REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

Effects of key operational parameters on biohydrogen production via anaerobic fermentation in a sequencing batch reactor

In this study, a series of tests were conducted in a 6 L anaerobic sequencing batch reactor (ASBR) to investigate the effect of pH, hydraulic retention time (HRT) and organic loading rate on biohydrogen production at 28 °C. Sucrose was used as the main substrate to mimic carbohydrate-rich wastewater and inoculum was prepared from anaerobic digested sludge without pretreatment. The reactor was operated initially with nitrogen sparging to form anaerobic condition. Results showed that methanogens were effectively suppressed. The optimum pH value would vary depending on the HRT. Maximum hydrogen production rate and yield of 3.04 L H₂/L reactor d and 2.16 mol H₂/mol hexose respectively were achieved at pH 4.5, HRT 30 h, and OLR 11.0 kg/m³ d. Two relationships involving the propionic acid/acetic acid ratio and ethanol/acetic acid ratio were derived from the analysis of the metabolites of fermentation. Ethanol/acetic acid ratio of 1.25 was found to be a threshold value for higher hydrogen production.     

Effect of feeding and sludge age on acclimated bacterial community and fate of slowly biodegradable substrate

The study investigated the effect of feeding regime and sludge age on starch utilization. For this purpose, parallel sequencing batch reactors were operated with pulse and continuous feeding of soluble starch at sludge ages of 8 and 2 days. Pulse feeding induced almost complete conversion of starch to glycogen, while storage was lowered and accompanied with direct growth under continuous feeding, regardless of sludge age. Low sludge age did not alter simultaneous storage and utilization for direct growth but it slightly favoured direct utilization due to faster growing biomass. Experimental results suggested adsorption of starch onto biomass as a preliminary removal mechanism prior to hydrolysis at sludge age of 8 days. Adsorption was not noticeable as substrate removal, glycogen generation and dissolved oxygen decrease were synchronous at sludge age of 2 days. Bacterial community always included fractions storing glycogen although sludge age only affected the relative magnitude of filamentous growth.     

Aerobic granular sludge formation for high strength agro-based wastewater treatment

The present study investigates the formation of aerobic granular sludge in sequencing batch reactor (SBR) fed with palm oil mill effluent (POME). Stable granules were observed in the reactor with diameters between 2.0 and 4.0 mm at a chemical oxygen demand (COD) loading rate of 2.5 kg COD m⁻³ d⁻¹. The biomass concentration was 7600 mg L⁻¹ while the sludge volume index (SVI) was 31.3 mL g SS⁻¹ indicating good biomass accumulation in the reactor and good settling properties of granular sludge, respectively. COD and ammonia removals were achieved at a maximum of 91.1% and 97.6%, respectively while color removal averaged at only 38%. This study provides insights on the development and the capabilities of aerobic granular sludge in POME treatment.     

The influence of fundamental design parameters on ciliates community structure in Irish activated sludge systems

The protozoan community in eleven activated sludge wastewater treatment plants (WWTPs) in the greater Dublin area has been investigated and correlated with key physio-chemical operational and effluent quality parameters. The plants represented various designs, including conventional and biological nutrient removal (BNR) systems. The aim of the study was to identify differences in ciliate community due to key design parameters including anoxic/anaerobic stages and to identify suitable bioindicator species for performance evaluation. BNR systems supported significantly different protozoan communities compared to conventional systems. Total protozoan abundance was reduced in plants with incorporated anoxic and anaerobic stages, whereas species diversity was either unaffected or increased. Plagiocampa rouxi and Holophrya discolor were tolerant to anoxic/anaerobic conditions and associated with high denitrification. Apart from process design, influent wastewater characteristics affect protozoan community structure. Aspidisca cicada was associated with low dissolved oxygen and low nitrate concentrations, while Trochilia minuta was indicative of good nitrifying conditions and good sludge settleability. Trithigmostoma cucullulus was sensitive to ammonia and phosphate and could be useful as an indicator of high effluent quality. The association rating assessment procedure of Curds and Cockburn failed to predict final effluent biological oxygen demand (BOD₅) indicating the method might not be applicable to treatment systems of different designs.     

Notch signaling and Notch signaling modifiers

Originally discovered nearly a century ago, the Notch signaling pathway is critical for virtually all developmental programs and modulates an astounding variety of pathogenic processes. The DSL (Delta, Serrate, LAG-2 family) proteins have long been considered canonical activators of the core Notch pathway. More recently, a wide and expanding network of non-canonical extracellular factors has also been shown to modulate Notch signaling, conferring newly appreciated complexity to this evolutionarily conserved signal transduction system. Here, I review current concepts in Notch signaling, with a focus on work from the last decade elucidating novel extracellular proteins that up- or down-regulate signal potency.     

