Fiber-assisted detection with photon number resolution

We report the development of a photon-number resolving detector based on a fiber-optical setup and a pair of standard avalanche photodiodes. The detector is capable of resolving individual photon numbers, and operates on the well-known principle by which a single mode input state is split into a large number (eight) of output modes. We reconstruct the photon statistics of weak coherent input light from experimental data, and show that there is a high probability of inferring the input photon number from a measurement of the number of detection events on a single run.Comment: 4 pages, 2 figures; Submitted for publicatio

Mimicking the extracellular matrix – a biomaterials approach to inhibit tissue fibrosis

Epithelial tissue is marked by the presence of a specialized, highly cross-linked, sheet-like extracellular matrix, the basement membrane. Tissue-invasive events, such as the epithelial-to-mesenchymal transition (EMT) - a key event in gastrulation, tissue fibrosis and cancer metastasis – are characterized by irreversible structural changes of the basement membrane through proteolytic processing by matrix metalloproteinases (MMPs). We have recently reported a previously unidentified laminin fragment that is released during EMT by MMP2 and that modulates key EMT-signalling pathways. Specifically, interaction of the laminin fragment with α3β1-integrin triggers the down-regulation of MMP2 expression, thereby constituting a cell-basement membrane-cell feedback mechanism. Inhibiting MMPs has been proposed as a strategy to prevent pathological cell migration and basement membrane breakdown in the course of EMT. Here, we explore this cell-matrix-cell feedback mechanism to target pathological EMT in the course of tissue fibrosis. We present an electrospun biomaterial that is functionalized with the recombinant laminin fragment and that can be directly interfaced with epithelial tissue to interfere with EMT pathways and inhibit MMP2 expression and activity in vitro and in vivo. We demonstrate how interaction of the functionalized synthetic membrane with peritoneal tissue inhibits mesothelial EMT in a mouse model of TGFβ-induced peritoneal fibrosis by decreasing active MMP2 levels, and propose a mechanism of how the laminin fragment acts downstream of α3β1-integrin in epithelial cells, after it is released from the basement membrane

Variations in Benthic Macroinvertebrate Communities and Biological Quality in the Aguarico and Coca River Basins in the Ecuadorian Amazon

Adequate environmental management in tropical aquatic ecosystems is imperative. Given the lack of knowledge about functional diversity and bioassessment programs, management is missing the needed evidence on pollution and its effect on biodiversity and functional ecology. Therefore, we investigated the composition and distribution of the macroinvertebrate community along two rivers. Specifically, 15 locations were sampled in the Coca and Aguarico Rivers (Ecuadorian Amazon) and the macroinvertebrates were used to indicate water quality (WQ), expressed as the Biological Monitoring Working Party Colombia (BMWP-Col) classes. Results indicate that elevation, pH, temperature, width, and water depth played an important role in the taxa and functional feeding groups (FFG) composition. The results show that diversity of taxa and FFG were generally scarce but were more abundant in good quality sites. Collector-gathers (CG) were, in general, dominant and were particularly abundant at low WQ and downstream sites. Scrapers (SC) were the second most abundant group, dominating mostly at good WQ and upstream sites. Predators (PR) were homogeneously distributed among the sites, without clear dominance, and their abundance was slightly higher in sites with medium-low WQ and downstream sites. Lastly, both shredders (SH) and collector-filterers (CF) were almost absent and were more abundant in good quality sites. The findings of this research can be used as baseline information in the studied region since a dam was constructed two years after the sampling campaign, which has been operating since. Furthermore, the results can be used to fill the knowledge gaps related to the bioassessments of other similar systems, particularly for a tropical rainforest

Systematic review finds that study data not published in full text articles have unclear impact on meta-analyses results in medical research.

A meta-analysis as part of a systematic review aims to provide a thorough, comprehensive and unbiased statistical summary of data from the literature. However, relevant study results could be missing from a meta-analysis because of selective publication and inadequate dissemination. If missing outcome data differ systematically from published ones, a meta-analysis will be biased with an inaccurate assessment of the intervention effect. As part of the EU-funded OPEN project (www.open-project.eu) we conducted a systematic review that assessed whether the inclusion of data that were not published at all and/or published only in the grey literature influences pooled effect estimates in meta-analyses and leads to different interpretation. Systematic review of published literature (methodological research projects). Four bibliographic databases were searched up to February 2016 without restriction of publication year or language. Methodological research projects were considered eligible for inclusion if they reviewed a cohort of meta-analyses which (i) compared pooled effect estimates of meta-analyses of health care interventions according to publication status of data or (ii) examined whether the inclusion of unpublished or grey literature data impacts the result of a meta-analysis. Seven methodological research projects including 187 meta-analyses comparing pooled treatment effect estimates according to different publication status were identified. Two research projects showed that published data showed larger pooled treatment effects in favour of the intervention than unpublished or grey literature data (Ratio of ORs 1.15, 95% CI 1.04-1.28 and 1.34, 95% CI 1.09-1.66). In the remaining research projects pooled effect estimates and/or overall findings were not significantly changed by the inclusion of unpublished and/or grey literature data. The precision of the pooled estimate was increased with narrower 95% confidence interval. Although we may anticipate that systematic reviews and meta-analyses not including unpublished or grey literature study results are likely to overestimate the treatment effects, current empirical research shows that this is only the case in a minority of reviews. Therefore, currently, a meta-analyst should particularly consider time, effort and costs when adding such data to their analysis. Future research is needed to identify which reviews may benefit most from including unpublished or grey data

Depletion of the gut microbiota differentially affects the impact of whey protein on high-fat diet-induced obesity and intestinal permeability

