Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Structured modeling and state estimation in a fermentation process: Lipase production by Candida rugosa

A simple structured mathematical model coupled with a methodology of state and parameter estimation is developed for lipase production by Candida rugosa in batch fermentation. The model describes the system according to the following qualitative observations and hypothesis: Lipase production is induced by extracellular oleic acid present in the medium. The acid is transported into the cell where it is consumed, transformed, and stored. Lipase is excreted to the medium where it is distributed between the available oil-water interphase and aqueous phase. Cell growth is modulated by the intracellular substrate concentration. Model parameters have been determined and the whole model validated against experiments not used in their determination. The estimation problem consists in the estimation of three state variables (biomass, intra- and extracellular substrate) and two kinetic parameters by using only the on-line measurement provided by exhaust gas analysis. The presented estimation strategy divides the complex problem into three subproblems that can be solved by stable algorithms. The estimation of biomass (X) and the specific growth rate (mu), is achieved by a recursive prediction error algorithm using the on-line measurement of the carbon dioxide evolution rate. mu is then used to perform an estimation of intracellular substrate and the other kinetic parameter related to substrate transport (A) by an adaptive observer. Extracellular substrate is then evaluated by means of the estimated values of intracellular substrate and biomass through the material balance of the reactor. Simulation and experimental tests showed good performance of the developed estimator, which appears suitable to be used for process control and monitoring. (c) 1995 John Wiley & Sons, Inc.     

Optimized nitrate reductase assay predicts the rate of nitrate utilization in the halotolerant microalga Dunaliella viridis

An in situ method for measuring nitrate reductase (NR) activity in Dunaliella viridis was optimized in terms of incubation time, concentration of KNO₃, permeabilisers (1-propanol and toluene), pH, salinity, and reducing power (glucose and NADH). NR activity was measured by following nitrite production and was best assayed with 50 mM KNO₃, 1.2 mM NADH, 5% 1-propanol (v/v), at pH 8.5. The estimated half-saturation constant (K_s) for KNO₃ was 5 mM. Glucose had no effect as external reducing power source, and NADH concentrations >1.2 mM inhibited NR activity. Nitrite production was linear up to 20 min; longer incubation did not lead to higher nitrate reduction. The use of the optimized assay predicted the rate of NO ₃ ⁻ removal from the external medium by D. viridis with high degree of precision. This revised version was published online in September 2006 with corrections to the Cover Date.     

Effects of CO2 and nitrogen supply on the biochemical composition of Ulva rigida with especial emphasis on lipid class analysis

Lipid class composition was analysed in the green macroalga Ulva rigida grown under normal (350 ppm) and high (10,000 ppm) CO₂ levels, and in nitrate saturated and nitrogen limited conditions. A new protocol for the extraction of lipids has been defined. Culture conditions altered the fate of assimilated carbon, and significant changes were observed in protein and total lipid content in particular. A CO₂-enriched atmosphere conditioned the effects of nitrogen limitation on lipid class composition, revealing deep qualitative changes in carbon metabolism. Triglycerides accumulated at high CO₂ and under nitrogen limitation, while chloroplast-related lipids showed an inverse response. Changes in phospholipids could be related to carbon availability as they did not respond to nitrogen limitation. The ratio sterols/acetone-mobile polar lipids followed a negative linear relation with the optimum quantum yield for photosynthetic electron transport (F_v/F_m), and was considered as an index of the «light status» of the cell. The specificity of the response of lipid classes to growth conditions in U. rigida emphasizes the potential role of lipid class analyses as a diagnostic tool for environmental stress.     

Glacidorbidae (Gastropoda: Heterobranchia) in South America: revision and description of a new genus and three new species from Patagonia

The Glacidorbidae, a family restricted to the Gondwanan realm (Tasmania, southeastern and southwestern Australia, and southern Argentina and Chile), previously included five genera with 20 identified species; 19 of them are Australian, with one genus and species, Gondwanorbis magallanicus (Meier-Brook & Smith, 1976 Meier-Brook, K. & Smith, B.J. (1976) Glacidorbis Iredale, 1943, a genus of freshwater prosobranchs with a Tasmanian-Southeast Australian-South Andean distribution. Archive für Molluskenkunde 106, 191–198. [Google Scholar]), from South America. Here we describe two new species of Gondwanorbis: Gondwanorbis fueguensis n. sp. from the freshwater gastropods province of Southern Patagonia (Argentina) and Gondwanorbis tricarinatus n. sp. from Chile, and a new genus and species from the freshwater gastropods province of northern Patagonia (Argentina), Patagonorbis nahuelhuapensis n. sp and n. gen.

http://www./zoobank.org/urn:lsid:zoobank.org:pub:62EA0972-3AEF-4188-8E6D-F10895CE2BEF