scholarly journals Immobilized Native Bacteria as a Tool for Bioremediation of Soils and Waters: Implementation and Modeling

2002 ◽  
Vol 2 ◽  
pp. 1361-1368 ◽  
Author(s):  
C. Lobo ◽  
M. Sanchez ◽  
C. Garbi ◽  
E. Ferrer ◽  
M.J. Martinez-Iñigo ◽  
...  
Keyword(s):  
Fluid Dynamics ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Biofilm Formation ◽  
Sequence Data ◽  
Soil Samples ◽  
Soil Bioremediation ◽  
Dna Sequence Data ◽  
Homologous Genes ◽  
Degrading Bacteria

Based on 3,4-dihydroxyphenylacetate (3,4-DHPA) dioxygenase amino acid sequence and DNA sequence data for homologous genes, two different oligonucleotides were designed. These were assayed to detect 3,4-DHPA related aromatic compound—degrading bacteria in soil samples by using the FISH method. Also, amplification by PCR using a set of ERIC primers was assayed for the detection ofPseudomonasGCH1 strain, which used in the soil bioremediation process. A model was developed to understand and predict the behavior of bacteria and pollutants in a bioremediation system, taking into account fluid dynamics, molecular/cellular scale processes, and biofilm formation.

Expression patterns of the genes that encode lectin or lectin-related polypeptides in Robinia pseudoacacia

1999 ◽  
Vol 26 (5) ◽  
pp. 495 ◽  
Author(s):  
Kazumasa Yoshida ◽  
Kiyoshi Tazaki
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Expression Patterns ◽  
Robinia Pseudoacacia ◽  
Regulation Of Expression ◽  
Nucleotide Sequence Data ◽  
Reading Frame ◽  
Inner Bark

Three genomic clones (Rplec2, Rplec5 and Rplec6) and a cDNA clone (LECRPA4) that encoded lectin or lectin-related polypeptides were isolated from Robinia pseudoacacia L. A comparison of the nucleotide sequences of Rplec2 and a previously reported cDNA for the subunit indicated that Rplec2 encoded the 29 kDa subunit of the inner-bark lectin RPbAI. Rplec5 encoded a polypeptide whose deduced amino acid sequence was 96.1% identical to that of a subunit of seed lectin. The amino acid sequence deduced from the open reading frame of Rplec6 showed 61.1% identity to that encoded by Rplec5. LECRPA4 was isolated from an inner bark cDNA library and appeared to encode the 26 kDa subunit of inner-bark lectin RPbAII. The expression patterns of the various genes in tissues were examined by the reverse transcriptase-polymerase chain reaction (RT-PCR) with appropriate primers. Rplec2 transcripts were detected in the inner bark and roots. Rplec5 transcripts were detected in the inner bark, seeds and roots. No Rplec6 transcripts were detected in all tissues examined. LECRPA4 transcripts were found in leaves and in the inner bark. The level of expression of Rplec2 in the inner bark appeared to be similar in samples collected in different years and from different trees, whereas levels of expression of Rplec5 and LECRPA4 varied. These results suggest the differential regulation of expression of members of the lectin gene family in tissues of R. pseudoacacia. The nucleotide sequence data reported herein will appear in the DDBJ, EMBL and GenBank Nucleotide Sequence Databases under the accession numbers AB 012632 (Rplec2), AB012633 (Rplec5), AB012634 (Rplec6) and AB012635 (LECRPA4).

scholarly journals Studies on the primary structure of chicken erythrocyte histone fraction V

1971 ◽  
Vol 124 (2) ◽  
pp. 319-325 ◽  
Author(s):  
P. J. Greenaway
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Primary Structure ◽  
Sequence Data ◽  
Acid Extraction ◽  
Chicken Erythrocyte ◽  
Histone Fraction

Histone fraction V was prepared by selective acid extraction from chicken erythrocyte nuclei. Amino acid sequence studies on the tryptic and thermolytic peptides are reported. Only a limited amount of overlapping sequence data was obtained.

