The Arabidopsis TAC Position Viewer: a high‐resolution map of transformation‐competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia‐0 genome

We present a high‐resolution map of genomic transformation‐competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library consisting of more than 10 000 TAC clones harboring large genomic DNA fragments extending over the whole Arabidopsis genome. Here, we determined 13 577 end sequences from 6987 Arabidopsis TAC clones and mapped 5937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large‐scale data set of TAC clones with high‐resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready‐to‐go transformable genomic DNA clones corresponding to certain loci on Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants and DNA transformation for heterologous gene expression.     

Unusual features in the photosynthetic machinery of Halorhodospira halochloris DSM 1059 revealed by complete genome sequencing

Halorhodospira halochloris is an anaerobic, halophilic, purple photosynthetic bacterium belonging to γ-Proteobacteria. H. halochloris is also characteristic as a thermophilic phototrophic isolate producing bacteriochlorophyll (BChl) b. Here, we report the complete genome sequence of H. halochloris DSM 1059. The genetic arrangement for this bacterium’s photosynthetic apparatus is of particular interest; its genome contains two sets of puf operons encoding the reaction center and core light-harvesting 1 (LH1) complexes having almost identical nucleotide sequences (e.g., 98.8–99.9% of nucleotide identities between two sets of pufLM genes, but 100% of deduced amino acid sequence identities). This duplication of photosynthetic genes may provide a glimpse at natural selection in action. The β-polypeptides of the LH1 complex in purple bacteria usually contain two histidine residues to bind BChl a; however, those of H. halochloris were revealed to have four histidine residues, indicating unusual pigment organization in the LH1 complex of this species. Like in other BChl b-producing phototrophs, the genome of H. halochloris lacks the divinyl reductase genes bciA and bciB. The phylogeny of chlorophyllide a oxidoreductase, which catalyzes committed steps in the synthesis of BChl a and BChl b, indicates that evolution toward BChl b production is convergent. Geranylgeranyl reductase (BchP) of H. halochloris has an insertion region in its primary structure, which could be important for its unusual sequential reduction reactions.

     

Anaplastic oligodendroglioma: a case report with characteristic cytologic features, including minigemistocytes

BACKGROUND: Absolute criteria for grading oligodendrogliomas are somewhat poorly defined in contrast to those for grading astrocytic tumors, and cytologic features of anaplastic oligodendrogliomas have been poorly described. CASE: A 63-year-old man presented with a toppling gait. Radiologic examination revealed a 7-cm mass with calcifications in the right frontal lobe. Intraoperative smears of the tumor showed hypercellular, loosely cohesive cell clusters and single cells with nuclear pleomorphism, numerous apoptotic cells and no discernible fibrillary processes. Many bland-looking round cells with cyanophilic cytoplasm and eccentrically located nuclei, so-called minigemistocytes, were intermingled among atypical cells. Cryostat sections showed cellular nests consisting of tumor cells with oval nuclei and clear cytoplasm. These cells were proliferating in the finely reticulated vascular stroma, and the tumor had an infiltrative margin with areas of focal necrosis and numerous calcifications. The diagnosis of anaplastic oligodendroglioma, World Health Organization grade 3, was made, and the results of fluorescence in situ hybridization (chromosome 1q deletion) supported the diagnosis. CONCLUSION: Intraoperative diagnosis of anaplastic oligodendroglioma may not be easy but is possible with judicious consideration of several features: high cellularity, no fibrillary processes, nuclear atypia, pleomorphism, abundant apoptotic cells, occasional mitotic figures, coagulative necrosis, endothelial hyperplasia and characteristic conspicuous minigemistocytes.     

Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus

In the human HOXA locus a number of ncRNAs are transcribed from the intergenic regions in the opposite direction to HOXA mRNAs. We observed that the genomic organization of genes for the ncRNAs and HOXA proteins is highly conserved between human and mouse. We examined the expression profiles of these ncRNAs and HOXA mRNAs in various human tissues. The expression patterns of ncRNAs in human tissues coincide with those of the adjacent HOXA mRNAs that are collinearly expressed along the anteroposterior axis. This coordinated expression was observed even in transformed tumors and cancer cell lines, suggesting that the expression of ncRNAs is prerequisite for the regulated expression of HOXA genes. HIT18844 ncRNA transcribed from the most upstream position of the HOXA cluster possesses an ultra-conserved short stretch which potentially forms an evolutionarily conserved secondary structure. Our data suggest a critical role for ncRNAs in the regulation of HOXA gene expression.     

