Data Cubes and Matrix Formulae for Convenient Handling of Physical Flow Data

If the technosphere and the biosphere are divided into cells, the presence and turnover of a substance in a study area can be summarized in a vector of stocks and a matrix of flows between different pairs of cells. Likewise the stocks and flows of several substances or materials in one or more time periods can be summarized in multidimensional data cubes. In this article, we provide a theoretical framework for handling physical flow data, and we demonstrate how a set of matrix operations can facilitate exploratory analysis and quality assessment of such data regardless of the number of substances, materials, and time periods considered. In particular, we show how matrices and cubes of flow data can be recalculated when the collection of cells is modified by joining cells, and also what information is required to recalculate flows when cells are split. Furthermore, we illustrate how and under what circumstances substance-flow data originating from different studies with different collections of cells can be compared or merged. The generic character of the given formulae facilitates the development of software for physical flow data.     

A novel manual pooling system for preparing three-dimensional pools of a deep coverage soybean bacterial artificial chromosome library

Compared with hybridization‐based techniques, polymerase chain reaction‐based screening of large insert libraries has been used widely as it is fast, easy and sensitive. However, various pooling strategies are needed to ensure efficient screening. It is time‐consuming and labourious to prepare three‐dimensional pools for a deep coverage bacterial artificial chromosome (BAC) library of soybean (1.12 × 10⁹ bp) in the absence of robotic facility. In the present study, we describe a novel manual pooling system for preparing three‐dimensional pools of a soybean BAC library. This simple technique enables a single researcher to construct three‐dimensional pools for a deep‐coverage (12 haploid genome equivalents) BAC library of soybean in less than 2 months without any robotic manipulation. When the prepared three‐dimensional pools were screened with 29 polymerase chain reaction‐based markers, an average of 9.2 clones per marker were identified. These identified clones will be useful either in quantitative trait loci gene isolation or in synteny study between soybean and other legumes including Lotus japonicus. This efficient pooling system could be applied to any other BAC libraries without the need for robotic manipulation.     

Qualitative and quantitative methodologies for determination of airborne microorganisms at concentrated animal-feeding operations

The generation of airborne microorganisms from concentrated animal-feeding operations (CAFOs) is a concern from a human and animal health perspective. To better understand the airborne microorganisms found in these environments, a number of collection and analytical techniques have been utilized and will be discussed in this review. The most commonly used bioaerosol collection method is the liquid impingement format, which is suitable with a number of culture-based and non-culture molecular-based approaches, such as polymerase chain reaction. However, the vast majority of airborne microorganism studies conducted at CAFOs utilize culture-based analyses. Because of the limitations often associated with culture-based analyses, we focused our discussion on the application of molecular-based techniques to identify and/or quantify microorganisms, as they have promising application in bioaerosol research. The ability to rapidly characterize airborne microorganisms will help to ensure protection of public and environmental health. The use or mention of any commercial products does not imply any endorsement of that product by either the authors or the US Department of Agriculture.     

An optimal DNA pooling strategy for progressive fine mapping

We present a cost-effective DNA pooling strategy for fine mapping of a single Mendelian gene in controlled crosses. The theoretical argument suggests that it is potentially possible for a single-stage pooling approach to reduce the overall experimental expense considerably by balancing costs for genotyping and sample collection. Further, the genotyping burden can be reduced through multi-stage pooling. Numerical results are provided for practical guidelines. For example, the genotyping effort can be reduced to only a small fraction of that needed for individual genotyping at a small loss of estimation accuracy or at a cost of increasing sample sizes slightly when recombination rates are 0.5% or less. An optimal two-stage pooling scheme can reduce the amount of genotyping to 19.5%, 14.5% and 6.4% of individual genotyping efforts for identifying a gene within 1, 0.5, and 0.1 cM, respectively. Finally, we use a genetic data set for mapping the rice xl(t) gene to demonstrate the feasibility and efficiency of the DNA pooling strategy. Taken together, the results demonstrate that this DNA pooling strategy can greatly reduce the genotyping burden and the overall cost in fine mapping experiments.     

Screening for the rice blast resistance gene Pi-ta using LNA displacement probes and real-time PCR

Single nucleotide polymorphisms (SNPs) will become a molecular breeding tool of increasing significance as a growing range of SNP data becomes available. In order for these markers to be incorporated into breeding programs, simple, high throughput and low cost detection methods need to be available. We have developed such an assay using LNA containing displacement probes for the Pi-ta gene, an important blast resistance gene in rice. This assay gave superior performance in comparison with TaqMan MGB probes and was able to accurately identify the presence of low frequency genotypes in artificially created mixed samples. The ability to pool samples for screening purposes offers the potential to significantly increase throughput and reduce per sample detection cost, particularly for low frequency alleles.     

Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling

The objective of this study was to identify QTL for growth rate in the blacklip abalone Haliotis rubra using selective DNA pooling. Three full-sibling families of H. rubra derived from crosses of wild broodstock were used. DNA was extracted from the largest and smallest 10% of progeny and combined into two pools for each phenotypic tail. The DNA pools were typed with 139 microsatellites, and markers showing significant differences between the peak height ratios of alleles inherited from the parents were individually genotyped and analysed by interval mapping. A strong correlation (r = 0.94, P < 0.001) was found between the t-values from the analysis of pools and the t-values from the analysis of individual genotypes. Based on the interval mapping analysis, QTL were detected on nine linkage groups at a chromosome-wide P < 0.01 and one linkage group at a chromosome-wide P < 0.05. The study demonstrated that selective DNA pooling is efficient and effective as a first-pass screen for the discovery of QTL in an aquaculture species.     

Within-breed heterozygosity of canine single nucleotide polymorphisms identified by across-breed comparison

Identification of single nucleotide polymorphisms (SNPs) by DNA sequence comparison across breeds is a strategy for developing genetic markers that are useful for many breeds. However, the heterozygosity of SNPs identified in this way might be severely reduced within breeds by inbreeding or genetic drift in the small effective population size of a breed (population subdivision). The effect of inbreeding and population subdivision on heterozygosity of SNPs in dog breeds has never been investigated in a systematic way. We determined the genotypes of dogs from three divergent breeds for SNPs in four canine genes (ACTC, LMNA, SCGB, and TYMS) identified by across-breed DNA sequence comparison, and compared the genotype frequencies to those expected under Hardy-Weinberg equilibrium (HWE). Although population subdivision significantly skewed allele frequencies across breeds for two of the SNPs, the deviations of observed heterozygosities compared with those expected within breeds were minimal. These results indicate that across-breed DNA sequence comparison is a reasonable strategy for identifying SNPs that are useful within many canine breeds.     

Examining the role of particle size on ammonia‐based bioprocessing of maize stover

The role of particle size in carbohydrate fractionation upon pretreatment and glucan yields upon enzymatic hydrolysis was investigated at two different temperatures, to examine the possibility of pretreating under milder conditions smaller particles, in order to satisfy pilot‐scale operational constraints. Maize stover was knife‐milled through 1‐mm and 0.5‐mm screens and pretreated by soaking in aqueous ammonia pretreatment at 60 or 110°C for 6 h. Pretreated solids were analyzed for composition and a material balance calculated for glucan, xylan, and lignin. At 60°C, milling resulted in greater delignification compared to unmilled biomass. Delignification was more uniform at 110°C. Pretreated solids were washed and cellulase hydrolysis carried out at 10% w/w solids loading, with low and high enzyme loadings. Liquid samples were drawn and concentration data developed through HPLC to calculate 48‐h glucan and xylan hydrolytic yields. The differences in hydrolytic yield between milled and unmilled treatments were found to vary with pretreatment temperature and enzyme loading. The results show that while particle size impacts carbohydrate recovery and hydrolytic yield, it is less important in bioprocessing than pretreatment temperature and enzyme loading, possibly owing to the particles’ morphology rather than the size. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:134–140, 2016     

Effective High-Throughput Blood Pooling Strategy before DNA Extraction for Detection of Malaria in Low-Transmission Settings

In the era of (pre) elimination setting, the prevalence of malaria has been decreasing in most of the previously endemic areas. Therefore, effective cost- and time-saving validated pooling strategy is needed for detection of malaria in low transmission settings. In this study, optimal pooling numbers and lowest detection limit were assessed using known density samples prepared systematically, followed by genomic DNA extraction and nested PCR. Pooling strategy that composed of 10 samples in 1 pool, 20 µl in 1 sample, was optimal, and the parasite density as low as 2 p/µl for both falciparum and vivax infection was enough for detection of malaria. This pooling method showed effectiveness for handling of a huge number of samples in low transmission settings (<9% positive rate). The results indicated that pooling of the blood samples before DNA extraction followed by usual nested PCR is useful and effective for detection of malaria in screening of hidden cases in low-transmission settings.     

Empirical evaluation of selective DNA pooling to map QTL in dairy cattle using a half-sib design by comparison to individual genotyping and interval mapping

This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow) product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information from phenotypic differences between individuals in the same pool and from neighbouring markers, which is lost in a DNA pooling design. These errors cause some differences between the markers detected as significant by pooling and those found significant by interval mapping based on individual selective genotyping. Therefore, it is recommended that pooled genotyping only be used as part of an initial screen with significant results to be confirmed by individual genotyping. Strategies for improving the efficiency of the DNA pooling design are also presented.