An emerging role for the exocyst : plant morphogenesis

Plants develop a vast array of cell shapes and sizes by selectively modifying their surrounding cell walls to expand in some regions and not in others. This process of morphogenesis requires the delivery of secretory vesicles to specific locations at the cell periphery, where exocytosis adds new membrane and proteins to the plasma membrane, and secretes materials to build and modify the cell wall. In yeast and mammals, the process of localized exocytosis has been found to involve an eight protein complex, the exocyst. Prior to my work, genes encoding all eight components of the exocyst had been identified in sequenced plant genomes, but no function had yet been determined for any of them. Utilizing T-DNA insertion mutants of putative exocyst components in Arabidopsis thaliana, I demonstrated that one component, SEC8, is required for pollen germination and competitive pollen tube growth. Subsequently, through genetic analyses, phenotypic observation, and cell biological experiments, I provided evidence that, combined with biochemical studies by my collaborators, demonstrated that the putative exocyst components function together as a complex (or complexes) in plants. Multiple components of the exocyst all localize to the tips of growing pollen tubes, the site of localized exocytosis, and strong mutations in exocyst components result in the formation of pollen tubes that are shorter and wider than wild-type. Exocyst mutants also have both an etiolated hypocotyl elongation defect and a root growth defect in the vegetative plant. Unexpectedly, characterization of these mutant plants implicated the exocyst for a role in phytohormone signaling, specifically, in the efficient reception of brassinosteroid signals. This work firmly establishes that the exocyst complex functions in plants to affect plant morphogenesis in at least three developmental processes: polarized growth in pollen tubes, cell elongation in etiolated hypocotyls, and both cell division and cell elongation in growing roots. It also links the exocyst with at least two brassinosteroid -mediated developmental pathways. Finally, it strongly suggests that the exocyst also has a role in defining the cell elongation zone in roots, with exocyst mutants showing that the establishment of this zone can be disconnected from establishment of the root meristem.Keywords: polarized growth, plant morphogenesis, Arabidopsis, root apical meristem, cell expansion, hypocotyl elongation, pollen tube growth, exocys

Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus

Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation

Genome-wide discovery and characterization of maize long non-coding RNAs

BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. RESULTS By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans-genetic factors. CONCLUSIONS We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping

The decline and rise of neighbourhoods: the importance of neighbourhood governance

There is a substantial literature on the explanation of neighbourhood change. Most of this literature concentrates on identifying factors and developments behind processes of decline. This paper reviews the literature, focusing on the identification of patterns of neighbourhood change, and argues that the concept of neighbourhood governance is a missing link in attempts to explain these patterns. Including neighbourhood governance in the explanations of neighbourhood change and decline will produce better explanatory models and, finally, a better view about what is actually steering neighbourhood change

Putting the squeeze on "Generation Rent": housing benefit claimants in the private rented sector - transitions, marginality and stigmatisation

The term 'Generation Rent' has gained currency in recent years to reflect the fact that more 25 to 34 year olds in Britain now live in rented accommodation rather than owner-occupation. The term also conveys the extent to which age-related divisions in the housing market are becoming as significant as longer standing tenure divisions. However, this portmanteau term covers a wide array of different housing circumstances - from students, young professionals and transient households to the working and non-working poor. This paper focuses on the position of a specific category of this age cohort - those 25 to 34 year olds living in self-contained accommodation in the private rented sector who are in receipt of Housing Benefit. On the basis of survey evidence and qualitative interviews with landlords and housing advisers, the paper considers how the marginal economic and housing market position of this age group is being reinforced by the stigmatising attitudes of landlords which formerly applied to tenants in their late teens and early 20s and are now being extended further along the age band. The paper suggests that the use of a 'housing pathways' approach to signify the housing transitions of young adults needs to be revisited, to give greater weight to collective and creative responses to constraints in the housing market and to recognise the key role played by gatekeepers such as landlords in stigmatising groups according to assumed age-related attributes

Structure and Measurement of Depression in Youth: Applying Item Response Theory to Clinical Data

