Amino acid insertions near Gag cleavage sites restore the otherwise compromised replication of human immunodeficiency virus type 1 variants resistant to protease inhibitors

A variety of amino acid substitutions in the protease and Gag proteins have been reported to contribute to the development of human immunodeficiency virus type 1 (HIV-1) resistance to protease inhibitors. In the present study, full-length molecular infectious HIV-1 clones were generated by using HIV-1 variants isolated from heavily drug-experienced and therapy-failed AIDS patients. Of six full-length infectious clones generated, four were found to have unique insertions (TGNS, SQVN, AQQA, SRPE, APP, and/or PTAPPA) near the p17/p24 and p1/p6 Gag cleavage sites, in addition to the known resistance-related multiple amino acid substitutions within the protease. The addition of such Gag inserts mostly compromised the replication of wild-type HIV-1, whereas the primary multidrug-resistant HIV infectious clones containing inserts replicated significantly better than those modified to lack the inserts. Western blot analyses revealed that the processing of Gag proteins by wild-type protease was impaired by the presence of the inserts, whereas that by mutant protease was substantially improved. The present study represents the first report clearly demonstrating that the inserts seen in the proximity of the Gag cleavage sites in highly multi-PI resistant HIV-1 variants restore the otherwise compromised enzymatic activity of mutant protease, enabling the multi-PI-resistant HIV-1 variants to remain replication competent.     

Ability of a Microbial Consortium to Remove Pesticide,Carbendazim and 2,4-Dichlorophenoxyacetic Acid

A bacterial consortium capable of simultaneously degrading the fungicide, carbendazim, and the herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D) was obtained by enrichment of soil samples collected from paddy fields in Japan. This consortium was acclimated in a continuously fed culture with 20 M carbendazim and 2 mM 2,4-D as sole carbon sources using a glass column reactor. By denaturing gradient gel electrophoresis, we observed changes in the bacterial population following the degradation of the both pesticides. This acclimated consortium completely degraded up to 100 M carbendazim and 3 mM 2,4-D within 36 and 24 h, respectively, in batch culture, but a lag time was observed after precultivation in a rich medium. The immobilization of the consortium on a polyester support enhanced the degradation ability of this consortium compared with the use of free cells. This microbial consortium could be useful for bioremediation at sites contaminated with these pesticides.     

Mhc class II B gene evolution in East African cichlid fishes

 A distinctive feature of essential major histocompatibility complex (Mhc) loci is their polymorphism characterized by large genetic distances between alleles and long persistence times of allelic lineages. Since the lineages often span several successive speciations, we investigated the behavior of the Mhc alleles during or close to the speciation phase. We sequenced exon 2 of the class II B locus 4 from 232 East African cichlid fishes representing 32 related species. The divergence times of the (sub)species ranged from 6000 to 8.4 million years. Two types of evolutionary analysis were used to elucidate the pattern of exon 2 sequence divergence. First, phylogenetic methods were applied to reconstruct the most likely evolutionary pathways leading from the last common ancestor of the set to the extant sequences, and to assess the probable mechanisms involved in allelic diversification. Second, pairwise comparisons of sequences were carried out to detect differences seemingly incompatible with origin by nonparallel point mutations. The analysis revealed point mutations to be the most important mechanism behind allelic divergences, with recombination playing only an auxiliary part. Comparison of sequences from related species revealed evidence of random allelic (lineage) losses apparently associated with speciation. Sharing of identical alleles could be demonstrated between species that diverged 2 million years ago. The phylogeny of the exon was incongruent with that of the flanking introns, indicating either a high degree of convergent evolution at the peptide-binding region-encoding sites, or intron homogenization. Received: 6 December 1999 / Revised: 15 February 2000     

Switching characteristics of a model for biochemical-reaction networks describing autophosphorylation versus dephosphorylation of Ca2+/calmodulin-dependent protein kinase II