Prediction of fat quality in pig carcasses by near-infrared spectroscopy

This study was conducted to evaluate the potential of near-infrared (NIR) spectroscopy (NIRS) technology for prediction of the chemical composition (moisture content and fatty acid composition) of fat from fast-growing, lean slaughter pig samples coming from breeding programmes. NIRS method I: a total of 77 samples of intact subcutaneous fat from pigs were analysed with the FOSS FoodScan NIR spectrophotometer (850 to 1050 nm) and then used to predict the moisture content by using partial least squares (PLS) regression methods. The best equation obtained has a coefficient of determination for cross-validation (CV; R(2)(cv)) and a root mean square error of a CV (RMSECV) of 0.88 and 1.18%, respectively. The equation was further validated with (n = 15) providing values of 0.83 and 0.42% for the coefficient of determination for validation (R(2)(val)) and root mean square error of prediction (RMSEP), respectively. NIRS method II: in this case, samples of melted subcutaneous fat were analysed in an FOSS XDS NIR rapid content analyser (400 to 2500 nm). Equations based on modified PLS regression methods showed that NIRS technology could predict the fatty acid groups, the main fatty acids and the iodine value accurately with R(2)(cv), RMSECV, R(2)(val) and RMSEP of 0.98, 0.38%, 0.95 and 0.49%, respectively (saturated fatty acids), 0.94, 0.45%, 0.97 and 0.65%, respectively (monounsaturated fatty acids), 0.97, 0.28%, 0.99 and 0.34%, respectively (polyunsaturated fatty acids), 0.76, 0.61%, 0.84 and 0.87%, respectively (palmitic acid, C16:0), 0.75, 0.16%, 0.89 and 0.10%, respectively (palmitoleic acid, C16:1n-7), 0.93, 0.41%, 0.96 and 0.64%, respectively (steric acid, C18:0), 0.90, 0.51%, 0.94 and 0.44%, respectively (oleic acid, C18:1n-9), 0.97, 0.25%, 0.98 and 0.29% (linoleic acid, C18:2n-6), 0.68, 0.09%, 0.57 and 0.16% (α-linolenic acid, C18:3n-3) and 0.97, 0.57, 0.97 and 1.22, respectively (iodine value, calculated). The magnitude of this error showed quite good accuracy using these rapid methods in prediction of the moisture and fatty acid composition of fat from pigs involved in breeding schemes.     

Comparative assessment of fermentation techniques useful in the processing of ogi

Ogiis processed traditionally by the use of uncontrolled spontaneous fermentation of maize, sorghum and millet. In this study, traditionally applied spontaneous fermentation was compared with accelerated batch fermentation (or back-slopping) and the use of starter cultures to initiate fermentation. Lactic acid bacteria populations comprised 95 of the total viable bacteria and remained prominent throughout the fermentations, while number of moulds and coliform bacteria declined as the fermentation progressed. The fermentation method involving the application of starter culture helps most to control the prevalence of coliforms and moulds. Lactic acid bacteria, such as Lactococcus raffinolactis, Pediococcussp.,Pediococcus pentosaceus, Lactobacillus plantarum, Lb. suebicus and Lb. brevis,were isolated at different processing stages of ogi using accelerated batch fermentation (back-slopping) technique. Highest increase in acidity was observed immediately after wet-milling and sieving fermenting maize grains at 28 and 48 h. Sharp increases in the reducing sugar levels were noted between 24 and 28 h of fermentations during wet-milling and sieving processes.     

Evaluation of agro-food byproducts for gluconic acid production by <Emphasis Type="Italic">Aspergillus niger</Emphasis> ORS-4.410

Certain cost-effective carbohydrate sources in crude as well as after purification were utilized as the sole sources of carbon for gluconic acid production using Aspergillus niger ORS-4.410 under submerged fermentation. Crude grape must (GM) and banana-must (BM) resulted into significant levels of gluconic acid production i.e. 62.6 and 54.6 g/l, respectively. The purification of grape and banana-must led to a 20–21% increase in gluconic acid yield. Molasses as such did not favour gluconate production (12.0 g/l) but a significant increase in production (60.3 g/l) was observed following hexacyanoferrate (HCF) treatment of the molasses. Rectified grape must (RGM) appeared to be best suitable substrate which after 144 h resulted in 73.2 g of gluconic acid/l with 80.6% yield followed by the yield obtained from the rectified banana must (RBM) (72.4%) and treated cane molasses (TM) (61.3%). Abundant growth of mould A. niger ORS-4.410 was observed with crude grape (0.131 g/l/h) and banana must (0.132 g/l/h).     

Production of fuculose-1-phosphate aldolase using operator-repressor titration for plasmid maintenance in high cell density Escherichia coli fermentations

We report a novel application for the operator-repressor titration (ORT) plasmid maintenance system. The ability of ORT to maintain a plasmid during production of DNA has been demonstrated previously. In this study, we have used the ORT system to maintain a plasmid during high cell density cultivation and expression of a recombinant protein. No evidence of plasmid loss was seen during protein expression at high cell densities. In addition, the quantity of protein produced using this system was similar to traditional plasmid maintenance systems.