FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences

Background: Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. Findings: FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. Conclusions: The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data

Pulsed-laser studies on the free-radical polymerization kinetics of styrene in microemulsion

A mean value of 339 L mol-1 s-1 was obtained for the propagation const. derived from pulsed-laser polymn. (PLP) of styrene in aq. AOT microemulsions. For accurate detns., simulations accounting for the esp. high radical concn. after the laser pulse in microemulsions were recommended. PLP with microemulsions apparently permitted specific kinetic aspects such as transfer to monomer and influence of droplet size on bimol. termination to be studied in detai

Mithramycin and Analogs for Overcoming Cisplatin Resistance in Ovarian Cancer

Ovarian cancer is a highly deadly malignancy in which recurrence is considered incurable. Resistance to platinum-based chemotherapy bodes a particularly abysmal prognosis, underscoring the need for novel therapeutic agents and strategies. The use of mithramycin, an antineoplastic antibiotic, has been previously limited by its narrow therapeutic window. Recent advances in semisynthetic methods have led to mithramycin analogs with improved pharmacological profiles. Mithramycin inhibits the activity of the transcription factor Sp1, which is closely linked with ovarian tumorigenesis and platinum-resistance. This article summarizes recent clinical developments related to mithramycin and postulates a role for the use of mithramycin, or its analog, in the treatment of platinum-resistant ovarian cancer

Microbial community responses determine how soil–atmosphere exchange of carbonyl sulfide, carbon monoxide, and nitric oxide responds to soil moisture

Carbonyl sulfide (OCS) plays an important role in the global sulfur cycle and is relevant for climate change due to its role as a greenhouse gas, in aerosol formation and atmospheric chemistry. The similarities of the carbon dioxide (CO2) and OCS molecules within chemical and plant metabolic pathways have led to the use of OCS as a proxy for global gross CO2 fixation by plants (gross primary production, GPP). However, unknowns such as the OCS exchange from soils, where simultaneous OCS production (POCS) and consumption (UOCS) occur, currently limits the use of OCS as a GPP proxy. We estimated POCS and UOCS by measuring net fluxes of OCS, carbon monoxide (CO), and nitric oxide (NO) in a dynamic chamber system fumigated with air containing different mixing ratios [OCS]. Nine soils with different land use were rewetted and soil–air exchange was monitored as soils dried out to assess responses to changing moisture. A major control of OCS exchange was the total amount of available sulfur in the soil. POCS production rates were highest for soils at WFPS (water-filled pore space) &gt;60&thinsp;% and rates were negatively related to thiosulfate concentrations. These moist soils switched from a net source to a net sink activity at moderate moisture levels (WFPS 15&thinsp;% to 37&thinsp;%). For three soils we measured NO and CO mixing ratios at different mixing ratios of OCS and revealed that NO and potentially CO exchange rates are linked to UOCS at moderate soil moisture. High nitrate concentrations correlated with maximum OCS release rates at high soil moisture. For one of the investigated soils, the moisture and OCS mixing ratio was correlated with different microbial activity (bacterial 16S rRNA, fungal ITS RNA relative abundance) and gene transcripts of red-like cbbL and amoA.</p

Acyl chain-dependent effect of lysophosphatidylcholine on endothelial prostacyclin production

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