A compact setup for behavioral studies measuring limb acceleration

Behavioral studies contribute largely to a broader understanding of human brain mechanisms and the process of learning and memory. An established method to quantify motor learning is the analysis of thumb activity. In combination with brain stimulation, the effect of various treatments on neural plasticity and motor learning can be assessed. So far, the setups for thumb abduction measurements employed consist of bulky amplifiers and digital-to-analog devices to record the data. We developed a compact hardware setup to measure acceleration data which can be integrated into a wearable, including a sensor board and a microcontroller board which can be connected to a PC via USB. Additionally, we provide two software packages including graphical user interfaces, one to communicate with the hardware and one to evaluate and process the data. This work demonstrates the construction and application of our setup at the example of thumb acceleration measurement with a custom made glove and its use for research. Using integrated circuits, the size of the measurement devices is reduced to this wearable. It is simple to construct and can be operated easily by non-technical staff.

Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway

Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, in the presence of arginine, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle.

Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism

Glyphosate (GS) specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that converts phosphoenolpyruvate (PEP) and shikimate-3-phosphate to EPSP in the shikimate pathway of bacteria and other organisms. The inhibition of the EPSP synthase depletes the cell of the EPSP-derived aromatic amino acids as well as of folate and quinones. A variety of mechanisms (e.g., EPSP synthase modification) has been described that confer GS resistance to bacteria. Here, we show that the Burkholderia anthina strain DSM 16086 quickly evolves GS resistance by the acquisition of mutations in the ppsR gene. ppsR codes for the pyruvate/ortho-Pi dikinase PpsR that physically interacts and regulates the activity of the PEP synthetase PpsA. The mutational inactivation of ppsR causes an increase in the cellular PEP concentration, thereby abolishing the inhibition of the EPSP synthase by GS that competes with PEP for binding to the enzyme. Since the overexpression of the Escherichia coli ppsA gene in Bacillus subtilis and E. coli did not increase GS resistance in these organisms, the mutational inactivation of the ppsR gene resulting in PpsA overactivity is a GS resistance mechanism that is probably unique to B. anthina.

Low energy magnetic stimulation of the phrenic nerve - a simulation study

Peripheral magnetic stimulation is a promising assistive technique for rehabilitation. Today's magnetic stimulation devices, designed for transcranial stimulation, operate at currents of 6 kA and higher. This makes them expensive and bulky. Many motor neurons in peripheral nerves are more accessible, have large diameters, and require significantly lower field strengths for stimulation. In this work, we present a simulation environment to determine the threshold current required to trigger an action potential in phrenic nerve motor neurons for different coil geometries. An anatomical model was used for coil placement and realistic field calculations. The field distribution was calculated using the finite integration technique and then applied to a neuronal model to simulate the axon membrane dynamics. For general applicability, the coil-nerve distance and the axon diameter were varied. We show that the required current was approximately 1.3 kA for a nerve-coil distance of 35 mm, which corresponds to 20% of the available power of a commercial TMS device. By including the nearby vagus nerve in the simulations, we showed that accidental stimulation of this nerve is highly unlikely. Our results pave the way for the development of smaller, less complex, and more affordable stimulators and promise to increase the use of peripheral magnetic stimulators in clinical settings.

Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production

Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders. Comparison of "cluster-specific" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.

Helicobacter pylori Modulates Heptose Metabolite Biosynthesis and Heptose-Dependent Innate Immune Host Cell Activation by Multiple Mechanisms

