Sequential immunization with V3 peptides from primary human immunodeficiency virus type 1 produces cross-neutralizing antibodies against primary isolates with a matching narrow-neutralization sequence motif

An antibody response capable of neutralizing not only homologous but also heterologous forms of the CXCR4-tropic human immunodeficiency virus type 1 (HIV-1) MNp and CCR5-tropic primary isolate HIV-1 JR-CSF was achieved through sequential immunization with a combination of synthetic peptides representing HIV-1 Env V3 sequences from field and laboratory HIV-1 clade B isolates. In contrast, repeated immunization with a single V3 peptide generated antibodies that neutralized only type-specific laboratory-adapted homologous viruses. To determine whether the cross-neutralization response could be attributed to a cross-reactive antibody in the immunized animals, we isolated a monoclonal antibody, C25, which neutralized the heterologous primary viruses of HIV-1 clade B. Furthermore, we generated a humanized monoclonal antibody, KD-247, by transferring the genes of the complementary determining region of C25 into genes of the human V region of the antibody. KD-247 bound with high affinity to the "PGR" motif within the HIV-1 Env V3 tip region, and, among the established reference antibodies, it most effectively neutralized primary HIV-1 field isolates possessing the matching neutralization sequence motif, suggesting its promise for clinical applications involving passive immunizations. These results demonstrate that sequential immunization with B-cell epitope peptides may contribute to a humoral immune-based HIV vaccine strategy. Indeed, they help lay the groundwork for the development of HIV-1 vaccine strategies that use sequential immunization with biologically relevant peptides to overcome difficulties associated with otherwise poorly immunogenic epitopes.     

cDNA cloning and sequencing of tobacco chloroplast ribosomal protein L12

Tobacco chloroplast ribosomal protein L12 was isolated as a ssDNA-cellulose-binding protein from a chloroplast soluble protein fraction. Based on the N-terminal amino acid sequence of chloroplast L12, a cDNA clone was isolated and characterized. The precursor protein deduced from the DNA sequence consists of a transit peptide of 53 amino acid residues and a mature L12 protein of 133 amino acid residues. The chloroplast L12 protein was synthesized with a reticulocyte lysate and subjected to nucleic acid-binding assays. L12 synthesized in vitro does not bind to ssDNA, dsDNA nor ribonucleotide homopolymers, but it binds to cellulose matrix.     

K‐distribution three‐dimensional mapping of biological tissues in optical coherence tomography

Probability density function (PDF) analysis with K‐distribution model of optical coherence tomography (OCT) intensity signals has previously yielded a good representation of the average number of scatterers in a coherence volume for microspheres‐in‐water systems, and has shown initial promise for biological tissue characterization. In this work, we extend these previous findings, based on single point M‐mode or two‐dimenstional slice analysis, to full three‐dimensional (3D) imaging maps of the shape parameter α of the K‐distribution PDF. After selecting a suitably sized 3D evaluation window, and verifying methodology in phantoms, the resultant parametric α images obtained in different animal tissues (rat liver and brain) show new contrasting ability not seen in conventional OCT intensity images.      

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis

Seborrheic dermatitis (SD) is a chronic inflammatory dermatologic condition in which erythema and itching develop on areas of the body with sebaceous glands, such as the scalp, face and chest. The inflammation is evoked directly by oleic acid, which is hydrolyzed from sebum by lipases secreted by skin microorganisms. Although the skin fungal genus, Malassezia, is thought to be the causative agent of SD, analysis of the bacterial microbiota of skin samples of patients with SD is necessary to clarify any association with Malassezia because the skin microbiota comprises diverse bacterial and fungal genera. In the present study, bacterial microbiotas were analyzed at non‐lesional and lesional sites of 24 patients with SD by pyrosequencing and qPCR. Principal coordinate analysis revealed clear separation between the microbiota of non‐lesional and lesional sites. Acinetobacter, Corynebacterium, Staphylococcus, Streptococcus and Propionibacterium were abundant at both sites. Propionibacterium was abundant at non‐lesional sites, whereas Acinetobacter, Staphylococcus and Streptococcus predominated at lesional sites; however, the extent of Propionibacterium colonization did not differ significantly between lesional and non‐lesional sites according to qPCR. Given that these abundant bacteria hydrolyze sebum, they may also contribute to SD development. To the best of our knowledge, this is the first comprehensive analysis of the bacterial microbiotas of the skin of SD patients.     

Temporal variation of δ<Superscript>13</Superscript>C of larch leaves from a montane boreal forest in Mongolia

