The Importance of Serine Metabolism in Cancer
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Monosaccharides and Their Derivatives in Carbonaceous Meteorites: a Scenario for Their Synthesis and Onset of Enantiomeric Excesses
life Review Monosaccharides and Their Derivatives in Carbonaceous Meteorites: A Scenario for Their Synthesis and Onset of Enantiomeric Excesses George Cooper 1,*, Andro C. Rios 1,2,* and Michel Nuevo 1,3 ID 1 NASA-Ames Research Center, Moffett Field, CA 94035, USA; [email protected] 2 Blue Marble Space, 1001 4th Ave, Ste 3201, Seattle, WA 98154, USA 3 Bay Area Environmental Research Institute, NASA Research Park, Moffett Field, CA 94035, USA * Correspondence: [email protected] (G.C.); [email protected] (A.C.R.) Received: 5 June 2018; Accepted: 22 August 2018; Published: 27 August 2018 Abstract: Carbonaceous meteorites provide the best glimpse into the solar system’s earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic reactions. Collectively, chemical reactions resulted in an insoluble kerogen-like carbon phase and a complex mixture of discrete soluble compounds including amino acids, nucleobases, and monosaccharide (or “sugar”) derivatives. This review presents the documented search for sugars and their derivatives in carbonaceous meteorites. We examine early papers, published in the early 1960s, and note the analytical methods used for meteorite analysis as well as conclusions on the results. We then present the recent finding of sugar derivatives including sugar alcohols and several sugar acids: The latter compounds were found to possess unusual “D” enantiomeric (mirror-image) excesses. After discussions on the possible roles of interstellar grain chemistry and meteorite parent body aqueous activity in the synthesis of sugar derivatives, we present a scenario that suggests that most of Earth’s extraterrestrial sugar alcohols (e.g., glycerol) were synthesized by interstellar irradiation and/or cold grain chemistry and that the early solar disk was the location of the initial enantiomeric excesses in meteoritic sugar derivatives. -
Gene Loci Associated with Insulin Secretion in Islets from Nondiabetic Mice
Gene loci associated with insulin secretion in islets from nondiabetic mice Mark P. Keller, … , Gary A. Churchill, Alan D. Attie J Clin Invest. 2019;129(10):4419-4432. https://doi.org/10.1172/JCI129143. Research Article Cell biology Genetics Graphical abstract Find the latest version: https://jci.me/129143/pdf The Journal of Clinical Investigation RESEARCH ARTICLE Gene loci associated with insulin secretion in islets from nondiabetic mice Mark P. Keller,1 Mary E. Rabaglia,1 Kathryn L. Schueler,1 Donnie S. Stapleton,1 Daniel M. Gatti,2 Matthew Vincent,2 Kelly A. Mitok,1 Ziyue Wang,3 Takanao Ishimura,2 Shane P. Simonett,1 Christopher H. Emfinger,1 Rahul Das,1 Tim Beck,4 Christina Kendziorski,3 Karl W. Broman,3 Brian S. Yandell,5 Gary A. Churchill,2 and Alan D. Attie1 1University of Wisconsin-Madison, Biochemistry Department, Madison, Wisconsin, USA. 2The Jackson Laboratory, Bar Harbor, Maine, USA. 3University of Wisconsin-Madison, Department of Biostatistics and Medical Informatics, Madison, Wisconsin, USA. 4Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom. 5University of Wisconsin-Madison, Department of Horticulture, Madison, Wisconsin, USA. Genetic susceptibility to type 2 diabetes is primarily due to β cell dysfunction. However, a genetic study to directly interrogate β cell function ex vivo has never been previously performed. We isolated 233,447 islets from 483 Diversity Outbred (DO) mice maintained on a Western-style diet, and measured insulin secretion in response to a variety of secretagogues. Insulin secretion from DO islets ranged greater than 1000-fold even though none of the mice were diabetic. -
Genetic Drivers of Pancreatic Islet Function