Heptose metabolites including ADP-d-glycero-β-d-manno-heptose (ADP-heptose) are involved in bacterial lipopolysaccharide and cell envelope biosynthesis. Recently, heptoses were also identified to have potent proinflammatory activity on human cells as novel microbe-associated molecular patterns. The gastric pathogenic bacterium Helicobacter pylori produces heptose metabolites, which it transports into human cells through its Cag type 4 secretion system. Using H. pylori as a model, we have addressed the question of how proinflammatory ADP-heptose biosynthesis can be regulated by bacteria. We have characterized the interstrain variability and regulation of heptose biosynthesis genes and the modulation of heptose metabolite production by H. pylori, which impact cell-autonomous proinflammatory human cell activation. HldE, a central enzyme of heptose metabolite biosynthesis, showed strong sequence variability between strains and was also variably expressed between strains. Amounts of gene transcripts in the hldE gene cluster displayed intrastrain and interstrain differences, were modulated by host cell contact and the presence of the cag pathogenicity island, and were affected by carbon starvation regulator A (CsrA). We reconstituted four steps of the H. pylori lipopolysaccharide (LPS) heptose biosynthetic pathway in vitro using recombinant purified GmhA, HldE, and GmhB proteins. On the basis of one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry, the structures of major reaction products were identified as β-d-ADP-heptose and β-heptose-1-monophosphate. A proinflammatory heptose-monophosphate variant was also identified for the first time as a novel cell-active product in H. pylori bacteria. Separate purified HldE subdomains and variant HldE allowed us to uncover additional strain variation in generating heptose metabolites. IMPORTANCE Bacterial heptose metabolites, intermediates of lipopolysaccharide (LPS) biosynthesis, are novel microbe-associated molecular patterns (MAMPs) that activate proinflammatory signaling. In the gastric pathogen Helicobacter pylori, heptoses are transferred into host cells by the Cag type IV secretion system, which is also involved in carcinogenesis. Little is known about how H. pylori, which is highly strain variable, regulates heptose biosynthesis and downstream host cell activation. We report here that the regulation of proinflammatory heptose production by H. pylori is strain specific. Heptose gene cluster activity is modulated by the presence of an active cag pathogenicity island (cagPAI), contact with human cells, and the carbon starvation regulator A. Reconstitution with purified biosynthesis enzymes and purified bacterial lysates allowed us to biochemically characterize heptose pathway products, identifying a heptose-monophosphate variant as a novel proinflammatory metabolite. These findings emphasize that the bacteria use heptose biosynthesis to fine-tune inflammation and also highlight opportunities to mine the heptose biosynthesis pathway as a potential therapeutic target against infection, inflammation, and cancer.

Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry

Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high sample-throughput. However, FI-MS is prone to in-source modifications of analytes because samples are directly injected into the electrospray ionization source of a mass spectrometer without prior chromatographic separation. Here, we spiked authentic standards of 160 primary metabolites individually into an Escherichia coli metabolite extract and measured the thus derived 160 spike-in samples by FI-MS. Our results demonstrate that FI-MS can capture a wide range of chemically diverse analytes within 30 s measurement time. However, the data also revealed extensive in-source modifications. Across all 160 spike-in samples, we identified significant increases of 11,013 ion peaks in positive and negative mode combined. To explain these unknown m/z features, we connected them to the m/z feature of the (de-)protonated metabolite using information about mass differences and MS2 spectra. This resulted in networks that explained on average 49 % of all significant features. The networks showed that a single metabolite undergoes compound specific and often sequential in-source modifications like adductions, chemical reactions, and fragmentations. Our results show that FI-MS generates complex MS1 spectra, which leads to an overestimation of significant features, but neutral losses and MS2 spectra explain many of these features.

Analysis of Fast Fluorescence Kinetics of a Single Cyanobacterium Trapped in an Optical Microcavity

Photosynthesis is one the most important biological processes on earth, producing life-giving oxygen, and is the basis for a large variety of plant products. Measurable properties of photosynthesis provide information about its biophysical state, and in turn, the physiological conditions of a photoautotrophic organism. For instance, the chlorophyll fluorescence intensity of an intact photosystem is not constant as in the case of a single fluorescent dye in solution but shows temporal changes related to the quantum yield of the photosystem. Commercial photosystem analyzers already use the fluorescence kinetics characteristics of photosystems to infer the viability of organisms under investigation. Here, we provide a novel approach based on an optical Fabry-Pérot microcavity that enables the readout of photosynthetic properties and activity for an individual cyanobacterium. This approach offers a completely new dimension of information, which would normally be lost due to averaging in ensemble measurements obtained from a large population of bacteria.

The Global Influence of Sodium on Cyanobacteria in Resuscitation from Nitrogen Starvation

Dormancy and resuscitation are key to bacterial survival under fluctuating environmental conditions. In the absence of combined nitrogen sources, the non-diazotrophic model cyanobacterium Synechocystis sp. PCC 6803 enters into a metabolically quiescent state during a process termed chlorosis. This state enables the cells to survive until nitrogen sources reappear, whereupon the cells resuscitate in a process that follows a highly orchestrated program. This coincides with a metabolic switch into a heterotrophic-like mode where glycogen catabolism provides the cells with reductant and carbon skeletons for the anabolic reactions that serve to re-establish a photosynthetically active cell. Here we show that the entire resuscitation process requires the presence of sodium, a ubiquitous cation that has a broad impact on bacterial physiology. The requirement for sodium in resuscitating cells persists even at elevated CO₂ levels, a condition that, by contrast, relieves the requirement for sodium ions in vegetative cells. Using a multi-pronged approach, including the first metabolome analysis of Synechocystis cells resuscitating from chlorosis, we reveal the involvement of sodium at multiple levels. Not only does sodium play a role in the bioenergetics of chlorotic cells, as previously shown, but it is also involved in nitrogen compound assimilation, pH regulation, and synthesis of key metabolites.