CD3 and immunoglobulin G Fc receptor regulate cerebellar functions

The immune and nervous systems display considerable overlap in their molecular repertoire. Molecules originally shown to be critical for immune responses also serve neuronal functions that include normal brain development, neuronal differentiation, synaptic plasticity, and behavior. We show here that FcgammaRIIB, a low-affinity immunoglobulin G Fc receptor, and CD3 are involved in cerebellar functions. Although membranous CD3 and FcgammaRIIB are crucial regulators on different cells in the immune system, both CD3epsilon and FcgammaRIIB are expressed on Purkinje cells in the cerebellum. Both CD3epsilon-deficient mice and FcgammaRIIB-deficient mice showed an impaired development of Purkinje neurons. In the adult, rotarod performance of these mutant mice was impaired at high speed. In the two knockout mice, enhanced paired-pulse facilitation of parallel fiber-Purkinje cell synapses was shared. These results indicate that diverse immune molecules play critical roles in the functional establishment in the cerebellum.     

Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1gamma gene

Fox-1 is a regulator of tissue-specific splicing, via binding to the element (U)GCAUG in mRNA precursors, in muscles and neuronal cells. Fox-1 can regulate splicing positively or negatively, most likely depending on where it binds relative to the regulated exon. In cases where the (U)GCAUG element lies in an intron upstream of the alternative exon, Fox-1 protein functions as a splicing repressor to induce exon skipping. Here we report the mechanism of exon skipping regulated by Fox-1, using the hF1γ gene as a model system. We found that Fox-1 induces exon 9 skipping by repressing splicing of the downstream intron 9 via binding to the GCAUG repressor elements located in the upstream intron 8. In vitro splicing analyses showed that Fox-1 prevents formation of the pre-spliceosomal early (E) complex on intron 9. In addition, we located a region of the Fox-1 protein that is required for inducing exon skipping. Taken together, our data show a novel mechanism of how RNA-binding proteins regulate alternative splicing.     

Serological evidence of leptospiral infection in pig populations in different districts in Japan

Serum samples were collected from 938 pigs of 24 farms in Hokkaido, Kagoshima, and Okinawa prefectures in Japan in 2001-2005. Enzyme-linked immunosorbent assay (ELISA) was used for the detection of antibodies to LipL32 antigen which is common to Leptospira interrogans. Samples positive in ELISA were then investigated by microscopic agglutination test for the identification of causal leptospires. Antibodies specific to leptospires of serovars Copenhageni, Bratislava, Australis and Javanica were detected in serum samples of pigs from each of the three districts. In addition, antibodies to leptospires of serovars Autumnalis and Tarassovi were predominantly detected in those from Kagoshima. The present study, thus, revealed that leptospires belonging to different serovars prevail in the pig population in Japan. In addition, it is the first detection of antibodies to leptospires belonging to serovars Javanica and Tarassovi in pigs in Japan.     

N-Acetyl Transferase,Shati/Nat8l,in the Dorsal Hippocampus Suppresses Aging-induced Impairment of Cognitive Function in Mice

As the elderly population rapidly increases worldwide, the onset of cognitive dysfunction is expected to increase. Although neuronal plasticity, neurogenesis, and mitochondrial dysfunction have been reported to be involved in cognitive function, the detailed mechanism of cognitive impairment accompanied by aging is poorly understood as there are many confounding factors associated with aging. Therefore, effective treatments for aging have not yet been developed, and the establishment of therapeutic strategies has not progressed accordingly. We have previously found a decline of cognitive function in the developmental stage in mice who lack the expression of Shati/Nat8l, an N-acetyl transferase However, the contribution of Shati/Nat8l to cognitive impairment in aged mice has not yet been investigated. In this study, we aimed to investigate the role of Shati/Nat8l in cognitive function during aging. We observed a reduction in Shati/Nat8l mRNA expression in the dorsal hippocampus of mice as a result of their aging. Moreover, the cognitive dysfunction observed in aged mice was reversed by Shati/Nat8l overexpression in the dorsal hippocampus. Shati/Nat8l overexpression in the dorsal hippocampus of mice did not alter the expression of neurotrophic factors or mitochondrial function-related genes, including Bdnf or Pgc-1α, which are suggested to be downstream genes of Shati/Nat8l. Decreased N-acetyl aspartate (NAA) in aged mice was upregulated by Shati/Nat8l overexpression, suggesting that the Shati/Nat8l-NAA pathway determines cognitive function with aging. Taken together, Shati/Nat8l and NAA in the dorsal hippocampus may be novel targets for the treatment of cognitive impairment.

