Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing

We have developed a method to overcome sequencing problems caused by the presence of homopolymer stretches, such as polyA/T, in cDNA libraries. PolyA tails are shortened by cleaving before cDNA cloning with type IIS restriction enzymes, such as GsuI, placed next to the oligo-dT used to prime the polyA tails of mRNAs. We constructed four rice Cap-Trapper-selected, full-length normalized cDNA libraries, of which the average residual polyA tail was 4 bases or shorter in most of the clones analyzed Because of the removal of homopolymeric stretches, libraries prepared with this method can be used for direct sequencing and transcriptional sequencing without the slippage observed for libraries prepared with currently available methods, thus improving sequencing accuracy, operations, and throughput.

Expansion of human hepatocyte populations by a retroviral gene transfer of simian virus 40 large T antigen

A hybrid artificial liver (HAL) could be used to treat acute liver failure or to serve as a temporary support until orthotopic liver transplantation is available. Primary human hepatocytes are ideal as a source of hepatic function in a HAL device. However, the worldwide shortage of human livers available for hepatocyte isolation severely limits this form of therapy. A possible alternative is to use a tightly regulated cell line that can be economically grown in culture to have differentiated liver function. In this work, human hepatocytes were immortalized with a retroviral vector SSR#69 expressing the genes of simian virus 40 large T antigen and herpes simplex virus-thymidine kinase. One of the resulting clones, NKNT-3 , showed the gene expression of differentiated liver function and were sensitive to the antiviral agent ganciclovir. When transplanted into the spleen of rats subjected to 90% hepatectomy, NKNT-3 cells prolonged the survival of 90% hepatectomized rats. The cells provide the advantages of unlimited availability, sterility, uniformity, and freedom from pathogens. This work represents a potential novel strategy for resolving the organ shortage that currently limits the use of primary human hepatocytes to develop a HAL.

Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus

Plants with low levels of DNA methylation show a range of developmental abnormalities including homeotic transformation of floral organs. Two independent DNA METHYLTRANSFERASEI (METI) antisense transformants with low levels of DNA methylation had flowers with increased numbers of stamens which resembled flowers seen on the loss-of-function superman (sup) mutant plants and on transgenic plants that ectopically express APETALA3 (AP3). These METI antisense plants have both increased and decreased methylation in and around the sup gene, compared with untransformed controls. DNA from the antisense plants was demethylated at least 4 kb upstream of the sup gene, while there was dense methylation around the start of transcription and within the coding region of this gene; these regions were unmethylated in control DNA. Methylation within the sup gene was correlated with an absence of SUP transcripts. The pattern and density of methylation was heterogeneous among different DNA molecules from the same plant, with some molecules being completely unmethylated. Methylcytosine occurred in asymmetric sites and in symmetric CpA/TpG but rarely in CpG dinucleotides in the antisense plants. In contrast, segregants lacking the METI antisense construct and epimutants with a hypermethylated allele of sup (clark kent 3), both of which have active METI genes, showed a higher frequency of methylation of CpG dinucleotides and of asymmetric cytosines. We conclude that METI is the predominant CpG methyltransferase and directly or indirectly affects asymmetric methylation.

A new approach to develop a biohybrid artificial liver using a tightly regulated human hepatocyte cell line

Currently patients with liver failure have been treated with a various liver support systems including a whole liver perfusion, a non-biological artificial liver, and a biohybrid artificial liver. In a hepatocyte-based bioreactor, porcine hepatocytes or transformed human liver tumor cells have been utilized because of the ease of preparation. According to the clinical data reported as of now, satisfactory results have not been obtained from the use of currently available liver support devices. One of the problems is limited availability of primary human liver cells for developing live support systems because of the shortage of human liver. To resolve this issue, human hepatocytes were immortalized with a retroviral vector SSR#69 which contained the genes of simian virus 40 large T antigen (SV40Tag) and herpes simplex virus-thymidine kinase (HSV-TK). One of the immortal cell lines, NKNT-3, showed the gene expression of differentiated liver functions, grew steadily in chemically defined serum-free CS-C medium, and doubled in number in about 48 hours. Essentially unlimited availability of NKNT-3 cells supports their clinical use for liver support devices. To realize the high density culture of NKNT-3 cells in a bioartificial liver device, we have developed cellulose microspheres (CMS) which contain cell adhesive GRGDS (Gly-Arg-Gly-Asp-Ser) peptides. Within 24 hours after starting a stirring suspension culture, GRGDS-CMS efficiently immobilized NKNT-3 cells. An electron microscopic examination demonstrated that NKNT-3 cells attached on GRGDS-CMS had well-developed mitochondria, rough reticulums, and villous extensions. In this article, we review the history of extracorporeal liver support systems and describe an attractive strategy for developing a novel extracorporeal liver assist device using NKNT-3 cells and GRGDS-coated cellulose microspheres.

[A case of idiopathic pulmonary hemosiderosis of adult onset]

A 51-year-old man presenting with hemoptysis was admitted to our hospital. Chest radiography revealed air space consolidation in the right lung field. Laboratory data showed anemia, hypoxemia, and no evidence of inflammatory signs, bleeding tendency, renal dysfunction, or collagen vascular diseases. Tests of anti-GBM antibody, P-ANCA, and C-ANCA were negative. Microscopic examination of the lung tissue specimens obtained by video assisted thoracic surgery revealed hemorrhage and numerous hemosiderin-laden macrophages in the alveoli. No deposition of immunoglobulin and vasculitis were seen. These findings were consistent with a diagnosis of idiopathic pulmonary hemosiderosis. Steroid therapy had a limited effect, and the patient died. Idiopathic pulmonary hemosiderosis of adult onset is rare in Japan.

Cryofiltration and oral corticosteroids provide successful treatment for an elderly patient with cryoglobulinemic glomerulonephritis associated with hepatitis C virus infection

A 75-year-old man was admitted due to nephrotic syndrome, purpura on the legs, which was associated with hepatitis C virus (HCV), and type II mixed cryoglobulinemia. Renal biopsy revealed features of cryoglobulinemic glomerulonephritis. Since the patient was elderly and the HCV genotype was Ib, interferon-alpha for reducing HCV was not indicated. Four sessions of cryofiltration and the administration of corticosteroids improved the proteinuria and renal function strikingly without adverse effects. This case demonstrates that an elderly patient who has nephrotic syndrome caused by cryoglobulinemic glomerulonephritis associated with HCV can be treated safely by cryofiltration with low doses of oral corticosteroids.

Multiple pathways regulating fission yeast mitosis upon environmental stresses

Environmental signals, such as nutrient availability and physiological stresses, modulate the cell cycle and cell size of the fission yeast Schizosaccharomyces pombe. However, little is known about how these signals are transmitted to the central cell cycle regulator, Cdc2, the cyclin-dependent kinase that induces mitosis. We show here genetic evidence that medium alkalization stimulates mitosis and consequently reduces cell size, either through the Nim1-Wee1 cascade, which regulates the inhibitory phosphorylation of Cdc2 at Tyr(15), or through the Cdc2-activating phosphatase, Cdc25. Alkaline stress stimulates phosphorylation of Nim1, accumulation of Cdc25 and dephosphorylation of Cdc2 at Tyr(15). We also show that osmostress stimulates mitosis through two independent pathways: one stimulates accumulation of Cdc25, and another dephosphorylation of Cdc2 at Tyr(15). However, our analysis demonstrates that these environmental stresses can stimulate mitosis independently of dephosphorylation of Cdc2 at Tyr(15). The S. pombe MAP kinase, Spc1, was required for the steady-state level of Cdc25 in the normal cell cycle and for its accumulation in response to alkaline stress and nutritional starvation.

Cyclic AMP regulates cell size of Schizosaccharomyces pombe through Cdc25 mitotic inducer

Nutritional state modulates the cell size of the fission yeast Schizosaccharomyces pombe, such that cells grown in rich medium are larger in size than those in poor medium. This signal is transduced partly through the cyclic AMP-dependent protein kinase cascade. However, little is known about how cyclic AMP interacts with the central cell cycle machinery, Cdc2, the cyclin-dependent kinase that induces mitosis. We show here that cyclic AMP regulates mitosis and cell size, in part, through regulation of protein stability of the Cdc2-activating phosphatase, Cdc25. However, our analysis demonstrates that cyclic AMP can negatively regulate mitosis independently of dephosphorylation of Cdc2 at Tyr(15).

[Effects of corticosteroid on porcine retinal pigment epithelial cells in culture--2. Effects on phagocytosis and lysosomal activity]

PURPOSE

The effects of a corticosteoid on the phagocytosis and lysosomal activity of cultured porcine retinal pigment epithelium (RPE) cells were investigated.

METHODS

After exposing cultured RPE cells to various concentrations (10, 50, 100, 500, 1,000 nM) of betamethasone sodium phosphate (betamethasone), the cells were incubated with latex microspheres for 6 hours.

