Characterization of genes expressed during vegetative organ development in potato (Solanum tuberosum L.)

The cp rps16 cDNA encoding the chloroplast ribosomal protein S16 and a MADS-box gene cDNA, POTM1-1, were isolated and characterized in potato (Solanum tuberosum L.) to understand molecular mechanisms of plant vegetative organ development;The rps16 gene is located between the trnK gene for tRNA Lys(UUU) and trnQ gene for tRNA Gln (UUG) on the same strand in the chloroplast genome. The ribosomal binding site, 5\u27-AGGA-3\u27, is located at nucleotide position -6 to -9 from the initiation codon ATG. The coding sequence contains an 88 amino acid open reading frame (ORF) that is interrupted by an 855 bp intron. Five different inverted repeat sequences are located at the 3\u27 end. The deduced amino acid sequence of the rps16 coding sequence shows 33% homology to the E. coli ribosomal protein S16 and 95% homology to the tobacco chloroplast ribosomal protein S16. The 13 amino acids encoded by exon-1 are highly conserved (100% identity) among higher plants. Two sizes of rps16 transcripts have been identified from northern blot analysis. The 1.5 kb transcript contains the 855 bp intron and represents an unprocessed RNA molecule, whereas the 0.7 kb transcript represents the mature form. The expression of rps16 is developmentally regulated, with transcript levels decreasing during tuber development and increasing during shoot development. The potato cp rps16 gene appears to be constitutively expressed in unswollen stolons and axillary buds, and its expression is enhanced by light;A [underline]potato [underline] MADS-box gene cDNA (POTM1-1) from an early tuber cDNA library has been isolated and further characterized. The deduced amino acid sequence of POTM1-1 encodes a 250 a.a. of a putative transcription factor which contained a MADS-box domain (56 a.a.) and a K-box domain (53 a.a). The MADS-box domain shared high homology to that of flower specific homeotic proteins, TM4 of tomato (100% identity) and AP1 of Arabidopsis (92.9%). The K-box domain shared high similarity to those of TM4 (96.2% identity) and AP1 (66.0% identity). The putative secondary structure of K-box domain, however, showed an amphipathic helix-turn-helix structure that is remarkably similar to that of other plant homeotic proteins. A potential phosphorylation and four potential glycosylation sites are located in POTM1-1, suggesting that posttranslational modification processes may be involved in the activation and specificity of POTM1-1. The levels of POTM1-1 transcripts were high in leaves, roots, aerial shoot tips, underground stolon tips, and late flowers, but relatively low in stems, early flowers, and mature tubers. In the axillary-bud-tuber induction system, the levels of POTM1-1 transcripts were increased along with the shoot development, but decreased along with tuber development. We propose that POTM1-1 may function as a constitutive transcription factor that may be involved in the fundamental functions such as cell division and/or growth, or in housekeeping, or in morphologically and metabolically active tissues in all types of plant organs;Results indicated that these two genes, cp rps16 and POTM1-1, are involved in vegetative tissue development

Continuous Decomposition of Granularity for Neural Paraphrase Generation

While Transformers have had significant success in paragraph generation, they treat sentences as linear sequences of tokens and often neglect their hierarchical information. Prior work has shown that decomposing the levels of granularity~(e.g., word, phrase, or sentence) for input tokens has produced substantial improvements, suggesting the possibility of enhancing Transformers via more fine-grained modeling of granularity. In this work, we propose a continuous decomposition of granularity for neural paraphrase generation (C-DNPG). In order to efficiently incorporate granularity into sentence encoding, C-DNPG introduces a granularity-aware attention (GA-Attention) mechanism which extends the multi-head self-attention with: 1) a granularity head that automatically infers the hierarchical structure of a sentence by neurally estimating the granularity level of each input token; and 2) two novel attention masks, namely, granularity resonance and granularity scope, to efficiently encode granularity into attention. Experiments on two benchmarks, including Quora question pairs and Twitter URLs have shown that C-DNPG outperforms baseline models by a remarkable margin and achieves state-of-the-art results in terms of many metrics. Qualitative analysis reveals that C-DNPG indeed captures fine-grained levels of granularity with effectiveness.Comment: Accepted to be published in COLING 202

An efficient strategy for cell-based antibody library selection using an integrated vector system

BACKGROUND: Cell panning of phage-displayed antibody library is a powerful tool for the development of therapeutic and imaging agents since disease-related cell surface proteins in native complex conformation can be directly targeted. Here, we employed a strategy taking advantage of an integrated vector system which allows rapid conversion of scFv-displaying phage into scFv-Fc format for efficient cell-based scFv library selection on a tetraspanin protein, CD9. RESULTS: A mouse scFv library constructed by using a phagemid vector, pDR-D1 was subjected to cell panning against stable CD9 transfectant, and the scFv repertoire from the enriched phage pool was directly transferred to a mammalian cassette vector, pDR-OriP-Fc1. The resulting constructs enabled transient expression of enough amounts of scFv-Fcs in HEK293E cells, and flow cytometric screening of binders for CD9 transfectant could be performed simply by using the culture supernatants. All three clones selected from the screening showed correct CD9-specificity. They could immunoprecipitate CD9 molecules out of the transfectant cell lysate and correctly stain endogenous CD9 expression on cancer cell membrane. Furthermore, competition assay with a known anti-CD9 monoclonal antibody (mAb) suggested that the binding epitopes of some of them overlap with that of the mAb which resides within the large extracellular loop of CD9. CONCLUSIONS: This study demonstrates that scFv-Fc from mammalian transient expression can be chosen as a reliable format for rapid screening and validation in cell-based scFv library selection, and the strategy described here will be applicable to efficient discovery of antibodies to diverse cell-surface targets

Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae

Virulence of wild-type and mutant Xoo strains on rice. (DOCX 16 kb

Femtosecond-Resolved Excited State Relaxation Dynamics of Copper (II) Tetraphenylporphyrin (CuTPP) After Soret Band Excitation

Excited state relaxation dynamics of Copper (II) tetraphenylporphyrin (CuTPP) after Soret band excitation have been investigated in various solvents by femtosecond broadband transient absorption spectroscopy. Significant role of charge transfer state has been confirmed from fast relaxation of triplet CuTPP in pyridine, giving τ ~ 26.5 ps. In piperidine, the transient measured at 480 nm shows biexponential behavior with distinct time constants of 300 fs and 27.4 ps. The fast component with τ ~ 300 fs is attributed to relaxation of the CuTPP-piperidine adduct populated in the ground state, giving the intrinsic relaxation rate of the CuTPP exciplex for the first time. For CuTPP in O-coordinating solvents of 1,4-dioxane and tetrahydrofuran (THF), a completely new relaxation channel via the 2[dz2, dx2−y2] state is opened. As the exciplex formation is diffusion controlled, triplet CuTPP lifetimes in pure solvents employed here are all measured to be more or less same to give ~30 ps, whereas the 2[dz2, dx2−y2] exciplex formed by the ligation with O-coordinating solvents is found to relax much slowly to the ground state, giving lifetimes of ~360 and ~270 ps in 1,4-dioxane and THF, respectively.11sciescopu

Echovirus 30 Induced Neuronal Cell Death through TRIO-RhoA Signaling Activation

BACKGROUND: Echovirus 30 (Echo30) is one of the most frequently identified human enteroviruses (EVs) causing aseptic meningitis and encephalitis. However the mechanism underlying the pathogenesis of Echo30 infection with significant clinical outcomes is not completely understood. The aim of this investigation is to illustrate molecular pathologic alteration in neuronal cells induced by Echo30 infection using clinical isolate from young patient with neurologic involvement. METHODOLOGY/PRINCIPAL FINDINGS: To characterize the neuronal cellular response to Echo30 infection, we performed a proteomic analysis based on two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF Mass Spectrophotometric (MS) analysis. We identified significant alteration of several protein expression levels in Echo30-infected SK-N-SH cells. Among these proteins, we focused on an outstanding up-regulation of Triple functional domain (TRIO) in Echo30-infected SK-N-SH cells. Generally, TRIO acts as a key component in the regulation of axon guidance and cell migration. In this study, we determined that TRIO plays a role in the novel pathways in Echo30 induced neuronal cell death. CONCLUSIONS/SIGNIFICANCE: Our finding shows that TRIO plays a critical role in neuronal cell death by Echo30 infection. Echo30 infection activates TRIO-guanine nucleotide exchange factor (GEF) domains (GEFD2) and RhoA signaling in turn. These results suggest that Echo30 infection induced neuronal cell death by activation of the TRIO-RhoA signaling. We expect the regulation of TRIO-RhoA signaling may represent a new therapeutic approach in treating aseptic meningitis and encephalitis induced by Echo30

Decreased expression of extracellular matrix proteins and trophic factors in the amygdala complex of depressed mice after chronic immobilization stress

BACKGROUND: The amygdala plays an essential role in controlling emotional behaviors and has numerous connections to other brain regions. The functional role of the amygdala has been highlighted by various studies of stress-induced behavioral changes. Here we investigated gene expression changes in the amygdala in the chronic immobilization stress (CIS)-induced depression model. RESULTS: Eight genes were decreased in the amygdala of CIS mice, including genes for neurotrophic factors and extracellular matrix proteins. Among these, osteoglycin, fibromodulin, insulin-like growth factor 2 (Igf2), and insulin-like growth factor binding protein 2 (Igfbp2) were further analyzed for histological expression changes. The expression of osteoglycin and fibromodulin simultaneously decreased in the medial, basolateral, and central amygdala regions. However, Igf2 and Igfbp2 decreased specifically in the central nucleus of the amygdala. Interestingly, this decrease was found only in the amygdala of mice showing higher immobility, but not in mice displaying lower immobility, although the CIS regimen was the same for both groups. CONCLUSIONS: These results suggest that the responsiveness of the amygdala may play a role in the sensitivity of CIS-induced behavioral changes in mice