Shotgun proteomic analyses of Pseudomonas species isolated from fish products

Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens.

Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria

This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.

XEN-45 in the management of early glaucoma surgery: A national Delphi consensus study

BACKGROUND AND OBJECTIVE

Recommendations on general glaucoma management and the use of early minimally invasive and microincisional surgeries are limited. This study aimed to establish consensus regarding glaucoma management, focusing on the XEN-45 gel stent implant.

METHODS

A Delphi consensus-driven process was used. The scientific committee led the study, identified the expert panel, and participated in elaborating the questionnaire. Fifty-one panelists were invited to complete, on a nine-point Likert scale, an 89-item questionnaire covering three topic blocks. Two Delphi rounds were performed. Consensus was achieved if ≥66.6% of panelists reached agreement or disagreement.

RESULTS

Panelists agreed on 84 items related to the patients' quality of life, the therapeutic algorithm and patient profile, and surgical and pre- and post-operative management. Panelists agreed on the suitability of XEN stent implants to treat glaucoma at different stages and for different patient profiles: young patients, elderly or with significant comorbidities, and with myopic glaucoma, patients who failed previous surgeries, and with previous poor post-operative experience. XEN surgery was considered a therapeutic step prior to classic filtering surgery and a possible first surgical option in elderly patients with comorbidities and uncontrolled intraocular pressure. XEN surgery allows the patient to return to routine daily activities faster than conventional filtering surgeries and to reduce and/or eliminate topical treatments.

CONCLUSIONS

This Delphi-driven consensus resulted in a series of general recommendations for glaucoma management, including those related to patient quality of life, therapeutic algorithm, and patient profile, and specific ones regarding the use of XEN stent gel surgery.

High-Resolution Comparative and Quantitative Proteomics of Biogenic-Amine-Producing Bacteria and Virulence Factors Present in Seafood

The presence of biogenic amines (histamine, tyramine, putrescine, and cadaverine) in seafood is a significant concern for food safety. This review describes for the first time a shotgun quantitative proteomics strategy to evaluate and compare foodborne strains of bacteria that produce biogenic amines in seafoods. This approach recognized 35,621 peptide spectrum matches, belonging to 20,792 peptides, and 4621 proteins. It allowed the determination of functional pathways and the classification of the strains into hierarchical clusters. The study identified a protein-protein interaction network involving 1160 nodes/10,318 edges. Proteins were related to energy pathways, spermidine biosynthesis, and putrescine metabolism. Label-free quantitative proteomics allowed the identification of differentially regulated proteins in specific strains such as putrescine aminotransferase, arginine decarboxylase, and l-histidine-binding protein. Additionally, 123 peptides were characterized as virulence factors and 299 peptide biomarkers were selected to identify bacterial species in fish products. This study presents the most extensive proteomic repository and progress in the science of food biogenic bacteria and could be applied in the food industry for the detection of bacterial contamination that produces histamine and other biogenic amines during food processing/storage.

Immunomodulatory effect of marine lipids on food allergy

Seafood is highly enriched in n-3 long-chain polyunsaturated fatty acids (n-3 LCPUFAs), particularly eicosapentaenoic acid (EPA, 20:5 n-3) and docosahexaenoic acid (DHA, 22:6 n-3), in contrast to the ultra-processed foods included in the modern Western diet that have high levels of n-6 linoleic acid (LA, 18:2 n-6), precursor for the pro-inflammatory n-6 arachidonic acid (ARA, 20:4 n-6). The capacity of marine lipids to reduce plasmatic triglycerides and blood pressure have been well-described. Moreover, recent studies have also raised evidence of a potential regulatory action of marine lipids on inflammation, the immune system, and food allergy (FA). FA is considered one of the main concerns to become life threatening in food safety. The prevalence of this emerging global problem has been increasing during the last two decades, especially in industrialized countries. About a 6-8% of young children and 2-4% of adults is estimated to be affected by FA. The main objective of the current study is to update the existing knowledge, but also the limitations, on the potential impact of marine lipids and their lipid mediators in regulating immunity, inflammation, and ultimately, food allergies. In particular, the focus is on the effect of marine lipids in modulating the key factors that control the sensitization and effector phases of FA, including gut microbiota (GM), inflammation, and immune system response. Results in animal models highlight the positive effect that consuming marine lipids, whether as a supplement or through seafood consumption, may have a relevant role in improving gut dysbiosis and inflammation, and preventing or reducing the severity of FA. However, more systematic studies in humans are needed to optimize such beneficial actions to each particular FA, age, and medical condition to reach an effective clinical application of marine lipids to improve FAs and their outcomes.

