The functional decline of tomato plants infected by Liberbacter solanacearum: an RNA-seq transcriptomic analysis.

Introduction: Liberibacter solanacearum (Lso) is a regulated plant pathogen in European and some Asian countries, associated with severe diseases in economically important Apiaceous and Solanaceous crops, including potato, tomato, and carrot. Eleven haplotypes of Lso have been identified based on the difference in rRNA and conserved genes and host and pathogenicity. Although it is pathogenic to a wide range of plants, the mechanisms of plant response and functional decline of host plants are not well defined.

Clasnip: a web-based intraspecies classifier and multi-locus sequence typing for pathogenic microorganisms using fragmented sequences.

Bioinformatic approaches for the identification of microorganisms have evolved rapidly, but existing methods are time-consuming, complicated or expensive for massive screening of pathogens and their non-pathogenic relatives. Also, bioinformatic classifiers usually lack automatically generated performance statistics for specific databases. To address this problem, we developed Clasnip (www.

Atria: an ultra-fast and accurate trimmer for adapter and quality trimming.

With advances in next-generation sequencing, adapters attached to reads and low-quality bases directly and implicitly hinder downstream analysis. For example, they can produce false-positive single nucleotide polymorphisms (SNP), and generate fragmented assemblies. There is a need for a fast trimming algorithm to remove adapters precisely, especially in read tails with relatively low quality.

Diffuse reflectance spectroscopy to monitor murine colorectal tumor progression and therapeutic response (Erratum).

The erratum notes a correction to Fig. 5 for the published article.

Diffuse reflectance spectroscopy to monitor murine colorectal tumor progression and therapeutic response.

Significance: Many studies in colorectal cancer (CRC) use murine ectopic tumor models to determine response to treatment. However, these models do not replicate the tumor microenvironment of CRC. Physiological information of treatment response derived via diffuse reflectance spectroscopy (DRS) from murine primary CRC tumors provide a better understanding for the development of new drugs and dosing strategies in CRC.