Microsatellite markers used for genome-wide association mapping of partial resistance to <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in a world collection of <Emphasis Type="Italic">Brassica napus</Emphasis>

The fungal pathogen Sclerotinia sclerotiorum causes stem rot of oilseed rape (Brassica napus) worldwide. In preparation for genome-wide association mapping (GWAM) of sclerotinia resistance in B. napus, 152 accessions from diverse geographical regions were screened with a single Canadian isolate, #321. Plants were inoculated by attaching mycelium plugs to the main stem at full flower. Lesion lengths measured 7, 14 and 21 days after inoculation were used to calculate the area under the disease progress curve (AUDPC). Depth of penetration was noted and used to calculate percent soft and collapsed lesions (% s + c). The two disease traits were highly correlated (r = 0.93). Partially resistant accessions (AUDPC <7 and % s + c <2) were identified primarily from South Korea and Japan with a few from Pakistan, China and Europe. Genotyping of accessions with 84 simple sequence repeat markers provided 690 polymorphic loci for GWAM. The general linear model in TASSEL best fitted the data when adjusted for population structure (STRUCTURE), GLM + Q. After correction for positive false discovery rate, 34 loci were significantly associated with both disease traits of which 21 alleles contributed to resistance, while the remaining enhanced susceptibility. The phenotypic variation explained by the loci ranged from 6 to 25 %. Five loci mapped to published quantitative trait loci conferring sclerotinia resistance in Chinese lines.     

Geographical distribution and density of Ixodes dammini (Acari: Ixodidae) and relationship to Lyme disease transmission in New Jersey

As part of continuing studies of Lyme disease, deer were surveyed during three hunting seasons in 1981 to obtain information on geographic distribution and density of I. dammini in New Jersey. I. dammini occurred throughout central and southern New Jersey. Four deer management zones (DMZs) were shown to have high tick densities. Geographical distribution and density data were independently regressed against 25 environmental and physical factors. Elevation was shown to be the most important factor in explaining the variability in both I. dammini distribution and density. Lyme disease cases were closely associated with the distribution of I. dammini and 57.3 percent of 117 Lyme disease cases occurred in the four DMZs previously identified as having the highest tick density.     

Atopic manifestations in the acquired immune deficiency syndrome: response to recombinant interferon gamma.

Six patients with the acquired immune deficiency syndrome (AIDS) had exacerbations or recurrences of previously quiescent atopic disease when they developed immunodeficiency. Four developed a different atopic illness from that suffered previously. Atopic symptoms developed within three months after the patients developed AIDS or during prodromal illness. Two of the patients were treated with recombinant interferon gamma: both showed a striking improvement in symptoms and cellular immunity. These results indicate that cellular immunity, through interferon gamma, may have a role in regulating atopic disease.     

D.D.T. Impregnation of Sacks for the Protection of Stored Cereals Against Insect Infestation

Cotton flour sacks, jute flour sacks, jute bran sacks and jute grain sacks have been impregnated with 1 and 5 % by weight of D.D.T. Treated and untreated sacks, each containing 1 cwt. of a mixture of grain (5 parts) and weatings (1 part), were exposed to severe infestation by adults of Calandra granaria, Tribolium castaneum, Ptinus tectus, Oryzaephilus surina-mensis and Ephestia elutella . After storage for 15 weeks at a mean temperature of 21.3 C. and a mean relative humidity of 65 %, the numbers of adult insects in each sack were determined by sieving the contents.
The results with Ephestia elutella were inconclusive. The results with the four species of beetles showed that the eventual degree of infestation of the contents of the sacks was dependent upon the closeness of weave and the D.D.T. content of the sacking material. Impregnation of sacking with 1 % of D.D.T. should afford adequate protection against insect infestation to clean bagged goods stored in stowages which are not heavily infested. Impregnation with 5 % of D.D.T. should offer a very high degree of protection at all times and can almost entirely prevent infestation, if the treated material is of sufficiently close weave to afford some mechanical hindrance to penetration by insects.     

Crystal Structure of Reduced MsAcg,a Putative Nitroreductase from Mycobacterium smegmatis and a Close Homologue of Mycobacterium tuberculosis Acg

This paper presents the structure of MsAcg (MSMEG_5246), a Mycobacterium smegmatis homologue of Mycobacterium tuberculosis Acg (Rv2032) in its reduced form at 1.6 Å resolution using x-ray crystallography. Rv2032 is one of the most induced genes under the hypoxic model of tuberculosis dormancy. The Acg family turns out to be unusual flavin mononucleotide (FMN)-binding proteins that have probably arisen by gene duplication and fusion from a classical homodimeric nitroreductase such that the monomeric protein resembles a classical nitroreductase dimer but with one active site deleted and the other active site covered by a unique lid. The FMN cofactor is not reduced by either NADH or NADPH, but the chemically reduced enzyme is capable of reduction of nitro substrates, albeit at no kinetic advantage over free FMN. The reduced enzyme is rapidly oxidized by oxygen but without any evidence for a radical state commonly seen in oxygen-sensitive nitroreductases. The presence of the unique lid domain, the lack of reduction by NAD(P)H, and the slow rate of reaction of the chemically reduced protein raises a possible alternative function of Acg proteins in FMN storage or sequestration from other biochemical pathways as part of the bacteria''s adaptation to a dormancy state.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high‐density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole‐genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC‐FISH) coupled with PCR using primers specific to the rearranged region. Using a well‐known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.