Homeostasis of the biosynthetic E. coli metabolome

Metabolite concentrations vary across conditions and such metabolome changes are relevant for metabolic and gene regulation. Here, we used LC-MS/MS to explore metabolite concentration changes in Escherichia coli. We measured 101 primary metabolites in 19 experimental conditions that include various nutrients and stresses. Many metabolites showed little variation across conditions and only few metabolites correlated with the growth rate. The least varying metabolites were nucleotides (e.g. UTP had 10% variation) and amino acids (e.g. methionine had 13% variation). These results show that E. coli maintains protein and RNA building blocks within narrow concentration ranges, thus indicating that many feedback mechanisms in biosynthetic pathways contribute to end-product homeostasis.

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101 E coli metabolites were measured in 19 conditions

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Biosynthetic end-products vary little between conditions

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Few metabolites correlate with the growth rate

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Metabolome data identify active regulatory metabolites

Hybrid Chemoenzymatic Synthesis of C7-Sugars for Molecular Evidence of in vivo Shikimate Pathway Inhibition

The design of distinctive chemical synthesis strategies aims for the most efficient routes towards versatile compounds in drug target studies. Here, we establish a powerful hybrid synthetic approach of total chemical and chemoenzymatic synthesis to efficiently obtain various 7‐deoxy‐sedoheptulose (7dSh, 1) analogues, unique C₇ sugars, for structure‐activity relationship studies. 7dSh (1) is a rare microbial sugar with in planta herbicidal activity. As natural antimetabolite of 3‐dehydroquinate synthase (DHQS), 7dSh (1) inhibits the shikimate pathway, which is essential for the synthesis of aromatic amino acids in bacteria, fungi, and plants, but absent in mammals. As glyphosate, the most used chemical herbicide faces restrictions worldwide, DHQS has gained more attention as valid target of herbicides and antimicrobial agents. In vitro and in vivo analyses of the C₇‐deoxysugars confirm DHQS as enzymatic target, highlight the crucial role of uptake for inhibition and add molecular aspects to target mechanism studies of C₇‐sugars as our contribution to global efforts for alternative weed‐control strategies.

Strong coupling between an optical microcavity and photosystems in single living cyanobacteria

The first step in photosynthesis is an extremely efficient energy transfer mechanism that led to the debate to which extent quantum coherence may be involved in the energy transfer between the photosynthetic pigments. In search of such a coherent behavior, we have embedded living cyanobacteria between the parallel mirrors of an optical microresonator irradiated with low intensity white light. As a consequence, we observe vacuum Rabi splitting in the transmission and fluorescence spectra as a result of strong light matter coupling of the chlorophyll a molecules in the photosystems (PSs) and the cavity modes. The Rabi-splitting scales with the number of the PSs chlorophyll a pigments involved in strong coupling indicating a delocalized polaritonic state. Our data provide evidence that a delocalized polaritonic state can be established between the chlorophyll a molecule of the PSs in living cyanobacterial cells at ambient conditions in a microcavity.

In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria

7-Deoxysedoheptulose (7dSh) is a bioactive deoxy-sugar actively excreted by the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) but also Streptomyces setonensis. In our previous publications we have shown that in S. elongatus, 7dSh is exclusively synthesized by promiscuous enzyme activity from an inhibitory by-product of radical SAM enzymes, without a specific gene cluster being involved. Additionally, we showed that 7dSh inhibits the growth of cyanobacteria, but also the growth of plants and fungi, presumably by inhibiting the 3-dehydroquinate synthase (DHQS), the second enzyme of the shikimate pathway, as the substrate of this enzyme strongly accumulates in cells treated with 7dSh. In this study, by using purified DHQS of Anabaena variabilis ATCC 29413 (A. variabilis) we biochemically confirmed that 7dSh is a competitive inhibitor of this enzyme. By analyzing the effect of 7dSh on a subset of cyanobacteria from all the five subsections, we identified different species whose growth was inhibited by 7dSh. We also found that in some of the susceptible cyanobacteria import of 7dSh is mediated by structurally different and promiscuous transporters: 7dSh can be taken up by the fructose ABC-transporter in A. variabilis and via the glucose permease in Synechocystis sp. PCC 6803 (Synechocystis sp.). In both cases, an effective uptake and thereby intracellular enrichment of 7dSh was essential for the inhibitory activity. Importantly, spontaneous mutations in the sugar transporters of A. variabilis and Synechocystis sp. not only disabled growth of the two strains on fructose and glucose, respectively, but also almost abolished their sensitivity to 7dSh. Although we have clearly shown in these examples that the effective uptake plays an essential role in the inhibitory effect of 7dSh, questions remain about how 7dSh resistance works in other (cyano)bacteria. Also, the involvement of a putative ribokinase in 7dSh resistance in the producer strain S. elongatus remained to be further investigated. Overall, these data establish 7dSh as the first allelochemical targeting the shikimate pathway in other cyanobacteria and plants and suggest a role of 7dSh in niche competition.

