Standardized gene nomenclature for the Brassica genus

The genus Brassica (Brassicaceae, Brassiceae) is closely related to the model plant Arabidopsis, and includes several important crop plants. Against the background of ongoing genome sequencing, and in line with efforts to standardize and simplify description of genetic entities, we propose a standard systematic gene nomenclature system for the Brassica genus. This is based upon concatenating abbreviated categories, where these are listed in descending order of significance from left to right (i.e. genus – species – genome – gene name – locus – allele). Indicative examples are provided, and the considerations and recommendations for use are discussed, including outlining the relationship with functionally well-characterized Arabidopsis orthologues. A Brassica Gene Registry has been established under the auspices of the Multinational Brassica Genome Project that will enable management of gene names within the research community, and includes provisional allocation of standard names to genes previously described in the literature or in sequence repositories. The proposed standardization of Brassica gene nomenclature has been distributed to editors of plant and genetics journals and curators of sequence repositories, so that it can be adopted universally

A recursive kinematic random forest and alpha beta filter classifier for 2D radar tracks

In this work, we show that by using a recursive random forest together with an alpha beta filter classifier it is possible to classify radar tracks from the tracks’ kinematic data. The kinematic data is from a 2D scanning radar without Doppler or height information. We use random forest as this classifier implicit handles the uncertainty in the position measurements. As stationary targets can have an apparently high speed because of the measurement uncertainty, we use an alpha beta filter classifier to classify stationary targets from moving targets. We show an overall classification rate from simulated data at 82.6 % and from real world data 79.7 %. Additional to the confusion matrix we also show recordings of real world data

A rich TILLING resource for studying gene function in Brassica rapa

<p>Abstract</p> <p>Background</p> <p>The <it>Brassicaceae </it>family includes the model plant <it>Arabidopsis thaliana </it>as well as a number of agronomically important species such as oilseed crops (in particular <it>Brassica napus, B. juncea </it>and <it>B. rapa</it>) and vegetables (<it>eg. B. rapa </it>and <it>B. oleracea</it>).</p> <p>Separated by only 10-20 million years, <it>Brassica </it>species and <it>Arabidopsis thaliana </it>are closely related, and it is expected that knowledge obtained relating to <it>Arabidopsis </it>growth and development can be translated into Brassicas for crop improvement. Moreover, certain aspects of plant development are sufficiently different between <it>Brassica </it>and <it>Arabidopsis </it>to warrant studies to be carried out directly in the crop species. However, mutating individual genes in the amphidiploid Brassicas such as <it>B. napus </it>and <it>B. juncea </it>may, on the other hand, not give rise to expected phenotypes as the genomes of these species can contain up to six orthologues per single-copy <it>Arabidopsis </it>gene. In order to elucidate and possibly exploit the function of redundant genes for oilseed rape crop improvement, it may therefore be more efficient to study the effects in one of the diploid <it>Brassica </it>species such as <it>B. rapa</it>. Moreover, the ongoing sequencing of the <it>B. rapa </it>genome makes this species a highly attractive model for <it>Brassica </it>research and genetic resource development.</p> <p>Results</p> <p>Seeds from the diploid <it>Brassica </it>A genome species, <it>B. rapa </it>were treated with ethyl methane sulfonate (EMS) to produce a TILLING (Targeting Induced Local Lesions In Genomes) population for reverse genetics studies. We used the <it>B. rapa </it>genotype, R-o-18, which has a similar developmental ontogeny to an oilseed rape crop. Hence this resource is expected to be well suited for studying traits with relevance to yield and quality of oilseed rape. DNA was isolated from a total of 9,216 M₂plants and pooled to form the basis of the TILLING platform. Analysis of six genes revealed a high level of mutations with a density of about one per 60 kb. This analysis also demonstrated that screening a 1 kb amplicon in just one third of the population (3072 M₂plants) will provide an average of 68 mutations and a 97% probability of obtaining a stop-codon mutation resulting in a truncated protein. We furthermore calculated that each plant contains on average ~10,000 mutations and due to the large number of plants, it is predicted that mutations in approximately half of the GC base pairs in the genome exist within this population.</p> <p>Conclusions</p> <p>We have developed the first EMS TILLING resource in the diploid <it>Brassica </it>species, <it>B. rapa</it>. The mutation density in this population is ~1 per 60 kb, which makes it the most densely mutated diploid organism for which a TILLING population has been published. This resource is publicly available through the <it>RevGen</it>UK reverse genetics platform <url>http://revgenuk.jic.ac.uk</url>.</p

Joint Minimum Processing Beamforming and Near-end Listening Enhancement

We consider speech enhancement for signals picked up in one noisy environment that must be rendered to a listener in another noisy environment. For both far-end noise reduction and near-end listening enhancement, it has been shown that excessive focus on noise suppression or intelligibility maximization may lead to excessive speech distortions and quality degradations in favorable noise conditions, where intelligibility is already at ceiling level. Recently [1,2] propose to remedy this with a minimum processing framework that either reduces noise or enhances listening a minimum amount given that a certain intelligibility criterion is still satisfied. Additionally, it has been shown that joint consideration of both environments improves speech enhancement performance. In this paper, we formulate a joint far- and near-end minimum processing framework, that improves intelligibility while limiting speech distortions in favorable noise conditions. We provide closed-form solutions to specific boundary scenarios and investigate performance for the general case using numerical optimization. We also show that concatenating existing minimum processing far- and near-end enhancement methods preserves the effects of the initial methods. Results show that the joint optimization can further improve performance compared to the concatenated approach.Comment: Submitted to ICASSP 202