RESULTS

The number of latex microspheres phagocytized by the cultured RPE cells was inhibited by 50 nM betamethasone within 24 hours. Ten-nM betamethasone did not inhibit the proliferation of cultured RPE cells, but ingestion of latex microspheres by the cells was inhibited after 3 days. Lysosomal activity (acid phosphatase, beta-glucuronidase) of RPE cells was inhibited by a high concentration (500 nM) of betametasone.

CONCLUSION

These results suggest that corticosteroid inhibits the phagocytosis and lysosomal activity of cultured RPE cells.

High-resolution ultrastructural comparison of renal glomerular and tubular basement membranes

BACKGROUND/AIMS

Glomerular basement membranes (GBM) and tubular basement membranes (TBM) consist of a fine meshwork composed mainly of type IV collagen. Each segment of tubules has specialized physiologic functions, and thus we investigated the ultrastructure of various basement membranes in rat kidneys.

METHODS

Since purifying basement membranes from different tubule segments is technically challenging, we employed tissue negative staining rather than conventional negative staining to compare the ultrastructures of proximal and distal TBM and GBM in normal rats. We also assessed the distribution of extracellular matrix components including type IV collagen, laminin, heparan sulfate proteoglycan, and fibronectin in the basement membranes by immunohistochemistry.

RESULTS

TBM and GBM of normal rats showed a fine meshwork structure consisting of fibrils forming small round to oval pores. Short- and long-pore diameters in proximal tubules were 3.3 +/- 0.5 and 3.9 +/- 0.6 nm, respectively, and in distal tubules 3.5 +/- 0.7 and 4.3 +/- 0.8 nm, respectively. For GBM the respective diameters were 2.5 +/- 0.5 and 3.0 +/- 0.5 nm. Immunohistochemical analysis showed no significant difference in distribution of extracellular matrix components between proximal and distal TBM. However, immunofluorescence scores of alpha1 chain of type IV collagen, fibronectin, and laminin were higher in the TBM than in the GBM. On the other hand, heparan sulfate proteoglycan was higher in the GBM.

CONCLUSION

Ultrastructural differences in renal basement membranes may be related to differences in physiologic function in each segment.

[Effects of corticosteroid on porcine retinal pigment epithelial cells in culture--1. Inhibitory effect on cell proliferation]

PURPOSE

Proliferation is an important function of the retinal pigment epithelial (RPE) cells. The effect of a corticosteroid on the proliferation of cultured porcine RPE cells was investigated.

METHODS

After administration of various concentrations (10-1,000 nM) of betamethasone sodium phosphate (betamethasone), we counted RPE cell numbers at 1, 3, 6, 9, and 14 days.

RESULTS

Betamethasone administration resulted in a dose-dependent decrease in RPE cell proliferation. The proliferation of the cultured RPE cells was significantly inhibited by betamethasone, at a dose of 300 nM in 9 days. Ten-nM betamethasone neither inhibited nor promoted the RPE cell proliferation in culture.

CONCLUSIONS

These results suggest that corticosteroids inhibit proliferation of cultured porcine RPE cells.

RNA maturation of the rice SPK gene may involve trans-splicing

A gene encoding a calcium-dependent seed-specific protein kinase (SPK) is abundantly expressed in developing rice seeds (Kawasaki, T et al. Gene (1993) 129, 183-189). Rice genomic clones encoding SPK were isolated using the entire cDNA fragment as a probe. Physical mapping of these genomic clones indicated that the genomic region corresponding to the entire cDNA was divided into two different regions, SPK-A and SPK-B, located on different rice chromosomes. The results of RACE-PCR analyses showed that the respective transcripts from SPK-A and SPK-B contained additional sequences which were not found in the SPK cDNA, and that these sequences were removed like introns during maturation of the SPK mRNA. These results suggest that two different RNAs were independently transcribed from SPK-A and SPK-B and joined, possibly by trans-splicing.

[Myasthenia gravis presenting as isolated respiratory failure]

A 61-year-old woman in excellent health and taking no medications presented with progressive dyspnea on exertion. She did not exhibit diplopia, dysphagia, dysarthria or muscle weakness. Her condition deteriorated, and respiratory distress developed. The patient was intubated and placed on mechanical ventilation. A computed tomogram of her chest revealed a moderately enlarged thymus gland unsuspected on a plain x-ray film. Myasthenia gravis was diagnosed on the basis of a high acetylcholine receptor antibody titer. Treatment started with prednisolone, anticholinesterase agent, and plasma exchange. The patient underwent a thymectomy 3 weeks after her diagnosis. Her symptoms were brought under control by anticholinesterase agent and prednisolone. This case illustrates the need to consider myasthenia gravis as well as other motor-neuron disorders when evaluating individuals presenting acute respiratory failure of unknown origin.

