On the nature of fur evolution: A phylogenetic approach in Actinobacteria

<p>Abstract</p> <p>Background</p> <p>An understanding of the evolution of global transcription regulators is essential for comprehending the complex networks of cellular metabolism that have developed among related organisms. The <it>fur </it>gene encodes one of those regulators – the ferric uptake regulator Fur – widely distributed among bacteria and known to regulate different genes committed to varied metabolic pathways. On the other hand, members of the Actinobacteria comprise an ecologically diverse group of bacteria able to inhabit various natural environments, and for which relatively little is currently understood concerning transcriptional regulation.</p> <p>Results</p> <p>BLAST analyses revealed the presence of more than one <it>fur </it>homologue in most members of the Actinobacteria whose genomes have been fully sequenced. We propose a model to explain the evolutionary history of <it>fur </it>within this well-known bacterial phylum: the postulated scenario includes one duplication event from a primitive regulator, which probably had a broad range of co-factors and DNA-binding sites. This duplication predated the appearance of the last common ancestor of the Actinobacteria, while six other duplications occurred later within specific groups of organisms, particularly in two genera: <it>Frankia </it>and <it>Streptomyces</it>. The resulting paralogues maintained main biochemical properties, but became specialised for regulating specific functions, coordinating different metal ions and binding to unique DNA sequences. The presence of syntenic regions surrounding the different <it>fur </it>orthologues supports the proposed model, as do the evolutionary distances and topology of phylogenetic trees built using both Neighbor-Joining and Maximum-Likelihood methods.</p> <p>Conclusion</p> <p>The proposed <it>fur </it>evolutionary model, which includes one general duplication and two in-genus duplications followed by divergence and specialization, explains the presence and diversity of <it>fur </it>genes within the Actinobacteria. Although a few rare horizontal gene transfer events have been reported, the model is consistent with the view of gene duplication as a main force of microbial genomes evolution. The parallel study of Fur phylogeny across diverse organisms offers a solid base to guide functional studies and allows the comparison between response mechanisms in relation with the surrounding environment. The survey of regulators among related genomes provides a relevant tool for understanding the evolution of one of the first lines of cellular adaptability, control of DNA transcription.</p

SOLUS: Multimodal System Combining Ultrasounds and Diffuse Optics for Tomographic Imaging of Breast Cancer

An innovative multimodal system for breast imaging was developed combining in a single probe B-mode ultrasound, shear-wave elastography and multi-wavelength time-domain diffuse optical tomography. The clinical validation is ongoing aiming at improving the diagnostic specificity

Breast lesion classification based on absorption and composition parameters: a look at SOLUS first outcomes

A machine learning classification algorithm is applied to the SOLUS database to discriminate benign and malignant breast lesions, based on absorption and composition properties retrieved through diffuse optical tomography. The Mann-Whitney test indicates oxy-hemoglobin (p-value = 0.0007) and lipids (0.0387) as the most significant constituents for lesion classification, but work is in progress for further analysis. Together with sensitivity (91%), specificity (75%) and the Area Under the ROC Curve (0.83), special metrics for imbalanced datasets (27% of malignant lesions) are applied to the machine learning outcome: balanced accuracy (83%) and Matthews Correlation Coefficient (0.65). The initial results underline the promising informative content of optical data

Breast lesion classification based on absorption and composition parameters: a look at SOLUS first outcomes

A machine learning classification algorithm is applied to the SOLUS database to discriminate benign and malignant breast lesions, based on absorption and composition properties retrieved through diffuse optical tomography. The Mann-Whitney test indicates oxy-hemoglobin (p-value = 0.0007) and lipids (0.0387) as the most significant constituents for lesion classification, but work is in progress for further analysis. Together with sensitivity (91%), specificity (75%) and the Area Under the ROC Curve (0.83), special metrics for imbalanced datasets (27% of malignant lesions) are applied to the machine learning outcome: balanced accuracy (83%) and Matthews Correlation Coefficient (0.65). The initial results underline the promising informative content of optical data

Initial examples of the SOLUS multimodal potential

We present initial evidence of the SOLUS potential for the multimodal non-invasive diagnosis of breast cancer by describing the correlation between optical and standard radiological data and analyzing a case study

SOLUS: An innovative multimodal imaging system to improve breast cancer diagnosis through diffuse optics and ultrasounds

To improve non-invasively the specificity in the diagnosis of breast cancer after a positive screening mammography or doubt/suspicious ultrasound examination, the SOLUS project developed a multimodal imaging system that combines: B-mode ultrasound (US) scans (to assess morphology), Color Doppler (to visualize vascularization), shear-wave elastography (to measure stiffness), and time domain multi-wavelength diffuse optical tomography (to estimate tissue composition in terms of oxy- and deoxy-hemoglobin, lipid, water, and collagen concentrations). The multimodal probe arranges 8 innovative photonic modules (optodes) around the US transducer, providing capability for optical tomographic reconstruction. For more accurate estimate of lesion composition, US-assessed morphological priors can be used to guide the optical reconstructions. Each optode comprises: i) 8 picosecond pulsed laser diodes with different wavelengths, covering a wide spectral range (635-1064 nm) for good probing of the different tissue constituents; ii) a large-area (variable, up to 8.6 mm2) fast-gated digital Silicon Photomultiplier; iii) the acquisition electronics to record the distribution of time-of-flight of the re-emitted photons. The optode is the basic element of the optical part of the system, but is also a stand-alone, ultra-compact (about 4 cm3) device for time domain multi-wavelength diffuse optics, with potential application in various fields

SOLUS: a novel multimodal approach to ultrasound and diffuse optics imaging of breast cancer

A multimodal instrument for breast imaging was developed, combining ultrasound (morphology), shear wave elastography (stiffness), and time domain multiwavelength diffuse optical tomography (blood, water, lipid, collagen) to improve the non-invasive diagnosis of breast cancer

Risk Factors for Intra-Abdominal Candidiasis in Intensive Care Units: Results from EUCANDICU Study

Introduction: Intra-abdominal infections represent the second most frequently acquired infection in the intensive care unit (ICU), with mortality rates ranging from 20% to 50%. Candida spp. may be responsible for up to 10–30% of cases. This study assesses risk factors for development of intra-abdominal candidiasis (IAC) among patients admitted to ICU. Methods: We performed a case–control study in 26 European ICUs during the period January 2015–December 2016. Patients at least 18&nbsp;years old who developed an episode of microbiologically documented IAC during their stay in the ICU (at least 48&nbsp;h after admission) served as the case cohort. The control group consisted of adult patients who did not develop episodes of IAC during ICU admission. Matching was performed at a ratio of 1:1 according to time at risk (i.e. controls had to have at least the same length of ICU stay as their matched cases prior to IAC onset), ICU ward and period of study. Results: During the study period, 101 case patients with a diagnosis of IAC were included in the study. On univariate analysis, severe hepatic failure, prior receipt of antibiotics, prior receipt of parenteral nutrition, abdominal drain, prior bacterial infection, anastomotic leakage, recurrent gastrointestinal perforation, prior receipt of antifungal drugs and higher median number of abdominal surgical interventions were associated with IAC development. On multivariate analysis, recurrent gastrointestinal perforation (OR 13.90; 95%&nbsp;CI 2.65–72.82, p = 0.002), anastomotic leakage (OR 6.61; 95%&nbsp;CI 1.98–21.99, p = 0.002), abdominal drain (OR 6.58; 95%&nbsp;CI 1.73–25.06, p = 0.006), prior receipt of antifungal drugs (OR 4.26; 95%&nbsp;CI 1.04–17.46, p = 0.04) or antibiotics (OR 3.78; 95%&nbsp;CI 1.32–10.52, p = 0.01) were independently associated with IAC. Conclusions: Gastrointestinal perforation, anastomotic leakage, abdominal drain and prior receipt of antifungals or antibiotics may help to identify critically ill patients with higher probability of developing IAC. Prospective studies are needed to identify which patients will benefit from early antifungal treatment