Control of Fruit Patterning in Arabidopsis by INDEHISCENT

AbstractThe Arabidopsis seedpod opens through a spring-loaded mechanism known as pod shatter, which is essential for dispersal of the seeds. Here, we identify INDEHISCENT (IND), an atypical bHLH protein, that is necessary for fruit opening and is involved in patterning each of the three fruit cell types required for seed dispersal. Previous studies suggested that FRUITFULL (FUL), a member of the MADS-domain transcription factor family, is required for fruit growth since ful mutant fruit fail to undergo the dramatic enlargement that normally occurs after fertilization. Here we show, however, that FUL is not directly required for fruit elongation and instead is required to prevent ectopic activity of IND. Our molecular and genetic studies suggest a model for the regulatory interactions among the genes that control fruit development and the mechanism that results in the expression of IND in a narrow stripe of cells

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes

Background: Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results: We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions: Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service

ART influences HIV persistence in the female reproductive tract and cervicovaginal secretions

The recently completed HIV prevention trials network study 052 is a landmark collaboration demonstrating that HIV transmission in discordant couples can be dramatically reduced by treating the infected individual with antiretroviral therapy (ART). However, the cellular and virological events that occur in the female reproductive tract (FRT) during ART that result in such a drastic decrease in transmission were not studied and remain unknown. Here, we implemented an in vivo model of ART in BM/liver/thymus (BLT) humanized mice in order to better understand the ability of ART to prevent secondary HIV transmission. We demonstrated that the entire FRT of BLT mice is reconstituted with human CD4+ cells that are shed into cervicovaginal secretions (CVS). A high percentage of the CD4+ T cells in the FRT and CVS expressed CCR5 and therefore are potential HIV target cells. Infection with HIV increased the numbers of CD4+ and CD8+ T cells in CVS of BLT mice. Furthermore, HIV was present in CVS during infection. Finally, we evaluated the effect of ART on HIV levels in the FRT and CVS and demonstrated that ART can efficiently suppress cell-free HIV-RNA in CVS, despite residual levels of HIV-RNA+ cells in both the FRT and CVS

A comparison of sexual behaviour and attitudes of healthy adolescents in a Danish high school in 1982, 1996, and 2001

AIM: To assess changes in sexual behaviour among students at a high school in Denmark from 1982 to 2001. METHODS: An anonymous self-administered questionnaire was used to compare data from three identical cross-sectional surveys performed in 1982, 1996, and 2001. RESULTS: Girls: More girls reported their first sexual intercourse before their 16th birthday in 2001 (42%) than in 1996 (29%) In 1982 it was also 42% (Chi-square for trend: p = 0.003). Fewer girls with no regular partner used condoms for their personal protection in 2001 (2%) than in 1996 (9%) and 1982 (0%) (Chi-square for trend p = 0.016). The proportion of girls with no regular partner who considered protection from sexually transmitted disease important for their choice of contraception was 39% in 2001 compared with 71% in 1996 and only 10% in 1982 (Chi-square for trend: p < 0.0001). Boys: More boys reported sexual debut before their 16th birthday in 2001 (40%) than in 1996 (37%) and 1982 (24%) (Chi-square for trend: p = 0.023). For boys with no regular partner, condom was preferred for personal protection by 85% in 2001, 91% in 1996 and 61% in 1982 (Chi-square for trend p = 0.007). Protection against sexually transmitted infection declined, especially among boys with no regular partner, from 51% in 2001 to 72% in 1996 and 21% in 1982 Chi-square for trend: p < 0.0001). The tendency towards earlier sexual debut and less use of safe sex practices to protect against sexually transmitted infections (STI) was accompanied by a rise in the number of detected STIs during this period. CONCLUSIONS: The period from 1982 to 1996 during which sexual attitudes were directed toward safer sex seems to have given way to a reverse trend in the period from 1996 to 2001. These findings may have significant implications for health care authorities organising preventive strategies for healthy adolescents

MCP1 SNPs and Pulmonary Tuberculosis in Cohorts from West Africa, the USA and Argentina: Lack of Association or Epistasis with IL12B Polymorphisms

The monocyte chemotactic protein-1 (MCP-1) is a chemokine that plays an important role in the recruitment of monocytes to M. tuberculosis infection sites, and previous studies have reported that genetic variants in MCP1 are associated with differential susceptibility to pulmonary tuberculosis (PTB). We examined eight MCP1 single nucleotide polymorphisms (SNPs) in a multi-ethnic, case-control design that included: 321 cases and 346 controls from Guinea-Bissau, 258 cases and 271 controls from The Gambia, 295 cases and 179 controls from the U.S. (African-Americans), and an additional set of 237 cases and 144 controls of European ancestry from the U.S. and Argentina. Two locus interactions were also examined for polymorphisms in MCP1 and interleukin 12B (IL12B), another gene implicated in PTB risk. Examination of previously associated MCP1 SNPs rs1024611 (−2581A/G), rs2857656 (−362G/C) and rs4586 (+900C/T) did not show evidence for association. One interaction between rs2857656 and IL12B SNP rs2288831 was observed among Africans but the effect was in the opposite direction in Guineans (OR = 1.90, p = 0.001) and Gambians (OR = 0.64, p = 0.024). Our data indicate that the effect of genetic variation within MCP1 is not clear cut and additional studies will be needed to elucidate its role in TB susceptibility