This paper reports the temporal variation (2002–2004) in foliar δ¹³C values, which are indicative of long-term integrated photosynthetic and water use characteristics, of Siberian larch (Larix sibirica Ledeb.) trees in a montane forest at Mongonmorit, NE Mongolia. At the stand, the δ¹³C value for understory shaded leaves was more negative by 2‰ on average than that for sunlit leaves sampled concurrently from open and sun-exposed environments in a forest gap. The δ¹³C value of both sunlit and shaded leaves showed pronounced intra- but relatively small inter-seasonal variations. The δ¹³C value was more positive for juvenile than mature leaves. We conjecture that juvenile leaves may derive carbon reserves in woody tissues (e.g., stems). Regardless of leaf habitats, the δ¹³C value was also affected by insect herbivores occurred in mid summer of 2003, being more negative in newly emerging leaves from the twigs after defoliation than in non-defoliated mature leaves. This pattern seems to contrast with that for the juvenile leaves in the early growing season. We surmise that the newly emerging leaves used stored organic carbon that was depleted due to fractionation during remobilization and translocation for leaf regrowth. There was also intra- and inter-seasonal variation in the foliar N concentrations and C:N ratios. A good positive (negative) correlation between the foliar δ¹³C values and N concentrations (C:N ratios) was also observed for both sunlit and shaded leaves, suggesting that the relationship between water and nitrogen use is a crucial factor affecting the plant carbon–water relationship in this mid latitude forest with a cold semiarid climate. Our isotopic data demonstrate that the larches in NE Mongolia exhibits relatively higher water use efficiency with a distinct within-season variability.     

Macrophage-colony stimulating factor in obese adipose tissue: studies with heterozygous op/+ mice

Objective: We examined the gene expression of macrophage‐colony stimulating factor (M‐CSF) in mice with diet‐induced obesity and in genetically obese mice. We also examined the effect of decreased M‐CSF signaling on the susceptibility to obesity and macrophage recruitment into the adipose tissue of mice. Research Methods and Procedures: The adipose tissue from mice with diet‐induced obesity, obese KKA^y mice, and ob/ob obese mice was used for RNA preparation. Production of M‐CSF and monocyte chemoattractant protein‐1 (MCP‐1) was examined by quantitative real‐time polymerase chain reaction (PCR) and enzyme‐linked immunosorbent assay. The op/+ heterozygous mice, with decreased functional M‐CSF expression, were placed on a high‐fat diet or crossed with KKA^y mice to study the susceptibility to obesity. The gene expression of macrophage markers in adipose tissue was examined. Results: The expression of M‐CSF was not significantly changed in mice on a high‐fat diet or in either type of genetic obesity (KKA^y or ob/ob mice). No change in the degree of obesity or macrophage‐related gene expression (F4/80, CD68, and MCP‐1) in the adipose tissue was observed in op/+ mice compared with +/+ control mice, which were either treated with a high‐fat diet or crossed with KKA^y mice. Discussion: This study demonstrated that there was no significant change in the expression of M‐CSF in the adipose tissue from obese mice and only a minor phenotypic change, such as macrophage infiltration, in the adipose tissue from op/+ mice, suggesting that M‐CSF does not play a major role in macrophage recruitment in the adipose tissue of obese mice.     

Genes Encoding the Group I Intron-containing tRNALeu and Subunit L of NADH Dehydrogenase from the Cyanobacterium Synechococcus PCC 6301

A part of the tRNA^Leu (UAA) gene containing a 240-nucleotidegroup I intron was amplified by PCR from cyanobacterium SynechococcusPCC 6301 genomic DNA. The pre-tRNA synthesized from the clonedPCR product was efficiently self-spliced in vitro under physiologicalconditions. The gene encoding the tRNA^Leu (UAA), trnL-UAA, wasisolated from a Synechococcus PCC 6301 genomic library and thenucleotide sequence of a 2,167-bp portion was determined. ThetrnL-UAA consists of a 34-bp 5' exon, a 240-bp group I intronand a 50-bp 3' exon. In addition, three open reading frames(ORF1, ORF2 and ORF3) were found in the 5' and 3' flanking regionsof trnL-UAA. The predicted protein sequence of ORF3, which islocated 74-bp upstream from trnL-UAA on the opposite strand,shows 66.2% amino acid identity to that of the SynechocystisPCC 6803 gene encoding subunit L of NADH dehydrogenase (ndhL).     

Discovery of a new 2-aminobenzhydrol template for highly potent squalene synthase inhibitors

To obtain small and efficient squalene synthase inhibitors, a flexible 2-aminobenzhydrol open form structure was designed and showed potent inhibitory activity comparable to 4,1-benzoxazepin compounds. Further chemical modification led to the discovery of a novel template with a strong squalene synthase inhibitory activity, and its basic structure-activity relationship was revealed. The X-ray crystallographic data of compound 12 bound to the active site of squalene synthase provided an important insight into the binding mode of this alternative template that formed 11-membered ring conformations with an intramolecular hydrogen bond.     

Crystal structure of α5β1 integrin ectodomain: atomic details of the fibronectin receptor

Integrin α5β1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the α5β1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2.9-Å resolution both in the absence and presence of a ligand peptide containing the Arg-Gly-Asp (RGD) sequence. The antibody-bound β1 chain accommodated the RGD ligand with very limited structural changes, which may represent the initial step of cell adhesion mediated by nonactivated integrins. Furthermore, a molecular dynamics simulation pointed to an important role for Ca²⁺ in the conformational coupling between the ligand-binding site and the rest of the molecule. The RGD-binding pocket is situated at the center of a trenchlike exposed surface on the top face of α5β1 devoid of glycosylation sites. The structure also enabled the precise prediction of the acceptor residue for the auxiliary synergy site of fibronectin on the α5 subunit, which was experimentally confirmed by mutagenesis and kinetic binding assays.