Efficacy and safety of combined 27-G vitrectomy and Ahmed valve using same sclerotomy site for the tube placement: A case series

We report a retrospective case series describing the feasibility and outcomes of combined 27-G minimally invasive vitrectomy surgery (MIVS) and Ahmed® Glaucoma Valve (AGV) placement. Four eyes of four patients underwent a combined MIVS using 27-G technology and AGV implantation with the tube placement in the vitreous cavity. Preoperative and postoperative data up to 12 months were collected including the type of glaucoma, intraocular pressure (IOP), glaucoma medications, and complications. All AGVs tubes were placed in the vitreous cavity using the same sclerotomy, although a slight wound enlargement was required. After one year, IOP and glaucoma medications were reduced (41.5 ± 19.1-14.5 ± 3.1 mmHg and from 3(3-3) to 1.5 (1.5-3.5). Three patients developed cystoid macular edema. The first-reported cases of combined MIVS-27-G and AGV showed a reduction of IOP and antiglaucoma medication. Placing the tube using the same sclerotomy location is feasible but a slight enlargement may be required.

Activity and stability of bifunctional perovskite/carbon-based electrodes for the removal of antipyrine by electro-Fenton process

Bifunctional perovskite/carbon-black(CB)/polytetrafluoroethylene(PTFE) electrodes for electro-generation and catalytic decomposition of hydrogen peroxide to oxidizing hydroxyl radicals have been fabricated. These electrodes were tested for electroFenton (EF) removal of antipyrine (ANT) as a model antipyretic and analgesic drug. The influence of the binder loading (20 and 40 wt % PTFE) and type of solvent (1,3-dipropanediol and water) was studied for the preparation of CB/PTFE electrodes. The electrode prepared with 20 wt % PTFE and water exhibited a low impedance and remarkable H₂O₂ electro-generation (about 1 g/L after 240 min, a production rate of ca. 6.5 mg/h·cm²). The incorporation of perovskite on CB/PTFE electrodes was also studied following two different methods: i) direct deposition on the CB/PTFE electrode surface and ii) addition in the own CB/PTFE/water paste used for the fabrication. Physicochemical and electrochemical characterization techniques were used for the electrode's characterization. The dispersion of perovskite particles in the own electrode matrix (method ii) exhibited a higher EF performance than the immobilisation onto the electrode surface (method i). EF experiments at 40 mA/cm² and pH 7 (non-acidified conditions) showed ANT and TOC removals of 30% and 17%, respectively. The increase of current intensity up to 120 mA/cm² achieved the complete removal of ANT and 92% of TOC mineralisation in 240 min. The bifunctional electrode also proved high stability and durability after 15 h of operation.

Facile one-step synthesis of a versatile nitrogen-doped hydrochar from olive oil production waste, "alperujo", for removing pharmaceuticals from wastewater

In line with the principles of zero waste and recycling, alperujo (AL) was used in this study to produce a value-added product: hydrochar (HC) with high adsorption capacity. An optimization of the hydrothermal carbonization (HTC) conditions, such as temperature, residence time, and water/solid ratio, was carried out to maximize the adsorption capacity. Eight HCs were obtained, and an in-depth comparative characterization, as well as adsorption tests of two pharmaceuticals with very different physicochemical properties (fluoxetine (FLX) and cefazolin (CFZ)), were performed. This first step allowed for elucidation of the best candidates to carry out nitrogen grafting on their surface, resulting in the HC obtained at a higher water/solid ratio and temperature, and longer residence time: 3-220ºC-2.5 h with a maximum uptake of 4.6 and 0.4 mg/g for FLX and CFZ, respectively. After that, a facile one-step, one-pot synthesis of nitrogen-doped hydrochars (N-HC) was developed to prepare a versatile bio-adsorbent with enhanced adsorption capacity. Two N-HCs were prepared using urea (U-HC) and polyethyleneimine (PEI-HC) and were intensively characterized to shed light on the adsorption mechanism. In both cases, amide groups were formed, which favored the adsorption process. PEI-HC acquired an outstanding maximum adsorption capacity of 983.84 mg/g for CFZ, and 29.31 mg/g for FLX, and the process was well described by the Freundlich isotherm and pseudo-second-order kinetic model. A co-adsorption test was performed using PEI-HC for both pharmaceuticals, finding that the adsorption process occurs in different active sites because there was no interference between the pollutants. This fact corroborates the versatility of the new bio-adsorbent synthesized.

Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria

Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs.

Glaucoma progression. Clinical practice guide

OBJECTIVE

To provide general recommendations that serve as a guide for the evaluation and management of glaucomatous progression in daily clinical practice based on the existing quality of clinical evidence.

METHODS

After defining the objectives and scope of the guide, the working group was formed and structured clinical questions were formulated following the PICO (Patient, Intervention, Comparison, Outcomes) format. Once all the existing clinical evidence had been independently evaluated with the AMSTAR 2 (Assessment of Multiple Systematic Reviews) and Cochrane "Risk of bias" tools by at least two reviewers, recommendations were formulated following the Scottish Intercollegiate Guideline network (SIGN) methodology.

RESULTS

Recommendations with their corresponding levels of evidence that may be useful in the interpretation and decision-making related to the different methods for the detection of glaucomatous progression are presented.

CONCLUSIONS

Despite the fact that for many of the questions the level of scientific evidence available is not very high, this clinical practice guideline offers an updated review of the different existing aspects related to the evaluation and management of glaucomatous progression.

Advanced glaucoma. Clinical practice guideline

OBJECTIVE

To present an update clinical practice guideline that serve as a guide for the detection, evaluation and treatment of adults patients with advanced glaucoma.

METHODS

After defining the objectives and scope of the guide, the working group was formed and structured clinical questions were formulated following the PICO (Patient, Intervention, Comparison, Outcomes) format. Once all the existing clinical evidence had been independently evaluated with the AMSTAR 2 (Assessment of Multiple systematic Rewiews) and Cochrane "Risk of bias" tools by at least two reviewers, recommendations were formulated following the Scottish Intercollegiate methodology. Guideline Network (SIGN).

RESULTS

Recommendations with their corresponding levels of evidence that may be useful in the diagnosis, monitoring and treatment of adults patients with advanced glaucoma.

CONCLUSIONS

Despite the fact that for many of the questions the level of scientific evidence available is not very high, this clinical practice guideline offers an updated review of the different existing aspects related to the evaluation and management of advanced glaucoma.

Peptidoglycan maturation controls outer membrane protein assembly

Linkages between the outer membrane of Gram-negative bacteria and the peptidoglycan layer are crucial for the maintenance of cellular integrity and enable survival in challenging environments^1–5. The function of the outer membrane is dependent on outer membrane proteins (OMPs), which are inserted into the membrane by the β-barrel assembly machine^6,7 (BAM). Growing Escherichia coli cells segregate old OMPs towards the poles by a process known as binary partitioning, the basis of which is unknown⁸. Here we demonstrate that peptidoglycan underpins the spatiotemporal organization of OMPs. Mature, tetrapeptide-rich peptidoglycan binds to BAM components and suppresses OMP foldase activity. Nascent peptidoglycan, which is enriched in pentapeptides and concentrated at septa⁹, associates with BAM poorly and has little effect on its activity, leading to preferential insertion of OMPs at division sites. The synchronization of OMP biogenesis with cell wall growth results in the binary partitioning of OMPs as cells divide. Our study reveals that Gram-negative bacteria coordinate the assembly of two major cell envelope layers by rendering OMP biogenesis responsive to peptidoglycan maturation, a potential vulnerability that could be exploited in future antibiotic design.

Peptidoglycan stem peptides in the Gram-negative bacterial cell wall regulate the insertion of essential outer membrane proteins, thus representing a potential target for antibiotic design.

Lytic transglycosylase MltG cleaves in nascent peptidoglycan and produces short glycan strands

Bacteria encase their cytoplasmic membrane with peptidoglycan (PG) to maintain the shape of the cell and protect it from bursting. The enlargement of the PG layer is facilitated by the coordinated activities of PG synthesising and -cleaving enzymes. In Escherichia coli, the cytoplasmic membrane-bound lytic transglycosylase MltG associates with PG synthases and was suggested to terminate the polymerisation of PG glycan strands. Using pull-down and surface plasmon resonance, we detected interactions between MltG from Bacillus subtilis and two PG synthases; the class A PBP1 and the class B PBP2B. Using in vitro PG synthesis assays with radio-labelled or fluorophore-labelled B. subtilis-type and/or E. coli-type lipid II, we showed that both, BsMltG and EcMltG, are lytic tranglycosylases and that their activity is higher during ongoing glycan strand polymerisation. MltG competed with the transpeptidase activity of class A PBPs, but had no effect on their glycosyltransferase activity, and produced glycan strands with a length of 7 disaccharide units from cleavage in the nascent strands. We hypothesize that MltG cleaves the nascent strands to produce short glycan strands that are used in the cell for a yet unknown process.

