scholarly journals Formation of ultralong DH regions through genomic rearrangement

2019 ◽  
Author(s):  
Brevin A. Smider ◽  
Vaughn V. Smider
Keyword(s):  
Amino Acids ◽  
Heavy Chain ◽  
Genetic Basis ◽  
Genomic Rearrangement ◽  
The Other ◽  
Gene Length ◽  
Deletion Event ◽  
Evolutionary Genomic ◽  
Duplication Events ◽  
Immune Diversity

AbstractCow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8-2, encoding over fifty amino acids. Most bovine IGHD regions are homologous but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. The cluster containing IGHD8-2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8-2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8-2 gene. Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.

scholarly journals Formation of ultralong DH regions through genomic rearrangement

2019 ◽  
Author(s):  
Brevin A. Smider ◽  
Vaughn Smider
Keyword(s):  
Amino Acids ◽  
Heavy Chain ◽  
Genetic Basis ◽  
The Other ◽  
Deletion Event ◽  
Genomic Arrangement ◽  
Evolutionary Genomic ◽  
Duplication Events ◽  
Immune Diversity ◽  
The Relationship

Abstract Background: Cow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8-2, encoding over fifty amino acids. Most bovine IGHD regions are homologous but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. However, the relationship between the genomic arrangement and long CDR lengths is unclear. Results: The DH cluster containing IGHD8-2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8-2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8-2 gene. Conclusions: Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.

scholarly journals Formation of ultralong DH regions through genomic rearrangement

2020 ◽  
Author(s):  
Brevin A. Smider ◽  
Vaughn V. Smider
Keyword(s):  
Amino Acids ◽  
Genetic Basis ◽  
Sequence Similarity ◽  
The Other ◽  
Deletion Event ◽  
Genomic Arrangement ◽  
Evolutionary Genomic ◽  
Duplication Events ◽  
Immune Diversity ◽  
The Relationship

Abstract Background: Cow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8-2, encoding over fifty amino acids. Many bovine IGHD regions have sequence similarity but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. However, the relationship between the genomic arrangement and long CDR lengths is unclear. Results: The DH cluster containing IGHD8-2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8-2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8-2 gene. Conclusions: Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.

scholarly journals Formation of ultralong DH regions through genomic rearrangement

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Brevin A. Smider ◽  
Vaughn V. Smider
Keyword(s):  
Amino Acids ◽  
Genetic Basis ◽  
Sequence Similarity ◽  
The Other ◽  
Deletion Event ◽  
Genomic Arrangement ◽  
Evolutionary Genomic ◽  
Duplication Events ◽  
Immune Diversity ◽  
The Relationship

Abstract Background Cow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8–2, encoding over 50 amino acids. Many bovine IGHD regions have sequence similarity but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. However, the relationship between the genomic arrangement and long CDR lengths is unclear. Results The DH cluster containing IGHD8–2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8–2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8–2 gene. Conclusions Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.

scholarly journals Arrangement of the disulphide bridges in human low-Mr kininogen

1987 ◽  
Vol 247 (1) ◽  
pp. 15-21 ◽  
Author(s):  
J Kellermann ◽  
C Thelen ◽  
F Lottspeich ◽  
A Henschen ◽  
R Vogel ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Heavy Chain ◽  
Light Chain ◽  
The Other ◽  
Critical Importance

The arrangement of the disulphide bridges in human low-Mr kininogen has been elucidated. Low-Mr kininogen contains 18 half-cystine residues forming nine disulphide bridges. The first and the last half-cystine residues of the amino acid sequence form a disulphide loop which spans the heavy- and the light-chain portion of the kininogen molecule. The other 16 half-cystine residues are linked consecutively to form eight loops of 4-20 amino acids; these loops are lined up in the heavy-chain portion of the kininogen molecule. In this way, a particular pattern of disulphide loops is formed which seems to be of critical importance for the inhibitor function of human kininogen.

scholarly journals In Vivo Resistance to Ceftolozane/Tazobactam in Pseudomonas aeruginosa Arising by AmpC- and Non-AmpC-Mediated Pathways

2018 ◽  
Vol 2018 ◽  
pp. 1-4 ◽  
Author(s):  
Erik Skoglund ◽  
Henrietta Abodakpi ◽  
Rafael Rios ◽  
Lorena Diaz ◽  
Elsa De La Cadena ◽  
...  
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
The Other ◽  
Whole Genome ◽  
Apparent Loss ◽  
Lactamase Inhibitor ◽  
Hydrolysis Activity

