The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection

Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß-ß-a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated

Evaluation of Host Immune Response in Diabetic Foot Infection Tissues Using an RNA Sequencing-Based Approach

The normal continuity of skin tissue can be affected by invading pathogens and lead to a series of complicated physiological events. Using an RNA sequencing-based approach, we have captured a metatranscriptomic landscape from diabetic foot infections (DFIs). The hierarchical clustering of the top 2,000 genes showed the expression of four main clusters in DFIs (A, B, C, and D). Clusters A and D were enriched in genes mainly involved in the recruitment of inflammatory cells and immune responses and clusters B and C were enriched in genes related to skin cell development and wound healing processes such as extracellular structure organization and blood vessel development. Differential expression analysis showed more than 500 differentially expressed genes (DEGs) between samples with a low number of virulence factors and samples with a high number of virulence factors. Up-regulated and down-regulated genes were mainly involved in adaptive/native immune responses and transport of mature mRNAs, respectively. Our results demonstrated the importance of inflammatory cytokines of adaptive/native immunity in the progression of DFIs and provided a useful groundwork for capturing gene snapshots in DFIs. In addition, we have provided a general introduction to the challenges and opportunities of RNA sequencing technology in the evaluation of DFIs. Pathways identified in this study such as immune chemokines, Rho GTPases, and corresponding effectors might be important therapeutic targets in the management of DFIs

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported—high thermostability and high catalytic activity—compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered “superior” to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.France. Agence nationale de la recherch

Study protocol for a double blind, randomised, placebo-controlled trial of continuous subpectoral local anaesthetic infusion for pain and shoulder function following mastectomy: SUB-pectoral Local anaesthetic Infusion following MastEctomy (SUBLIME) study.

INTRODUCTION: Over 16 000 mastectomies are performed in England and Wales annually. Acute postoperative pain and nausea are common. The most frequently occurring long-term complications are chronic pain (up to 50%) and reduced shoulder function (reported at 35%). Regional techniques that improve acute postoperative pain relief may reduce the incidence of these complications. This study assesses the effectiveness of a 24-hour continuous local anaesthetic in the subpectoral plane in improving postoperative pain and quality of life in patients undergoing mastectomy. METHODS AND ANALYSIS: This is a randomised, double blind, placebo-controlled, two-centre, parallel group trial in women undergoing mastectomy with or without axillary involvement. One hundred and sixty participants will be randomised in a 1:1 ratio to receive either 0.25% levobupivacaine or 0.9% saline by subpectoral infusion postoperatively for 24 h. All participants will be provided with an intravenous morphine patient-controlled analgesia (PCA) system. Participants will be followed-up for 24 h in hospital and at approximately 14 days and 6 months postoperatively. Joint primary outcome measures are total morphine consumption and total pain score (captured via patient-recorded visual analogue scale (VAS) 4 hourly) during the first 24 h postoperatively. Primary statistical analysis of total pain is based on the area under the curve of pain versus time graph. Secondary outcomes include PCA attempts in first 24 h; VAS pain scores and shoulder function by goniometry at 24 h, 14 days (approximately) and 6 months; Verbal Rating Scale pain scores in first 24 h; Brief Pain Inventory and Oxford Shoulder Score at 6 months; duration of hospital stay; incidence of postoperative nausea and vomiting; cost-effectiveness. ETHICS AND DISSEMINATION: The study is approved by the South West England Research Ethics Committee (12/SW/0149). RESULTS: will be published in a peer-reviewed journal and presented at local, national and international scientific meetings. TRIAL REGISTRATION: ISRCTN46621916. EudraCT 2011-005775-16

Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex

<p>Abstract</p> <p>Background</p> <p>General iron-sulfur cluster biosynthesis proceeds through assembly of a transient cluster on IscU followed by its transfer to a recipient apo-protein. The efficiency of the second step is increased by the presence of HscA and HscB, but the reason behind this is poorly understood. To shed light on the function of HscB, we began a study on the nature of its interaction with IscU. Our work suggested that the binding site of IscU is in the C-terminal domain of HscB, and two different triple alanine substitutions ([L92A, M93A, F153A] and [E97A, E100A, E104A]) involving predicted binding site residues had detrimental effects on this interaction. However, the individual contribution of each substitution to the observed effect remains to be determined as well as the possible involvement of other residues in the proposed binding site.</p> <p>Results</p> <p>In the work reported here, we used isothermal titration calorimetry to characterize the affinity of single alanine HscB mutants for IscU, and subsequently confirmed our results with nuclear magnetic resonance spectroscopy. Alanine substitutions of L92, L96, and F153 severely impaired the ability of HscB to form a complex with IscU; substitutions of R87, R99, and E100 had more modest effects; and substitutions of T89, M93, E97, D103, E104, R152, K156, and S160 had only minor or no detectable effects.</p> <p>Conclusions</p> <p>Our results show that the residues of HscB most important for strong interaction with IscU include three hydrophobic residues (L92, L96, and F153); in addition, we identified a number of other residues whose side chains contribute to a lesser extent to the interaction. Our results suggest that the triple alanine substitution at HscB positions 92, 96, and 153 will destabilize the HscB-IscU complex by ΔΔ<it>G</it>_b≅ 5.7 kcal/mol, equivalent to a ≅ 15000-fold reduction in the affinity of HscB for IscU. We propose that this triple mutant could provide a more definitive test of the functional importance of the HscB-IscU interaction in vivo than those used previously that yielded inconclusive results.</p

