purification • Quantitation • Bisulfite conversion Review analysis methods • Advantages and disadvantages of each 2 Epigenetics in Action A Different Form of Gene Regulation Genetically Identical Mice X Normal Diet Altered Diet of Mother Normal Diet Epigenetic: Heritable changes in phenotype or gene expression caused by mechanisms other than changes in the DNA sequence. Obese, diabetic with increased risk of cancer 3 Epigenetic Mechanisms Changes in Chromatin Structure or DNA Methylation Chromatin Structure DNA Modification (Methylation) 5-methyl-CpG CH3 Nucleosome positioning TACGAG ATGCTC Histone variants CH3 Modified histones DNA methylation Alterations Cell division Progeny 4 CpG Islands Regions with High Concentrations of CpGs CpG Island Promoter Gene Gene Promoter Shores CpG Islands Shores • Definition • Regions flanking CpG islands • 200-3000bp regions • Suggested to be where regulated • >50% GC content methylation occurs • Genomic distribution • 70% of promoter regions contain CpG islands • Only 1% of remaining genome contains CpG islands 5 Epigenetic Mechanisms Regulation of Critical Biological Processes Differentiation Regulate Chromatin structure Development Gene DNA methylation Expression
    [Show full text]
  • Techniques to Overcome Bottlenecks in Epigenetics Research
    Scientific article Techniques to overcome bottlenecks in epigenetics research Gerald Schock and Thorsten Traeger QIAGEN GmbH, Qiagen Straße 1, 40724 Hilden, Germany Abstract: This article discusses the obstacles in bisulfite conversion of DNA for epigenetics research applications and uncovers possible solutions to overcome them. Furthermore, various methods for methylation analysis such as high-resolution melting (HRM®), methylation-specific PCR (MSP), MethyLight PCR, bisulfite sequencing, and Pyrosequencing® are described, and their respective uses and limitations are evaluated. Introduction Contents DNA methylation, the process of adding a methyl group to Introduction __________________________________________ 1 cytosines, is one of the key epigenetic mechanisms in mammals. DNA methylation — an important epigenetic mechanism ___ 2 It is closely associated with histone modification, and it alters DNA methylation in disease progression _________________ 2 the chromatin structure to enable control and modulation of Bisulfite conversion — the fundamental step in gene expression. DNA methylation plays a crucial role in DNA methylation analysis ______________________________ 2 mammalian development, genomic imprinting, and in genomic Increasing yield and PCR sensitivity through direct bisulfite stability. Because its deregulation can both cause or result conversion without prior DNA isolation __________________ 3 from abnormal cell regulation in cancer, studies in DNA Stability of bisulfite treatment — a challenge for storing methylation are expected to lead to the development of converted DNA for downstream analysis _________________ 4 effective biomarkers and drugs against cancer or other Overcoming limitations due to small sample amounts ______ 5 malignant diseases. Screening for unknown methylation CpG Assessing DNA methylation typically comprises three major positions — high-resolution melting analysis (HRM) ________ 5 steps — DNA isolation, bisulfite conversion, and analysis of Methylation-specific PCR (MSP) — an easy way to the bisulfite converted DNA.
    [Show full text]
  • Bisulfite Converted Human DNA Standard
    Bisulfite Converted Universal Methylated Human DNA Standard Cat. Nos. D5015 Storage: -20 °C Product Information Highlights: Protocol: Purified male human DNA that has been methylated at all Note: We recommend using ZymoTaq™ DNA Polymerase or other cytosine positions within the CG dinucleotide context by hot-start DNA polymerases for amplification of bisulfite-treated DNA. M.SssI methyltransferase and treated with sodium bisulfite for direct downstream methylation applications. 1. PCR Setup: Control primer pair is designed to amplify a fragment of the The following setup is designed for a 25 µl total reaction volume: human MLH1 mismatch repair gene following bisulfite conversion. Component Volume Final Conc. hMLH1 primer I* Variable 0.2 to 0.8 µM hMLH1 primer II* Variable 0.2 to 0.8 µM Product Contents: Bisulfite-converted DNA 1 µl 0.8 ng/µl 10 mM dNTP mix 0.5 µl 0.2 mM each dNTP Cat. # Standard PCR buffer Variable 1x Storage Temp. D5015 MgCl2 or MgSO4 Variable 1-4 mM, if needed Bisulfite Converted Universal Methylated ZymoTaq™ DNA Polymerase 1 µg/50 µl -20 °C Human DNA Standard (or other Hot-start DNA polymerase) Variable 1 to 2 units Add water to 25 µl hMLH1 Primers 20 µl -20 °C * Alternatively, you may substitute primers of your choice. 2. Recommended Thermocycler Conditions: Description: A. 95 °C, 10 minutes The Bisulfite Converted Universal Methylated Human DNA B. 95 °C, 30 seconds Standard contains bisulfite-treated DNA derived from the Universal C. 59 °C, 30 to 60 seconds Methylated Human DNA Standard. The supplied DNA has been D.
    [Show full text]