Two pairs of ceftolozane/tazobactam susceptible/resistant P. aeruginosa were isolated from 2 patients after exposure to β-lactams. The genetic basis of ceftolozane/tazobactam resistance was evaluated, and β-lactam-resistant mechanisms were assessed by phenotypic assays. Whole genome sequencing identified mutations in AmpC including the mutation (V213A) and a deletion of 7 amino acids (P210–G216) in the Ω-loop. Phenotypic assays showed that ceftolozane/tazobactam resistance in the strain with AmpCV213A variant was associated with increased β-lactamase hydrolysis activity. On the other hand, the deletion of 7 amino acids in the Ω-loop of AmpC did not display enhanced β-lactamase activity. Resistance to ceftolozane/tazobactam in P. aeruginosa is associated with changes in AmpC; however, the apparent loss of β-lactamase activity in AmpC∆7 suggests that non-AmpC mechanisms could play an important role in resistance to β-lactam/β-lactamase inhibitor combinations.

scholarly journals STRUCTURAL STUDIES OF HUMAN γG-MYELOMA PROTEINS OF DIFFERENT ANTIGENIC SUBGROUPS AND GENETIC SPECIFICITIES

1966 ◽  
Vol 124 (4) ◽  
pp. 715-732 ◽  
Author(s):  
B. Frangione ◽  
E. C. Franklin ◽  
H. H. Fudenberg ◽  
M. E. Koshland
Keyword(s):  
Amino Acids ◽  
Glutamic Acid ◽  
Heavy Chain ◽  
The Other ◽  
Structural Studies ◽  
Heavy Chains ◽  
Myeloma Proteins ◽  
Methionine Sulfone ◽  
Peptide Maps ◽  
Heavy Chain Disease

1. Peptide maps of Fc fragments or heavy chains of 36 G myeloma proteins and two "heavy chain disease" proteins belonging to the four γ-chain subgroups revealed very striking similarities between them. However differences in a few peptides were noted. This was most pronounced for the Ge(γ2d) subgroup which lacked three peptides characteristic of the other three subgroups. While Fc fragments from different proteins belonging to the same subgroup appeared very similar, minor differences in addition to those based on currently recognized Gm factors were occasionally noted. 2. Fc fragments from Gm(a+) We(γ2b) proteins had a peptide previously shown to be characteristic of normal Gm(a+) γG-globulins. Fc fragments from Gm(a-) molecules belonging to the We(γ2b), Vi(γ2c), or Ne(γ2a) subgroups, whether Gm(b+), Gm(f+), or Gm(-), had the peptide previously identified in Gm(b+f+) normal γG-globulin. This "non-a" peptide was absent in peptide maps from Gm(-) molecules of the Ge(γ2d) subgroup which contained instead another peptide with the same electrophoretic mobility but migrating slightly further on chromatography. 3. Both the "a" and "non-a" peptides were pentapeptides having three amino acids in common, and differing in the other two. The "a" peptide contained one residue of lysine, aspartic acid, threonine, leucine, and glutamic acid. The "non-a" peptides prepared from Gm(b+), Gm(f+), and Gm(-) proteins were identical and contained one residue of lysine, threonine, and methionine sulfone, and two residues of glutamic acid. 4. Several possible mechanisms for the origin of these differences, and their possible role in serologic specificity are discussed.

Human Platelet Antigen 3 (HPA-3): Localization of the Determinant of the Alloantibody Leka (HPA-3a) to the C-Terminus of Platelet Glycoprotein IIb Heavy Chain and Contribution of O-Linked Carbohydrates

1993 ◽  
Vol 69 (05) ◽  
pp. 485-489 ◽  
Author(s):  
Isabelle Djaffar ◽  
Didier Vilette ◽  
Dominique Pidard ◽  
Jean-Luc Wautier ◽  
Jean-Philippe Rosa
Keyword(s):  
Amino Acids ◽  
Heavy Chain ◽  
Human Platelet ◽  
Platelet Glycoprotein ◽  
Fibrinogen Receptor ◽  
C Terminus ◽  
Platelet Antigen ◽  
Human Platelet Antigen ◽  
Determinant Structure ◽  
Polymerase Chain

SummaryThe human platelet antigen (HPA) 3 system is expressed on GPIIb, one subunit of GPIIb-IIIa, the platelet fibrinogen receptor. It was recently shown that HPA-3 was associated with an Ile843/Ser polymorphism. To investigate further HPA-3 determinant structure, we localized an HPA-3a determinant, recognized by the alloantiserum Leka, within the last 29 amino acids of GPIIbα. This region encompasses the polymorphic Ile843, which, as expected, is substituted into Ser in Leka-negative individuals, as shown by DNA sequence after polymerase chain reaction on platelet RNA. In addition, contribution of glycosylation to the determinant structure was demonstrated since the Leka antigenicity was strongly decreased after specifically removing nonterminal O-linked sugars, but not terminal sialic acids. We have thus refined the localization of an HPA-3a determinant within the last 29 amino acids, including Ile843, of GPIIb heavy chain, and shown that the Leka HPA-3a determinant is dependent, in part, upon the serine-linked carbohydrates adjacent to Ile/Ser843.

scholarly journals Epistatic Control of Non-Mendelian Inheritance in Mouse Interspecific Crosses

