Deep-Sequencing Analysis of the Association between the Quasispecies Nature of the Hepatitis C Virus Core Region and Disease Progression

Variation of core amino acid (aa) 70 of hepatitis C virus (HCV) has been shown recently to be closely correlated with liver disease progression, suggesting that the core region might be present as a quasispecies during persistent infection and that this quasispecies nature might have an influence on the progression of disease. In our investigation, the subjects were 79 patients infected with HCV genotype 1b (25 with chronic hepatitis [CH], 29 with liver cirrhosis [LC], and 25 with hepatocellular carcinoma [HCC]). Deep sequencing of the HCV core region was carried out on their sera by using a Roche 454 GS Junior pyrosequencer. Based on a plasmid containing a cloned HCV sequence (pCV-J4L6S), the background error rate associated with pyrosequencing, including the PCR procedure, was calculated as 0.092 ± 0.005/base. Deep sequencing of the core region in the clinical samples showed a mixture of “mutant-type” Q/H and “wild-type” R at the core aa 70 position in most cases (71/79 [89.9%]), and the ratio of mutant residues to R in the mixture increased as liver disease advanced to LC and HCC. Meanwhile, phylogenetic analysis of the almost-complete core region revealed that the HCV isolates differed genetically depending on the mutation status at core aa 70. We conclude that the core aa 70 mixture ratio, determined by deep sequencing, reflected the status of liver disease, demonstrating a significant association between core aa 70 and disease progression in CH patients infected with HCV genotype 1b.     

The Effect of Potassium Nitrate on the Reduction of Phytophthora Stem Rot Disease of Soybeans, the Growth Rate and Zoospore Release of Phytophthora sojae

The effects of potassium nitrate (KNO₃) application on Phytophthora stem rot disease reduction of Glycine max (L.) Merr. cvs. Chusei-Hikarikuro and Sachiyutaka, and mycelium growth and zoospore release of a Phytophthora sojae isolate were investigated under laboratory conditions. The application of 4–30 m m KNO₃ prior to inoculation greatly reduced incidence of disease in the two soybean cultivars. Although a concentration of 20–30 m m KNO₃ led to a slight decrease in the growth rate of the PJ-H30 isolate on PDA medium, no significant relationship was observed between inhibition of the growth rate and disease reduction on application of 0.4–10 m m KNO₃. Disease suppression recorded in laboratory experiments using pathogen mycelium was due to the response of plant tissues rather than a direct inhibition of pathogen hyphal growth by the application of KNO₃. The extent of disease reduction was related to increased potassium concentration in plants of the two cultivars (except for some cases involving cv. Sachiyutaka), suggesting that differences existed between the two cultivars in terms of the effect of KNO₃ application on disease suppression. Scanning electron microscopic observation with fresh samples indicated marked accumulation of potassium at the penetration-stopping sites of P. sojae in the cortex layer of soybean plants treated with 30 m m KNO₃, compared with the non-treated control plants. The presence of 0.4–30 m m KNO₃ decreased the release of zoospores. These results suggest the possibility of applying a solution containing 20–30 m m of KNO₃ to decrease the incidence of disease in agricultural fields by the response of plant tissues to KNO₃.     

Evidence for Interference by Immune Complexes in the Serodiagnosis of Cryptococcosis

The latex agglutination test was used to compare cryptococcal antigen titers before and after protease treatment in 19 patients with pulmonary cryptococcosis. Antigen was detected by the LA test in 13 of 33 serum samples before protease treatment, and in an additional 13 samples following treatment. Of 26 antigen-positive serum samples, 22 (84.6%) showed an increased antigen titer after protease treatment. Using the cell slide agglutination test, antibody was detected in 3 of 19 cases. In one of these 3, antigen could only be detected after protease treatment. Soluble immune complex was prepared in vitro using anti-C. neoformans rabbit antiserum and polysaccharide antigen of C. neoformans, and the effects of immune complexes on the LA test were examined. In this experimental model, soluble immune complexes seemed to be observed in antibody excess region, because the antigen titers were increased after the protease treatment. We concluded that C. neoformans capsular polysaccharide antigen and anti-C. neoformans antibody formed soluble immune complexes in patients' sera, which interfered with antigen detection by the latex agglutination test without protease treatment.     

In Vitro Reconstitution of a CaMKII Memory Switch by an NMDA Receptor-Derived Peptide

Ca²⁺/Calmodulin-dependent protein kinase II (CaMKII) has been shown to play a major role in establishing memories through complex molecular interactions including phosphorylation of multiple synaptic targets. However, it is still controversial whether CaMKII itself serves as a molecular memory because of a lack of direct evidence. Here, we show that a single holoenzyme of CaMKII per se serves as an erasable molecular memory switch. We reconstituted Ca²⁺/Calmodulin-dependent CaMKII autophosphorylation in the presence of protein phosphatase 1 in vitro, and found that CaMKII phosphorylation shows a switch-like response with history dependence (hysteresis) only in the presence of an N-methyl-D-aspartate receptor-derived peptide. This hysteresis is Ca²⁺ and protein phosphatase 1 concentration-dependent, indicating that the CaMKII memory switch is not simply caused by an N-methyl-D-aspartate receptor-derived peptide lock of CaMKII in an active conformation. Mutation of a phosphorylation site of the peptide shifted the Ca²⁺ range of hysteresis. These functions may be crucial for induction and maintenance of long-term synaptic plasticity at hippocampal synapses.     

Exopolysaccharide production by a unicellular freshwater cyanobacterium Cyanothece sp. isolated from a rice field in Vietnam

A unicellular cyanobacterium that produces a large amount of exopolysaccharide (EPS) was isolated from a rice field in Phu Tho Province, Vietnam. Morphological characteristics and phylogenetic analysis using a partial sequence of the 16S rRNA gene revealed that the isolate was closely related to the genus Cyanothece. The isolate, named Cyanothece sp. Viet Nam 01, grew at a wide range of temperatures (25–40 °C), but was not viable below 20 °C. The isolate had an ability of aerobic nitrogen fixation. The EPS was purified using NaOH extraction and ethanol precipitation, and the absolute molecular weight was estimated to be 4.5?×?10⁴ kDa. The pattern of the Fourier transform infrared spectrum indicated that the EPS had carbonyl and sulfate groups, as well as the typical functional groups of sugars. The uronic acid and sulfur contents were 23 and 8.4 mol% per total monosaccharide, respectively. The EPS constituent monosaccharides were rhamnose, glucose, galactose, xylose, mannose, fucose, arabinose, ribose, and unknown sugar, with molar compositions of 38.6:13.8:4.8:4.8:2.4:3.5:2.0:0.6:6.5, respectively.     

Detection sensitivity of influenza rapid diagnostic tests

The sensitivity of influenza rapid diagnostic tests (IRDTs) currently available in Japan for various influenza virus strains, including human H7N9 and H5N1 isolates, were compared and it was found that all of the IRDTs examined detected these viruses; however, their detection sensitivities differed.