5-Deoxyadenosine Metabolism: More than "Waste Disposal"

5-Deoxyadenosine (5dAdo) is a by-product of many radical SAM enzyme reactions in all domains of life, and an inhibitor of the radical SAM enzymes themselves. Hence, pathways to recycle or dispose of this toxic by-product must exist but remain largely unexplored. In this review, we discuss the current knowledge about canonical and atypical 5dAdo salvage pathways that have been characterized in the last years. We highlight studies that report on how, in certain organisms, the salvage of 5dAdo via specific pathways can confer a growth advantage by providing either intermediates for the synthesis of secondary metabolites or a carbon source for the synthesis of metabolites of the central carbon metabolism. Yet, an alternative recycling route exists in organisms that use 5dAdo as a substrate to synthesize and excrete 7-deoxysedoheptulose, an allelopathic inhibitor of one enzyme of the shikimate pathway, thereby competing for their own niche. Remarkably, most steps of 5dAdo salvage are the result of the activity of promiscuous enzymes. This strategy enables even organisms with a small genome to synthesize bioactive compounds which they can deploy under certain conditions to gain a competitive growth advantage. We conclude emphasizing that, unexpectedly, 5dAdo salvage pathways seem not to be ubiquitously present, raising questions about the fate of such a toxic by-product in those species. This observation also suggests that additional 5dAdo salvage pathways, possibly relying on the activity of promiscuous enzymes, may exist. The future challenge will be to bring to light these "cryptic" 5dAdo recycling pathways.

Continuous capture scale down model: A comparison of a continuous and a discrete approach

In continuous pharmaceutical manufacturing, consisting of a perfused batch fermentation and integrated continuous downstream processing, the continuous capture is the linking unit operation. For the development of this unit operation, scale-down models (SDMs) are crucial, whereas discrete, noncontinuous SDMs are preferred over continuous SDM due to their simplistic nature, reduced material consumption, and shorter operation time. The results presented in this study show the suitability of a discrete SDM approach, compared to a continuous SDM for a continuous protein A purification step.

Flow management strategies for a connected purification process

This paper describes different flow management strategies for a connected purification process which includes two polishing steps, virus filtration and tangential flow filtration. Connecting these unit operations avoids introducing large intermediate product pool vessels in small manufacturing facilities. However, a connected-downstream process requires an elaborate control strategy enabling multiple unit operations to function as a single unit. The key strategy to enable the connected-downstream process is a robust management of flow disparities among unit operations. During a typical ultrafiltration step, product concentration increases as mass is added to the retentate tank, leading to a permeate flux decline. In a connected-downstream process, the inlet stream is directly connected to the prior unit operation and any decrease in permeate flow rate could cause a flow disparity. Four different flow management approaches are proposed to manage potential flow disparities and their advantages and challenges are discussed. Bench-scale results of these strategies are presented and evaluated.

Development of the materials analysis and particle probe for Proto-MPEX

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) is a linear plasma device being used in plasma source research and development (R&D) for the proposed MPEX. Once the R&D is completed, this device can also be used to perform plasma-material interaction studies. To perform these studies, a new materials analysis and particle probe (MAPP) has been constructed. The MAPP's components are a sample holder and manipulator and a custom vacuum chamber with ports to facilitate surface chemistry diagnostics. The MAPP's overall design enables rapid sample turnaround and in vacuo surface characterization. The surface analysis vacuum chamber has ports for x-ray photoelectron spectroscopy, thermal desorption spectroscopy, back-scatter ion scattering spectroscopy, forward-scatter ion scattering spectroscopy, and direct recoil spectroscopy. The sample manipulator and holder is a Lesker/UHV Multi-Centre Analytical Stage, which is used to place the samples in the exposure region of the Proto-MPEX or the analysis position in the MAPP vacuum chamber. The sample holder has a heating capability of up to 1200 °C for heated exposure and for desorption studies. In this work, we present the MAPP's design and the first tungsten sample exposure with ex situ analysis that shows a surface deposition layer on the exposed target, highlighting the need for additional in situ measurements on the Proto-MPEX.

Acute acral eruptions in children during the COVID-19 pandemic: Characteristics of 103 children and their family clusters

Background

A marked increase in frequency of acute acral eruptions (AAE) was observed in children during the COVID-19 pandemic in the spring period.

Objectives

In this observational multicenter study, based on children with AAE, we aimed to assess the proportion of household members possibly infected by SARS-CoV-2.

Methods

We collected data from all children observed with AAE, prospectively from April 7, 2020 to June 22, 2020, and retrospectively since February 28, 2020. The primary outcome was the household infection rate, defined as the proportion of family clusters having at least one member with COVID-19 infection other than the child with AAE (“index child”). The definition of a case was based on characteristic clinical signs and a positive PCR or serology.

