Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer

Pandemic 2009 influenza A virus (A/H1N1/2009) has emerged globally. In this study, we performed a comprehensive detection of potential pathogens by de novo sequencing using a next-generation DNA sequencer on total RNAs extracted from an autopsy lung of a patient who died of viral pneumonia with A/H1N1/2009. Among a total of 9.4×10⁶ 40-mer short reads, more than 98% appeared to be human, while 0.85% were identified as A/H1N1/2009 (A/Nagano/RC1-L/2009(H1N1)). Suspected bacterial reads such as Streptococcus pneumoniae and other oral bacteria flora were very low at 0.005%, and a significant bacterial infection was not histologically observed. De novo assembly and read mapping analysis of A/Nagano/RC1-L/2009(H1N1) showed more than ×200 coverage on average, and revealed nucleotide heterogeneity on hemagglutinin as quasispecies, specifically at two amino acids (Gly₁₇₂Glu and Gly₂₃₉Asn of HA) located on the Sa and Ca2 antigenic sites, respectively. Gly239 and Asn239 on antigenic site Ca2 appeared to be minor amino acids compared with the highly distributed Asp239 in H1N1 HAs. This study demonstrated that de novo sequencing can comprehensively detect pathogens, and such in-depth investigation facilitates the identification of influenza A viral heterogeneity. To better characterize the A/H1N1/2009 virus, unbiased comprehensive techniques will be indispensable for the primary investigations of emerging infectious diseases.     

Ectopic expression of a rice plasma membrane intrinsic protein (OsPIP1;3) promotes plant growth and water uptake

Plasma membrane intrinsic proteins (PIPs) are known to be major facilitators of the movement of a number of substrates across cell membranes. From a drought‐resistant cultivar of Oryza sativa (rice), we isolated an OsPIP1;3 gene single‐nucleotide polymorphism (SNP) that is mostly expressed in rice roots and is strongly responsive to drought stress. Immunocytochemistry showed that OsPIP1;3 majorly accumulated on the proximal end of the endodermis and the cell surface around the xylem. Expression of GFP‐OsPIP1;3 alone in Xenopus oocytes or rice protoplasts showed OsPIP1;3 mislocalization in the endoplasmic reticulum (ER)‐like neighborhood, whereas co‐expression of OsPIP2;2 recruited OsPIP1;3 to the plasma membrane and led to a significant enhancement of water permeability in oocytes. Moreover, reconstitution of 10×His‐OsPIP1;3 in liposomes demonstrated water channel activity, as revealed by stopped‐flow light scattering. Intriguingly, by patch‐clamp technique, we detected significant NO₃^? conductance of OsPIP1;3 in mammalian cells. To investigate the physiological functions of OsPIP1;3, we ectopically expressed the OsPIP1;3 gene in Nicotiana benthamiana (tobacco). The transgenic tobacco plants exhibited higher photosynthesis rates, root hydraulic conductivity (Lp_r) and water‐use efficiency, resulting in a greater biomass and a higher resistance to water deficit than the wild‐type did. Further experiments suggested that heterologous expression of OsPIP1;3 in cyanobacterium altered bacterial growth under different conditions of CO₂ gas supply. Overall, besides shedding light on the multiple functions played by OsPIP1;3, this work provides insights into the translational value of plant AQPs.     

Biochemical and pathophysiological characterization of Helicobacter pylori asparaginase

Asparaginase was purified from Helicobacter pylori 26695 and its pathophysiological role explored. The K(m) value of asparagine was 9.75 ± 1.81 μM at pH 7.0, and the optimum pH range was broad and around a neutral pH. H. pylori asparaginase converted extracellular asparagine to aspartate. H. pylori cells were unable to take up extracellular asparagine directly. Instead, aspartate produced by the action of the asparaginase was transported into H. pylori cells, where it was partially converted to β-alanine. Asparaginase exhibited striking cytotoxic activity against histiocytic lymphoma cell line U937 cells via asparagine deprivation. The cytotoxic activity of live H. pylori cells against U937 cells was significantly diminished by deletion of the asparaginase gene, indicating that asparaginase functions as a cytotoxic agent of the bacterium. The cytotoxic effect was negligible for gastric epithelial cell line AGS cells, suggesting that the effect differs across host cell types. An asparaginase-deficient mutant strain was significantly less capable of colonizing Mongolian gerbils. Since asparagine depletion by exogenous asparaginase has been shown to suppress lymphocyte proliferation in vivo, the present results suggest that H. pylori asparaginase may be involved in inhibition of normal lymphocyte function at the gastric niche, allowing H. pylori to evade the host immune system.     

Immunochemical detection of flavonoid glycosides: development, specificity, and application of novel monoclonal antibodies

Flavonoid-rich diets are expected to decrease the risk of cardiovascular diseases. The localization and target sites of flavonoids underlying the protective mechanism in vivo have not been fully investigated because the methods for detection of flavonoids have been limited to chemical analysis such as high-performance liquid chromatography. To further understand the actions of flavonoids in vivo, we developed a novel methodology that immunochemically evaluates flavonoids using specific antibodies. Quercetin-3-glucuronide (Q3GA), a major metabolite in human plasma, was coupled with keyhole limpet hemocyanin. Alternatively, the sugar moiety of quercetin-3-glucoside (Q3G) was succinylated and then coupled with a carrier protein. Using these two immunogens, we finally obtained two monoclonal antibodies, mAb14A2 and mAb11G6, from the immunogen using Q3GA and Q3G, respectively. Competitive enzyme-linked immunosorbent assay showed the unique difference in the specificity between the two similar antibodies: mAb14A2 recognized several quercetin-3-glycosides including Q3G and rutin but mAb11G6 was highly specific to the Q3G structure. The macrophage-derived foam cells in human atherosclerotic lesions were significantly stained with mAb14A2 but scarcely with mAb11G6. These results showed that the anti-flavonoid glycoside antibodies are useful tools for evaluating their localization in tissues and that the specificities strongly depend on the immunogen design for synthesizing the hapten-protein conjugates.     

