A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains

Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (V_L) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of V_L domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the V_L domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol⁻¹, which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in V_L domains of the κ family and not in V_Lλ or in V_H domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains.     

Genetic diversity of Microcystis cyanophages in two different freshwater environments

Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host’s phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes.     

Suitable Chemical Properties of Animal Manure Compost to Facilitate Pb Immobilization in Soil

Chemical immobilization using animal manure compost is one of the most useful for low-cost, in-situ soil remediation techniques. The present study aimed to determine suitable chemical properties of animal manure compost to facilitate lead (Pb) immobilization in soil. The level of mobile Pb in soil amended with swine compost was higher than that amended with cattle compost during the early stage of incubation. However, the level of mobile Pb was almost the same in soil amended with both types of compost on day 184 of incubation. The ratio of the residual fraction after sequential extraction was enhanced in soil amended with both types of compost, particularly swine compost. X-ray diffractometer (XRD) results demonstrated the precipitation of Pb phosphate minerals, such as pyromorphite, in Pb-sorbed composts, particularly swine compost. Amendment using swine compost could reduce Pb solubility even when it had a high content of water-soluble organic matter because it significantly lowered Pb phase solubility. The amendment with swine compost improved plant growth and microbial activity. This study suggests that composts with high phosphorus (P) content are suitable for Pb immobilization amendment even if they have a high water-soluble organic matter content.     

Screening the Expression of ABCB6 in Erythrocytes Reveals an Unexpectedly High Frequency of Lan Mutations in Healthy Individuals

Lan is a high-incidence blood group antigen expressed in more than 99.9% of the population. Identification of the human ABC transporter ABCB6 as the molecular basis of Lan has opened the way for studies assessing the relation of ABCB6 function and expression to health and disease. To date, 34 ABCB6 sequence variants have been described in association with reduced ABCB6 expression based on the genotyping of stored blood showing weak or no reactivity with anti-Lan antibodies. In the present study we examined the red blood cell (RBC) surface expression of ABCB6 by quantitative flow cytometry in a cohort of 47 healthy individuals. Sequencing of the entire coding region of the ABCB6 gene in low RBC ABCB6 expressors identified a new allele (IVS9+1G>A, affecting a putative splice site at the boundary of exon 9) and two nonsynonymous SNPs listed in the SNP database (R192Q (rs150221689) and G588 S (rs145526996)). The R192Q mutation showed co-segregation with reduced RBC ABCB6 expression in a family, and we found the G588 S mutation in a compound heterozygous individual with undetectable ABCB6 expression, suggesting that both mutations result in weak or no expression of ABCB6 on RBCs. Analysis of the intracellular expression pattern in HeLa cells by confocal microscopy indicated that these mutations do not compromise overall expression or the endolysosomal localization of ABCB6. Genotyping of two large cohorts, containing 235 and 1039 unrelated volunteers, confirmed the high allele frequency of Lan-mutations. Our results suggest that genetic variants linked to lower or absent cell surface expression of ABCB6/Langereis may be more common than previously thought.     

The expression of planarian brain factor homologs,DjFoxG and DjFoxD

Recent accumulating evidence revealed that planarian central nervous system (CNS) has numerous functional domains distinguished by a large number of neural markers, suggesting that primitive animals which developed CNS already had the framework of the brain development. It is of interest to investigate genes which have been acquired at an early stage of evolution for brain pattern formation. One such candidate is FoxG1 (BF-1), specifically expressed in the telencephalon and implicated in brain development. We identified a FoxG1 (BF-1) homolog gene in planarians (DjFoxG). We also identified a FoxD class gene, DjFoxD. DjFoxG is expressed in the body and brain, with strong expression in the mesenchyme surrounding the gut. During regeneration, an intense anterior signal is detected, but this is not restricted to the head. DjFoxD is expressed in the mid-apex of the head, between the two lobes of the brain. Strong expression was detected in the mid-anterior blastema. Thus, FoxG and FoxD homologs do exist in planarians, but are regulated differently than those in vertebrates.     

Total synthesis and adjuvant activity of all stereoisomers of pinellic acid

Pinellic acid is a novel and potentially useful oral adjuvant when used in conjunction with intranasal inoculation of influenza HA vaccines. All stereoisomers of pinellic acid have been synthesized via regioselective asymmetric dihydroxylation, regioselective inversion, and stereoselective reduction, and their adjuvant activities were characterized. Among this series of isomers, 9S, 12S, 13S compound has the most potent adjuvant activity. Structure-activity relationships are discussed.     

Inhibition of immunoglobulin G-catalyzed hydrogen peroxide generation by dexamethasone and piroxicam

In the present study, we established a simple and physiologically acceptable in vitro assay system to measure H2O2 generated by human immunoglobulin G (IgG) and other proteins. In addition, the effects of various drugs were also tested in this method. We found that UV irradiation (280 nm) of the test solutions for 1 h at 37 degrees C produced suitable conditions to test the effects of these drugs. The test solution contained 100 microg/ml IgG in 50 mM phosphate buffer (pH 7.4), and 1% dimethylformamide (DMF), a solvent used to dissolve each drug. Phosphate anions were preferable for H2O2 generation. H2O2 concentration in the irradiated sample was determined by continuous photometric measurement of absorption (O.D.) at 340 nm for 600 sec. The decrease in O.D. was due to the oxidation of NADPH by H2O2 mediated by the glutathione redox cycle. H2O2 generation was expressed as O.D.(340 nm decrease/400 sec). IgG (100 microg/ml) generated 6-7 microM H2O2/h. With irradiation, most cytokines, proteins and enzymes failed to generate significant amounts of H2O2. The formation of H2O2 from H2O and UV light-induced singlet oxygen (1O2) was demonstrated by the inhibitory effects of 1O2 quenchers. Dexamethasone (IC50: 6 ng/ml = 1.4x10(-8) M) blocked H2O2 generation catalyzed by IgG. This action was not mediated by binding to the glucocorticoid receptor. Piroxicam (IC50: 20 ng/ml = 6.0 x 10(-6) M) and diclofenac.Na (IC50: 500 ng/ml = 1.6 x 10(-5) M), but not indomethacin, also blocked H2O2 generation. The mechanism underlying the inhibition of IgG-catalyzed H2O2 generation is not clear; however, the possibility exists that these drugs intercept, or interfere with, the approach of water molecules at the catalytic interface(s) of the IgG.     

Enantioselective formation of (R)-9-HPODE and (R)-9-HPOTrE in marine green alga Ulva conglobata

When linoleic and linolenic acid were incubated with a crude enzyme of marine green alga Ulva conglobata, the corresponding (R)-9-hydroperoxy-(10E, 12Z)-10, 12-octadecadienoic acid [(R)-9-HPODE] and (R)-9-hydroperoxy-(10E, 12Z, 15Z)-10, 12, 15-octadecatrienoic acid [(R)-9-HPOTrE] were formed with a high enantiomeric excess (>99%), respectively.     

A practical synthesis and biological evaluation of 9-halogenated PGF analogues

A series of 9-halo PGF analogues 1-2 and 5-13 were synthesized and biologically evaluated. Among the compounds, 2 was the best EP2-receptor agonist. A practical method of synthesizing 2 via the Julia olefination of an aldehyde 3 with an optically active sulfone 4, which was prepared by Sharpless asymmetric epoxidation of 15, was developed. Other 9-halogenated PGF analogues were synthesized essentially by the same procedure and evaluated. The absolute configuration of 16-OH of 2 was determined as S by the X-ray analysis of a salt consisting of a 1/1 molar ratio of 2 and L-lysine.