Regulation and function of class A Penicillin-binding proteins

Most bacteria surround their cell membrane with a peptidoglycan sacculus that counteracts the turgor and maintains the shape of the cell. Class A PBPs are bi-functional glycosyltransferase-transpeptidases that polymerize glycan chains and cross-link peptides. They have a major contribution to the total peptidoglycan synthesized during cell growth and cell division. In recent years it became apparent that class A PBPs participate in multiple protein? protein interactions and that some of these regulate their activities. In this opinion article, we review and discuss the role of class A PBPs in peptidoglycan growth and repair. We hypothesize that class A PBP function is essential in walled bacteria unless they have (a) SEDS protein(s) capable of replacing their function.

Ultrasonic processes for the advanced remediation of contaminated sediments

Sediments play a fundamental role in the aquatic environment, so that the presence of contaminants poses severe concern for the possible negative effects on both environmental and human health. Sediment remediation is thus necessary to reduce pollutant concentrations and several techniques have been studied so far. A novel approach for sediment remediation is the use of Advanced Oxidation Processes, which include ultrasound (US). This paper focuses on the study of the ultrasonic effects for the simultaneous reduction of both organic and inorganic contaminants from sediments. To this end, the US technology was investigated as a stand-alone treatment as well as in combination with an electro-kinetic (EK) process, known to be effective in the removal of heavy metals from soil and sediments. The US remediation resulted in higher organic compound degradation, with an average 88% removal, but promising desorption yields (47-84%) were achieved for heavy metals as well. The combined EK/US process was found to be particularly effective for lead. Experimental outcomes highlighted the potential of the ultrasonic technology for the remediation of contaminated sediments and addressed some considerations for the possible scale-up.

Proteomics-Based Methodologies for the Detection and Quantification of Seafood Allergens

Seafood is considered one of the main food allergen sources by the European Food Safety Authority (EFSA). It comprises several distinct groups of edible aquatic animals, including fish and shellfish, such as crustacean and mollusks. Recently, the EFSA recognized the high risk of food allergy over the world and established the necessity of developing new methodologies for its control. Consequently, accurate, sensitive, and fast detection methods for seafood allergy control and detection in food products are highly recommended. In this work, we present a comprehensive review of the applications of the proteomics methodologies for the detection and quantification of seafood allergens. For this purpose, two consecutive proteomics strategies (discovery and targeted proteomics) that are applied to the study and control of seafood allergies are reviewed in detail. In addition, future directions and new perspectives are also provided.

Stability and reproducibility of 6013 deep inspiration breath-holds in left-sided breast cancer

Purpose

Patients with left-sided breast cancer frequently receive deep inspiration breath-hold (DIBH) radiotherapy to reduce the risk of cardiac side effects. The aim of the present study was to analyze intra-breath-hold stability and inter-fraction breath-hold reproducibility in clinical practice.

Material and methods

Overall, we analyzed 103 patients receiving left-sided breast cancer radiotherapy using a surface-guided DIBH technique. During each treatment session the vertical motion of the patient was continuously measured by a surface guided radiation therapy (SGRT) system and automated gating control (beam on/off) was performed using an audio-visual patient feedback system. Dose delivery was automatically triggered when the tracking point was within a predefined gating window. Intra-breath-hold stability and inter-fraction reproducibility across all fractions of the entire treatment course were analyzed per patient.

Results

In the present series, 6013 breath-holds during beam-on time were analyzed. The mean amplitude of the gating window from the baseline breathing curve (maximum expiration during free breathing) was 15.8 mm (95%-confidence interval: [8.5–30.6] mm) and had a width of 3.5 mm (95%-CI: [2–4.3] mm). As a measure of intra-breath-hold stability, the median standard deviation of the breath-hold level during DIBH was 0.3 mm (95%-CI: [0.1–0.9] mm). Similarly, the median absolute intra-breath-hold linear amplitude deviation was 0.4 mm (95%-CI: [0.01–2.1] mm). Reproducibility testing showed good inter-fractional reliability, as the maximum difference in the breathing amplitudes in all patients and all fractions were 1.3 mm on average (95%-CI: [0.5–2.6] mm).