Results

The study included 103 children in 10 French departments and in Quebec. The median age was 13 years and the interquartile range [8–15], with a female-to-male ratio of 1/1.15. In children with AAE, all PCR tests were negative (n = 18), and serology was positive in 2/14 (14.3%) cases. We found no significant anomalies in the lab results. A total of 66 of the 103 families (64.1%) of included children had at least one other infected member apart from the index child. The total number of household members was 292, of whom 119 (40.8%) were considered possibly infected by SARS-CoV-2. No index children or households exhibited severe COVID-19.

Discussion

Among the 103 households included, 64.1% had at least one infected member. Neither children with AAE nor their households showed severe COVID-19.

A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism

5-Deoxyadenosine (5dAdo) is the byproduct of many radical S-adenosyl-l-methionine enzyme reactions in all domains of life. 5dAdo is also an inhibitor of the radical S-adenosyl-l-methionine enzymes themselves, making it necessary for cells to construct pathways to recycle or dispose of this toxic metabolite. However, the specific pathways involved have long remained unexplored. Recent research demonstrated a growth advantage in certain organisms by using 5dAdo or intermediates as a sole carbon source and elucidated the corresponding salvage pathway. We now provide evidence using supernatant analysis by GC-MS for another 5dAdo recycling route. Specifically, in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus), the activity of promiscuous enzymes leads to the synthesis and excretion first of 5-deoxyribose and subsequently of 7-deoxysedoheptulose. 7-Deoxysedoheptulose is an unusual deoxy-sugar, which acts as an antimetabolite of the shikimate pathway, thereby exhibiting antimicrobial and herbicidal activity. This strategy enables organisms with small genomes and lacking canonical gene clusters for the synthesis of secondary metabolites, like S. elongatus, to produce antimicrobial compounds from primary metabolism and enzymatic promiscuity. Our findings challenge the view of bioactive molecules as sole products of secondary metabolite gene clusters and expand the range of compounds that microorganisms can deploy to compete for their ecological niche.

Microplastic ingestion by Atlantic chub mackerel (Scomber colias) in the Canary Islands coast

In recent years, due to the increasing concerns about their negative impact on wildlife and possible toxicity to living organisms (including humans), microplastics have become the subject of intense investigations. In the ocean, microplastics can be easily ingested by numerous marine organisms because of their small size (<5 mm). The Northwest African upwelling system is an important fishery area, and the present study is the first one in the region to reveal the presence of microplastic particles in the digestive tract of Atlantic chub mackerel (Scomber colias). From the 120 examined fish gastrointestinal tracts, 78.3% contained some type of microplastics, 74.2% contained fibres, 17.5% plastic fragments, and 16.7% paint. More studies are needed on fish, but S. colias is a candidate for being a good indicator of microplastic contamination in the region.

Cyanobacterial antimetabolite 7-deoxy-sedoheptulose blocks the shikimate pathway to inhibit the growth of prototrophic organisms

Antimetabolites are small molecules that inhibit enzymes by mimicking physiological substrates. We report the discovery and structural elucidation of the antimetabolite 7-deoxy-sedoheptulose (7dSh). This unusual sugar inhibits the growth of various prototrophic organisms, including species of cyanobacteria, Saccharomyces, and Arabidopsis. We isolate bioactive 7dSh from culture supernatants of the cyanobacterium Synechococcus elongatus. A chemoenzymatic synthesis of 7dSh using S. elongatus transketolase as catalyst and 5-deoxy-d-ribose as substrate allows antimicrobial and herbicidal bioprofiling. Organisms treated with 7dSh accumulate 3-deoxy-d-arabino-heptulosonate 7-phosphate, which indicates that the molecular target is 3-dehydroquinate synthase, a key enzyme of the shikimate pathway, which is absent in humans and animals. The herbicidal activity of 7dSh is in the low micromolar range. No cytotoxic effects on mammalian cells have been observed. We propose that the in vivo inhibition of the shikimate pathway makes 7dSh a natural antimicrobial and herbicidal agent.

Mother Nature is a valuable resource for the discovery of drug and agricultural chemicals. Here, the authors show that 7-deoxy-sedoheptulose produced by a cyanobacterium is an antimicrobial and herbicidal compound that acts through inhibition of 3-dehydroquniate synthase in the shikimate pathway.