| INVESTIGATION Genetic Drivers of Pancreatic Islet Function Mark P. Keller,*,1 Daniel M. Gatti,†,1 Kathryn L. Schueler,* Mary E. Rabaglia,* Donnie S. Stapleton,* Petr Simecek,† Matthew Vincent,† Sadie Allen,‡ Aimee Teo Broman,§ Rhonda Bacher,§ Christina Kendziorski,§ Karl W. Broman,§ Brian S. Yandell,** Gary A. Churchill,†,2 and Alan D. Attie*,2 *Department of Biochemistry, §Department of Biostatistics and Medical Informatics, and **Department of Horticulture, University of Wisconsin–Madison, Wisconsin 53706-1544, †The Jackson Laboratory, Bar Harbor, Maine 06409, and ‡Maine School of Science and Mathematics, Limestone, Maine 06409, ORCID IDs: 0000-0002-7405-5552 (M.P.K.); 0000-0002-4914-6671 (K.W.B.); 0000-0001-9190-9284 (G.A.C.); 0000-0002-0568-2261 (A.D.A.) ABSTRACT The majority of gene loci that have been associated with type 2 diabetes play a role in pancreatic islet function. To evaluate the role of islet gene expression in the etiology of diabetes, we sensitized a genetically diverse mouse population with a Western diet high in fat (45% kcal) and sucrose (34%) and carried out genome-wide association mapping of diabetes-related phenotypes. We quantified mRNA abundance in the islets and identified 18,820 expression QTL. We applied mediation analysis to identify candidate causal driver genes at loci that affect the abundance of numerous transcripts. These include two genes previously associated with monogenic diabetes (PDX1 and HNF4A), as well as three genes with nominal association with diabetes-related traits in humans (FAM83E, IL6ST, and SAT2). We grouped transcripts into gene modules and mapped regulatory loci for modules enriched with transcripts specific for a-cells, and another specific for d-cells. -
NATURAL KILLER CELLS, HYPOXIA, and EPIGENETIC REGULATION of HEMOCHORIAL PLACENTATION by Damayanti Chakraborty Submitted to the G
NATURAL KILLER CELLS, HYPOXIA, AND EPIGENETIC REGULATION OF HEMOCHORIAL PLACENTATION BY Damayanti Chakraborty Submitted to the graduate degree program in Pathology and Laboratory Medicine and the Graduate Faculty of the University of Kansas in partial fulfillment ofthe requirements for the degree of Doctor of Philosophy. ________________________________ Chair: Michael J. Soares, Ph.D. ________________________________ Jay Vivian, Ph.D. ________________________________ Patrick Fields, Ph.D. ________________________________ Soumen Paul, Ph.D. ________________________________ Michael Wolfe, Ph.D. ________________________________ Adam J. Krieg, Ph.D. Date Defended: 04/01/2013 The Dissertation Committee for Damayanti Chakraborty certifies that this is the approved version of the following dissertation: NATURAL KILLER CELLS, HYPOXIA, AND EPIGENETIC REGULATION OF HEMOCHORIAL PLACENTATION ________________________________ Chair: Michael J. Soares, Ph.D. Date approved: 04/01/2013 ii ABSTRACT During the establishment of pregnancy, uterine stromal cells differentiate into decidual cells and recruit natural killer (NK) cells. These NK cells are characterized by low cytotoxicity and distinct cytokine production. In rodent as well as in human pregnancy, the uterine NK cells peak in number around mid-gestation after which they decline. NK cells associate with uterine spiral arteries and are implicated in pregnancy associated vascular remodeling processes and potentially in modulating trophoblast invasion. Failure of trophoblast invasion and vascular remodeling has been shown to be associated with pathological conditions like preeclampsia syndrome, hypertension in mother and/or fetal growth restriction. We hypothesize that NK cells fundamentally contribute to the organization of the placentation site. In order to study the in vivo role of NK cells during pregnancy, gestation stage- specific NK cell depletion was performed in rats using anti asialo GM1 antibodies. -
Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize
