Combing Genomic DNA for Structural and Functional Studies

Abstract Three families with polycythemia inherited through apparently different modes are described. Secondary causes of polycythemia were ruled out. Erythropoietin (EPO) levels were normal or low, even after phlebotomy. In vitro erythroid colony growth in standard assay cultures containing EPO was normal; however, in the absence of added EPO, a few progenitors from most of the affected individuals were able to generate recognizable colonies of mature erythroblasts, although these were smaller and proportionately less numerous than seen in polycythemia vera (PV). To search for EPO-receptor changes as a possible pathophysiologic mechanism, we examined, by Southern blot analysis, genomic DNA samples from affected and nonaffected family members, as well as three patients with PV. Two different probes, derived from the human EPO-receptor, were used. We found no evidence for chromosomal rearrangements or gene amplification in hereditary polycythemia or PV patients. Further, no nucleotide sequences were found that were homologous to the Friend spleen focus-forming virus glycoprotein gp55, which has been shown to bind to and activate the murine EPO-receptor. Functional studies examining number and binding affinity of the EPO- receptor on erythroid progenitors from three hereditary polycythemia patients demonstrated no abnormalities. We conclude that the mechanism(s) for the erythrocytosis in familial and congenital polycythemia and in PV may not involve the EPO-receptor and, therefore, may result from alterations of postreceptor responses.

Download Full-text

Familial and congenital polycythemia in three unrelated families

Blood ◽

10.1182/blood.v79.11.3019.bloodjournal79113019 ◽

1992 ◽

Vol 79 (11) ◽

pp. 3019-3030

Author(s):

PD Emanuel ◽

CJ Eaves ◽

VC Broudy ◽

T Papayannopoulou ◽

MR Moore ◽

...

Keyword(s):

Genomic Dna ◽

Southern Blot Analysis ◽

Chromosomal Rearrangements ◽

Colony Growth ◽

Erythroid Progenitors ◽

Epo Receptor ◽

Functional Studies ◽

Standard Assay ◽

Or Gene

Three families with polycythemia inherited through apparently different modes are described. Secondary causes of polycythemia were ruled out. Erythropoietin (EPO) levels were normal or low, even after phlebotomy. In vitro erythroid colony growth in standard assay cultures containing EPO was normal; however, in the absence of added EPO, a few progenitors from most of the affected individuals were able to generate recognizable colonies of mature erythroblasts, although these were smaller and proportionately less numerous than seen in polycythemia vera (PV). To search for EPO-receptor changes as a possible pathophysiologic mechanism, we examined, by Southern blot analysis, genomic DNA samples from affected and nonaffected family members, as well as three patients with PV. Two different probes, derived from the human EPO-receptor, were used. We found no evidence for chromosomal rearrangements or gene amplification in hereditary polycythemia or PV patients. Further, no nucleotide sequences were found that were homologous to the Friend spleen focus-forming virus glycoprotein gp55, which has been shown to bind to and activate the murine EPO-receptor. Functional studies examining number and binding affinity of the EPO- receptor on erythroid progenitors from three hereditary polycythemia patients demonstrated no abnormalities. We conclude that the mechanism(s) for the erythrocytosis in familial and congenital polycythemia and in PV may not involve the EPO-receptor and, therefore, may result from alterations of postreceptor responses.

Download Full-text

A simple method to co-purify genomic DNA, RNA, and proteins for functional studies

10.1101/467928 ◽

2018 ◽

Author(s):

Jian Jiang ◽

Junfei Ma ◽

Bin Liu ◽

Ying Wang

Keyword(s):

Gene Expression ◽

Molecular Biology ◽

High Throughput ◽

Genomic Dna ◽

Molecular Mechanisms ◽

Rapid Development ◽

Regulation Of Gene Expression ◽

Robust Method ◽

Simple Method ◽

Functional Studies

AbstractUnderstanding the regulation of gene expression, from the epigenetic modifications on genomes to posttranscriptional and translational controls, are critical for elucidating molecular mechanisms underlying distinct phenotypes in biology. With the rapid development of Multi-Omics analyses, it is desirable to minimize sample variations by using DNA, RNA, and proteins co-purified from the same samples. Currently, most of the co-purification protocols rely on Tri Reagent (Trizol as a common representative) and require protein precipitation and dissolving steps, which render difficulties in experimental handling and high-throughput analyses. Here, we established a simple and robust method to minimize the precipitation steps and yield ready-to-use RNA and protein in solutions. This method can be applied to samples in small quantity, such as protoplasts. We demonstrated that the protoplast system equipped with this method may facilitate studies on viroid biogenesis. Given the ease and the robustness of this new method, it will have broad applications for plant research and other disciplines in molecular biology.

Download Full-text

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100075932 ◽

1983 ◽

Vol 41 ◽

pp. 440-441

Author(s):

A. Engel ◽

D.L. Dorset ◽

A. Massalski ◽

J.P. Rosenbusch

Keyword(s):

Crystal Packing ◽

3D Structure ◽

Gram Negative Bacteria ◽

Protein Ratio ◽

Crystal Forms ◽

Large Molecules ◽

Functional Studies ◽

Voltage Dependent ◽

Planar Membranes ◽

Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

Download Full-text

Ionic homeostasis and subcellular element compartmentation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010013434x ◽

1990 ◽

Vol 48 (2) ◽

pp. 150-151

Author(s):

Ann LeFurgey ◽

Peter Ingram ◽

J.J. Blum ◽

M.C. Carney ◽

L.A. Hawkey ◽

...