Conclusion

The clinical integration of an optical surface scanner enables a stable and reliable DIBH treatment delivery during SGRT for left-sided breast cancer in clinical routine.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli

The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh‐like sacculus requires the combined activity of peptidoglycan synthases and hydrolases. In Escherichia coli, the activity of two PG synthases is driven by lipoproteins anchored in the outer membrane (OM). However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the OM lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and division biosynthetic complexes based on its localization and genetic interactions. Consistent with such a role, we reconstitute PG multi‐enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that peptidoglycan regulators and adaptors are part of PG biosynthetic multi‐enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.

Application of Strategically Designed Sample Composition to the Rapid Analytical Screening of Milk Samples for Polychlorinated Biphenyls

Strategically designed sample composition (SSC) is a new technique that decreases the number of analytical determinations needed in routine screening to as few as the number of original sample specimens while providing information that is specific to them. Although this new technique has been applied to environmental studies, this paper describes its first application to food safety studies. Contamination of milk samples with polychlorinated biphenyls (PCBs) was chosen as a case study to show the usefulness and potential of the SSC technique with a fast analytical procedure that involves saponification of the samples and solid-phase microextraction of the PCBs. A total of 20 sample specimens can be analyzed in 11 determinations with excellent predictions of the positive samples and the concentration levels of the contaminants. The robustness of the strategy was investigated and demonstrated.

Optimized Protocol for the Incorporation of FDAA (HADA Labeling) for in situ Labeling of Peptidoglycan

The essential peptidoglycan (PG) layer surrounds the cytoplasmic membrane in nearly all bacteria. It is needed to maintain the shape of the cell and protect it from lysis due to high turgor. Growth of the PG layer is a complex process that involves the activities of PG synthases and hydrolases during elongation and cell division. PG growth sites can be labeled by the recently developed fluorescent D-amino acid (FDAA) probes in a range of different bacteria. FDAAs are incorporated into PG by dd-transpeptidases (Penicillin-binding proteins, PBPs) or, if present, ld-transpeptidase (LDTs). Long-pulse in situ labeling of E. coli cells with the FDAA 7-hydroxycoumarincarbonylamino-D-alanine (HADA) is expected to result in a uniform label at the side wall of cells and enhanced label at cell division sites due to the intense PG synthesis. However, we observed reduced label at mid-cell when labeling E. coli cells with HADA. We reasoned that probe incorporated at cell division sites may be removed by PG hydrolases and modified the labeling protocol to better preserve PG-incorporated HADA for fluorescence microscopy. Here, we report the optimized HADA-labeling protocol by which cells retain an enhanced HADA signal at the division septum.

Selecting the best piping arrangement for scaling-up an annular channel reactor: An experimental and computational fluid dynamics study

This study is focused on the selection of the best piping arrangement for a pilot scale annular channel reactor intended for the remediation of waters and wastewaters. Two annular channel reactors composed of a single UV lamp and distinct piping arrangements were considered: (i) a novel reactor with tangential inlet/outlet pipes - the FluHelik reactor, and (ii) a conventional Jets reactor. These two reactors were manufactured at lab scale and characterized in terms of residence time distribution (RTD), radiant power and ability to degrade aqueous solutions spiked with a model compound - 3-amino-5-methylisoxazole (AMI) - by H₂O₂/UVC and UVC processes. Computational fluid dynamics (CFD) simulations were used to assess the hydrodynamics, RTD and UV radiation intensity distribution of both reactors at pilot scale. In general, experimental results at lab scale revealed quite similar RTDs, radiant powers and AMI degradation rates for both reactors. On the other hand, CFD simulations at pilot scale revealed the generation of a helical motion of fluid around the UVC lamp in the FluHelik reactor, inducing: (i) a longer contact time between fluid particles and UV light, (ii) more intense dynamics of macromixing as a result of larger velocity gradients, turbulent intensities and dispersion of RTD values around the peak, and (iii) a more homogeneous UV radiation distribution. In addition, the design of the FluHelik reactor can favor the implementation of various reactors in series, promoting its application at industrial scale. The FluHelik reactor was chosen for scaling-up. A pre-pilot scale treatment unit containing this reactor was constructed and its feasibility was proven.