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1739-1752 ◽  
Author(s):  
Xavier Montagutelli ◽  
Rowena Turner ◽  
Joseph H Nadeau
Keyword(s):  
X Chromosome ◽  
Genetic Basis ◽  
Mendelian Inheritance ◽  
The Other ◽  
Interspecific Crosses ◽  
Chromosome 2 ◽  
Mus Spretus ◽  
F1 Hybrid ◽  
Strong Deviation ◽  
Marker Loci

Abstract Strong deviation of allele frequencies from Mendelian inheritance favoring Mus spretus-derived alleles has been described previously for X-linked loci in four mouse interspecific crosses. We reanalyzed data for three of these crosses focusing on the location of the gene(s) controlling deviation on the X chromosome and the genetic basis for incomplete deviation. At least two loci control deviation on the X chromosome, one near Xist (the candidate gene controlling X inactivation) and the other more centromerically located. In all three crosses, strong epistasis was found between loci near Xist and marker loci on the central portion of chromosome 2. The mechanism for this deviation from Mendelian expectations is not yet known but it is probably based on lethality of embryos carrying particular combinations of alleles rather than true segregation distortion during oogenesis in F1 hybrid females.

Natural Vulcanization Accelerators in Hevea Latex

1948 ◽  
Vol 21 (4) ◽  
pp. 853-859
Author(s):  
R. F. A. Altman
Keyword(s):  
Amino Acids ◽  
Experimental Results ◽  
The Other ◽  
Active Nitrogen ◽  
Nitrogen Bases ◽  
Other Hand ◽  
Decomposition Processes ◽  
Volatile Products ◽  
Nitrogenous Substances ◽  
The One

Abstract As numerous investigators have shown, some of the nonrubber components of Hevea latex have a decided accelerating action on the process of vulcanization. A survey of the literature on this subject points to the validity of certain general facts. 1. Among the nonrubber components of latex which have been investigated, certain nitrogenous bases appear to be most important for accelerating the rate of vulcanization. 2. These nitrogen bases apparently occur partly naturally in fresh latex, and partly as the result of putrefaction, heating, and other decomposition processes. 3. The nitrogen bases naturally present in fresh latex at later stages have been identified by Altman to be trigonelline, stachhydrine, betonicine, choline, methylamine, trimethylamine, and ammonia. These bases are markedly active in vulcanization, as will be seen in the section on experimental results. 4. The nitrogenous substances formed by the decomposition processes have only partly been identified, on the one hand as tetra- and pentamethylene diamine and some amino acids, on the other hand as alkaloids, proline, diamino acids, etc. 5. It has been generally accepted that these nitrogenous substances are derived from the proteins of the latex. 6. Decomposition appears to be connected with the formation of a considerable amount of acids. 7. The production of volatile nitrogen bases as a rule accompanies the decomposition processes. These volatile products have not been identified. 8. The active nitrogen bases, either already formed or derived from complex nitrogenous substances, seem to be soluble in water but only slightly soluble in acetone.

METABOLISM OF AROMATIC COMPOUNDS IN HEALTHY AND RUST-INFECTED PRIMARY LEAVES OF WHEAT: II. STUDIES WITH L-PHENYLALANINE-U-14C, L-TYROSINE-U-14C, AND FERULATE-U-14C

1967 ◽  
Vol 45 (11) ◽  
pp. 2137-2153 ◽  
Author(s):  
A. Fuchs ◽  
R. Rohringer ◽  
D. J. Samborski
Keyword(s):  
Amino Acids ◽  
Stem Rust ◽  
Aromatic Compounds ◽  
The Other ◽  
Major Portion ◽  
Insoluble Residue ◽  
Resistant Reaction ◽  
Wheat Leaves

Wheat leaves infected with stem rust, especially those of susceptible plants, contained more phenylalanine and tyrosine than healthy leaves. The utilization of phenylalanine was increased in both the susceptible and resistant reaction, but the utilization of tyrosine was increased only in the susceptible reaction. No evidence of interconversion of these amino acids was obtained.In n-butanol extracts, which contained glycosides, many constituents were labelled after feeding of L-phenylalanine-U-14C. Most of the n-butanol extractives from resistant-reacting leaves contained more label than those from susceptible-reacting leaves or from healthy leaves. However, one of the n-butanol extractives from susceptible-reacting leaves was 5–10 times as active as that isolated from the other tissues.With L-phenylalanine-U-14C and ferulate-U-14C as precursors, more activity was recovered in insoluble than in soluble esters (of ferulate and p-coumarate). With L-tyrosine-U-14C as precursor, the reverse was observed. After infection, the proportion of label in insoluble esters increased more in resistant leaves than it did in susceptible leaves, regardless of the precursor used.A major portion of the activity from these precursors was recovered in the insoluble residue that contained protein and other polymers. In the experiment with L-phenylalanine-U-14C, this residue was fractionated into protein and non-hydrolyzable material. Susceptible-reacting leaves contained equal amounts of activity in these fractions, while resistant-reacting leaves incorporated 2.5 times as much activity into the non-hydrolyzable material as into protein.

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