Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

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A chromosome conformation capture ordered sequence of the barley genome

As in previous years, the consensus group to consider the use of biological agents in the treatment of rheumatic diseases met during the 13th Annual Workshop on Advances in Targeted Therapies in April, 2011. The group consisted of rheumatologists from a number of universities among the continents of Europe, North America, South America, Australia and Asia.

Pharmaceutical industry support was obtained from a number of companies for the annual workshop itself, but these companies had no part in the decisions about the specific programme or about the academic participants at this conference. Representatives of the supporting sponsors participated in the initial working groups to supply factual information. The sponsors did not participate in the drafting of the consensus statement.

This consensus was prepared from the perspective of the treating physician.

In view of the new data for abatacept, B cell-specific agents, interleukin 1 (IL-1) antagonists, tocilizumab (TCZ) and tumour necrosis factor α blocking agents (TNF inhibitors), an update of the previous consensus statement is appropriate. To allow ease of updating, the 2010 (data from March 2009 to January 2010) updates are incorporated into the body of the article, while 2011 updates (February 2010–January 2011) are separated and highlighted. The consensus statement is annotated to document the credibility of the data supporting it as much as possible. This annotation is that of Shekelle et al and is described in appendix 1.1 We have modified the Shekelle annotation by designating all abstracts as ‘category D evidence’, whether they describe well-controlled trials or not, as details of the study were often not available in the abstracts. Further, the number of possible references has become so large that reviews are sometimes included; if they contain category A references, they will be referred to as category A evidence.

The rheumatologists and bioscientists who attended …

https://ard.bmj.com/content/annrheumdis/72/suppl_2/ii2.full.pdf

Updated consensus statement on biological agents for the treatment of rheumatic diseases, 2010

This paper describes a qualitative approach to analysing students' concept maps. The classification highlights three major patterns which are referred to as 'spoke', 'chain' and 'net' structures. Examples are given from Year 8 science classes. The patterns are interpreted as being indicators of progressive levels of understanding. It is proposed that identification of these differences may help the classroom teacher to focus teaching for more effective learning and may be used as a basis for structuring groups in collaborative settings. This approach to analysing concept maps is of value because it suggests teaching approaches that help students integrate new knowledge and build upon their existing naive concepts. We also refer to the teacher's scheme of work and to the National Curriculum for science in order to consider their influence in the construction of understanding. These ideas have been deliberately offered for early publication to encourage debate and generate feedback. Further work is in progr...

How a qualitative approach to concept map analysis can be used to aid learning by illustrating patterns of conceptual development

B chromosomes are extra chromosomes to the standard complement that occur in many organisms They can originate in a number of ways including derivation from autosomes and sex chromosomes in intraa

/pdf/b-chromosome-evolution-25cmhcd0kp.pdf

B-chromosome evolution.

Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.

Histone methylation in higher plants

Strong methylation of lysine 4 (K4) and low methylation of lysine 9 (K9) have been proposed as modifications of histone H3, typical for transcriptionally active euchromatin and the opposite for inactive heterochromatin. We have analysed the correlation between the global distribution of histone H3, methylated at either lysine 4 or lysine 9, and of microscopically detectable euchromatic or heterochromatic regions in relation to genome size for 24 plant species. Two different distribution patterns of methylated (K9)H3 (Met(K9)H3) were found that depend on genome size. For most species with small genomes (1C <500 Mbp), including Arabidopsis thaliana, strong methylation of (K9)H3 was restricted to constitutive heterochromatin. Species with larger genomes showed a uniform distribution of Met(K9)H3. Contrary to this and regardless of the genome size, methylated (K4)H3 (Met(K4)H3) was found to be enriched within the euchromatin of all species. Transcriptionally less active B chromosomes showed the same patterns as basic A chromosomes. We thus propose that large genomes with high amounts of dispersed repetitive sequences (mainly retroelements) have to silence these sequences and therefore display epigenetic modifications such as methylation of DNA and (K9)H3 also within euchromatic regions.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2003.01681.x

Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content.