G C A T T A C G G C A T genes Article Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize Zhixuan Zhao 1, Shuai Li 1, Chen Ji 2 , Yong Zhou 2, Changsheng Li 2 and Wenqin Wang 1,* 1 School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; [email protected] (Z.Z.); [email protected] (S.L.) 2 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; [email protected] (C.J.); [email protected] (Y.Z.); [email protected] (C.L.) * Correspondence: [email protected]; Tel.: +86-21-34206942 Abstract: Improving sulfur assimilation in maize kernels is essential due to humans and animals’ inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a sequence homology search. The RNA-seq quantification indicates that they are highly expressed in leaves, other than root and seeds, consistent with their biological functions in sulfur assimilation. With the recently released 25 genomes of nested association mapping (NAM) founders representing the diverse maize stock, we had the opportunity to investigate the SAT genetic variation comprehensively. The abundant transposon insertions into SAT genes indicate their driving power in terms of gene structure and genome evolution. We found that the transposon insertion into exons could change SAT gene transcription, whereas there was no significant correlation between transposable element (TE) insertion into introns and their gene expression, indicating that other Citation: Zhao, Z.; Li, S.; Ji, C.; Zhou, regulatory elements such as promoters could also be involved. -
WO2011085347A2.Pdf
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 14 July 2011 (14.07.2011) WO 2011/085347 A2 (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, C12N 15/113 (2010.01) A61K 48/00 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, A61K 31/7088 (2006.01) C12N 15/63 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (21) International Application Number: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, PCT/US201 1/020768 ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (22) International Filing Date: NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 11 January 201 1 ( 11.01 .201 1) SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, 61/293,739 11 January 2010 ( 11.01 .2010) US ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (71) Applicant (for all designated States except US): OPKO EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, ΓΓ, LT, LU, CURNA, LLC [US/US]; 440 Biscayne Boulevard, Mia LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, mi, FL 33 137 (US). -
Photosynthetic Productivity: Can Plants Do Better?
3 Photosynthetic Productivity: Can Plants do Better? John B. Skillman1, Kevin L. Griffin2, Sonya Earll1 and Mitsuru Kusama1 1Department of Biology, California State University, San Bernardino, California 2Lamont-Doherty Earth Observatory, Columbia University, New York, New York USA 1. Introduction By the time you finish this paragraph you will be a changed person. Change, of course, takes a variety of forms, from eroding mountains and melting snowflakes to the major changes we experience in our own lives - birth, growth, reproduction, and death. Less tangible, but changes nonetheless, are the small shifts in perspective that occur as we go through our days - new ideas, new feelings, and new understandings. But, as the Second Law of Thermodynamics reminds us, these varied and seemingly unrelated expressions of change do, in fact have a common source. All change arises from the decay of order - an increase in entropy. Sometimes the increased disarray that defines change is obvious, as when a crystalline cube of ice turns into a higgledy-piggledy puddle of water. Other times, the increased disorder is less obvious. Indeed, in living systems, change often seems to be associated with an increase in order. The gradual recovery of a lush and materially diverse living forest in the years following a catastrophic fire would seem to represent a net increase in order. The sequential nature of biological development, from zygote to adult, or from acorn to ancient oak, would seem to represent a net increase in order. The regulated changes in neuronal connectivity and brain architecture that occurs as the mind grasps new insights would seem to represent a net increase in order. -
Sigma Sugars and Carbohydrates
