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.

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

I. the origin of species by means of natural selection

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.

/pdf/seed-dormancy-and-the-control-of-germination-4tdhm2985s.pdf

Seed dormancy and the control of germination

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.

/pdf/ccl2-recruits-inflammatory-monocytes-to-facilitate-breast-3bhsa2s5gr.pdf

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

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.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

Sisymbrium linifolium and Sisymbriopsis schugnana, previously confined to western North America and Tajikistan, respectively, were discovered in Xinjiang during a recent field trip to this autonomous region of China. The identity of these two species was subsequently confirmed by extensive morphological and molecular studies. The biogeographical significance of these new floristic records is briefly addressed.

Sisymbrium linifolium and Sisymbriopsis schugnana (Brassicaceae), two new records from Xinjiang, China

The present revision focuses on the enigmatic Southwest Asian genus Aethionema in Iran based on taxonomic literature, fieldwork, and study of over 400 herbarium specimens. As a result of the present study, A . diastrophis and A. transhyrcanum are newly found for Iran. The former is morphologically closer to A . membranaceum and A . kopetdaghi rather than to A. spinosum, under which it was previously synonymized. Aethionema edentulum and A . levandowskyi are placed in the synonymy of A . membranaceum and A . grandiflorum, respectively. The genus is represented in Iran by 16 species, of which six are endemic. Detailed descriptions, distribution maps, IUCN conservation status assessments, and illustrations of the species are provided. The lectotypes of A . cordatum , A . elongatum, A . fimbriatum , A . grandiflorum , A . koenigii , A . moricandianum , A . pallidiflorum , A . pulchellum , A . recurvum , A . schelkownikowii , A . sintenisii , A . spinosum , A . stenopterum , A . umbellatum , A . virgatum , A . woronowii , Lepidium intricatum , and Moriera gracilis are designated.

A taxonomic revision of the genus Aethionema s.l. (Brassicaceae) in Iran

New or noteworthy Draba (Brassicaceae) from South America

Synonymy, typification, distribution, and key to the 23 species of Braya are given, along with an updated generic description. The new species B. sichuanica is described and illustrated. The new combinations B.fengii, B. parvia, B. piasezkii, B. qingshuiheense, and B. stigmatosa are proposed. A list of taxa excluded from Braya is given, along with their current generic and tribal placements. The following taxa are lectotypified: Beketowia tianschanica, Braya aenea var. multicaulis, B. aenea var. simplicior, B. pectinata, B. purpurascens var. longisiliquosa, B. rosea var. angustifolia, B. tibetica var. breviscapa, B. versicolor, Erysimum pamiricum, E. stigmatosum, Pilosella richardsonii, Sisymbrium nanum var. leiocarpum, and Torularia humilis prol. venusta. Previous designations are narrowed for Arabis sinuata, Braya aenea, B. rosea, B. thomsonii, and B. tibetica.

A Synopsis of the Genus Braya (Brassicaceae)

Pseudofortuynia leucoclada (Boiss.) Khosravi was initially described and was long treated as a member of Hesperis L. whereas Tchihatchewia isatidea Boiss. has never hitherto been assigned to this genus. Currently these species represent monospecific genera, Pseudofortuynia Hedge and Tchihatchewia Boiss., endemic to restricted areas in Iran and Turkey, respectively. Based on a re-evaluation of morphological characters in light of available molecular data, the merger of Pseudofortuynia with Sisymbrium L. and Tchihatchewia with Hesperis is proposed. Relevant combinations are validated.

Ihsan A. Al-Shehbaz

Papers

Sisymbrium linifolium and Sisymbriopsis schugnana (Brassicaceae), two new records from Xinjiang, China

A taxonomic revision of the genus Aethionema s.l. (Brassicaceae) in Iran

New or noteworthy Draba (Brassicaceae) from South America

A Synopsis of the Genus Braya (Brassicaceae)

A reconsideration of Pseudofortuynia and Tchihatchewia as synonyms of Sisymbrium and Hesperis, respectively (Brassicaceae).