Chemical structure of light chains: amino acid sequence of type K Bence-Jones proteins

1966 ◽  
Vol 166 (1003) ◽  
pp. 124-137 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Single Point ◽  
Structural Difference ◽  
Light Chains ◽  
Single Point Mutation ◽  
Amino Terminal ◽  
Type K ◽  
Bence Jones Proteins

Bence-Jones proteins are the light chains of the autologous myeloma globulin and are analogous to the light chains of normal human immunoglobulins. Peptide mapping has demonstrated that Bence-Jones proteins share a fixed portion of their sequence (the ‘constant’ portion) and also have a mutable part (the ‘variable’ portion). Sequence analysis and ordering of the tryptic and chymotryptic peptides has provided the tentative complete amino acid sequence of one Bence-Jones protein of antigenic type K. Comparison with partial sequence data for other type K Bence-Jones proteins has revealed many structural differences in the amino terminal half of the molecules, but only one structural difference in the carboxyl terminal half. The latter is strongly correlated with the Inv genetic factor. The points of interchange in the amino terminal half occur in clusters close to the half cystine residues and the ‘switch peptide’ (positions 102 through 105), after which the sequence becomes essentially invariant. This suggests that the major areas subject to sequence variation are part of a single topographical region which may define a portion of the antigen combining site in the light chains of antibodies. Many, but not all, the amino acid interchanges are compatible with a single point mutation. As yet, no single mutational theory suffices to explain the manifold differences in structure of the light chains. Such structural variation, however, could result from the presence of many related genes.

scholarly journals The principal site of glycation of human complement factor B

1991 ◽  
Vol 274 (2) ◽  
pp. 473-480 ◽  
Author(s):  
M A Niemann ◽  
A S Bhown ◽  
E J Miller
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Complement Factor ◽  
Human Complement ◽  
Factor B ◽  
Complement Factor B ◽  
Functional Regions ◽  
High Concentrations

Accumulating amino acid sequence data have made it increasingly evident that many essential complement proteins have potentially modifiable lysine residues in putative critical functional regions. Evidence is now presented that glucose is covalently attached to lysine-266 of purified human complement Factor B as a result of glycation. Purified B was treated with NaB3H4, which reduces such bound glucose to a mixture of radiolabelled hexitols. Amino acid analysis revealed the expected radiolabelled hexitol-lysine epimers. In addition, fluorography of dried gels resolving the major high-molecular-mass h.p.l.c.-fractionated CNBr-cleavage peptides of NaB3H4-reduced B indicated that this radioactivity was specifically associated with the 15 kDa fragment derived from the N-terminal region of fragment Bb. Amino acid sequence analysis suggested that the C-terminal lysine (residue 266 of B) of the N-terminal Lys-Lys doublet of this peptide is preferentially modified. If such glycation can subsequently be shown to occur in vivo, then perhaps this modification might also be found to affect the functional activity of B and offer a potential explanation for some of the immunopathological complications of diseases exposing key plasma proteins, such as this active-site-containing proteinase of the multimeric alternative-complement-pathway C3/C5 convertases, to long-term high concentrations of glucose, such as the decreased resistance to infection and impaired chemotaxis and phagocytosis characteristic of diabetes.

scholarly journals Partial amino acid sequence and mRNA analysis of cytosolic pyridoxine-beta-d-glucoside hydrolase from porcine intestinal mucosa: proposed derivation from the lactase-phlorizin hydrolase gene

2004 ◽  
Vol 380 (1) ◽  
pp. 211-218 ◽  
Author(s):  
Chi-Wah TSEUNG ◽  
Laura G. McMAHON ◽  
Jorge VÁZQUEZ ◽  
Jan POHL ◽  
Jesse F. GREGORY
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Northern Blot ◽  
Sequence Data ◽  
Cdna Probe ◽  
Protein Mass ◽  
Sds Page ◽  
Mrna Analysis ◽  
Hydrolysis Of

