Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.     

Chromatic Regulation of Photosystem Composition in the Cyanobacterial Photosynthetic System: Kinetic Relationship between Change of Photosystem Composition and Cell Proliferation

Kinetics of the change of photosystem (PS) composition in cyanobacteriainduced by chromatic light were studied in relation to cellproliferation. The study was made for two unicellular strains,Synechococcus NIBB 1059 and Synechocystis (Aphanocapsa) PCC6714. We found that (1) the change to a higher or lower PS I/IIratio was due to acceleration or suppression of apparent PSI formation, and (2) it progressed on a similar time scale tothat of the cell proliferation. The apparent rate constant ofthe change in the PS I/II ratio was proportional to that ofcell proliferation, µ, when this was low, but at highvalues of µ the increase in the rate constant of the changein the PS I/II ratio became smaller, causing a deviation fromthe linear relationship. Results indicate that under autotrophicconditions, the photoregulated composition change occurs asa result of thylakoid development, which accompanies cell proliferation. (Received June 23, 1986; Accepted December 5, 1986)     

Dynamics of appearance and disappearance of the ripple structure in multilamellar liposomes of dipalmitoylphosphatidylcholine

The physical properties of the pretransition (P beta'----L beta') of dipalmitoylphosphatidylcholine liposomes were investigated using freeze-fracture electron microscopy. The kinetics of pretransition examined in the previous paper using TEMPO spin probe (Tsuchida, K., et al. (1985) Biochim. Biophys. Acta 812, 249-254) was extensively studied by observing the ripple structures in the freeze-fractured surfaces at different time intervals. When the temperature is decreased from 38 degrees C to 30 degrees C, the ripple structure disappears in the following steps. The intervals between ripples begin to expand with the decrease of ripple density upon the temperature shift, and this process continues for several tens minutes. Then, each ripple disappears gradually and changes into a completely smooth surface at 3 h after the temperature shift. The comparison of relaxation times between the previous ESR measurement and the present experiment suggests that the fast relaxation observed in the previous study corresponds to the expansion of the intervals between ripples. On the other hand, the ripple structure of regular intervals appears rapidly in some places and then spreads over the whole area of fractured surface when the temperature is increased from 23 degrees C to 35 degrees C. The results obtained in this work and the previous ESR work strongly suggest that the formation and disappearance of ripple structure is closely related to the relaxation processes near the pretransition temperature.     

A complete deletion mutant of the Escherichia coli dnaKdnaJ operon

Southern hydridization analyses of genomic DNAs from various dnaJ mutants of Escherichia coli showed that mutant K7052, which has well characterized dnaK706 and dnaJ705 double mutantions, is a deletion mutant. The deletion is about 8.0 kb long and encompasses the whole of the dnaKdnaJ operon.     

A region-matched hydrophobic interaction between melittin and dimyristoylphosphatidylcholine in a ternary mixture of phosphatidylcholines

Interaction of melittin with phosphatidylcholine molecules in pure vesicles, binary mixtures and a ternary mixture of dimyristoylphosphatidylcholine IDMPC), dipalmitoylphosphatidylcholine (DPPC) and distearoylphosphatidylcholine (DSPC) was investigated by differential scanning calorimetry. Melittin binds preferentially with DMPC, and results in segregation of DMPC in binary mixtures of DMPC/DPPC and DMPC/DSPC and in a ternary mixture of DMPC/DPPC/DSPC. The results indicate that the hydrophobic part of peptide interacts preferentially with the phospholipid which has the same size of hydrophobic region or fatty acyl chains.     

Demonstration of a dawn phenomenon in normal adolescents

To ascertain whether the dawn phenomenon occurs in normal adolescents and, if so, to determine its mechanism, we measured nocturnal plasma glucose, insulin, glucagon, growth hormone, cortisol, and adrenocorticotropic hormone (ACTH) levels between 01.00 and 08.00 h in 10 healthy adolescents. The prehepatic insulin secretion rate was calculated based on C peptide levels. The metabolic clearance rate of insulin (MCRI) was calculated as the ratio of mean insulin secretion rate to mean insulin concentration. There was no change in plasma glucose, insulin, and glucagon between 01.00-04.00 and 05.00-08.00 h (paired t test). The MCRI was higher at 05.00-08.00 h compared to 01.00-04.00 h (9.30 +/- 1.50 vs. 4.87 +/- 1.11 ml.kg-1.min-1; p = 0.008). The prehepatic insulin secretion increased at 05.00-08.00 h relative to 01.00-04.00 h (1.1 +/- 0.2 vs. 0.6 +/- 0.1 pmol.kg-1.min-1; p = 0.013). Similarly, cortisol and ACTH levels were higher at 05.00-08.00 versus 01.00-04.00 h (323 +/- 33 vs. 102 +/- 22 nmol/l, p less than 0.001; 3.6 +/- 0.5 vs. 1.8 +/- 0.4 pmol/l, p = 0.006, respectively). Growth hormone was higher at 01.00-04.00 versus 05.00-08.00 h (7.6 +/- 1.2 and 3.0 +/- 0.9 microgram/l; p = 0.019). ACTH correlated with MCRI (r = 0.66; p = 0.002) and prehepatic insulin secretion (r = 0.75; p less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)     