ABCB1 and ABCG2 drug transporters are differentially expressed in non-small cell lung cancers (NSCLC) and expression is modified by cisplatin treatment via altered Wnt signaling

BACKGROUND

Lung cancer (LC) is still the most common cause of cancer related deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for 85% of all LC cases but is not a single entity. It is now accepted that, apart from the characteristic driver mutations, the unique molecular signatures of adeno- (AC) and squamous cell carcinomas (SCC), the two most common NSCLC subtypes should be taken into consideration for their management. Therapeutic interventions, however, frequently lead to chemotherapy resistance highlighting the need for in-depth analysis of regulatory mechanisms of multidrug resistance to increase therapeutic efficiency.

METHODS

Non-canonical Wnt5a and canonical Wnt7b and ABC transporter expressions were tested in primary human LC (n = 90) resections of AC and SCC. To investigate drug transporter activity, a three dimensional (3D) human lung aggregate tissue model was set up using differentiated primary human lung cell types. Following modification of the canonical, beta-catenin dependent Wnt pathway or treatment with cisplatin, drug transporter analysis was performed at mRNA, protein and functional level using qRT-PCR, immunohistochemistry, immune-fluorescent staining and transport function analysis.

RESULTS

Non-canonical Wnt5a is significantly up-regulated in SCC samples making the microenvironment different from AC, where the beta-catenin dependent Wnt7b is more prominent. In primary cancer tissues ABCB1 and ABCG2 expression levels were different in the two NSCLC subtypes. Non-canonical rhWnt5a induced down-regulation of both ABCB1 and ABCG2 transporters in the primary human lung aggregate tissue model recreating the SCC-like transporter pattern. Inhibition of the beta-catenin or canonical Wnt pathway resulted in similar down-regulation of both ABC transporter expression and function. In contrast, cisplatin, the frequently used adjuvant chemotherapeutic agent, activated beta-catenin dependent signaling that lead to up-regulation of both ABCB1 and ABCG2 transporter expression and activity.

CONCLUSIONS

The difference in the Wnt microenvironment in AC and SCC leads to variations in ABC transporter expression. Cisplatin via induction of canonical Wnt signaling up-regulates ABCB1 and ABCG2 drug transporters that are not transporters for cisplatin itself but are transporters for drugs that are frequently used in combination therapy with cisplatin modulating drug response.

Enantioselective Reduction of Citral Isomers in NCR Ene Reductase: Analysis of an Active-Site Mutant Library

A deeper understanding of the >99 % S-selective reduction of both isomers of citral catalyzed by NCR ene reductase was achieved by active-site mutational studies and docking simulation. Though structurally similar, the E/Z isomers of citral showed a significantly varying selectivity response to introduced mutations. Although it was possible to invert (E)-citral reduction enantioselectivity to ee 46 % (R) by introducing mutation W66A, for (Z)-citral it remained ≥88 % (S) for all single-residue variants. Residue 66 seems to act as a lever for opposite binding modes. This was underlined by a W66A-based double-mutant library that enhanced the (E)-citral derived enantioselectivity to 63 % (R) and significantly lowered the S selectivity for (Z)-citral to 44 % (S). Formation of (R)-citronellal from an (E/Z)-citral mixture is a desire in industrial (-)-menthol synthesis. Our findings pave the way for a rational enzyme engineering solution.

Increased Wnt5a in squamous cell lung carcinoma inhibits endothelial cell motility

BACKGROUND

Angiogenesis is important both in normal tissue function and disease and represents a key target in lung cancer (LC) therapy. Unfortunately, the two main subtypes of non-small-cell lung cancers (NSCLC) namely, adenocarcinoma (AC) and squamous cell carcinoma (SCC) respond differently to anti-angiogenic e.g. anti-vascular endothelial growth factor (VEGF)-A treatment with life-threatening side effects, often pulmonary hemorrhage in SCC. The mechanisms behind such adverse reactions are still largely unknown, although peroxisome proliferator activator receptor (PPAR) gamma as well as Wnt-s have been named as molecular regulators of the process. As the Wnt microenvironments in NSCLC subtypes are drastically different, we hypothesized that the particularly high levels of non-canonical Wnt5a in SCC might be responsible for alterations in blood vessel growth and result in serious adverse reactions.

METHODS

PPARgamma, VEGF-A, Wnt5a, miR-27b and miR-200b levels were determined in resected adenocarcinoma and squamous cell carcinoma samples by qRT-PCR and TaqMan microRNA assay. The role of PPARgamma in VEGF-A expression, and the role of Wnts in overall regulation was investigated using PPARgamma knock-out mice, cancer cell lines and fully human, in vitro 3 dimensional (3D), distal lung tissue aggregates. PPARgamma mRNA and protein levels were tested by qRT-PCR and immunohistochemistry, respectively. PPARgamma activity was measured by a PPRE reporter system. The tissue engineered lung tissues expressing basal level and lentivirally delivered VEGF-A were treated with recombinant Wnts, chemical Wnt pathway modifiers, and were subjected to PPARgamma agonist and antagonist treatment.