We have previously identified and purified a novel β-glucosidase, designated PNGH (pyridoxine-5´-β-d-glucoside hydrolase), from the cytosolic fraction of pig intestinal mucosal. PNGH catalyses the hydrolysis of PNG (pyridoxine-5´-β-d-glucoside), a plant derivative of vitamin B6 that exhibits partial nutritional bioavailability in humans and animals. Preliminary amino acid sequence analysis indicated regions of close similarity of PNGH to the precursor form of LPH (lactase–phlorizin hydrolase), the β-glucosidase localized to the brush-border membrane. We report in the present study amino acid sequence data for PNGH and results of Northern blot analyses, upon which we propose a common genomic origin of PNGH and LPH. Internal Edman sequencing of the PNGH band isolated by SDS/PAGE yielded data for 16 peptides, averaging 10.8 amino acids in length. These peptides from PNGH (approx. 140 kDa) were highly similar to sequences existing over most of the length of the >200 kDa precursor of rabbit LPH; however, we found no PNGH sequences that corresponded to approx. 350 amino acids between positions 463 and 812 of the LPH precursor, a region encoded by exon 7 of the LPH precursor gene (amino acids 568–784), and no sequences that corresponded to regions near the N-terminus. MS analysis of tryptic peptides yielded 25 peptides, averaging 15 amino acids, with masses that matched segments of the rabbit LPH precursor. Northern blot analysis of pig and human small intestinal polyadenylated mRNA using a non-specific LPH cDNA probe showed an expected approx. 6 kb transcript of the LPH precursor, but also an approx. 4 kb transcript that was consistent with the size predicted from the PNGH protein mass. Using a probe specific to the region encoded by exon 7, hybridization occurred only with the 6 kb transcript. Based on these observations, we propose that both PNGH and LPH enzymes have the same genomic origin, but differ in transcriptional and, possibly, post-translational processing.

scholarly journals Can Power Laws Help Us Understand Gene and Proteome Information?

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
J. A. Tenreiro Machado ◽  
António C. Costa ◽  
Maria Dulce Quelhas
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Genetic Code ◽  
Protein Function ◽  
Sequence Data ◽  
Proteome Analysis ◽  
Power Laws ◽  
Linear Sequence ◽  
Graphical Visualization

Proteins are biochemical entities consisting of one or more blocks typically folded in a 3D pattern. Each block (a polypeptide) is a single linear sequence of amino acids that are biochemically bonded together. The amino acid sequence in a protein is defined by the sequence of a gene or several genes encoded in the DNA-based genetic code. This genetic code typically uses twenty amino acids, but in certain organisms the genetic code can also include two other amino acids. After linking the amino acids during protein synthesis, each amino acid becomes a residue in a protein, which is then chemically modified, ultimately changing and defining the protein function. In this study, the authors analyze the amino acid sequence using alignment-free methods, aiming to identify structural patterns in sets of proteins and in the proteome, without any other previous assumptions. The paper starts by analyzing amino acid sequence data by means of histograms using fixed length amino acid words (tuples). After creating the initial relative frequency histograms, they are transformed and processed in order to generate quantitative results for information extraction and graphical visualization. Selected samples from two reference datasets are used, and results reveal that the proposed method is able to generate relevant outputs in accordance with current scientific knowledge in domains like protein sequence/proteome analysis.

scholarly journals A monoclonal antibody that defines an idiotope with two subsites in galactan-binding myeloma proteins.

1981 ◽  
Vol 154 (6) ◽  
pp. 1946-1956 ◽  
Author(s):  
M Pawlita ◽  
E Mushinski ◽  
R J Feldmann ◽  
M Potter
Keyword(s):  
Monoclonal Antibody ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Molecular Models ◽  
Myeloma Protein ◽  
Amino Acid Sequence Data ◽  
Myeloma Proteins ◽  
Igg1 Monoclonal Antibody ◽  
Hybridoma Technology

An IgG1 monoclonal antibody HyX24-14 was derived from A/J mice that were immunized with the IgA XRPC24 (X24) galactan binding myeloma protein (GalBMP) of BALB/c origin by the Kohler-Milstein hybridoma technology. HyX24-14 specifically binds some but all GalBMP. Different patterns of binding using a panel of nine Gal BMP were found, depending upon the concentration of antibody and the antigenic target. From molecular models and amino acid sequence data, ti was proposed that the idiotope defined by HyX24-14 had two subsites, each of which appeared to be able to bind independently to the antibody.

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