Optical Surface Scanning for Patient Positioning in Radiation Therapy: A Prospective Analysis of 1902 Fractions

Purpose/Objective:

Reproducible patient positioning remains one of the major challenges in modern radiation therapy. Recently, optical surface scanners have been introduced into clinical practice in addition to well-established positioning systems, such as room laser and skin marks. The aim of this prospective study was to evaluate setup errors of the optical surface scanner Catalyst HD (C-RAD AB) in different anatomic regions.

Material/Methods:

Between October 2016 and June 2017 a total of 1902 treatment sessions in 110 patients were evaluated. The workflow of this study included conventional setup procedures using laser-based positioning with skin marks and an additional registration of the 3-dimensional (3D) deviations detected by the Catalyst system. The deviations of the surface-based method were then compared to the corrections of cone beam computed tomography alignment which was considered as gold standard. A practical Catalyst setup error was calculated between the translational deviations of the surface scanner and the laser positioning. Two one-sided t tests for equivalence were used for statistical analysis.

Results:

Data analysis revealed total deviations of 0.09 mm ± 2.03 mm for the lateral axis, 0.07 mm ± 3.21 mm for the longitudinal axis, and 0.44 mm ± 3.08 mm vertical axis for the Catalyst system, compared to −0.06 ± 3.54 mm lateral, 0.53 ± 3.47 mm longitudinal, and 0.19 ± 3.49 mm vertical for the laser positioning compared to cone beam computed tomography. The lowest positional deviations were found in the cranial region, and larger deviations occurred in the thoracic and abdominal sites. A statistical comparison using 2 one-sided t tests showed a general concordance of the 2 methods (P ≤ 0.036), excluding the vertical direction of the abdominal region (P = 0.198).

Conclusion:

The optical surface scanner Catalyst HD is a reliable and feasible patient positioning system without any additional radiation exposure. From the head to the thoracic and abdominal region, a decrease in accuracy was observed within a comparable range for Catalyst and laser-assisted positioning.

Publisher Correction: Z-ring membrane anchors associate with cell wall synthases to initiate bacterial cell division

The original version of this Article contained errors in Figures 1 and 3. In Fig. 1b, the label 'IP-PBP3' above the second of the three blots incorrectly read 'IP-PBP1B'. In Fig. 3b, the label 'PBP1B' under the first bar of each chart incorrectly read 'PBP1A'. These errors have been corrected in both the PDF and HTML versions of the Article.

Z-ring membrane anchors associate with cell wall synthases to initiate bacterial cell division

During the transition from elongation to septation, Escherichia coli establishes a ring-like peptidoglycan growth zone at the future division site. This preseptal peptidoglycan synthesis does not require the cell division-specific peptidoglycan transpeptidase PBP3 or most of the other cell division proteins, but it does require FtsZ, its membrane-anchor ZipA and at least one of the bi-functional transglycosylase-transpeptidases, PBP1A or PBP1B. Here we show that PBP1A and PBP1B interact with ZipA and localise to preseptal sites in cells with inhibited PBP3. ZipA stimulates the glycosyltransferase activity of PBP1A. The membrane-anchored cell division protein FtsN localises at preseptal sites and stimulates both activities of PBP1B. Genes zipA and ftsN can be individually deleted in ftsA* mutant cells, but the simultaneous depletion of both proteins is lethal and cells do not establish preseptal sites. Our data support a model according to which ZipA and FtsN-FtsA have semi-redundant roles in connecting the cytosolic FtsZ ring with the membrane-anchored peptidoglycan synthases during the preseptal phase of envelope growth.

Proteins FtsZ, ZipA, and either PBP1A or PBP1B are required for the synthesis of preseptal peptidoglycan at the future cell division site in E. coli. Here, Pazos et al. provide evidence that ZipA and FtsA-FtsN connect the cytosolic FtsZ ring with the membrane-anchored PBPs.