Acknowledgement: The authors thank Fiona Crispie and Amanda Brechon from Teagasc Moorepark Food Research Centre for their assistance in 16S library preparation and sequencing. The authors thank Thomaz Bastiaanssen for generating the pictures for caecal metabolomics analysis. The authors thank Joana Pereira, Eoin Sherwin and Marina Shverer for helping with the Ussing chambers experiment. S. B. was funded under the Teagasc Walsh Fellowship scheme (grant number 2016007). K. N. N. was supported by Teagasc, Ireland and in part by a research grant from Science Foundation Ireland (SFI) under grant numbers SFI/16/BBSRC/3389 and BBSRC under the grant number BB/P009875/1 (to K.N.N. and J.R.S). Funding information Teagasc Walsh Fellowship Programme, Grant/Award Number: 2016007; Science Foundation Ireland, Grant/Award Number: SFI/16/BBSRC/3389; Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/P009875/1Peer reviewedPublisher PD

Accessory proteins of the zDHHC family of S-acylation enzymes

Almost two decades have passed since seminal work in Saccharomyces cerevisiae identified zinc finger DHHC domain-containing (zDHHC) enzymes as S-acyltransferases. These enzymes are ubiquitous in the eukarya domain, with 23 distinct zDHHC-encoding genes in the human genome. zDHHC enzymes mediate the bulk of S-acylation (also known as palmitoylation) reactions in cells, transferring acyl chains to cysteine thiolates, and in so-doing affecting the stability, localisation and function of several thousand proteins. Studies using purified components have shown that the minimal requirements for S-acylation are an appropriate zDHHC enzyme-substrate pair and fatty acyl-CoA. However, additional proteins including GCP16 (also known as Golga7), Golga7b, huntingtin and selenoprotein K, have been suggested to regulate the activity, stability and trafficking of certain zDHHC enzymes. In this Review, we discuss the role of these accessory proteins as essential components of the cellular S-acylation system

Unravelling the removal mechanisms of bacterial and viral surrogates in aerobic granular sludge systems

The aerobic granular sludge (AGS) process is an effective wastewater treatment technology for organic matter and nutrient removal that has been introduced in the market rapidly. Until now, limited information is available on AGS regarding the removal of bacterial and viral pathogenic organisms present in sewage. This study focussed on determining the relation between reactor operational conditions (plug flow feeding, turbulent aeration and settling) and physical and biological mechanisms on removing two faecal surrogates, Escherichia coli and MS2 bacteriophages. Two AGS laboratory-scale systems were separately fed with influent spiked with 1.0 × 106 CFU/100 mL of E. coli and 1.3 × 108 PFU/100 mL of MS2 bacteriophages and followed during the different operational phases. The reactors contained only granular sludge and no flocculent sludge. Both systems showed reductions in the liquid phase of 0.3 Log10 during anaerobic feeding caused by a dilution factor and attachment of the organisms on the granules. Higher removal efficiencies were achieved during aeration, approximately 1 Log10 for E. coli and 0.6 Log10 for the MS2 bacteriophages caused mainly by predation. The 18S sequencing analysis revealed high operational taxonomic units (OTUs) of free-living protozoa genera Rhogostoma and Telotrochidium concerning the whole eukaryotic community. Attached ciliates propagated after the addition of the E. coli, an active contribution of the genera Epistylis, Vorticella, and Pseudovorticella was found when the reactor reached stability. In contrast, no significant growth of predators occurred when spiking the system with MS2 bacteriophages, indicating a low contribution of protozoa on the phage removal. Settling did not contribute to the removal of the studied bacterial and viral surrogates.M.L. Barrios-Hernández acknowledges the Technological Institute of Costa Rica for providing the fellowship (Grant Number 007-2014-M) to pursue her PhD programme (2016-2020) at IHE-Delft, the Netherlands. K. Mora-Cabrera acknowledges the Generalitat Valenciana (GRISOLIAP/2017/173) and the European Social Funds (BEFPI/2019/065) for their financial support

Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.

Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions

Antimicrobial Activity of the Rhizospheric Bacillus Species Isolated from Potato (Solanum tuberosum) Organic Farm Soils in the Philippines

The purpose of this study is to determine the potential of rhizospheric bacteria belonging to the genus Bacillus isolated from the organic soil of Solanum tuberosum (potato) as an untapped and promising source of novel antimicrobials to combat infections, particularly multidrug-resistant strains. The rhizospheric Bacillus species were isolated using serial dilution and aerobic cultivation. Hydrolytic exoenzyme production was determined using plate techniques, whereas antimicrobial activity was determined using the cross-streak method and agar-disc diffusion assay. The data indicate that the Bacillus isolates possess antimicrobial property against gram-positive bacterial pathogens. The activities were compared to those of the antibiotic Rifampicin as a control. Notably, several Bacillus isolates inhibited the growth of methicillin-resistant Staphylococcus aureus (MRSA). The top performing Bacillus isolates were identified by 16s rRNA gene sequence analysis, which showed the similarities of the isolates to known soil-associated and plant-growth-promoting species; B. velezensis, B. mojavensis, B. subtilis, B. sonorensis, B. tequilensis, B. clausii, B. amyloliquefaciens, B. altitudinis, and B. siamensis from those sequences available in GENBANK. The present investigation establishes the presence of antagonistic Bacillus species in S. tuberosum's rhizosphere. The findings may form the basis for further investigation of the active compounds produced by the isolates and the mechanisms underlying their antimicrobial activity, while optimizing the culture medium for efficient production of potent antimicrobial compounds to combat infectious agents may further be investigated