Dispensable, supernumerary (B) chromosomes are found in diverse eukaryotic species. The origin and genetic consequences of B chromosomes have been the subjects of speculation for more than a century. Until now, there has been no molecular evidence that B chromosome DNA is transcribed and there is no unequivocal evidence as to their origin. B chromosomes are considered to be genetically inert although they appear to cause a variety of phenotypic effects. We report that members of one of two ribosomal RNA gene families that are confined to the B chromosomes of a plant, Crepis capillaris, are transcribed—thus providing the first molecular evidence of gene activity on B chromosomes. Sequence analysis of part of the A and B chromosome rRNA genes, together with comparisons with related species, indicates that the B chromosome rRNA genes originate from the A chromosome.

https://www.genetics.org/content/genetics/171/1/269.full.pdf

Molecular evidence for transcription of genes on a B chromosome in Crepis capillaris.

Dot-like micro B chromosomes of Brachycome dichromosomatica were analysed for their sequence composition. Southern hybridization patterns of a total micro B probe to genomic DNA from plants with and without micro Bs demonstrated that the micro Bs shared sequences with the A chromosomes. In addition to telomere, rDNA and common A and B chromosome sequences, a new B-specific, highly methylated tandem repeat (Bdm29) was detected. After in situ hybridization with Bdm29 the entire micro B chromosome was labelled and clustering of the condensed micro Bs could be observed at interphase. A high number of Bdm29-like sequences were also found in the larger B chromosomes of B. dichromosomatica and in other Bs within the genus Brachycome.

A repetitive DNA sequence common to the different B chromosomes of the genus Brachycome.

Brachycome dichromosomatica is an Australian native daisy that has two pairs of A chromosomes and up to three B chromosomes in some populations. A putative B-specific tandem repeat DNA sequence (Bd49) was isolated previously. Here we describe further characterisation of this sequence and investigate its possible origin. Southern analysis showed that all individual B chromosomes examined have highly methylated tandem repeats of Bd49 but differences in banding pattern for distinct B isolates suggested that the sequence is in a state of flux. Using in situ hybridisation, the sequence was shown to be located at the centromeric region of the B chromosome. Southern analysis of genomic DNA with Bd49 demonstrated that multiple copies of the sequence exist in the genomes of B. eriogona, B. ciliaris, B. segmentosa and B. multifida (none of which have B chromosomes) whereas other species tested (including 0B plants of B. dichromosomatica and 0B and +B B. curvicarpa and B. dentata) have few or no copies. Genomic clones and Bd49-like sequences derived by the polymerase chain reaction (PCR) were obtained from five species but determination of phylogenetic relationships within the genus and inference as to the possible origin of the B chromosome were problematic because of extensive intragenomic heterogeneity of the sequences.

Organisation and origin of a B chromosome centromeric sequence from Brachycome dichromosomatica.

Supernumerary B chromosomes represent one of many causes of numerical chromosome variation that exist in higher plants and animals. Sequences of DNA unique to B chromosomes of Brachycome dichromosomatica were enriched prior to cloning and resultant clones hybridizing only to plants containing B chromosomes were further investigated. Sequences of DNA that were characterised include members of a family of 176-bp tandem repeats that are specific to the B chromosomes of B. dichromosomatica, an annual Australian native plant species with only two pairs of A chromosomes and up to three dispensable B chromosomes. Sequence analysis of these six related clones indicated that some regions of the sequence are more highly conserved than others or, alternatively, that some adenine residues at the NdeII site are methylated. The repeat is homologous to DNA from Brachycome ciliaris var. languinosa but not to DNA from other related taxa growing in the vicinity of the B. dichromosomatica populations.

Carolyn R. Leach

Papers

Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content.

Molecular evidence for transcription of genes on a B chromosome in Crepis capillaris.

A repetitive DNA sequence common to the different B chromosomes of the genus Brachycome.

Organisation and origin of a B chromosome centromeric sequence from Brachycome dichromosomatica.

A sequence specific to B chromosomes of Brachycome dichromosomatica.