Genomic and molecular characterization of a novel quorum sensing molecule in Bacillus licheniformis

Quorum sensing molecules (QSMs) are involved in the regulation of complicated processes helping bacterial populations respond to changes in their cell-density. Although the QS gene cluster (comQXPA) has been identified in the genome sequence of some bacilli, the QS system B. licheniformis has not been investigated in detail, and its QSM (ComX pheromone) has not been identified. Given the importance of this antagonistic bacterium as an industrial workhorse, this study was aimed to elucidate B. licheniformis NCIMB-8874 QS. The results obtained from bioinformatics studies on the whole genome sequence of this strain confirmed the presence of essential quorum sensing-related genes. Although polymorphism was verified in three proteins of this cluster, ComQ, precursor-ComX and ComP, the transcription factor ComA was confirmed as the most conserved protein. The cell–cell communication of B. licheniformis NCIMB-8874 was investigated through further elucidation of the ComX pheromone as 13-amino acid peptide. The peptide sequence of the pheromone has been described through biochemical characterisation

Source Apportionment of Brown Carbon Absorption by Coupling Ultraviolet-Visible Spectroscopy with Aerosol Mass Spectrometry

The impact of brown carbon (BrC) on climate has been widely acknowledged but remains uncertain, because either its contribution to absorption is being ignored in most climate models or the associated mixed emission sources and atmospheric lifetime are not accounted for. In this work, we propose positive matrix factorization as a framework to apportion the contributions of individual primary and secondary organic aerosol (OA) source components of BrC absorption, by combining long-term aerosol mass spectrometry (AMS) data with concurrent ultraviolet-visible (UV-vis) spectroscopy measurements. The former feature time-depend ent factor contributions to OA mass, and the latter consist of wavelength-dependent absorption coefficients. Using this approach for a full-year case study, we estimate for the first time the mass absorption efficiency (MAE) of major light-absorbing water soluble OA components in the atmosphere. We show that secondary biogenic OA contributes negligibly to absorption despite dominating the mass concentration in the summer. In contrast, primary and secondary wood burning emissions are highly absorbing up to 500 nm. The approach allowed us to constrain their MAE within a confined range consistent with previous laboratory work, which can be used in climate models to estimate the impact of BrC from these emissions on the overall absorption.The impact of brown carbon (BrC) on climate has been widely acknowledged but remains uncertain, because either its contribution to absorption is being ignored in most climate models or the associated mixed emission sources and atmospheric lifetime are not accounted for. In this work, we propose positive matrix factorization as a framework to apportion the contributions of individual primary and secondary organic aerosol (OA) source components of BrC absorption, by combining long-term aerosol mass spectrometry (AMS) data with concurrent ultraviolet-visible (UV-vis) spectroscopy measurements. The former feature time-depend ent factor contributions to OA mass, and the latter consist of wavelength-dependent absorption coefficients. Using this approach for a full-year case study, we estimate for the first time the mass absorption efficiency (MAE) of major light-absorbing water soluble OA components in the atmosphere. We show that secondary biogenic OA contributes negligibly to absorption despite dominating the mass concentration in the summer. In contrast, primary and secondary wood burning emissions are highly absorbing up to 500 nm. The approach allowed us to constrain their MAE within a confined range consistent with previous laboratory work, which can be used in climate models to estimate the impact of BrC from these emissions on the overall absorption.Peer reviewe

Prognostic value of B cells in cutaneous melanoma

Background: Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell density and function have considerable prognostic and predictive value in skin cutaneous melanoma (SKCM). Less is known about the significance of tumor-infiltrating B cells in SKCM. Our goal was to understand the prognostic and predictive value of B cell phenotypic subsets in SKCM using RNA sequencing. Methods: We used our previously published algorithm, V'DJer, to assemble B cell receptor (BCR) repertoires and estimate diversity from short-read RNA sequencing (RNA-seq). We applied machine learning-based cellular phenotype classifiers to measure relative similarity of bulk tumor sample gene expression profiles and different B cell phenotypes. We assessed these aspects of B cell biology in 473 SKCM from the Cancer Genome Atlas Project (TCGA) as well as in RNA-seq data corresponding to tumor samples procured from patients who received CTLA-4 and PD-1 inhibitors for metastatic SKCM. Results: We found that the BCR repertoire was associated with different clinical factors, such as tumor tissue site and sex. However, increased clonality of the BCR repertoire was favorably prognostic in SKCM and was prognostic even after first conditioning on various clinical factors. Mutation burden was not correlated with any BCR measurement, and no specific mutation had an altered BCR repertoire. Lack of an assembled BCR in pre-treatment tumor tissues was associated with a lack of anti-tumor response to a CTLA-4 inhibitor in metastatic SKCM. Conclusions: These findings suggest an important prognostic and predictive role for B cell characteristics in SKCM. This has implications for melanoma immunobiology and potential development of immunogenomics features to predict survival and response to immunotherapy