Peptidoglycan editing by a specific LD-transpeptidase controls the muramidase-dependent secretion of typhoid toxin

Protein secretion mechanisms are essential for the virulence of most bacterial pathogens. Typhoid toxin is an essential virulence factor for Salmonella Typhi, the cause of typhoid fever in humans. This toxin is unique in that it is only produced within mammalian cells, and it must be trafficked to the extracellular space before intoxicating target cells. An essential and poorly understood aspect of this transport pathway is the secretion of typhoid toxin from the bacterium into the S. Typhi-containing vacuole. We show here that typhoid toxin secretion requires its translocation to the trans side of the peptidoglycan layer at the bacterial poles for subsequent release through the outer membrane. This translocation process depends on a specialized muramidase, the activity of which requires the localized editing of peptidoglycan by a specific ld-transpeptidase. These studies describe a protein export mechanism that is probably conserved in other bacterial species.

Real-time intra-fraction motion management in breast cancer radiotherapy: analysis of 2028 treatment sessions

BACKGROUND

Intra-fraction motion represents a crucial issue in the era of precise radiotherapy in several settings, including breast irradiation. To date, only few data exist on real-time measured intra-fraction motion in breast cancer patients. Continuous surface imaging using visible light offers the capability to monitor patient movements in three-dimensional space without any additional radiation exposure. The aim of the present study was to quantify the uncertainties of possible intra-fractional motion during breast radiotherapy.

MATERIAL AND METHODS

One hundred and four consecutive patients that underwent postoperative radiotherapy following breast conserving surgery or mastectomy were prospectively evaluated during 2028 treatment sessions. During each treatment session the patients' motion was continuously measured using the Catalyst™ optical surface scanner (C-RAD AB, Sweden) and compared to a reference scan acquired at the beginning of each session. The Catalyst system works through an optical surface imaging with light emitting diode (LED) light and reprojection captured by a charge coupled device (CCD) camera, which provide target position control during treatment delivery with a motion detection accuracy of 0.5 mm. For 3D surface reconstruction, the system uses a non-rigid body algorithm to calculate the distance between the surface and the isocentre and using the principle of optical triangulation. Three-dimensional deviations and relative position differences during the whole treatment fraction were calculated by the system and analyzed statistically.

RESULTS

Overall, the maximum magnitude of the deviation vector showed a mean change of 1.93 mm ± 1.14 mm (standard deviation [SD]) (95%-confidence interval: [0.48-4.65] mm) and a median change of 1.63 mm during dose application (beam-on time only). Along the lateral and longitudinal axis changes were quite similar (0.18 mm ± 1.06 mm vs. 0.17 mm ± 1.32 mm), on the vertical axis the mean change was 0.68 mm ± 1.53 mm. The mean treatment session time was 154 ± 53 (SD) seconds and the mean beam-on time only was 55 ± 16 s. According to Friedman's test differences in the distributions of the three possible directions (lateral, longitudinal and vertical) were significant (p < 0.01), in post-hoc analysis there were no similarities between any two of the three directions.

CONCLUSION

The optical surface imaging system is an accurate and easy tool for real-time motion management in breast cancer radiotherapy. Intra-fraction motion was reported within five millimeters in all directions. Thus, intra-fraction motion in our series of 2028 treatment sessions seems to be of minor clinical relevance in postoperative radiotherapy of breast cancer.

Heterogeneous electro-Fenton as plausible technology for the degradation of imidazolinium-based ionic liquids

Conventional water treatments are generally inadequate for degradation of emerging pollutants such as ionic liquids (ILs). The use of heterogeneous electro-Fenton (HEF) has attracted great interest, due to its ability to efficiently oxidize a wide range of organic pollutants operating in cycles or in continuous mode. In this study, the removal of a complex IL from the imidazolinium family (1,3-Bis(2,4,6-trimethylphenyl)imidazolinium chloride), by means of HEF using iron alginate spheres as catalyst has been investigated, resulting in significant TOC decay after 6 h. The optimization of the key process parameters (current, IL concentration and catalyst dosage) has been performed using a Box-Behnken experimental design and achieving 76.98% of TOC abatement in 2 h of treatment. Current proved to be a crucial parameter and high catalyst dosage is required to achieve the maximum removal. In addition, an insight about the availability of iron into the reactor and the evolution of several intermediates has been carried out by employing differential pulse voltammetry on screen-printed carbon electrodes. The evolution of the different voltammetric peaks confirmed the influence of iron release, and the generation of several iron complexes has permitted the comprehension of the degradation pathway, which has been validated by chromatographic techniques.

Bacterial Cell Wall Precursor Phosphatase Assays Using Thin-layer Chromatography (TLC) and High Pressure Liquid Chromatography (HPLC)

Peptidoglycan encases the bacterial cytoplasmic membrane to protect the cell from lysis due to the turgor. The final steps of peptidoglycan synthesis require a membrane-anchored substrate called lipid II, in which the peptidoglycan subunit is linked to the carrier lipid undecaprenol via a pyrophosphate moiety. Lipid II is the target of glycopeptide antibiotics and several antimicrobial peptides, and is degraded by 'attacking' enzymes involved in bacterial competition to induce lysis. Here we describe two protocols using thin-layer chromatography (TLC) and high pressure liquid chromatography (HPLC), respectively, to assay the digestion of lipid II by phosphatases such as Colicin M or the LXG toxin protein TelC from Streptococcus intermedius. The TLC method can also monitor the digestion of undecaprenyl (pyro)phosphate, whereas the HPLC method allows to separate the di-, mono- or unphosphorylated disaccharide pentapeptide products of lipid II.

p-Nitrophenol degradation by electro-Fenton process: Pathway, kinetic model and optimization using central composite design

The chemical process scale-up, from lab studies to industrial production, is challenging and requires deep knowledge of the kinetic model and the reactions that take place in the system. This knowledge is also useful in order to be employed for the reactor design and the determination of the optimal operational conditions. In this study, a model substituted phenol such as p-nitrophenol was degraded by electro-Fenton process and the reaction products yielded along the treatment were recorded. The kinetic model was developed using Matlab software and was based on main reactions that occurred until total mineralization which allowed predicting the degradation pathway under this advanced oxidation process. The predicted concentration profiles of p-nitrophenol, their intermediates and by-products in electro-Fenton process were validated with experimental assays and the results were consistent. Finally, based on the developed kinetic model the degradation process was optimized using central composite design taking as key parameters the ferrous ion concentration and current density.

A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial habitats of importance to human health and industry. Although these communities are often densely colonized, a broadly distributed contact-dependent mechanism of interbacterial antagonism utilized by Firmicutes has not been elucidated. Here we show that proteins belonging to the LXG polymorphic toxin family present in Streptococcus intermedius mediate cell contact- and Esx secretion pathway-dependent growth inhibition of diverse Firmicute species. The structure of one such toxin revealed a previously unobserved protein fold that we demonstrate directs the degradation of a uniquely bacterial molecule required for cell wall biosynthesis, lipid II. Consistent with our functional data linking LXG toxins to interbacterial interactions in S. intermedius, we show that LXG genes are prevalent in the human gut microbiome, a polymicrobial community dominated by Firmicutes. We speculate that interbacterial antagonism mediated by LXG toxins plays a critical role in shaping Firmicute-rich bacterial communities.

DOI:http://dx.doi.org/10.7554/eLife.26938.001

Most bacteria live in densely colonized environments, such as the human gut, in which they must constantly compete with other microbes for space and nutrients. As a result, bacteria have evolved a wide array of strategies to directly fight their neighbors. For example, some bacteria release antimicrobial compounds into their surroundings, while others ‘inject’ protein toxins directly into adjacent cells.

Bacteria can be classified into two groups known as Gram-positive and Gram-negative. Previous studies found that Gram-negative bacteria inject toxins into neighboring cells, but no comparable toxins in Gram-positive bacteria had been identified. Before a bacterium can inject molecules into an adjacent cell, it needs to move the toxins from its interior to the cell surface. It had been suggested that a transport system in Gram-positive bacteria called the Esx pathway may export toxins known as LXG proteins. However, it was not clear whether these proteins help Gram-positive bacteria to compete against other bacteria.

Whitney et al. studied the LXG proteins in Gram-positive bacteria known as Firmicutes. The experiments reveal that Firmicutes found in the human gut possess LXG genes. A Firmicute known as Streptococcus intermedius produces three LXG proteins that are all toxic to bacteria. To avoid being harmed by its own LXG proteins, S. intermedius also produces matching antidote proteins. Further experiments show that LXG proteins are exported out of S. intermedius cells and into adjacent competitor bacteria by the Esx pathway. Examining one of these LXG proteins in more detail showed that it can degrade a molecule that bacteria need to make their cell wall.

Together, these findings suggest that LXG proteins may influence the species living in many important microbial communities, including the human gut. Changes in the communities of gut microbes have been linked with many diseases. Therefore, understanding more about how the LXG proteins work may help us to develop ways to manipulate these communities to improve human health.

DOI:http://dx.doi.org/10.7554/eLife.26938.002