Sigma Sugars and Carbohydrates Library Listing – 614 spectra This library represents a material-specific subset of the larger Sigma Biochemical Condensed Phase Library relating to sugars and carbohydrates found in the Sigma Biochemicals and Reagents catalog. Spectra acquired by Sigma-Aldrich Co. which were examined and processed at Thermo Fisher Scientific. The spectra include compound name, molecular formula, CAS (Chemical Abstract Service) registry number, and Sigma catalog number. Sigma Sugars and Carbohydrates Index Compound Name Index Compound Name 255 (+/-)-Epi-inosose-2 475 2,3,4,6-Tetra-O-methyl-D-glucopyranose 468 1,2,3,4-Tetra-O-acetyl-6- 487 2,3,5-Tri-O-benzoyl-1-O-p-nitrobenzoyl diphenylphosphoryl-b-D-manopyranose D-ribofuranoside 471 1,2,3,4-Tetra-O-acetyl-b-D- 490 2,3,5-Tri-O-benzyl-1-O-p-nitrobenzoyl- glucopyranose D-arabinofuranoside 472 1,2,3,5-Tetra-O-acetyl-b-D-ribofuranose 488 2,3,5-Tri-O-benzyl-b-D-arabinofuranose 473 1,2,3,5-Tetra-O-benzoyl-a-D- 489 2,3,5-Tri-O-benzyl-b-L-arabinofuranose xylofuranose 107 2,3-Dehydro-2-deoxy-N- 258 1,2-O-Isopropylidene-3-O-benzyl-rac- acetylneuraminic acid glycerol 142 2,3-Diphospho-D-glyceric acid, 261 1,2-O-Isopropylidene-5-O-p-tosyl-a-D- penta(CHA) salt xylofuranose 143 2,3-Diphospho-D-glyceric acid, 259 1,2-O-Isopropylidene-D-glucofuranose pentasodium salt 262 1,2-O-Isopropylidene-D-xylofuranose 144 2,3-Diphospho-D-glyceric acid, tris salt 135 1,2:3,4-Di-O-isopropylidene-D- 260 2,3-O-Isopropylidene-b-D- galactopyranose ribofuranosylamine, tosylate salt 141 1,2:3,5-Di-O-isopropylidene-D- -
The Clinical Significance of the Organic Acids Test
The Clinical Significance of the Organic Acids Test The Organic Acids Test (OAT) provides an accurate metabolic snapshot of what is going on in the body. Besides offering the most complete and accurate evaluation of intestinal yeast and bacteria, it also provides information on important neurotransmitters, nutritional markers, glutathione status, oxalate metabolism, and much more. The test includes 76 urinary metabolite markers that can be very useful for discovering underlying causes of chronic illness. Patients and physicians report that treating yeast and bacterial abnormalities reduces fatigue, increases alertness and energy, improves sleep, normalizes bowel function, and reduces hyperactivity and abdominal pain. The OAT Assists in Evaluating: ■ Krebs Cycle Abnormalities ■ Neurotransmitter Levels ■ Nutritional Deficiencies ■ Antioxidant Deficiencies ■ Yeast and Clostridia Overgrowth ■ Fatty Acid Metabolism ■ Oxalate Levels ■ And More! The OAT Pairs Well with the Following Tests: ■ GPL-TOX: Toxic Non-Metal Chemical Profile ■ IgG Food Allergy + Candida ■ MycoTOX Profile ■ Phospholipase A2 Activity Test Learn how to better integrate the OAT into your practice, along with our other top tests by attending one of our GPL Academy Practitioner Workshops! Visit www.GPLWorkshops.com for workshop dates and locations. The following pages list the 75 metabolite markers of the Organic Acids Test. Included is the name of the metabolic marker, its clinical significance, and usual initial treatment. INTESTINAL MICROBIAL OVERGROWTH Yeast and Fungal Markers Elevated citramalic acid is produced mainly by Saccharomyces species or Propionibacteria Citramalic Acid overgrowth. High-potency, multi-strain probiotics may help rebalance GI flora. A metabolite produced by Aspergillus and possibly other fungal species in the GI tract. 5-Hydroxy-methyl- Prescription or natural antifungals, along with high-potency, multi-strain probiotics, furoic Acid may reduce overgrowth levels. -
Secretory Signal Peptide Modification for Optimized Antibody-Fragment Expression-Secretion in Leishmania Tarentolae Stephan Klatt1,2 and Zoltán Konthur1*