Comparison of indocyanine green and fluorescein angiography of choroidal neovascularization

We compared indocyanine green (ICG) and fluorescein angiography for evaluation of choroidal neovascularization (CNV). Cast preparations of CNV induced in monkey eyes by laser photocoagulation were correlated with ICG and fluorescein angiographies of the same CNV formations. Fluorescein angiography was more effective, in general, than ICG angiography in detecting CNV; however, CNVs with subretinal hemorrhage (2 of 35 sites) were visible only with ICG angiography. In early phase ICG angiography, CNV formations that casts showed to be dense or composed of thick vessels were seen, but less dense areas were not visible. Lesions that ICG angiography revealed as leaking were not differentiated morphologically from non-leaking areas by the CNV casts. This study confirms that only ICG angiography can identify CNV hidden by subretinal hemorrhage, although fluorescein angiography is otherwise superior. Indocyanine green angiography is indicated as a valuable complement to fluorescein angiography for evaluation of CNV.

Type Ia supernovae: their origin and possible applications in cosmology

Spectroscopic and photometric evidence indicates that Type Ia supernovae (SNe Ia) are the thermonuclear explosions of accreting white dwarfs. However, the progenitor binary systems and hydrodynamical models for SNe Ia are still controversial. The relatively uniform light curves and spectral evolution of SNe Ia have led to their use as a standard candle for determining cosmological parameters, such as the Hubble constant, the density parameter, and the cosmological constant. Recent progress includes the calibration of the absolute maximum brightness of SNe Ia with the Hubble Space Telescope, the reduction of the dispersion in the Hubble diagram through the use of the relation between the light curve shape and the maximum brightness of SNe Ia, and the discovery of many SNe Ia with high red shifts.

[Alveolar hemorrhage, skin eruption, and gastrointestinal bleeding accompanied by crescentric glomerulonephritis in a patient with cytoplasmic anti-neutrophil cytoplasmic antibody]

A 69-year-old woman was admitted to our hospital because of hemoptysis, skin eruption, and gastrointestinal bleeding. A chest X-ray film revealed infiltrates in the left upper lung field. Analysis of bronchoalveolar lavage fluid revealed alveolar hemorrhage. Examination of skin biopsy specimens demonstrated leukocytoclastic vasculitis. Fiberoptic examination of the colon showed diffuse reddish and edematous mucosa. Histological examination of biopsy specimens from the sigmoid colon showed necrotizing vasculitis. The serum creatinine level was high: 2.2 mg/dl. Examination of transcutaneous renal biopsy specimens revealed crescentric glomerulonephritis. A test for perinuclear anti-neutrophil cytoplasmic antibody was negative, but a test for cytoplasmic anti-neutrophil cytoplasmic antibody was positive. The latter strongly suggests a diagnosis of Wegener's granulomatosis, although the association is not absolute. We diagnosed pulmonary-renal syndrome associated with anti-neutrophil cytoplasmic antibody. The findings in this case were compatible with microscopic polyangiitis.

Coordinated Regulation of the Genes Participating in Starch Biosynthesis by the Rice Floury-2 Locus

The recessive floury-2 (flo-2) locus of rice (Oryza sativa L.), which is located on chromosome 4, causes a strong reduction in expression of the gene encoding an isoform of branching enzyme RBE1 in immature seeds 10 d after flowering. Mapping of the RBE1 gene demonstrated the localization on rice chromosome 6, suggesting that the wild-type Floury-2 (Flo-2) gene regulates RBE1 gene expression in trans. However, reduced expression of the genes encoding some other starch-synthesizing enzymes, including another isoform of branching enzyme RBE3 and granule-bound starch synthase, was also found in the flo-2 seeds. In spite of the low level of RBE1 gene expression in the immature seeds of the flo-2 mutants, the RBE1 gene was equally expressed in the leaves of the wild type and flo-2 mutants. Thus, these results imply that the Flo-2 gene may co-regulate expression of some of the genes participating in starch synthesis possibly in a developing seed-specific manner.

