MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors.

SUMMARY: The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. AVAILABILITY AND IMPLEMENTATION: MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. CONTACT: dominik.heider@uni-marburg.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesorhizobium norvegicum sp. nov., a rhizobium isolated from a Lotus corniculatus root nodule in Norway.

Strain 10.2.2T was isolated from a root nodule of a Lotus corniculatus plant growing near Skammestein (Norway). Phenotypic and chemotaxonomic characterization revealed that colonies grown on yeast-mannitol broth agar were circular, convex and slimy. Growth occurred at 28 °C in 0-1 % NaCl and in a pH range from above 4 to 10. Cells were resistant to kanamycin and phosphomycin. They could assimilate carbon sources such as l-lysine, d-mannose, d-mannitol, and l-alanine. Major fatty acids found in the organism were 11-methyl C18  :  1ω7c, C16  :  0, C18  :  1ω7c, C18  :  0 and C19  :  0 cyclo ω8c. Genome sequencing and characterization of the genome revealed its size to be 8.27 Mbp with a G+C content of 62.4 mol%. Phylogenetic analyses based on the 16S rRNA gene and housekeeping gene alignments placed this strain within the genus Mesorhizobium. Pairwise genome-wide average nucleotide identity values supported that strain 10.2.2T represents a new species, for which we propose the name Mesorhizobium norvegicum sp. nov. with the type strain 10.2.2T (=DSM 108834T=LMG 31153T).

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage.

The extensive information capacity of DNA, coupled with decreasing costs for DNA synthesis and sequencing, makes DNA an attractive alternative to traditional data storage. The processes of writing, storing, and reading DNA exhibit specific error profiles and constraints DNA sequences have to adhere to. We present DNA-Aeon, a concatenated coding scheme for DNA data storage. It supports the generation of variable-sized encoded sequences with a user-defined Guanine-Cytosine (GC) content, homopolymer length limitation, and the avoidance of undesired motifs. It further enables users to provide custom codebooks adhering to further constraints. DNA-Aeon can correct substitution errors, insertions, deletions, and the loss of whole DNA strands. Comparisons with other codes show better error-correction capabilities of DNA-Aeon at similar redundancy levels with decreased DNA synthesis costs. In-vitro tests indicate high reliability of DNA-Aeon even in the case of skewed sequencing read distributions and high read-dropout.

Top soil physical and chemical properties in Kazakhstan across a north-south gradient.

Kazakhstan's soil properties have yet to be comprehensively characterized. We sampled 40 sites consisting of ten major soil types at spring (wet) and late-summer (dry) seasons. The sample locations range from semi-arid to arid with an annual mean air temperature from 1.2 to 10.7 °C and annual precipitation from less than 200 to around 400 mm. Overall topsoil total (STC), organic (SOC), and inorganic (SIC) carbon did not change significantly between spring and late summer. STC and SOC show a wave like pattern from north to south with two maxima in northern and southern Kazakhstan and one minimum in central Kazakhstan. With a few exceptions SIC content at northern sites is generally low, whereas at Lake Balkhash SIC can exceed 75% of STC. Independent of the seasons, SOC significantly differed among soil types. Total nitrogen content distribution among our sampling sites followed a similar pattern as SOC with significant differences between soil types occurring in northern, central and southern Kazakhstan.