Composite Polarons in Ferromagnetic Narrow-band Metallic Manganese Oxides

A new mechanism is proposed to explain the colossal magnetoresistance and related phenomena. Moving electrons accompanied by Jahn-Teller phonon and spin-wave clouds may form composite polarons in ferromagnetic narrow-band manganites. The ground-state and finite-temperature properties of such composite polarons are studied in the present paper. By using a variational method, it is shown that the energy of the system at zero temperature decreases with the formation of composite polaron; the energy spectrum and effective mass of the composite polaron at finite temperature is found to be strongly renormalized by the temperature and the magnetic field. It is suggested that the composite polaron contribute significantly to the transport and the thermodynamic properties in ferromagnetic narrow-band metallic manganese oxides.Comment: Latex, no figur

The microbiome of diabetic foot ulcers : a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing

Background: Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing. Results: Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs X = 32,014) compared to tissue (X = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon’s H diversity p = 0.009). However, based on a presence/ absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34). Conclusions: Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy. SOME OF THE SCIENTIC SYMBOLS CAN NOT BE REPRESENTED CORRECTLY IN THE ABSTRACT. PLEASE READ WITH CAUTION AND REFER TO THE ORIGINAL PUBLICATION

From ‘Young Women’ to ‘Female Adolescents’:Dutch Advice Literature during the Long Nineteenth Century

In late eighteenth-century Europe, there was a rapid expansion in the publication of advice books directed at young adult women. Based on an examination of conduct books published in the Netherlands, this chapter traces the changing format of the genre from the last quarter of the eighteenth century through to the early decades of the twentieth century. It explores how women pedagogues in the nineteenth century developed new ways of advising young women that gave readers greater control over their life choices. In the early twentieth century, the emerging social sciences drew attention to the physical and emotional changes involved in female adolescence, prescribing for the young woman strict forms of behaviour

Rearing goat kids away from their dams 2. Understanding farmers’ views on changing management practices

Improving animal welfare is an important aim of livestock industries and is dependent on human management. Understanding attitudes to change and perceived barriers is therefore a key consideration for welfare scientists. A survey that aimed to investigate farmers’ attitudes towards changing goat kid-rearing practices was distributed. Likert scales examined willingness to change and the importance of factors in decision-making alongside open-text responses for further explanation. A total of 242 farmers (United States of America (USA) 72; United Kingdom (UK) 71; Australia 33; Canada 23; New Zealand 20; European Union 14; Other 9) rearing goat kids away from their dams responded. All respondents rated from one (highly unwilling) to seven (highly willing), how willing they would be to supply three enrichment types. Willingness to provide enrichments differed (χ2(2) = 190.114, P < 0.001), with farmers most likely to provide climbing or loose items rather than swinging items. The most common reasons cited for unwillingness to provide enrichment were related to safety (101 responses/76.5%). Those currently abruptly weaning were asked how willing they would be to use gradual weaning methods. Those abruptly weaning from ad libitum milk systems (n = 47) showed no difference in willingness to change to different gradual weaning methods; the median (Interquartile Range (IQR)) for the willingness to change to removing teats was 2 (1–4), reducing milk temperature 3 (1–5) and diluting milk 2 (1–5), with most concerns relating to feasibility. Those abruptly weaning from bottle feeding (n = 18) also showed no difference in willingness to change to gradual weaning methods. Median (IQR) score for willingness to change to reduced number of bottle feeds was 4 (1–7), reducing milk quantity 3 (1–6.25), and diluting milk 1 (1–5), respectively. Health concerns were the most common reason for not being willing to change. All 242 respondents were asked to rate how important different factors are when deciding to implement a new management practice. There was a significant difference in importance between factors (χ2(2) = 34.779, P < 0.001). Median (IQR) importance of the factors was labour/time 5 (4–7), cost 5 (4–7), evidence beneficial to welfare 6 (5–7), evidence beneficial to health 6 (5–7), and evidence beneficial to growth 6 (4–7). To our knowledge, this is the first study to examine goat farmers’ attitudes towards changing management practices and could help ensure that future research addresses farmer concerns and therefore has the best opportunity to be implemented on-farm