Keyword(s):

Leishmania Major ◽

Ionic Homeostasis ◽

X Ray ◽

Functional Studies ◽

Cell Compartments ◽

X Ray Imaging ◽

Resolution Electron ◽

Multiple Cell ◽

Role Of Zn

Subcellular compartments commonly identified and analyzed by high resolution electron probe x-ray microanalysis (EPXMA) include mitochondria, cytoplasm and endoplasmic or sarcoplasmic reticulum. These organelles and cell regions are of primary importance in regulation of cell ionic homeostasis. Correlative structural-functional studies, based on the static probe method of EPXMA combined with biochemical and electrophysiological techniques, have focused on the role of these organelles, for example, in maintaining cell calcium homeostasis or in control of excitation-contraction coupling. New methods of real time quantitative x-ray imaging permit simultaneous examination of multiple cell compartments, especially those areas for which both membrane transport properties and element content are less well defined, e.g. nuclei including euchromatin and heterochromatin, lysosomes, mucous granules, storage vacuoles, microvilli. Investigations currently in progress have examined the role of Zn-containing polyphosphate vacuoles in the metabolism of Leishmania major, the distribution of Na, K, S and other elements during anoxia in kidney cell nuclel and lysosomes; the content and distribution of S and Ca in mucous granules of cystic fibrosis (CF) nasal epithelia; the uptake of cationic probes by mltochondria in cultured heart ceils; and the junctional sarcoplasmic retlculum (JSR) in frog skeletal muscle.

Download Full-text

Phytochemical and functional studies on the roots of Armoracia rusticana

10.1055/s-0037-1608402 ◽

2017 ◽

Author(s):

E Jimenez Negro ◽

J Sendker ◽

B Scharf ◽

M Kleinwächter ◽

B Lipowicz ◽

...

Keyword(s):

Armoracia Rusticana ◽

Functional Studies

Download Full-text

Paris I Dysfibrinogenemia: A Point Mutation in Intron 8 Results in Insertion of a 15 Amino Acid Sequence in the Fibrinogen γ-Chain

Thrombosis and Haemostasis ◽

10.1055/s-0038-1651583 ◽

1993 ◽

Vol 69 (03) ◽

pp. 217-220 ◽

Cited By ~ 12

Author(s):

Jonathan B Rosenberg ◽

Peter J Newman ◽

Michael W Mosesson ◽

Marie-Claude Guillin ◽

David L Amrani

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Point Mutation ◽

Genomic Dna ◽

Comparative Sequence Analysis ◽

Chain Gene ◽

Molecular Defect ◽

Nucleotide Position ◽

Normal Individuals ◽

Polymerase Chain

SummaryParis I dysfibrinogenemia results in the production of a fibrinogen molecule containing a functionally abnormal γ-chain. We determined the basis of the molecular defect using polymerase chain reaction (PCR) to amplify the γ-chain region of the Paris I subject’s genomic DNA. Comparative sequence analysis of cloned PCR segments of normal and Paris I genomic DNA revealed only an A→G point mutation occurring at nucleotide position 6588 within intron 8 of the Paris I γ-chain gene. We examined six normal individuals and found only normal sequence in this region, indicating that this change is not likely to represent a normal polymorphism. This nucleotide change leads to a 45 bp fragment being inserted between exons 8 and 9 in the mature γparis I chain mRNA, and encodes a 15 amino acid insert after γ350 [M-C-G-E-A-L-P-M-L-K-D-P-C-Y]. Alternative splicing of this region from intron 8 into the mature Paris I γ-chain mRNA also results after translation into a substitution of S for G at position γ351. Biochemical studies of 14C-iodoacetamide incorporation into disulfide-reduced Paris I and normal fibrinogen corroborated the molecular biologic predictions that two additional cysteine residues exist within the γpariS I chain. We conclude that the insertion of this amino acid sequence leads to a conformationallyaltered, and dysfunctional γ-chain in Paris I fibrinogen.

Download Full-text

Functional Characterization of a Variant Factor XII (F XII Locarno) in a Cross Reacting Material Positive F XII Deficient Plasma

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648416 ◽

1992 ◽

Vol 67 (02) ◽

pp. 219-225 ◽

Cited By ~ 6

Author(s):

Walter A Wuillemin ◽

Miha Furlan ◽

Hans Stricker ◽

Bernhard Lämmle

Keyword(s):

Dextran Sulfate ◽

Functional Characterization ◽

Healthy Woman ◽

Chain Molecule ◽

Plasma Kallikrein ◽

Factor Xii ◽

Single Chain ◽

Sulfate Adsorption ◽

Prolonged Incubation ◽

Functional Studies

SummaryThe plasma of a healthy woman was found to contain half normal factor XII (FXII) antigen level (0.46 U/ml) without any FXII clotting activity (<0.01 U/ml). The variant FXII in this plasma, denoted as FXII Locarno, was partially characterized by immunological and functional studies on the proposita’s plasma. FXII Locarno is a single chain molecule with the same size (M r = 80 kDa) as normal FXII. Isoelectric focusing suggested an excess of negative charge in the variant FXII as compared to normal FXII. In contrast to FXII in normal plasma, FXII Locarno was not proteolytically cleaved upon prolonged incubation of proposita’s plasma with dextran sulfate. Adsorption to kaolin was similar for both, abnormal and normal FXII. Incubation of the proposita’s plasma with dextran sulfate and exogenous plasma kallikrein showed normal cleavage of FXII Locarno outside of the tentative disulfide loop Cys340-Cys467, but only partial cleavage within this disulfide loop. Furthermore, plasma kallikrein-cleaved abnormal FXII showed neither amidolytic activity nor proteolytic activity against factor XI and plasma prekallikrein.These results suggest a structural alteration of FXII Locarno, affecting the plasma kallikrein cleavage site Arg353-Val354 and thus formation of activated FXII (a-FXIIa).

Download Full-text