Reversal by protein kinase C inhibitor of suppressive actions of phorbol-12-myristate-13-acetate on polyphosphoinositide metabolism and cytosolic Ca2+ mobilization in thrombin-stimulated human platelets

In the presence of 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H-7), a potent inhibitor of protein kinase C in vitro, phorbol-12-myristate-13-acetate (PMA) did not suppress the thrombin-induced increase of cytosolic Ca2+ concentration in human platelets. The H-7 reversal of the inhibitory action of PMA was also observed in thrombin-induced polyphosphoinositide breakdown by phospholipase C. These results provide additional support to the developing theory that the inhibition of PMA on Ca2+ mobilization and phosphoinositide turnover may be mediated by protein kinase C activation.     

Influence of washing on elemental analysis of leaves of fieldgrown crop plants

Summary Information is limited on soil contamination of leaves from field-grown row crops, especially with respect to aluminum (Al) analyses. The objective of this study was to determine the influence of washing leaf samples with either deionized water or detergent solution on elemental analyses for several agronomic crop plants. The crop plants sampled were corn (Zea mays L.), soybean (Glycine max L. Merr.), grain sorghum (Sorghum bicolor L. Moench), and wheat (Triticum aestivum L.). The crops were grown on a range of soil types, soil pH values, and tillage practices. Samples of upper leaves and lower leaves were collected separately. The samples were either not washed, washed with deionized water, or washed with detergent solution. After drying, grinding, and digesting, the samples were analyzed for Al, nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu). For all crop plants and conditions studied, there was no effect on measured N, P, K, Ca, Mg, Mn, Zn, or Cu concentrations, but measured Al and Fe concentrations were influenced by washing. In general, washing had a greater effect on Al analyses than on Fe analyses. Soybean samples were most affected by washing, while wheat samples seemed to be least affected. The results reflected greater contamination of lower leaves than upper leaves. Decontamination procedures appear necessary prior to Al and Fe analyses of field-grown crop plants.     

Constant Phycobilisome Size in Chromatically Adapted Cells of the Cyanobacterium Tolypothrix tenuis, and Variation in Nostoc sp

Phycobilisomes of Tolypothrix tenuis, a cyanobacterium capable of complete chromatic adaptation, were studied from cells grown in red and green light, and in darkness. The phycobilisome size remained constant irrespective of the light quality. The hemidiscoidal phycobilisomes had an average diameter of about 52 nanometers and height of about 33 nanometers, by negative staining. The thickness was equivalent to a phycocyanin molecule (about 10 nanometers). The molar ratio of allophycocyanin, relative to other phycobiliproteins always remained at about 1:3. Phycobilisomes from red light grown cells and cells grown heterotrophically in darkness were indistinguishable in their pigment composition, polypeptide pattern, and size. Eight polypeptides were resolved in the phycobilin region (17.5 to 23.5 kilodaltons) by isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Half of these were invariable, while others were variable in green and red light. It is inferred that phycoerythrin synthesis in green light resulted in a one for one substitution of phycocyanin, thus retaining a constant phycobilisome size. Tolypothrix appears to be one of the best examples of phycobiliprotein regulation with wavelength. By contrast, in Nostoc sp., the decrease in phycoerythrin in red light cells was accompanied by a decrease in phycobilisome size but not a regulated substitution.     

The Electrical Capacitance of Phospholipid Membranes

As one of the methods of finding out the structural change of lipid bilayers due to change of environmental solution, the capacitances of phosphatidyl choline (egg lecithin) and phosphatidyl serine (bovine brain) bilayer membranes in solutions of various pH and salt contents were measured. It was found that the capacitance of the bilayer depended upon pH and salt content. The capacitance had a minimum value around pH 4 for phosphatidyl choline and around pH 3-4 for phosphatidyl serine bilayers, respectively. The value of the capacitance increased as the pH of the solution became lower or higher. As the concentration of cholesterol in the phosphatidyl choline bilayer increased, the capacitance increased and reached a saturation value. A DC voltage across the phosphatidyl choline bilayer did not affect the value of the capacitance practically.