[A case of RSD with complete disappearance of symptoms following intravenous ketamine infusion combined with stellate ganglion block and continuous epidural block]

A 74 year-old woman with a 6-month history of RSD following herpes zoster on her right arm was treated with stellate ganglion blocks (SGB), continuous epidural block (CEB) and continuous intravenous infusion of ketamine known as one of the NMDA receptor blockers. Of the symptoms of RSD, burning pain and hyperperspiration but allodynia disappeared after the treatment with SGB 8 times and CEB for 4 days. Allodynia disappeared completely after ketamine treatment, where ketamine was infused once using a subanesthetic dose for 2 hours. It is considered that ketamine is one of the useful drugs for the treatment of neuropathic pain with allodynia.

Phylogenetic position of the menaquinone-containing acidophilic chemo-organotroph Acidobacterium capsulatum

The phylogenetic position of an acidophilic chemo-organotrophic menaquinone-containing bacterium, Acidobacterium capsulatum, was studied on the basis of 16S rRNA gene sequence information. A. capsulatum showed the highest level of sequence similarity to Heliobacterium chlorum, a member of the Gram-positive group, yet this level was only 81%. Distance matrix tree analysis suggested that A. capsulatum belongs to a unique lineage deeply branching from the Chlamydia-Planctomyces group or from the Gram-positive line.

[Dye leakage from choroidal neovascularization with indocyanine green angiography]

The ultrastructure of experimentally induced choroidal neovascularization was studied in correlation with dye leakage in indocyanine green (ICG) infrared fluorescence angiography. Newly formed vessels which demonstrated leakage of ICG extended into the subretinal space without enclosure of retinal pigment epithelium (RPE), and the endothelial cells were immature. Choroidal neovascularization which did not demonstrate leakage of ICG was enclosed by RPE without retinal detachment, and the endothelial cells were mature. The newly formed vessels with immature endothelium in the subretinal space that were covered with multiple layers of RPE demonstrated no leakage. These results show that ICG leaks form choroidal neovascularization which has immature vessels that are not enclosed by RPE and that extend into the subretinal space.

[Effects of interferon-beta on repair of the retinal pigment epithelium after laser photocoagulation]

We studied the morphological effects of human interferon-beta on repair of the retinal pigment epithelium (RPE) after moderate dye laser photocoagulation in monkey eyes. In the control eyes, RPE cells were proliferating towards the center from the margin of the laser burn 3 days after photocoagulation. At day 14 after photocoagulation, a newly formed monolayer of RPE cells covered Burch's membrane to repair the lesion. In the eyes treated with interferon-beta by systemic administration, RPE cells had proliferated remarkably 3 days after photocoagulation. The RPE cells proliferated to form multiple layers on Burch's membrane even at day 14 after photocoagulation. These results suggest that interferon-beta promotes the proliferation to repair damaged RPE.

Structure, organization, and chromosomal location of the gene encoding a form of rice soluble starch synthase

A rice (Oryza sativa L.) genomic clone encoding the gene for a form of soluble starch synthase (SSS1) and its 5'- and 3'-flanking regions has been isolated and sequenced. The SSS1 gene contained 15 exons interrupted by 14 introns. The exon/intron organization of the SSS1 gene was divergent from that of the rice Waxy gene coding for granule-bound starch synthase, thus suggesting that the SSS1 and granule-bound starch synthase genes have evolved from an ancestral gene in a different way or that the two genes are products of different ancestral genes that have converged during evolution. However, these two genes were closely located to each other on rice chromosome 6 at an approximate map distance of 5 centimorgans. The nucleotide sequence of the 5'-end region of the gene is unique because of the presence of some repetitive sequences.

[Effect of human interferon-beta on reconstruction of the choriocapillaris in monkeys following laser photocoagulation]

We studied the effect of human interferon-beta on reconstruction of the choriocapillaris following laser photocoagulation in monkey eyes. Moderate dye laser photocoagulation caused the occlusion of the choriocapillaris by the intraluminal thrombus in the photocoagulated lesions on the retina. After 3 days, immature endothelial cells began to migrate towards the center from the edge of the lesions. After 7 days capillaries were newly formed, and after 14 days the choriocapillaris in the lesions was almost reconstructed. Systemic administration of interferon-beta after photocoagulation suppressed the reconstruction of the choriocapillaris remarkably. These results suggest that interferon-beta inhibits proliferation and migration of the capillary endothelium on the retina. Interferon-beta may be effective as medication for the treatment of age-related macular degeneration.