Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

The development and contribution of surface charge by crop residues in two Malawian acid soils

The effects of maize and soya bean residues on the pH and charge of a loamy sand (Kawalazi) and a sandy clay loam (Naming'omba) from Malawi were measured to determine both the indirect effect of the residues on soil charge through the changes in pH, and the direct contribution of charge carried on the residue surfaces. The soils had pH values (10 mM CaCl2) of 4.3 and 5.0 and organic matter contents were 1.4% and 2.7%, respectively. The clay fractions were dominated by kaolinite and goethite, and mica was present in both samples. The soils were incubated for 28 days with maize (Zea mays) and soya bean (Glycine max) residues. The maximum addition of residue (12.0%) in the Kawalazi and Naming'omba soils increased the pH from 4.3 and 5.0 to 4.8 and 5.3 (maize) and to 9.0 and 8.8 (soya bean), respectively. Negative charge increased from 2.1 and 4.7 cmol(c) kg(-1) to 3.8 and 7.5 (maize) and to 5.3 and 9.3 cmol(c) kg(-1) (soya bean). Positive charge increased from 0.72 and 0.62 to 0.87 and 0.85 cmol(c) kg(-1) (maize) and to 0.75 and 0.68 (soya bean). The charge contribution by the residues was calculated by difference between the charge on a sample incubated with residue and the charge on a soil without residue limed to the same pH value. Up to 100 cmolc negative charge and 10 cmol(c) of positive charge per kg of residue were directly contributed to the soil-residue mixture, the amounts depending on the type of residue, the extent to which the residue was decomposed in the soil and the pH of the mixture. The Anderson and Sposito method [Soil Sci. Soc. Am. J. 55 (1991) 1569] was used to partition the permanent negative charge (holding Cs+) from variable negative charge (holding Li+). In the pH range 3.7-6.5 the maize residue contributed between 3 and 26 cmol(c) of variable charge per kg of residue in the Kawalazi soil and between 6 and 25 cmol(c) per kg of residue in the Naming'omba soil. For soya bean the values were between I and 28 and between 4 and 68 cmolc per kg of residue, respectively. At a given pH value, the charge tended to increase with time of incubation and for a given addition of residue, pH decreased during incubation. Addition of residues contributed no permanent negative charge and the charge on the soil measured by Cs adsorption was independent of pH change caused by the residue showing that the method is valid for soil-residue mixtures. With time there was a decrease in the amount of permanent charge probably due to masking as humic material become adsorbed on mineral surfaces. (C) 2003 Elsevier Science B.V. All rights reserved.

Molecular identification and anti-pathogenic activities of putative probiotic bacteria isolated from faeces of healthy elderly individuals

One hundred and nine lactic acid bacterial strains (56 bifidobacteria-like and 53 lactobacilli-like) were isolated from faecal samples donated by healthy elderly individuals (>65 years old). Isolates were identified to species level by phenotypic analysis (by API) and by 16S rDNA sequencing. Eleven species of Lactobacillus and six species of Bifidobacterium were identified. The most frequently isolated lactobacillus was L. fermentum and the most frequently isolated bifidobacterium was closely related to B. infantis by 16S rDNA sequence alignment. The isolates were characterized for their antimicrobial activity against Clostridium difficile, enteropathogenic Escherichia coli (EPEC), verocytotoxigenic E. coli (VTEC) and Campylobacter jejuni. The lactobacilli displayed variations in their antimicrobial activity with few strains showing inhibitory activity against all pathogens. The bifidobacteria displayed higher levels of inhibitory activity against C. jejuni and Cl. difficile than against the E. coli strains. Keywords: Lactobacillus, Bifidobacterium, elderly, gastrointestinal microbiota, inhibition, Clostridium difficile, enteropathogenic Escherichia coli (EPEC), verocytotoxigenic E. coli (VTEC), Campylobacter jejuni.