Ca2+/calmodulin-dependent protein kinase II (CaMKII) has been suggested to participate in various cellular phenomena triggered by Ca2+ signalling. In the present study, we addressed the functional role of CaMKII in molecular-signal transduction in cells by mathematical modelling of putative biochemical-reaction networks thought to represent an essential part of molecular events responsible for CaMKII-related cellular phenomena. These networks include Ca2+/calmodulin-dependent threonine-286/287 (Thr286/287) autophosphorylation of CaMKII versus dephosphorylation of the enzyme. Computer simulation of the model was performed to examine the relation between the Ca2+-signalling pattern as an input and the resulting degree of Thr286/287 autophosphorylation (m) as an output. Under the simplified condition that the Ca2+ concentration during Ca2+ signalling was set to remain constant with time, the biochemical-reaction networks were shown to function as a switch. There is a threshold for gamma, a parameter representing the probability that the Thr286/287-dephosphorylated CaMKII subunit binds with the Ca2+/calmodulin complex; if gamma is above this threshold, m increases with time to a large degree (switch-on); otherwise, it remains near zero (switch-off). Mathematically, this sharp onset of m at the threshold can be accounted for by a change in the structure of the dynamic system describing the model, from bistability to monostability; this is analogous to the first-order phase transition in statistical physics. For the oscillatory time course of [Ca2+], switching characteristics were also shown with respect to the frequency and the maximum amplitude of the oscillation. These results suggest that graded information mediated by Ca2+ signalling is digitized into all-or-non information mediated by Thr286/287 autophosphorylation of CaMKII.     

A molecular phylogenetic framework for the Ryukyu endemic rodents Tokudaia osimensis and Diplothrix legata

Diplothrix legata and Tokudaia osimensis are rodent species endemic to the Ryukyu Islands (Okinawa area) of the southern part of Japan. To place them within a phylogenetic framework of Asian rodent species, we examined the molecular relationships among these species and Apodemus, Micromys, Mus, and Rattus, using an analysis of mitochondrial cytochrome b gene (1140 bp) and nuclear IRBP gene (782 bp) sequences. The results indicate that the four main murine genera and Tokudaia diverged at similar evolutionary times, namely at the time of the radiation of Murinae, 14 to 40 million years ago, depending on different concepts for the divergence times of Rattus and Mus. In contrast, Diplothrix separated from the Rattus group more recently. Our results indicate that D. legata and the Rattus group diverged at 20-30% of the divergence time of Rattus and Mus under the assumption of the molecular clock, suggesting that D. legata established its lineage at least by the beginning of the Pleistocene era. It is thus evident that the Okinawa area preserves rare indigenous species with various levels of genetic endemicity.     

Synergistic tumor suppression by a <Emphasis Type="Italic">Perilla frutescens</Emphasis>-derived methoxyflavanone and anti-cancer tyrosine kinase inhibitors in A549 human lung adenocarcinoma

Anti-cancer tyrosine kinase inhibitors (TKIs) are effective in many types of cancers including non-small cell lung cancer, while appearance of TKI-resistant tumors suggests a need for the development of their potentiation strategies. We have previously shown that a methoxyflavanone derivative from the Asian medicinal herb Perilla frutescens (Perilla-derived methoxyflavanone; PDMF) shows a prominent anti-tumor activity against A549 human lung adenocarcinoma. Here we show that PDMF and anti-cancer TKIs (nilotinib, bosutinib, dasatinib, and ponatinib) synergistically suppress proliferation of A549 cells. Flow cytometric analysis indicated that co-stimulation with nilotinib (4 μM) and PDMF induced G₂/M cell cycle arrest in low PDMF doses (10–50 μM), whereas this combination triggered de novo G₁ arrest in higher PDMF dosages (50–125 μM). We also found that co-administration with nilotinib and PDMF significantly suppressed in vivo tumorigenicity of A549 cells in athymic nude mice.     

Sitosterol prevents obesity-related chronic inflammation

The physiological roles of phytosterols in chronic inflammation, which are believed to be involved in the underlying mechanisms for metabolic diseases, have yet to be elucidated. Therefore, in the present study, we aimed to elucidate the physiological roles of phytosterols in both clinical studies and animal experiments. We observed the existence of rather specific negative correlations between the serum sitosterol level and the serum IL-6 and the TNF-α levels in both diabetic subjects (n = 46) and non-diabetic subjects (n = 178). Multiple regression analyses also revealed that the serum IL-6 and TNF-α levels exhibited strong negative correlations with the serum sitosterol levels. When ABCG5/8 KO mice with markedly elevated plasma sitosterol levels and ABCG5/8 hetero mice were fed a high-fat diet, we observed that the increase in body weight, the fatty liver changes, and the expansion of perigonadal adipose tissues were suppressed in ABCG5/8 KO mice without any modulation of food intake. We also observed that the plasma IL-6 and TNF-α levels, the expressions of TNF-α and PAI-1 in the liver and the expressions of the IL-6, TNF-α, and MCP-1 levels in the adipose tissue were lower in ABCG5/8 KO mice. These results suggest that sitosterol might suppress obesity-related chronic inflammation and might be applicable to the treatment of metabolic diseases.     

