Regulation of D-galacturonate metabolism in Caulobacter crescentus by HumR, a LacI-family transcriptional repressor

The oligotrophic freshwater bacterium Caulobacter crescentus encodes a cluster of genes (CC_1487 to CC_1495) shown here to be necessary for metabolism of D-galacturonate, the primary constituent of pectin, a major plant polymer. Sequence analysis suggests that these genes encode a version of the bacterial hexuronate isomerase pathway. A conserved 14 bp sequence motif is associated with promoter regions of three operons within this cluster, and is conserved in homologous gene clusters in related alpha-Proteobacteria. Embedded in the hexuronate gene cluster is a gene (CC_1489) encoding a member of the LacI family of bacterial transcription factors. This gene product, designated here as HumR (hexuronate metabolism regulator), represses expression of the uxaA and uxaC operon promoters by binding to the conserved operator sequence. Repression is relieved in the presence of galacturonate or, to a lesser extent, by glucuronate. Other genes potentially involved in pectin degradation and hexuronate transport are also under the control of HumR. Adoption of a LacI-type repressor to control hexuronate metabolism parallels the regulation of xylose, glucose, and maltose utilization in C. crescentus, but is distinct from the use of GntR-type repressors to control pectin and hexuronate utilization in gamma-Proteobacteria such as Escherichia coli

Optimal management of older people with frailty non-weight bearing after lower limb fracture: a scoping review

BackgroundPatients with lower limb fractures who are non-weight bearing are at risk of the complications of the associated immobility and disability, particularly people with frailty, but there is lack of clarity about what constitutes optimal care for such patients. A scoping literature review was conducted to explore what evidence is available for the management of this patient group.MethodsMEDLINE (PubMed) CINAHL, EMBASE and the Cochrane databases of published literature and the HMIC and SIGLE sites for grey literature were searched for primary research studies and expert reports, using an iterative approach initially including the key term ‘non-weight bearing’. All study types were included. Analysis was by narrative synthesis.ResultsNo papers were identified from a search using the key phrase ‘non-weight bearing’. With this term removed, 11 indirectly relevant articles on lower limb fractures were retrieved from the searches of the electronic databases comprising three observational studies, five non-systematic review articles, a systematic review, an opinion piece and a survey of expert opinion that had relevance to restricted weight bearing patients. The observational studies indicated depression, cognition and nutrition affect outcome and hence have indirect relevance to management. The non-systematic reviews articles emphasised the importance of maintaining strength and range of movement during immobilisation and advised an orthogeriatric model of care. Fourteen UK and 97 non-UK guidelines relevant to fragility fractures, falls and osteoporosis management were found in the grey literature, but none made specific recommendations regarding the management of any period of non-weight bearing.DiscussionThese findings provide a summary of the evidence base that can be used in the development of a clinical guideline for these patients but is not sufficient. We propose that, a guideline should be developed for these patients using an expert consensus process

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.</p

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution

APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast DCIS, and in pre-invasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx pre-invasive to invasive NSCLC lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models, revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in pre-invasive disease, providing fuel for selection early in cancer evolution

Implementing a Mach Debugger for Multithreaded Applications

Multiple threads of control add new challenges to the task of application debugging, and require the development of new debuggers to meet these challenges. This paper describes the design and implementation of modifications to an existing debugger (gdb) for debugging multithreaded applications under the Mach operating system. It also describes the operating system facilities that support it. Although certain implementation details are specific to Mach, the underlying design principles are applicable to other systems that support threads in a Unix compatible environment