Rare Copy Number Variants Are a Common Cause of Short Stature

Human growth has an estimated heritability of about 80%–90%. Nevertheless, the underlying cause of shortness of stature remains unknown in the majority of individuals. Genome-wide association studies (GWAS) showed that both common single nucleotide polymorphisms and copy number variants (CNVs) contribute to height variation under a polygenic model, although explaining only a small fraction of overall genetic variability in the general population. Under the hypothesis that severe forms of growth retardation might also be caused by major gene effects, we searched for rare CNVs in 200 families, 92 sporadic and 108 familial, with idiopathic short stature compared to 820 control individuals. Although similar in number, patients had overall significantly larger CNVs (p-value<1×10⁻⁷). In a gene-based analysis of all non-polymorphic CNVs>50 kb for gene function, tissue expression, and murine knock-out phenotypes, we identified 10 duplications and 10 deletions ranging in size from 109 kb to 14 Mb, of which 7 were de novo (p<0.03) and 13 inherited from the likewise affected parent but absent in controls. Patients with these likely disease causing 20 CNVs were smaller than the remaining group (p<0.01). Eleven (55%) of these CNVs either overlapped with known microaberration syndromes associated with short stature or contained GWAS loci for height. Haploinsufficiency (HI) score and further expression profiling suggested dosage sensitivity of major growth-related genes at these loci. Overall 10% of patients carried a disease-causing CNV indicating that, like in neurodevelopmental disorders, rare CNVs are a frequent cause of severe growth retardation.     

Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris)

Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.     

Hierarchical establishment of information sources during foraging decision-making process involving Acromyrmex subterraneus (Forel, 1893) (Hymenoptera,Formicidae)

During foraging, worker ants are known for making use of many information sources to guide themselves in external environments, especially individual (memory) and social (trail pheromone) information. Both kinds of information act in a synergic way, keeping the foraging process efficient and organized. However, when social and individual information is conflicting face a trail bifurcation, it is necessary to establish a hierarchical order so prioritizing one of them. This study aims to verify which information (social or individual) is prioritized by Acromyrmex subterraneus workers when facing a bifurcation in a Y-trail system. Only one branch of the Y-trail leads to food resource and it had a section covered by filter paper where trail pheromone was deposited by workers. Pheromone deposition was here estimated by worker flow. After an individually marked forager (target-worker) made 1, 3 or 5 trips to the food resource, the filter paper was transferred to the branch which did not lead to the food. The time spent by target workers on branch selection and their right choice (branch with food) frequency were registered. Regardless of the target worker's previous trips to the resource, right choice frequency stood over 70%. In addition, the number of previous trips did not influence the time spent on decision making. However, the higher the flow of workers, the longer the time spent on decision making. By simulating a situation with conflicting information, it was possible to verify that a hierarchical order is established by A. subterraneus, which prioritized individual information (memory).     

Temperature-sensitive step in Ti plasmid vir-region induction and correlation with cytokinin secretion by Agrobacteria

Summary DNA transfer from Agrobacteria to plant cells requires activation of functions which are inactive under normal growth conditions. We studied two aspects with nopaline plasmid pGV3850: (1) conditions required for induction of a representative vir-region protein (virD2); for this we prepared antiserum against the protein and used the Western blot technique, and (2) correlation between vir-region induction and secretion of plant hormones. The results show that three factors are necessary and sufficient: the previously identified acetosyringone and acidic pH and, in addition, a carbon/energy source. Induction correlates with cytokinin secretion, suggesting that release of this hormone by the bacteria may play a role in tumor induction. No pronounced correlation is observed with release of indole-3-acetic acid. VirD2 induction and cytokinin secretion are temperature-dependent with similar optima. It is proposed that the thermosensitive step discovered decades ago with tumor induction in planta is in the activation of the vir functions.Abbreviations vir virulence gene - iP N⁶-(2-isopentenyl)adenine - iPA N⁶-(2-isopentenyl)adenosine - trans-Z trans-Zeatin - trans ZR, trans-Zeatinriboside - IAA indole-3-acetic acid - IPTG isopropyl--D-thiogalactoside     

Use of anion-exchange high-performance liquid chromatography for the study of smooth muscle myosin light-chain kinase and its catalytic domain

Avian myosin light-chain kinase from smooth muscle of the gizzard and its catalytic domain, derived from the intact enzyme by trypsin digestion, was purified within 30–40 min by both analytical and preparative anion-exchange high-performance liquid chromatography. The proteins obtained were more than 95% pure and retained their biological activity. The high-performance anion-exchange chromatography protocols represent a significant decrease in purification time when compared with conventional ion-exchange chromatography.     

Caldesmon: anomalous electrophoretic behaviour in polyacrylamide gel

In SDS gels caldesmon (Mr = 140 kDa) and myosin light chain kinase (Mr = 130 kDa) migrate as a closely separated doublet. When glycerol is added to the gel caldesmon is characterized by an anomalous migration. In fact under this latter condition, the distance between caldesmon and myosin light chain kinase is enhanced by two-three times. The nature of putative caldesmon and myosin light chain kinase was confirmed by physicochemical, enzymatic and immunological methods.     

CMView: interactive contact map visualization and analysis

SUMMARY: Contact maps are a valuable visualization tool in structural biology. They are a convenient way to display proteins in two dimensions and to quickly identify structural features such as domain architecture, secondary structure and contact clusters. We developed a tool called CMView which integrates rich contact map analysis with 3D visualization using PyMol. Our tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods. A unique feature is the interactive refinement of structural alignments based on user selected substructures. AVAILABILITY: CMView is freely available for Linux, Windows and MacOS. The software and a comprehensive manual can be downloaded from http://www.bioinformatics.org/cmview/. The source code is licensed under the GNU General Public License.     

A β-Lactamase based reporter system for ESX dependent protein translocation in mycobacteria

Protein secretion is essential for all bacteria in order to interact with their environment. Mycobacterium tuberculosis depends on protein secretion to subvert host immune response mechanisms. Both the general secretion system (Sec) and the twin-arginine translocation system (Tat) are functional in mycobacteria. Furthermore, a novel type of protein translocation system named ESX has been identified. In the genome of M. tuberculosis five paralogous ESX regions (ESX-1 to ESX-5) have been found. Several components of the ESX translocation apparatus have been identified over the last ten years. The ESX regions are composed of a basic set of genes for the translocation machinery and the main substrate - a heterodimer. The best studied of these heterodimers is EsxA (ESAT-6)/EsxB (CFP-10), which has been shown to be exported by ESX-1. EsxA/B is heavily involved in virulence of M. tuberculosis. EsxG/H is exported by ESX-3 and seems to be involved in an essential iron-uptake mechanism in M. tuberculosis. These findings make ESX-3 components high profile drug targets. Until now, reporter systems for determination of ESX protein translocation have not been developed. In order to create such a reporter system, a truncated β-lactamase ('bla TEM-1) was fused to the N-terminus of EsxB, EsxG and EsxU, respectively. These constructs have then been tested in a β-lactamase (BlaS) deletion strain of Mycobacterium smegmatis. M. smegmatis ΔblaS is highly susceptible to ampicillin. An ampicillin resistant phenotype was conferred by translocation of Bla TEM-1-Esx fusion proteins into the periplasm. BlaTEM-1-Esx fusion proteins were not found in the culture filtrate suggesting that plasma membrane translocation and outer membrane translocation are two distinct steps in ESX secretion. Thus we have developed a powerful tool to dissect the molecular mechanisms of ESX dependent protein translocation and to screen for novel components of the ESX systems on a large scale.