Characterization of factors affecting the activity of photosystem I cyclic electron transport in chloroplasts

PSI cyclic electron transport is essential for photosynthesis and photoprotection. In higher plants, the antimycin A-sensitive pathway is the main route of electrons in PSI cyclic electron transport. Although a small thylakoid protein, PGR5 (PROTON GRADIENT REGULATION 5), is essential for this pathway, its function is still unclear, and there are numerous debates on the rate of electron transport in vivo and its regulation. To assess how PGR5-dependent PSI cyclic electron transport is regulated in vivo, we characterized its activity in ruptured chloroplasts isolated from Arabidopsis thaliana. The activity of ferredoxin (Fd)-dependent plastoquinone (PQ) reduction in the dark is impaired in the pgr5 mutant. Alkalinization of the reaction medium enhanced the activity of Fd-dependent PQ reduction in the wild type. Even weak actinic light (AL) illumination also markedly activated PGR5-dependent PSI cyclic electron transport in ruptured chloroplasts. Even in the presence of linear electron transport [11 mumol O2 (mg Chl)(-1) h(-1)], PGR5-dependent PSI electron transport was detected as a difference in Chl fluorescence levels in ruptured chloroplasts. In the wild type, PGR5-dependent PSI cyclic electron transport competed with NADP+ photoreduction. These results suggest that the rate of PGR5-dependent PSI cyclic electron transport is high enough to balance the production ratio of ATP and NADPH during steady-state photosynthesis, consistently with the pgr5 mutant phenotype. Our results also suggest that the activity of PGR5-dependent PSI cyclic electron transport is regulated by the redox state of the NADPH pool.     

Antennal motor system of the cockroach, <Emphasis Type="Italic">Periplaneta americana</Emphasis>

The organization of the antennal muscles, nerves, and motor neurons has been investigated in the cockroach, Periplaneta americana. Antennal movements have been observed by video analysis, muscle actions have been determined by dissection and direct mechanical testing, and the motor neurons innervating each muscle have been defined with a recently developed selective backfill method. A model of the antennomotor system of Periplaneta has thus been established and compared with that of crickets. Five muscles located within the head capsule insert on the most proximal antennal segment, the scape. By their action, they allow the scape to move in essentially any direction within the dorsoventral and anteroposterior planes. An additional pair of muscles, one dorsal and one ventral, are found within the scape. They insert on the pedicel and move the pedicel in the dorsal-ventral plane. These seven muscles are controlled by at least 17 motor neurons with somata located in the deutocerebrum. By their action, these motor neurons enable cockroaches to move the long flagellum of each antenna through a wide range of positions in the frontal space, medio-laterally, and also allow depression toward the substrate and elevation well above the level of the head. The antennal motor neurons have been classified into five morphological types based on soma and axon location. Each morphological type has been correlated with a particular pattern of muscle innervation and control. The neurites of all motor neurons are located along the medial aspect of the dorsal lobe of the deutocerebrum. This research was supported by grant nos. IBN 96-04629 and 04-22883 from the National Science Foundation.     

Spike‐dependent calcium influx in dendrites of the cricket giant interneuron

Identified wind‐sensitive giant interneurons in the cricket's cercal sensory system integrate cercal afferent signals and release an avoidance behavior. A calcium‐imaging technique was applied to the giant interneurons to examine the presence of the voltage‐dependent Ca²⁺ channels (VDCCs) in their dendrites. We found that presynaptic stimuli to the cercal sensory nerve cords elevated the cytosolic Ca²⁺ concentration ([Ca²⁺]_i) in the dendrites of the giant interneurons. The dendritic Ca²⁺ rise coincided with the spike burst of the giant interneurons, and the rate of Ca²⁺ rise depended on the frequency of the action potentials. These results suggest that the action potentials directly caused [Ca²⁺]_i increase. Observation of the [Ca²⁺]_i elevation induced by depolarizing current injection demonstrates the presence of the VDCCs in the dendrites. Although hyperpolarizing current injection into the giant interneuron suppressed action potential generation, EPSPs could induce no [Ca²⁺]_i increase. This result means that ligand‐gated channels do not contribute to the synaptically stimulated Ca²⁺ elevation. On the other hand, antidromically stimulated spikes also increased [Ca²⁺]_i in all cellular regions including the dendrites. And bath application of a mixture of Ni²⁺, Co²⁺, and Cd²⁺ or tetrodotoxin inhibited the [Ca²⁺]_i elevation induced by the antidromic stimulation. From these findings, we suppose that the axonal spikes antidromically propagate and induce the Ca²⁺ influx via VDCCs in the dendrites. The spike‐dependent Ca²⁺ elevation may regulate the sensory signals processing via second‐messenger cascades in the giant interneurons. © 2000 John Wiley & Sons, Inc. J Neurobiol 44: 45–56, 2000     

Alteration in Gene Expression during Cold Treatment of Rice Plant

Alteration of gene expression during cold stress was examinedby study of the in vitro translation products of poly(A)⁺RNAextracted from rice leaves. Upon in vitro translation of poly(A)⁺-RNAof cold tolerant rice seedlings (variety, Somewake), severalnew polypeptides were found to be induced or repressed by coldstress. In particular, a 14 kDa polypeptide was strongly inducedat 5?C but not at 15?C or 42?C. ¹ Present address: National Institute of Agrobiological Resources,Tsukuba Science City, Ibaraki, 305 Japan (Received January 25, 1991; Accepted June 24, 1991)