Discontinuation of adalimumab after attaining disease activity score 28-erythrocyte sedimentation rate remission in patients with rheumatoid arthritis (HONOR study): an observational study

Introduction

Evidences of biologics-free disease control after discontinuing adalimumab (ADA) in rheumatoid arthritis (RA) patients in clinical practice have not been sufficiently investigated. Purpose of this study is to investigate whether disease activity score 28 (DAS28)- erythrocyte sedimentation rate (ESR) remission was preserved after discontinuation of ADA in patients with RA.

Methods

This is an observational but not a randomized controlled study. Among 197 RA patients who initiated with combination of ADA with concomitant MTX, 69 (35%) acquired DAS28 (ESR) < 2.6 for at least 24 weeks. Of those 69 patients, 51 went on ADA discontinuation with their consent, and finally 50 of those with follow-up of > 24 weeks were evaluated. The effect of discontinuing ADA on clinical disease activity, functional disability and radiographic progression were evaluated by DAS28 (ESR), the clinical disease activity index (CDAI) and the simplified disease activity index (SDAI), by a health assessment questionnaire-disability index (HAQ-DI) and by the modified total Sharp score (mTSS), respectively.

Results

The mean age of the participants was 59.5 years with the mean disease duration of 7.1 years. Out of the 50 patients, 29 (58%) were maintained in DAS28 (ESR) < 2.6 at 24 weeks after discontinuing ADA. A logistic regression analysis showed that DAS28 (ESR) at baseline significantly predicted a DAS28 (ESR) < 2.6 maintained after discontinuation of ADA, and a receiver-operating characteristic (ROC) analysis showed that the cut-off value of DAS28 (ESR) at discontinuation was 2.16. The mean HAQ-DI at six months after discontinuing ADA was 0.1 in patients who kept in DAS28 (ESR) < 2.6, and 94.9% (37/39) showed no evidence of radiographic progression (> 0.5 per year of a change in mTSS) at 1 year.

Conclusions

It was possible to maintain DAS28 (ESR) < 2.6 after discontinuation of ADA without functional and radiographic progression and very low DAS28 (ESR) at the discontinuation was associated with successful ADA-free DAS28 (ESR) < 2.6 in patients with RA.

Trial registration

University Hospital Medical Information Network Identifier: UMIN000006669.     

Structural and phylogenetic comparison of napsin genes: The duplication,loss of function and human-specific pseudogenization of napsin B

Aspartic proteinases form a widely distributed protein superfamily, including cathepsin D, cathepsin E, pepsins, renin, BACE and napsin. Human napsin genes are located on human chromosome 19q13, which comprises napsin A and napsin B. Napsin B has been annotated as a pseudogene because it lacks an in-frame stop codon; its nascent chains are cotranslationally degraded. Until recently, there have been no studies concerning the molecular evolution of the napsin protein family in the human genome. In the present study, we investigated the evolution and gene organization of the napsin protein family. Napsin B orthologs are primarily distributed in primates, while napsin A orthologs are the only napsin genes in other species. The corresponding regions of napsin B in the available sequences from primate species contain an in-frame stop codon at a position equivalent to that of human napsin A. In addition, a rare single-nucleotide polymorphism (SNP) that creates a proper stop codon in human napsin B was identified using HapMap populations. Recombinant protein expression and three-dimensional comparative modeling revealed that napsin B exhibits residual activity toward synthetic aspartic protease substrates compared with napsin A, presumably through a napsin B-specific Arg287 residue. Thus, napsin B was duplicated from napsin A during the early stages of primate evolution, and the subsequent loss of napsin B function during primate evolution reflected ongoing human-specific napsin B pseudogenization.