Goals of the paper were to use item response theory (IRT) to assess the relation of depressive symptoms to the underlying dimension of depression and to demonstrate how IRT-based measurement strategies can yield more reliable data about depression severity than conventional symptom counts. Participants were 3403 clinic and nonclinic children and adolescents from 12 contributing samples, all of whom received the Kiddie Schedule of Affective Disorders and Schizophrenia for school-aged children. Results revealed that some symptoms reflected higher levels of depression and were more discriminating than others. Results further demonstrated that utilization of IRT-based information about symptom severity and discriminability in the measurement of depression severity can reduce measurement error and increase measurement fidelity

Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity

This study used 16S rRNA-based pyrosequencing to examine the microbial community that is closely associated with the colonic mucosa of five healthy individuals. Spatial heterogeneity in microbiota was measured at right colon, left colon and rectum, and between biopsy duplicates spaced 1 cm apart. The data demonstrate that mucosal-associated microbiota is comprised of Firmicutes (50.9%±21.3%), Bacteroidetes (40.2%±23.8%) and Proteobacteria (8.6%±4.7%), and that interindividual differences were apparent. Among the genera, Bacteroides, Leuconostoc and Weissella were present at high abundance (4.6% to 41.2%) in more than 90% of the studied biopsy samples. Lactococcus, Streptococcus, Acidovorax, Acinetobacter, Blautia, Faecalibacterium, Veillonella, and several unclassified bacterial groups were also ubiquitously present at an abundance <7.0% of total microbial community. With the exception of one individual, the mucosal-associated microbiota was relatively homogeneous along the colon (average 61% Bray-Curtis similarity). However, micro-heterogeneity was observed in biopsy duplicates within defined colonic sites for three of the individuals. A weak but significant Mantel correlation of 0.13 was observed between the abundance of acidomucins and mucosal-associated microbiota (P-value  =  0.04), indicating that the localized biochemical differences may contribute in part to the micro-heterogeneity. This study provided a detailed insight to the baseline mucosal microbiota along the colon, and revealed the existence of micro-heterogeneity within defined colonic sites for certain individuals

Randomized controlled trial of a family cognitive-behavioral preventive intervention for children of depressed parents.

A family cognitive-behavioral preventive intervention for parents with a history of depression and their 9–15-year-old children was compared with a self-study written information condition in a randomized clinical trial (n = 111 families). Outcomes were assessed at postintervention (2 months), after completion of 4 monthly booster sessions (6 months), and at 12-month follow-up. Children were assessed by child reports on depressive symptoms, internalizing problems, and externalizing problems; by parent reports on internalizing and externalizing problems; and by child and parent reports on a standardized diagnostic interview. Parent depressive symptoms and parent episodes of major depression also were assessed. Evidence emerged for significant differences favoring the family group intervention on both child and parent outcomes; strongest effects for child outcomes were found at the 12-month assessment with medium effect sizes on most measures. Implications for the prevention of adverse outcomes in children of depressed parents are highlighted

Tenants' campaigns for tenure neutrality and a general needs model of social housing: making universal claims

The policy of tenure neutrality championed by the International Union of Tenants as essential to a right to adequate housing advances a model of general needs or, in other words, universal social rented housing provision unrestricted by income limits or needs-based rationing. Support for this model has been severely undermined by recent European Commission rulings that have restricted access to social housing to those least capable of coping in a competitive market place. As general needs demand for affordable housing continues to swell, the challenge for adherents of tenure neutrality is to demonstrate that universal social housing can meet both the needs of the most vulnerable and the demands of those excluded from homeownership by price inflation and credit limits. This paper examines the promotion of universal social housing by tenants’ organisations and challenges the extent to which this model is intended ‘for all’. In a case study of the defence of municipal housing by English tenants’ movements, it identifies the exclusionary narratives that render the particular housing needs of advantaged social groups as universal. The paper concludes by reviewing strategies to resolve the tensions between the universal and the particular to reinvigorate support for tenure neutrality in arguments for widening access and supply of social housing

Genome-wide discovery and characterization of maize long non-coding RNAs

BACKGROUND: Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. RESULTS: By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans-genetic factors. CONCLUSIONS: We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping