Direct Cloning of Human 10q25 Neocentromere DNA Using Transformation-Associated Recombination (TAR) in Yeast

The transformation-associated recombination (TAR) procedure allows rapid, site-directed cloning of specific human chromosomal regions as yeast artificial chromosomes (YACs). The procedure requires knowledge of only a single, relatively small genomic sequence that resides adjacent to the chromosomal region of interest. We applied this approach to the cloning of the neocentromere DNA of a marker chromosome that we have previously shown to have originated through the activation of a latent centromere at human chromosome 10q25. Using a unique 1.4-kb DNA fragment as a “hook” in TAR experiments, we achieved single-step isolation of the critical neocentromere DNA region as two stable, 110- and 80-kb circular YACs. For obtaining large quantities of highly purified DNA, these YACs were retrofitted with the yeast–bacteria–mammalian-cells shuttle vector BRV1, electroporated intoEscherichia coliDH10B, and isolated as bacterial artificial chromosomes (BACs). Extensive characterization of these YACs and BACs by PCR and restriction analyses revealed that they are identical to the corresponding regions of the normal chromosome 10 and provided further support for the formation of the neocentromere within the marker chromosome through epigenetic activation.     

Health-related quality of life in children with craniofacial anomalies

The purpose of this study was to examine parents' perceptions of the health and health-related quality of life in a series of children and adolescents with cleft and other craniofacial anomalies. The subjects for this prospective study were a consecutive series of 54 children and adolescents presenting to an outpatient craniofacial anomalies surgery clinic, ages 5 to 18 years (mean, 8.9 +/- 4.2 years), 50 percent with cleft lip and/or palate, 9 percent synostotic (two coronal, two bicoronal, and one sagittal), 17 percent syndromic (two Apert, one Crouzon, one Noonan, two Goldenhar, two Smith-Lemli-Opitz, and one brachio-oto-renal), and 24 percent with other diagnoses. Subjects were divided into two groups, those with primary cleft lip and/or palate and those with other craniofacial anomalies. Health and health-related quality of life were assessed with the Child Health Questionnaire version PF28, a reliable and valid 28-Likert-item questionnaire completed by parents and yielding physical and psychosocial status scale scores. Physical and psychosocial scale scores largely fell within normal limits for the subset of children with cleft lip and/or palate. There were significant group differences in parents' ratings of global health status, with greater health concerns noted in the non-cleft lip and/or palate group. There were no significant associations between either age or sex and physical or psychosocial health. Physical health, behavior, and psychological status were highly correlated. Using a health status and quality-of-life assessment instrument, findings indicate perceived health differences between groups with and without primary cleft lip and/or palate. In contrast to normative data with the Child Health Questionnaire, findings suggest that there is a significant association between perceived physical health and psychosocial adjustment in the population of children with craniofacial anomalies. The significant perceived health needs of the non-cleft lip and/or palate group and the association between physical health and psychological adjustment highlight the importance of the interdisciplinary nature of craniofacial teams.     

GB Non-native Species Information Portal: documenting the arrival of non-native species in Britain

Information on non-native species (NNS) is often scattered among a multitude of sources, such as regional and national databases, peer-reviewed and grey literature, unpublished research projects, institutional datasets and with taxonomic experts. Here we report on the development of a database designed for the collation of information in Britain. The project involved working with volunteer experts to populate a database of NNS (hereafter called “the species register”). Each species occupies a row within the database with information on aspects of the species’ biology such as environment (marine, freshwater, terrestrial etc.), functional type (predator, parasite etc.), habitats occupied in the invaded range (using EUNIS classification), invasion pathways, establishment status in Britain and impacts. The information is delivered through the Great Britain Non-Native Species Information Portal hosted by the Non-Native Species Secretariat. By the end of 2011 there were 1958 established NNS in Britain. There has been a dramatic increase over time in the rate of NNS arriving in Britain and those becoming established. The majority of established NNS are higher plants (1,376 species). Insects are the next most numerous group (344 species) followed by non-insect invertebrates (158 species), vertebrates (50 species), algae (24 species) and lower plants (6 species). Inventories of NNS are seen as an essential tool in the management of biological invasions. The use of such lists is diverse and far-reaching. However, the increasing number of new arrivals highlights both the dynamic nature of invasions and the importance of updating NNS inventories.     

Putative CENP-B paralogues are not present at mammalian centromeres

Although centromere protein B (CENP-B) is a highly conserved mammalian centromere protein, its function remains unknown. The presence of the protein is required to form artificial satellite DNA-based centromeres de novo, yet cenpb knockout mice are viable for multiple generations with no mitotic or meiotic defects, and the protein is not present at fully functional neocentromeres. Previous studies have suggested that the presence of functionally redundant paralogues of CENP-B may explain the lack of a phenotype in knockout mice, and the related Tigger-derived (TIGD) family of proteins has been implicated as the most likely candidate for such paralogues. Here, we describe an investigation of the centromere-binding properties of the three TIGD proteins most highly related to CENP-B through phylogenetic analysis through EGFP fusion studies and immunocytochemistry. Although two of the three proteins bound to human centromeres with low affinity when overexpressed as fusion proteins, the strongest candidate, TIGD3, demonstrated no native centromeric binding when using raised antibodies, either in human cells or in cenpb ^−/− mouse ES cells. We conclude that the existence of functional CENP-B paralogues is highly unlikely and that CENP-B acts alone at the centromere. Based on these data, we suggest a new, meiotic drive model of CENP-B action during centromere repositioning in evolution.     

A novel quantitative proteomics strategy to study phosphorylation-dependent peptide-protein interactions

Phosphorylation-dependent protein-protein interactions provide the mechanism for a large number of intracellular signal transduction pathways. One of the goals of signal transduction research is to understand more precisely the nature of these phosphorylation-dependent interactions. Here, we report a novel strategy based on quantitative proteomics that allows for the rapid analysis of peptide-protein interactions with more than one phosphorylation site involved. The phosphorylation of two tyrosine residues, Y342 and Y346, within the linker B region of the protein-tyrosine kinase Syk is important for optimal signaling from the B cell receptor for antigen. We employed four amino-specific, isobaric reagents to differentially label proteins interacting in vitro with four Syk peptides containing none, one, or two phosphates on tyrosine residues Y342 and Y346, respectively. In total, 76 proteins were identified and quantified, 11 of which were dependent on the phosphorylation of individual tyrosine residues. One of the proteins, peroxiredoxin 1, preferably bound to phosphorylated Y346, which was further verified by Western blotting results. Thus, we demonstrate that the use of 4-fold multiplexing allows for relative protein measurements simultaneously for the identification of interacting proteins dependent on the phosphorylation of specific residues.     

Assortative mating by size: A meta-analysis of mating patterns in water striders

Summary Assortative mating by size is a common mating pattern that can be generated by several different behavioural mechanisms, with different evolutionary implications. Assortative mating is typically associated with sexual selection and has been regarded as an attribute of populations, species, mating systems or even higher order taxa. In most animal groups, however, appropriate analyses of assortative mating at these different levels are lacking and the causes and forms of assortative mating are poorly understood. Here, we analyse 45 different population level estimates of assortative mating and non-random mating by size in seven confamiliar species of water striders that share a common mating system. A hierarchical comparative analysis shows that virtually all the variance within the clade occurs among samples within species. We then employ meta-analysis to estimate the overall strength of assortative mating, to determine the form of assortative mating and to further assess potential differences among species as well as the probable causes of assortative mating in this group of insects. We found overall weak but highly significant positive assortative mating. We show that analyses of the degree of heteroscedasticity in plots of male versus female size are critical, since the evolutionary implications of true and apparent assortative mating differ widely and conclude that the positive assortative mating observed in water striders was of the true rather than the apparent form. Further, within samples, mating individuals were significantly larger than non-mating individuals in both males and females. All of these non-random mating patterns were consistent among species and we conclude that weak positive assortative mating by size is a general characteristic of those water strider species that share this mating system. We use our results to illustrate the importance of distinguishing between different forms of assortative mating, to discriminate between various behavioural causes of assortative mating and to assess potential sources of interpopulational variance in estimates of assortative mating. Finally, we discuss the value of using meta-analytic techniques for detecting overall patterns in multiple studies of non-random mating.     

Cloning and expression of Burkholderia polyyne biosynthetic gene clusters in Paraburkholderia hosts provides a strategy for biopesticide development

Burkholderia have potential as biocontrol agents because they encode diverse biosynthetic gene clusters (BGCs) for a range of antimicrobial metabolites. Given the opportunistic pathogenicity associated with Burkholderia species, heterologous BGC expression within non-pathogenic hosts is a strategy to construct safe biocontrol strains. We constructed a yeast-adapted Burkholderia-Escherichia shuttle vector (pMLBAD_yeast) with a yeast replication origin 2 μ and URA3 selection marker and optimised it for cloning BGCs using the in vivo recombination ability of Saccharomyces cerevisiae. Two Burkholderia polyyne BGCs, cepacin (13 kb) and caryoynencin (11 kb), were PCR-amplified as three overlapping fragments, cloned downstream of the pBAD arabinose promoter in pMLBAD_yeast and mobilised into Burkholderia and Paraburkholderia heterologous hosts. Paraburkholderia phytofirmans carrying the heterologous polyyne constructs displayed in vitro bioactivity against a variety of fungal and bacterial plant pathogens similar to the native polyyne producers. Thirteen Paraburkholderia strains with preferential growth at 30°C compared with 37°C were also identified, and four of these were amenable to genetic manipulation and heterologous expression of the caryoynencin construct. The cloning and successful heterologous expression of Burkholderia biosynthetic gene clusters within Paraburkholderia with restricted growth at 37°C opens avenues for engineering non-pathogenic biocontrol strains.     

Analysis of retinal cell development in chick embryo by immunohistochemistry and in ovo electroporation techniques

Background

Endogenous peptides such as neuropeptides are involved in numerous biological processes in the fully developed brain but very little is known about their role in brain development. Japanese quail is a commonly used bird model for studying sexual dimorphic brain development, especially adult male copulatory behavior in relation to manipulations of the embryonic endocrine system. This study uses a label-free liquid chromatography mass spectrometry approach to analyze the influence of age (embryonic days 12 vs 17), sex and embryonic day 3 ethinylestradiol exposure on the expression of multiple endogenous peptides in the developing diencephalon.

Results

We identified a total of 65 peptides whereof 38 were sufficiently present in all groups for statistical analysis. Age was the most defining variable in the data and sex had the least impact. Most identified peptides were more highly expressed in embryonic day 17. The top candidates for EE₂ exposure and sex effects were neuropeptide K (downregulated by EE₂ in males and females), gastrin-releasing peptide (more highly expressed in control and EE₂ exposed males) and gonadotropin-inhibiting hormone related protein 2 (more highly expressed in control males and displaying interaction effects between age and sex). We also report a new potential secretogranin-2 derived neuropeptide and previously unknown phosphorylations in the C-terminal flanking protachykinin 1 neuropeptide.

Conclusions

This study is the first larger study on endogenous peptides in the developing brain and implies a previously unknown role for a number of neuropeptides in middle to late avian embryogenesis. It demonstrates the power of label-free liquid chromatography mass spectrometry to analyze the expression of multiple endogenous peptides and the potential to detect new putative peptide candidates in a developmental model.