Ihsan A. Al-Shehbaz

Bio: Ihsan A. Al-Shehbaz is an academic researcher from Missouri Botanical Garden. The author has contributed to research in topics: Genus & Brassicaceae. The author has an hindex of 44, co-authored 305 publications receiving 8770 citations. Previous affiliations of Ihsan A. Al-Shehbaz include Heidelberg University & University of Missouri–St. Louis.

Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview

Abstract: A critical review of characters used in the systematics of the Brassicaceae is given, and aspects of the origin, classification, and generic delimitation of the family discussed. Molecular phylogenetic studies of the family were reviewed, and major clades identified. Based on molecular studies, especially from the ndhF chloroplast gene, and careful evaluation of morphology and generic circumscriptions, a new tribal alignment of the Brassicaceae is proposed. In all, 25 tribes are recognized, of which seven (Aethionemeae, Boechereae, Descurainieae, Eutremeae, Halimolobeae, Noccaeeae, and Smelowskieae) are described as new. For each tribe, the center(s) of distribution, morphology, and number of taxa are given. Of the 338 genera currently recognized in the Brassicaceae, about 260 genera (or about 77%) were either assigned or tentatively assigned to the 25 tribes. Some problems relating to various genera and tribes are discussed, and future research developments are briefly covered.

Brassicaceae phylogeny and trichome evolution

Abstract: To estimate the evolutionary history of the mustard family (Brassicaceae or Cruciferae), we sampled 113 species, representing 101 of the roughly 350 genera and 17 of the 19 tribes of the family, for the chloroplast gene ndhF. The included accessions increase the number of genera sampled over previous phylogenetic studies by four-fold. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the Shimodaira-Hasegawa test (S-H test) to compare the phylogenetic results with the most recent tribal classification for the family. The resultant phylogeny allowed a critical assessment of variations in fruit morphology and seed anatomy, upon which the current classification is based. We also used the S-H test to examine the utility of trichome branching patterns for describing monophyletic groups in the ndhF phylogeny. Our phylogenetic results indicate that 97 of 114 ingroup accessions fall into one of 21 strongly supported clades. Some of these clades can themselves be grouped into strongly to moderately supported monophyletic groups. One of these lineages is a novel grouping overlooked in previous phylogenetic studies. Results comparing 30 different scenarios of evolution by the S-H test indicate that five of 12 tribes represented by two or more genera in the study are clearly polyphyletic, although a few tribes are not sampled well enough to establish para- or polyphyly. In addition, branched trichomes likely evolved independently several times in the Brassicaceae, although malpighiaceous and stellate trichomes may each have a single origin.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Seed dormancy and the control of germination

Abstract: Seed dormancy is an innate seed property that defines the environmental conditions in which the seed is able to germinate. It is determined by genetics with a substantial environmental influence which is mediated, at least in part, by the plant hormones abscisic acid and gibberellins. Not only is the dormancy status influenced by the seed maturation environment, it is also continuously changing with time following shedding in a manner determined by the ambient environment. As dormancy is present throughout the higher plants in all major climatic regions, adaptation has resulted in divergent responses to the environment. Through this adaptation, germination is timed to avoid unfavourable weather for subsequent plant establishment and reproductive growth. In this review, we present an integrated view of the evolution, molecular genetics, physiology, biochemistry, ecology and modelling of seed dormancy mechanisms and their control of germination. We argue that adaptation has taken place on a theme rather than via fundamentally different paths and identify similarities underlying the extensive diversity in the dormancy response to the environment that controls germination.

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

Abstract: Macrophages, which are abundant in the tumour microenvironment, enhance malignancy. At metastatic sites, a distinct population of metastasis-associated macrophages promotes the extravasation, seeding and persistent growth of tumour cells. Here we define the origin of these macrophages by showing that Gr1-positive inflammatory monocytes are preferentially recruited to pulmonary metastases but not to primary mammary tumours in mice. This process also occurs for human inflammatory monocytes in pulmonary metastases of human breast cancer cells. The recruitment of these inflammatory monocytes, which express CCR2 (the receptor for chemokine CCL2), as well as the subsequent recruitment of metastasis-associated macrophages and their interaction with metastasizing tumour cells, is dependent on CCL2 synthesized by both the tumour and the stroma. Inhibition of CCL2-CCR2 signalling blocks the recruitment of inflammatory monocytes, inhibits metastasis in vivo and prolongs the survival of tumour-bearing mice. Depletion of tumour-cell-derived CCL2 also inhibits metastatic seeding. Inflammatory monocytes promote the extravasation of tumour cells in a process that requires monocyte-derived vascular endothelial growth factor. CCL2 expression and macrophage infiltration are correlated with poor prognosis and metastatic disease in human breast cancer. Our data provide the mechanistic link between these two clinical associations and indicate new therapeutic targets for treating metastatic breast cancer.

Image Processing

Abstract: MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.