RESULTS

PPARgamma down-regulation and VEGF-A up-regulation are characteristic to both AC and SCC. Increased VEGF-A levels are under direct control of PPARgamma. PPARgamma levels and activity, however, are under Wnt control. Imbalance of both canonical (in AC) and non-canonical (in SCC) Wnts leads to PPARgamma down-regulation. While canonical Wnts down-regulate PPARgamma directly, non-canonical Wnt5a increases miR27b that is known regulator of PPARgamma.

CONCLUSION

During carcinogenesis the Wnt microenvironment alters, which can downregulate PPARgamma leading to increased VEGF-A expression. Differences in the Wnt microenvironment in AC and SCC of NSCLC lead to PPARgamma decrease via mechanisms that differentially alter endothelial cell motility and branching which in turn can influence therapeutic response.

Design of a digital holography system for PFC erosion measurements on Proto-MPEX

A project has been started at ORNL to develop a dual-wavelength digital holography system for plasma facing component erosion measurements on prototype material plasma exposure experiment. Such a system will allow in situ real-time measurements of component erosion. Initially the system will be developed with one laser, and first experimental laboratory measurements will be made with the single laser system. In the second year of development, a second CO₂ laser will be added and measurements with the dual wavelength system will begin. Adding the second wavelength allows measurements at a much longer synthetic wavelength.

First results from the Thomson scattering diagnostic on proto-MPEX

A Thomson scattering (TS) diagnostic has been successfully implemented on the prototype Material Plasma Exposure eXperiment (Proto-MPEX) at Oak Ridge National Laboratory. The diagnostic collects the light scattered by plasma electrons and spectroscopically resolves the Doppler shift imparted to the light by the velocity of the electrons. The spread in velocities is proportional to the electron temperature, while the total number of photons is proportional to the electron density. TS is a technique used on many devices to measure the electron temperature (T_e) and electron density (n_e) of the plasma. A challenging aspect of the technique is to discriminate the small number of Thomson scattered photons against the large peak of background photons from the high-power laser used to probe the plasma. A variety of methods are used to mitigate the background photons in Proto-MPEX, including Brewster angled windows, viewing dumps, and light baffles. With these methods, first results were measured from argon plasmas in Proto-MPEX, indicating T_e ∼ 2 eV and n_e ∼ 1 × 10¹⁹ m^-3. The configuration of the Proto-MPEX TS diagnostic will be described and plans for improvement will be given.

Heat flux estimates of power balance on Proto-MPEX with IR imaging

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) at Oak Ridge National Laboratory (ORNL) is a precursor linear plasma device to the Material Plasma Exposure eXperiment (MPEX), which will study plasma material interactions (PMIs) for future fusion reactors. This paper will discuss the initial steps performed towards completing a power balance on Proto-MPEX to quantify where energy is lost from the plasma, including the relevant diagnostic package implemented. Machine operating parameters that will improve Proto-MPEX's performance may be identified, increasing its PMI research capabilities.

Advanced Thomson scattering system for high-flux linear plasma generator

An advanced Thomson scattering system has been built for a linear plasma generator for plasma surface interaction studies. The Thomson scattering system is based on a Nd:YAG laser operating at the second harmonic and a detection branch featuring a high etendue (f/3) transmission grating spectrometer equipped with an intensified charged coupled device camera. The system is able to measure electron density (n(e)) and temperature (T(e)) profiles close to the output of the plasma source and, at a distance of 1.25 m, just in front of a target. The detection system enables to measure 50 spatial channels of about 2 mm each, along a laser chord of 95 mm. By summing a total of 30 laser pulses (0.6 J, 10 Hz), an observational error of 3% in n(e) and 6% in T(e) (at n(e) = 9.4 × 10(18) m(-3)) can be obtained. Single pulse Thomson scattering measurements can be performed with the same accuracy for n(e) > 2.8 × 10(20) m(-3). The minimum measurable density and temperature are n(e) < 1 × 10(17) m(-3) and T(e) < 0.07 eV, respectively. In addition, using the Rayleigh peak, superimposed on the Thomson scattered spectrum, the neutral density (n(0)) of the plasma can be measured with an accuracy of 25% (at n(0) = 1 × 10(20) m(-3)). In this report, the performance of the Thomson scattering system will be shown along with unprecedented accurate Thomson-Rayleigh scattering measurements on a low-temperature argon plasma expansion into a low-pressure background.

The new WMO RA VI Regional Climate Centre Node on Climate Monitoring

Abstract. Regional Climate Centres are institutions with the capacity and mandate by WMO to develop high quality regional-scale products using global products, national input and incorporating regional information. Recently a pilot network of three Regional Climate Centre consortia was established for the WMO region RA VI (Europe and Middle East). Germany (Deutscher Wetterdienst) has taken the responsibility of the Regional Climate Centre Node on Climate Monitoring. The main basic functions of this centre are the publication of annual and monthly climate diagnostic bulletins, monthly monitoring maps, monitoring of significant events, implementation of a climate watch system, capacity building and offering reference climatologies and trend maps.