Specific effects of bortezomib against experimental malignant pleural effusion: a preclinical study

BACKGROUND: We have previously shown that nuclear factor (NF)-κB activation of mouse Lewis lung carcinoma (LLC) specifically promotes the induction of malignant pleural effusions (MPE) by these cells. In the present studies we hypothesized that treatment of immunocompetent mice with bortezomib tailored to inhibit cancer cell NF-κB activation and not proliferation specifically inhibits MPE formation by LLC cells. RESULTS: Treatment of LLC cells with low concentrations of bortezomib (100 ng/ml) inhibited NF-κB activation and NF-κB-dependent transcription, but not cellular proliferation. Bortezomib treatment of immunocompetent C57BL/6 mice bearing LLC-induced subcutaneous tumors and MPEs significantly blocked tumor-specific NF-κB activation. However, bortezomib treatment did not impair subcutaneous LLC tumor growth, but was effective in limiting LLC-induced MPE. This specific effect was evidenced by significant reductions in effusion accumulation and the associated mortality and was observed with both preventive (beginning before MPE formation) and therapeutic (beginning after MPE establishment) bortezomib treatment. The favorable impact of bortezomib on MPE was associated with suppression of cardinal MPE-associated phenomena, such as inflammation, vascular hyperpermeability, and angiogenesis. In this regard, therapeutic bortezomib treatment had identical favorable results on MPE compared with preventive treatment, indicating that the drug specifically counteracts effusion formation. CONCLUSIONS: These studies indicate that proteasome inhibition tailored to block NF-κB activation of lung adenocarcinoma specifically targets the effusion-inducing phenotype of this tumor. Although the drug has limited activity against advanced solid lung cancer, it may prove beneficial for patients with MPE

The Impact of Chronic Tobacco Smoking on Retinal and Choroidal Thickness in Greek Population

Aim. To investigate the effect of more than 25-year cigarette smoking on choroidal and retinal thickness, using spectral domain optical coherence tomography (SD-OCT). Methods. Thirty-one smokers and 25 age- and sex-matched nonsmokers, serving as control group, were submitted to slit-lamp biomicroscopy and dilated fundoscopy, SD-OCT, measurements of intraocular pressure (IOP), central corneal thickness (CCT), and axial length (AL). Heidelberg Spectralis was used to calculate choroidal thickness (CT), ganglion cell complex (GCC), outer retina layers (ORL), and macular thicknesses (MT). Results. The smokers’ group consisted of 17 males and 14 females with mean age of 57.8 ± 4.5 years, while the controls’ group consisted of 14 males and 11 females with mean age of 68.0 ± 4.1 years. CT and GCC thicknesses were significantly reduced in smokers compared to control group. The differences in thicknesses of ORL were marginally significant between two groups. The measurements of MT, IOP, CCT, and AL had the same distributions between smokers and nonsmokers. Conclusions. Tobacco smoking seems to result in thinner choroid and retina compared to nonsmokers. This is the first study in literature that investigates the anatomical effect of smoking for more than 25 years on the choroid and retina

Microbial adaptation to venom is common in snakes and spiders

Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane disrupting activity against multi-drug resistant bacteria. However, bite wound infections are common in developing nations. Investigating the oral and venom microbiome of five snake and two spider species, we evidence viable microorganisms potentially unique to venom for black-necked spitting cobras (Naja nigricollis). Among these are two novel sequence types of Enterococcus faecalis misidentified by commonly used clinical biochemistry procedures as Staphylococcus; the genome sequence data of venom-specific isolates feature an additional 45 genes, at least 11 of which improve membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds

Keratoconus associated with choroidal neovascularization: a case report

<p>Abstract</p> <p>Introduction</p> <p>Keratoconus and choroidal neovascularization can occur as a result of dysfunction of the epithelium and its basement membrane.</p> <p>Case presentation</p> <p>A 17-year-old Asian man, who was diagnosed with myopic choroidal neovascularization in both eyes and who subsequently underwent intravitreal injection of ranibizumab (Lucentis^®) five times over six months, presented with further vision decrease and pain in his right eye. Examination showed corneal steepening and stromal edema in the inferocentral cornea of his right eye, both of which were indicative of advanced keratoconus with acute hydrops. Corneal topography also showed features consistent with keratoconus in his left eye. Fluorescein angiography and optical coherence tomography revealed choroidal neovascularization-associated subretinal hemorrhages and lacquer cracks in both eyes.</p> <p>Conclusion</p> <p>Keratoconus and choroidal neovascularization, possibly resulting from dysfunction of the epithelium and its basement membrane, can occur together in the same individual. This would suggest a possible connection in pathogenesis between these two conditions.</p

Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood

The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT- qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log- linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource- limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats