A toolbox for manipulating the genome of the major goat pathogen, Mycoplasma capricolum subsp. capripneumoniae

Mycoplasma capricolum subspecies capripneumoniae (Mccp) is the causative agent of contagious caprine pleuropneumonia (CCPP), a devastating disease listed by the World Organisation for Animal Health (WOAH) as a notifiable disease and threatening goat production in Africa and Asia. Although a few commercial inactivated vaccines are available, they do not comply with WOAH standards and there are serious doubts regarding their efficacy. One of the limiting factors to comprehend the molecular pathogenesis of CCPP and develop improved vaccines has been the lack of tools for Mccp genome engineering. In this work, key synthetic biology techniques recently developed for closely related mycoplasmas were adapted to Mccp. CReasPy-Cloning was used to simultaneously clone and engineer the Mccp genome in yeast, prior to whole-genome transplantation into M. capricolum subsp. capricolum recipient cells. This approach was used to knock out an S41 serine protease gene recently identified as a potential virulence factor, leading to the generation of the first site-specific Mccp mutants. The Cre-lox recombination system was then applied to remove all DNA sequences added during genome engineering. Finally, the resulting unmarked S41 serine protease mutants were validated by whole-genome sequencing and their non-caseinolytic phenotype was confirmed by casein digestion assay on milk agar. The synthetic biology tools that have been successfully implemented in Mccp allow the addition and removal of genes and other genetic features for the construction of seamless targeted mutants at ease, which will pave the way for both the identification of key pathogenicity determinants of Mccp and the rational design of novel, improved vaccines for the control of CCPP.

The small stellated dodecahedron code and friends

We explore a distance-3 homological CSS quantum code, namely the small stellated dodecahedron code, for dense storage of quantum information and we compare its performance with the distance-3 surface code. The data and ancilla qubits of the small stellated dodecahedron code can be located on the edges respectively vertices of a small stellated dodecahedron, making this code suitable for three-dimensional connectivity. This code encodes eight logical qubits into 30 physical qubits (plus 22 ancilla qubits for parity check measurements) in contrast with one logical qubit into nine physical qubits (plus eight ancilla qubits) for the surface code. We develop fault-tolerant parity check circuits and a decoder for this code, allowing us to numerically assess the circuit-based pseudo-threshold.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'.

The promiscuous nature of the cardiac sodium current

Voltage-gated sodium channels (Na(V)s) are essential in propagating neuronal electrical impulse and triggering muscle contraction. In the heart, the Na(+) channel isoform Na(V)1.5 is strongly expressed and in the past was thought to be solely responsible for generating the cardiac Na(+) current (I(Na)). Recent studies, however, revealed that neuronal and skeletal muscle Na(+) channel isoforms are also expressed in the heart and contribute to cardiac I(Na). Amongst the findings is that many neuronal type Na(V)s are expressed in specific areas of the conduction system and ventricles. The contribution of these TTX-sensitive channels to normal cardiac function remains unclear but these data raise the possibility of a more prominent role of TTX-sensitive channels in conduction. Moreover, cardiac arrhythmias are commonly observed in many neuronal and musculoskeletal diseases despite their exclusive linkage to mutations in the neuronal and skeletal muscle sodium channel isoforms. The cause for these arrhythmias remains poorly understood. These recent findings indicate that neuronal and skeletal muscle sodium channels are expressed in areas of the heart that may be involved in the clinical phenotypes observed. The purpose of this review is to give an overview of the evidence for the presence of TTX-sensitive Na(V) isoforms in the heart and present the hypothesis brought forward so far for their direct role in cardiac function. These data demonstrate the promiscuous nature of the cardiac sodium current at the molecular level and should help us to bridge the gap that exists between our understanding of cardiac physiology and arrhythmias associated to brain and myotonic diseases.

The peer relations of dropouts: a comparative study of at-risk and not at-risk youths

Little research has been devoted to exploring the relationship between high school disengagement and friendship network changes. In this study, the characteristics of friends, the environments of the friendship network and the nature of peer relations of students at-risk and not at-risk of dropping out of high school were compared. A questionnaire was given to 191 high school students (109 males, 82 females) from a middle class environment at the beginning and end of the school year. Results indicated that at-risk students had more dropout friends, more working friends, fewer school friends and fewer same-sex friends. Sex differences were discovered in several areas. Findings are discussed in relation to research and theories pertaining to dropouts and adolescent development.

Visualization of elementary DNA replication units in human nuclei corresponding in size to DNA loop domains

Newly synthesized DNA in mammalian nuclei is concentrated in discrete nuclear granules called replication foci. These foci may be visualized using antibodies against 5-bromodeoxyuridine. In the early S-phase cells 100-250 foci are usually detected. On average, individual foci range between 0.5 and 2 microns in diameter and can be seen as clusters of more than ten average-sized (60-100 kb) synchronously activated replicons. In this study, employing minor modifications of the previous methods, we report the visualization of small replication foci of about 0.3 micron diameter (mini-foci). Some foci are clustered into folded chains consisting of 2-40 subunits. DNA content of one mini-focus is estimated to be 50-120 kb and there are 500-1500 mini-foci per cell in the early S-phase. Experimentally induced decrease in replicon size does not affect the size of mini-foci, suggesting that these represent elementary units of DNA replication in mammalian nuclei and are probably identical to the basic structural DNA loop domains.

The structure of human S-phase chromosome fibres

Recent in situ hybridization studies suggested that within the range of 0.1-1.0 Mb, human interphase chromosomes follow a random walk model (i.e. they behave as flexible polymers without major constraints). However, chromosome structure may differ in the G1, S, and G2 phases, and phase-specific constraints may be masked if the chromosome analysis does not discriminate between the phases. Therefore, using confocal microscopy, we examined the structure of S-phase chromosomes labelled with 5-iododeoxyuridine after prolonged treatment with 5-fluorodeoxyuridine. In the S-phase, labelled 0.32 mu chromosome fibres mostly appear as semi-circles with an average diameter of 0.83 +/- 0.03 mu. These semi-circles are joined together to form different 3D structures, and two semicircles frequently adopt s- or omega-like conformations involving about 2.5 mu of the chromosome contour length (L). Morphometric analysis of the S-phase fibres suggests that our data fit both the random flexible polymer model and also a model in which two constrained semi-circles are attached to each other by a flexible joint, thus eliminating constraints at long distances (L more than 2 mu).

Up-regulation of a thymic epithelial ligand after contact with thymocytes

Thymic medullary epithelial cells of the E-5 line were shown to form in vitro complexes with thymocytes resulting in no apparent modification to the thymocytes participating in the complex, but in tyrosine phosphorylation on a glycoprotein associated with the epithelial adhesion molecule. Because signal transduction from lymphocytes to stromal cells is poorly documented, we examine in this work events which follow epithelial cell activation. Our findings indicate that one chain of the epithelial adhesion molecule (gp23), after complex formation with thymocytes, undergoes a rapid and transient tyrosine kinase-dependent up-regulation.