Suppression of tritium retention in remote areas of ITER by nonperturbative reactive gas injection

A technique based on reactive gas injection in the afterglow region of the divertor plasma is proposed for the suppression of tritium-carbon codeposits in remote areas of ITER when operated with carbon-based divertor targets. Experiments in a divertor simulator plasma device indicate that a 4  nm/min deposition can be suppressed by addition of 1  Pa·m³ s⁻¹ ammonia flow at 10 cm from the plasma. These results bolster the concept of nonperturbative scavenger injection for tritium inventory control in carbon-based fusion plasma devices, thus paving the way for ITER operation in the active phase under a carbon-dominated, plasma facing component background.

EPR spectroscopy and electrospray ionization mass spectrometry reveal distinctive features of the iron site in leukocyte 12-lipoxygenase

The procedure for the expression and purification of recombinant porcine leukocyte 12-lipoxygenase using Escherichia coli [K.M. Richards, L.J. Marnett, Biochemistry 36 (1997) 6692-6699] was updated to make it possible to produce enough protein for physical measurements. Electrospray ionization tandem mass spectrometry confirmed the amino acid sequence. The redox properties of the cofactor iron site were examined by EPR spectroscopy at 25K following treatment with a variety of fatty acid hydroperoxides. Combination of the enzyme in a stoichiometric ratio with the hydroperoxides led to a g4.3 signal in EPR spectra instead of the g6 signal characteristic of similarly treated soybean lipoxygenase-1. Native 12-lipoxygenase was also subjected to electrospray ionization mass spectrometry. There was evidence for loss of the mass of an iron atom from the protein as the pH was lowered from 5 to 4. Native ions in these samples indicated that iron was lost without the protein completely unfolding.

Construction of a five-marker protein-based model for stage-independent assessment of prognosis in breast cancer

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Background: While the TNM method for assessment of stage in breast cancer is simple and robust, molecular methods for limited patient subsets are gaining popularity (i.e Oncotype Dx or Mammaprint). We hypothesized that multiplexed quantitative measurement of proteins known to be involved in breast cancer signaling pathways of growth, proliferation, survival, and metastasis can enhance clinical methods of predicting prognosis in all patients. Methods: We assessed the expression of twenty-three proteins (ER, PR, EGFR, HER2, HER3, HER4, ERK, PTEN, PI3Kp85α, PI3Kp110α, p27/Kip1,EIF4E, FOXO3,AKT1, AKT2, AKT3, MYC, cyclinD1, FOXO1, mTOR, p70S6Kb, NFkB and BCL2) in four subcellular compartments by automated quantitative analysis of protein expression (AQUA) on tissue microarrays of the archival Yale breast cancer cohort (n=676). To project future performance of these markers including clinicopathological parameters, we constructed univariate and multivariate logistic regression models using leave-one-out cross-validation and calculated prediction error (PE) estimates of each model's value to predict a binary endpoint of 10 year survival. In addition, we constructed univariate and multivariate Cox models of ten year disease specific survival (DSS). Results: By Cox univariate analysis, ER, PR, PTEN, and BCL2 were directly correlated with DSS, while FOXO1, HER2, HER3, and PI3Kp110α were inversely correlated with DSS. A five-variable logistic regression model of 10 year survival including nuclear AKT1, BCL2, nuclear FOXO1, cytoplasmic mTOR, and nuclear p70S6Kb (prediction error= .274) surpasses performance of TNM staging (PE=.367) and the Nottingham Prognostic Index (PE=.326). The same model is associated with 10-year DSS by Cox proportional hazard (p=<.00001) independent of TNM stage and NPI. Conclusions: Our protein-based, multiplexed approach to prognostic classification was superior to traditional methods (TNM or NPI) and single biomarkers in this retrospective cohort. Current outcomes are influenced by modern therapies, limiting the direct impact of this analysis. However, molecular profiling of primary tumor linked to outcome paves the way for the incorporation of new prognostic models into prospective studies.

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Monitoring Alfvén cascades with interferometry on the JET Tokamak

A microwave interferometry technique is applied for the first time for detecting a discrete spectrum of Alfvén cascade (AC) eigenmodes excited with fast ions in reversed magnetic shear plasmas of the Joint European Torus. The interferometry measurements of plasma density perturbations associated with ACs show an unprecedented frequency and time resolution superior to that obtained with external magnetic coils. The measurements of ACs are used for monitoring the evolution of the safety factor and density of rational magnetic surfaces in the region of maximum plasma current.