Supporting material affects the growth and development of in vitro sweet potato plantlets cultured photoautotrophically

Summary A comparative study was conducted to optimize the vegetative growth of sweet potato (Ipomoea batatas L. (Lam), cv. Beniazuma) plantlets cultured in vitro in five different types of supporting materials: agar matrix (a seaweed derivative; Kanto Chemical Co. Inc., Tokyo), gellan gum (a Pseudomonas derivative; Kanto Chemical Co. Inc., Tokyo), vermiculite (a kind of hydrous silicates), a mixture of vermiculite and cellulose fiber (Florialite; Nisshinbo Industries, Inc., Tokyo) and cellulose plug (Sorbarod; Baumgartner Rapiers SA., Switzerland). Single nodal cuttings were cultured photoautotrophically (without any sugar in the medium and with enriched CO₂ and high photosynthetic photon flux) for 21 d on MS basal medium. Plantlets exhibited the greatest growth when Florialite was used as supporting material. The leaf and root fresh and dry mass were 2.4× and 2.9×, and 2.2× and 2.8× greater, respectively, than those of the plantlets grown in the agar matrix (control). Plantlets cultured in Sorbarod supporting material exhibited the second greatest fresh and dry mass of leaves and roots followed by vermiculite and gellan gum supporting material. The most interesting feature was the development of a large number of fine lateral roots from the main adventitious root in the Florialite treatment. Among the treatments, the highest net photosynthetic rate was evident in the Florialite grown plantlets. The percent porosity of the supporting materials was highest in Sorbarod followed by Florialite and vermiculite. Plantlets transplanted from the Florialite supporting material exhibited the highest acclimatization percentage followed by that of the Sorbarod treatment.     

Fifteen hub genes associated with progression and prognosis of clear cell renal cell carcinoma identified by coexpression analysis

Renal cell carcinoma (RCC) is the most common type of renal tumor, and the clear cell renal cell carcinoma (ccRCC) is the most frequent subtype. In this study, our aim is to identify potential biomarkers that could effectively predict the prognosis and progression of ccRCC. First, we used The Cancer Genome Atlas (TCGA) RNA-sequencing (RNA-seq) data of ccRCC to identify 2370 differentially expressed genes (DEGs). Second, the DEGs were used to construct a coexpression network by weighted gene coexpression network analysis (WGCNA). Moreover, we identified the yellow module, which was strongly related to the histologic grade and pathological stage of ccRCC. Then, the functional annotation of the yellow module and single-samples gene-set enrichment analysis of DEGs were performed and mainly enriched in cell cycle. Subsequently, 18 candidate hub genes were screened through WGCNA and protein–protein interaction (PPI) network analysis. After verification of TCGA’s ccRCC data set, Gene Expression Omnibus (GEO) data set (GSE73731) and tissue validation, we finally identified 15 hub genes that can actually predict the progression of ccRCC. In addition, by using survival analysis, we found that patients of ccRCC with high expression of each hub gene were more likely to have poor prognosis than those with low expression. The receiver operating characteristic curve showed that each hub gene could effectively distinguish between localized and advanced ccRCC. In summary, our study indicates that 15 hub genes have great predictive value for the prognosis and progression of ccRCC, and may contribute to the exploration of the pathogenesis of ccRCC.     

Was total primary production in the western Wadden Sea stimulated by nitrogen loading?

Borum and Sand-Jensen (1996) described empirical relationships between nitrogen (N) loadings from land and total (benthic + pelagic) primary production rates in shallow coastal marine waters. We applied these relationships to N loadings of the western Wadden Sea system, and compared the production estimates with actually observed primary production rates of autotrophic components (phytoplankton, microphytobenthos, macroalgae and seagrasses) for those years for which field data were available. During the 1980s and early 1990s, primary production values appear in good agreement with those derived from the empirical relationships. During the 1960s and early 1970s, however, these relationships substantially overestimated the total primary production in the western Wadden Sea. Based on ambient nutrient concentrations and the Redfield ratio, production in that period was considered not to be limited by N but by phosphorus (P) during most of the time. It is concluded that primary production is not invariably stimulated by N loading from land. If other factors (i.e. additional nutrient sources, N:P ratios, internal nutrient dynamics and co-limiting effects of nutrients and light) are not taken into account, management regulations that are targeted at diminishing the effects of eutrophication hold the risk of seriously under- or overestimating nutrient reductions that are thought necessary to achieve their goals. Received: 30 November 1998 / Received in revised form: 12 July 1999 / Accepted: 15 July 1999     

An eight-long noncoding RNA expression signature for colorectal cancer patients’ prognosis

Long noncoding RNAs (lncRNAs) have recently emerged as important biomarkers of cancer progression. Here, we proposed to develop a lncRNA-based signature with a prognostic value for colorectal cancer (CRC) overall survival (OS). Through mining microarray datasets, we analyzed the lncRNA expression profiles of 122 patients with CRC from Gene Expression Omnibus. Associations between lncRNA and CRC OS were firstly evaluated through univariate Cox regression analysis. A random survival forest method was applied for further screening of the lncRNA signature, which resulted in eight lncRNAs, including PEG3-AS1, LOC100505715, MINCR, DBH-AS1, LINC00664, FAM224A, LOC642852, and LINC00662. Combination of the eight lncRNAs weighted by their multivariate Cox regression coefficients formed a prognostic signature, through which, we could divide the 122 patients with CRC into two subgroups with significantly different OS. Good robustness of the lncRNA signature's prognostic value was verified through an independent data set consisting of 55 patients with CRC. In addition, gene set enrichment analysis indicated the potential association between high prognostic value and oxygen metabolism-related processes. This result should indicate that lncRNAs could be a useful signature for CRC prognosis.     

Modified method for selective enrichment and isolation of Bacillus thuringiensis from soil

Many colonies of Bacillus thuringiensis (Bt) were found to be lost using the isolation technique described by Martin and Travers modified by Morris (Morris method). Hence, a modified method for isolation of B. thuringiensis is described and compared with the Morris method. Screening methodology adopted by this method delivers an immensely rich and potentially more useful library of Bt colonies with ‘presumptive-positive’ morphology and 10-fold higher per cent frequency of Bt colonies as compared to the Morris method.