The automatic identification and prioritisation of criminal networks from police crime data

The identification of criminal networks is not a routine exploratory process within the current practice of the law enforcement authorities; rather it is triggered by specific evidence of criminal activity being investigated. A network is identified when a criminal comes to notice and any associates who could also be potentially implicated would need to be identified if only to be eliminated from the enquiries as suspects or witnesses as well as to prevent and/or detect crime. However, an identified network may not be the one causing most harm in a given area.. This paper identifies a methodology to identify all of the criminal networks that are present within a Law Enforcement Area, and, prioritises those that are causing most harm to the community. Each crime is allocated a score based on its crime type and how recently the crime was committed; the network score, which can be used as decision support to help prioritise it for law enforcement purposes, is the sum of the individual crime scores.

An experimental approach to project risk identification and prioritization

One of the aims of a broad ethnographic study into how the apportionment of risk influences pricing levels of contactors was to ascertain the significant risks affecting contractors in Ghana, and their impact on prices. To do this, in the context of contractors, the difference between expected and realized return on a project is the key dependent variable examined using documentary analyses and semi-structured interviews. Most work in this has focused on identifying and prioritising risks using relative importance indices generated from the analysis of questionnaire survey responses. However, this approach may be argued to constitute perceptions rather than direct measures of the project risk. Here, instead, project risk is investigated by examining two measures of the same quantity; one ‘before’ and one ‘after’ construction of a project has taken place. Risks events are identified by ascertaining the independent variables causing deviations between expected and actual rates of return. Risk impact is then measured by ascertaining additions or reductions to expected costs due to the occurrence of risk events. So far, data from eight substantially complete building projects indicates that consultants’ inefficiency, payment delays, subcontractor-related problems and changes in macroeconomic factors are significant risks affecting contractors in Ghana.

Dynamic recurrent neural network for system identification and control

A dynamic recurrent neural network (DRNN) that can be viewed as a generalisation of the Hopfield neural network is proposed to identify and control a class of control affine systems. In this approach, the identified network is used in the context of the differential geometric control to synthesise a state feedback that cancels the nonlinear terms of the plant yielding a linear plant which can then be controlled using a standard PID controller.

A potential lag between the open solar magnetic source flux and solar EUV and X-ray emissions as measured by the Earth's ionosphere during total solar eclipses

Measurements of the ionospheric E-region during total solar eclipses have been used to provide information about the evolution of the solar magnetic field and EUV and X-ray emissions from the solar corona and chromosphere. By measuring levels of ionisation during an eclipse and comparing these measurements with an estimate of the unperturbed ionisation levels (such as those made during a control day, where available) it is possible to estimate the percentage of ionising radiation being emitted by the solar corona and chromosphere. Previously unpublished data from the two eclipses presented here are particularly valuable as they provide information that supplements the data published to date. The eclipse of 23 October 1976 over Australia provides information in a data gap that would otherwise have spanned the years 1966 to 1991. The eclipse of 4 December 2002 over Southern Africa is important as it extends the published sequence of measurements. Comparing measurements from eclipses between 1932 and 2002 with the solar magnetic source flux reveals that changes in the solar EUV and X-ray flux lag the open source flux measurements by approximately 1.5 years. We suggest that this unexpected result comes about from changes to the relative size of the limb corona between eclipses, with the lag representing the time taken to populate the coronal field with plasma hot enough to emit the EUV and X-rays ionising our atmosphere.

Identification and minimization of IIR tap coefficients for the cancellation of complex multipath in terrestrial television

By using a deterministic approach, an exact form for the synchronous detected video signal under a ghosted condition is presented. Information regarding the phase quadrature-induced ghost component derived from the quadrature forming nature of the vestigial sideband (VSB) filter is obtained by crosscorrelating the detected video with the ghost cancel reference (GCR) signal. As a result, the minimum number of taps required to correctly remove all the ghost components is subsequently presented. The results are applied to both National Television System Committee (NTSC) and phase alternate line (PAL) television.

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.