Klatt and Konthur Microbial Cell Factories 2012, 11:97 http://www.microbialcellfactories.com/content/11/1/97 RESEARCH Open Access Secretory signal peptide modification for optimized antibody-fragment expression-secretion in Leishmania tarentolae Stephan Klatt1,2 and Zoltán Konthur1* Abstract Background: Secretory signal peptides (SPs) are well-known sequence motifs targeting proteins for translocation across the endoplasmic reticulum membrane. After passing through the secretory pathway, most proteins are secreted to the environment. Here, we describe the modification of an expression vector containing the SP from secreted acid phosphatase 1 (SAP1) of Leishmania mexicana for optimized protein expression-secretion in the eukaryotic parasite Leishmania tarentolae with regard to recombinant antibody fragments. For experimental design the online tool SignalP was used, which predicts the presence and location of SPs and their cleavage sites in polypeptides. To evaluate the signal peptide cleavage site as well as changes of expression, SPs were N-terminally linked to single-chain Fragment variables (scFv’s). The ability of L. tarentolae to express complex eukaryotic proteins with highly diverse post-translational modifications and its easy bacteria-like handling, makes the parasite a promising expression system for secretory proteins. Results: We generated four vectors with different SP-sequence modifications based on in-silico analyses with SignalP in respect to cleavage probability and location, named pLTEX-2 to pLTEX-5. To evaluate their functionality, we cloned four individual scFv-fragments into the vectors and transfected all 16 constructs into L. tarentolae. Independently from the expressed scFv, pLTEX-5 derived constructs showed the highest expression rate, followed by pLTEX-4 and pLTEX-2, whereas only low amounts of protein could be obtained from pLTEX-3 clones, indicating dysfunction of the SP. -
Research Article a Urine Metabonomics Study of Rat Bladder Cancer by Combining Gas Chromatography-Mass Spectrometry with Random Forest Algorithm
Hindawi International Journal of Analytical Chemistry Volume 2020, Article ID 8839215, 9 pages https://doi.org/10.1155/2020/8839215 Research Article A Urine Metabonomics Study of Rat Bladder Cancer by Combining Gas Chromatography-Mass Spectrometry with Random Forest Algorithm MengchanFang,1 FanLiu,2 LinglingHuang,1 LiqingWu,3 LanGuo ,1,2 andYiqunWan 1,2 1College of Chemistry, Nanchang University, Nanchang 330031, China 2Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang 330031, China 3Department of Pathology, 3rd Affiliated Hospital of Nanchang University, Nanchang 330008, China Correspondence should be addressed to Lan Guo; [email protected] and Yiqun Wan; [email protected] Received 15 June 2020; Revised 6 September 2020; Accepted 9 September 2020; Published 21 September 2020 Academic Editor: David M. Lubman Copyright © 2020 Mengchan Fang et al. .is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A urine metabolomics study based on gas chromatography-mass spectrometry (GC-MS) and multivariate statistical analysis was applied to distinguish rat bladder cancer. Urine samples with different stages were collected from animal models, i.e., the early stage, medium stage, and advanced stage of the bladder cancer model group and healthy group. After resolving urea with urease, the urine samples were extracted with methanol and, then, derived with N, O-Bis(trimethylsilyl) trifluoroacetamide and tri- methylchlorosilane (BSTFA + TMCS, 99 :1, v/v), before analyzed by GC-MS. .ree classification models, i.e., healthy control vs. early- and middle-stage groups, healthy control vs. -
The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life
catalysts Review The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life Maheen Gull * and Matthew A. Pasek School of Geosciences, University of South Florida, 4202 E Fowler Ave., NES 204, Tampa, FL 33620, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-813-974-8979 Abstract: The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life. Citation: Gull, M.; Pasek, M.A. The Keywords: glycerol; phosphorylation; catalysis; prebiotic syntheses; origin of life; evolution of cell Role of Glycerol and Its Derivatives in membranes; deep eutectic solvents; extremophiles; glycerol biochemistry; phospholipids; early Earth the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life.