     

Targeted Disruption of Ig-Hepta/Gpr116 Causes Emphysema-like Symptoms That Are Associated with Alveolar Macrophage Activation

Ig-Hepta/GPR116 is a member of the G protein-coupled receptor family predominantly expressed in the alveolar type II epithelial cells of the lung. Previous studies have shown that Ig-Hepta is essential for lung surfactant homeostasis, and loss of its function results in high accumulation of surfactant lipids and proteins in the alveolar space. Ig-Hepta knock-out (Ig-Hepta^−/−) mice also exhibit emphysema-like symptoms, including accumulation of foamy alveolar macrophages (AMs), but its pathogenic mechanism is unknown. Here, we show that the bronchoalveolar lavage fluid obtained from Ig-Hepta^−/− mice contains high levels of inflammatory mediators, lipid hydroperoxides, and matrix metalloproteinases (MMPs), which are produced by AMs. Accumulation of reactive oxygen species was observed in the AMs of Ig-Hepta^−/− mice in an age-dependent manner. In addition, nuclear factor-κB (NF-κB) is activated and translocated into the nuclei of the AMs of Ig-Hepta^−/− mice. Release of MMP-2 and MMP-9 from the AMs was strongly inhibited by treatment with inhibitors of oxidants and NF-κB. We also found that the level of monocyte chemotactic protein-1 is increased in the embryonic lungs of Ig-Hepta^−/− mice at 18.5 days postcoitum, when AMs are not accumulated and activated. These results suggest that Ig-Hepta plays an important role in regulating macrophage immune responses, and its deficiency leads to local inflammation in the lung, where AMs produce excessive amounts of reactive oxygen species and up-regulate MMPs through the NF-κB signaling pathway.     

Pathogenic Role of a Proliferation-Inducing Ligand (APRIL) in Murine IgA Nephropathy

A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor (TNF) superfamily. Despite advances in clinical and genetic studies, the details of the pathological roles of APRIL in IgA nephropathy (IgAN) remain to be fully defined. The present study aimed to further assess the pathological role of APRIL using a mouse model of IgAN. Mice with IgAN designated “grouped ddY” (gddY) were intraperitoneally administered an anti-APRIL monoclonal antibody (anti-APRIL Ab) or control IgG (Control Ab) twice each week for 2 weeks starting during the early stage of IgAN (6–7 weeks of age). Urinary albumin, serum IgA, and glomerular IgA deposition were evaluated. We further assessed the inflammatory responses during treatment by measuring the levels of the chemokine fractalkine (FKN) and its receptor CX3CR1 as well as the level of peripheral blood monocytosis. Anti-APRIL Ab treatment significantly decreased albuminuria and tissue damage combined with decreases in serum IgA levels and deposition of glomerular IgA. In contrast, the abundance of IgA⁺/B220⁺ or CD138⁺/B220⁺ B cells in the spleen and bone marrow, respectively, was unchanged. Treating gddY mice with anti-April Ab reduced the overexpression of FKN/CX3CR1 in the kidney and the increase in the population of circulating Gr1⁻/CD115⁺ monocytes. The size of the population of Gr1⁻/CD115⁺ monocytes correlated with renal FKN and urinary albumin levels. Moreover, mice treated with anti-APRIL Ab exhibited reduced progression of IgAN, serum IgA levels, and glomerular IgA deposition as well as an attenuated inflammatory process mediated by FKN-associated activation of monocytes. To the best of our knowledge, this is the first study to implicate the APRIL signal transduction pathway in the pathogenesis of nephrogenic IgA production. Moreover, our findings identify APRIL as a potential target of therapy.