Abiotic stresses limit the plant growth and productivity. Plants have developed various responsive mechanisms to survive these adverse environmental conditions. To better understand plants how to adapt environmental stress, we retrieved the Arabidopsis root responsive genes related to eight abiotic stresses (salt, cold, drought, osmotic, UV, wounding, heat, and heavy metal stresses) from the Gene Expression Omnibus (GEO) database. After quantile normalization of microarray data, a robust rank aggregation (RRA) algorithm was applied to determine the differentially expressed genes (DEGs). The resultant 213 DEGs, including 139 up-regulated and 74 down-regulated genes out of more than 20,000 genes, were further analyzed by the integrated bioinformatics approaches of PUBMED, PANTHER, DAVID, and STRING. The results indicated that the up-regulated DEGs were more positively involved in response to oxidative stress, regulation of transcription, and structure organization than the down-regulated DEGs. The former also had more complicated PPI interactions than the latter. Furthermore, qRT-PCR and enzyme activity have been done to validate the outcome of integrated bioinformatics analysis. Our work will facilitate to demonstrate the common molecular mechanisms responsive to differential abiotic stresses and these DEGs might be potential biomarkers for future abiotic stress-resistance studies.

Cold stress is a major environmental factor that limits plant growth and productivity. Plants have evolved various strategies to adapt to these environmental conditions. To better explain the mechanisms used to survive environmental challenges, we retrieved the cold-responsive genes of Arabidopsis thaliana from the Gene Expression Omnibus (GEO) database. The GEO raw data were normalized by the quantile method, and then the differentially expressed genes (DEGs) under cold stress were screened using the robust rank aggregation (RRA) algorithm, including 261 upregulated and 177 downregulated genes out of more than 20,000 genes. Further, the integrated bioinformatics analyses of PUBMED, PANTHER, DAVID, and STRING indicated that the upregulated DEGs were involved in cellular response to red light, negative regulation of circadian rhythm, photoprotection, monosaccharide transport, cold acclimation, and phosphate ion homeostasis, while the downregulated DEGs were associated with the indole glucosinolate biosynthetic process, regulation of RNA splicing, water transport, cell wall modification, cell wall loosening, cellular water homeostasis, and cell wall homeostasis. Furthermore, the up-regulated DEGs had about four times protein-protein-interactions (PPIs) than the down-regulated DEGs, and the cold-responsive genes were identified using Cytoscape software. Furthermore, qRT-PCR of low-temperatureresponsive protein 78 (LTI78), transducin family protein (SWA1), and arginine methyltransferase 11 (PRMT11) were performed to validate the outcome of integrated bioinformatics analysis. Our work will improve our knowledge of cold-responsive mechanisms and these DEGs might be targets for plant cold stress-resistance research.

Background Cryptococcal meningitis (CM) has a high morbidity and mortality due to the low detection of Cryptococcus in cerebrospinal fluid (CSF) during the early stage of the disease with traditional methods. Case presentation In addition to the traditional methods of India ink staining and cryptococcal antigen (CrAg), we used nanopore sequencing and next-generation sequencing (NGS) to detect pathogenic DNA in CSF samples of three patients with CM. The CSF samples of all three patients were positive by India ink staining and CrAg. NGS also detected Cryptococcus in all three CSF samples. Nanopore sequencing detected Cryptococcus in two CSF samples. Conclusion Nanopore sequencing may be useful in assisting with the clinical diagnosis of CM. Further research is needed to determine the sensitivity and specificity of nanopore sequencing of CSF.

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Plant growth and crop productivity has been adversely affected by salt stress around the world. Arabidopsis root is an important model to demonstrate how the glycophyte adapts to salt stress. To better understand the salt-responsive genes in Arabidopsis root, a rank aggregation method has been applied to disclose 836 dysregulated genes including 449 upregulated and 387 downregulated genes out of more than 20,000 genes in NaCl-treated Arabidopsis root from the Gene Expression Omnibus (GEO) database. Then, the integrated approaches of PANTHER, DAVID, KEGG, Cytoscape and STRING have been used for bioinformatic analysis. Our results showed that these salt-responsive genes were involved in various gene ontology enrichments (transcription, oxidative stress, cell wall organization), differential pathways (MAPK signaling pathway, hormone signal transduction), and complicated interactions (cross-talking with wounding stress, abscisic acid stress, heat stress, water deprivation stress, cold stress). Furthermore, the activities of the oxidative stress related gene, peroxidase, were determined under salt stress, cold stress and water deprivation stress, which validated the bioinformatic outcome of cross-tolerance to different stresses. Our work will throw new lights on the response of Arabidopsis roots to salt stress, and provide potential salttargets to improve plant growth and increase crop output.