Regulation of carbon dioxide fixation in the chemoautotroph Xanthobacter flavus

Autotrophic bacteria and plants are able to convert the greenhouse gas carbon dioxide, CO2, into cell material. Although there are a number of metabolic pathways supporting autotrophic growth, the Calvin cycle is the most widely distributed of these. CO2 fixation requires a large amount of energy which originates from light or chemical oxidation, supporting respectively photoautotrophic or chemoautotrophic growth.... Zie: Chapter

Use of QuEChERS as a manual and automated high-throughput protocol for investigating environmental matrices

Environmental pollution has strong links to adverse human health outcomes with risks of pollution through production, use, ineffective wastewater (WW) remediation, and/or leachate from landfill. 'Fit-for-purpose' monitoring approaches are critical for better pollution control and mitigation of harm, with current sample preparation methods for complex environmental matrices typically time-consuming and labour intensive, unsuitable for high-throughput screening. This study has shown that a modified 'Quick Easy Cheap Effective Rugged and Safe' (QuEChERS) sample preparation is a viable alternative for selected environmental matrices required for pollution monitoring (e.g. WW effluent, treated sludge cake and homogenised biota tissue). As a manual approach, reduced extraction times (hours to ∼20 min/sample) with largely reproducible (albeit lower) recoveries of a range of pharmaceuticals and biocidal surfactants have been reported. Its application has shown clear differentiation of matrices via chemometrics, and the measurement of pollutants of interest to the UK WW industry at concentrations significantly above suggested instrument detection limits (IDL) for sludge, indicating insufficient removal and/or bioaccumulation during WW treatment. Furthermore, new pollutant candidates of emerging concern were identified - these included detergents, polymers and pharmaceuticals, with quaternary ammonium compound (QAC) biocides observed at 2.3-70.4 mg/kg, and above levels associated with priority substances for environmental quality regulation (EQSD). Finally, the QuEChERS protocol was adapted to function as a fully automated workflow, further reducing the resource to complete both the preparation and analysis to 62%), and when applied to a largely un-investigated clay matrix, acceptable recovery (88.0-131.1%) and precision (≤10.3% RSD) for the tested pharmaceuticals and biocides was maintained. Therefore, this preliminary study has shown the successful application of a high-throughput QuEChERS protocol across a range of environmental solids for potential deployment in a regulated laboratory

Complimentary protein extraction methods increase the identification of the Park Grass Experiment metaproteome

Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of “protein metabolism”, “membrane transport”, “carbohydrate metabolism”, “respiration” “ribosomal and nitrogen cycle” proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phylum level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. The newly identified Park Grass metaproteome thus provides a baseline on which future targeted studies of important soil processes and their control can be built

Negatively-Marked MCQ Assessments That Reward Partial Knowledge Do Not Introduce Gender Bias Yet Increase Student Performance and Satisfaction and Reduce Anxiety

Multiple-choice question (MCQ) examinations are increasingly used as the assessment method of theoretical knowledge in large class-size modules in many life science degrees. MCQ-tests can be used to objectively measure factual knowledge, ability and high-level learning outcomes, but may also introduce gender bias in performance dependent on topic, instruction, scoring and difficulty. The ‘Single Answer’ (SA) test is often used in which students choose one correct answer, in which they are unable to demonstrate partial knowledge. Negatively marking eliminates the chance element of guessing but may be considered unfair. Elimination testing (ET) is an alternative form of MCQ, which discriminates between all levels of knowledge, while rewarding demonstration of partial knowledge. Comparisons of performance and gender bias in negatively marked SA and ET tests have not yet been performed in the life sciences. Our results show that life science students were significantly advantaged by answering the MCQ test in elimination format compared to single answer format under negative marking conditions by rewarding partial knowledge of topics. Importantly, we found no significant difference in performance between genders in either cohort for either MCQ test under negative marking conditions. Surveys showed that students generally preferred ET-style MCQ testing over SA-style testing. Students reported feeling more relaxed taking ET MCQ and more stressed when sitting SA tests, while disagreeing with being distracted by thinking about best tactics for scoring high. Students agreed ET testing improved their critical thinking skills. We conclude that appropriately-designed MCQ tests do not systematically discriminate between genders. We recommend careful consideration in choosing the type of MCQ test, and propose to apply negative scoring conditions to each test type to avoid the introduction of gender bias. The student experience could be improved through the incorporation of the elimination answering methods in MCQ tests via rewarding partial and full knowledge

From nostrils to crocodile blood – ten surprising places to look for antibiotics

One in ten people’s noses contain bacteria that could be the source of a powerful new antibiotic, German scientists say. Even resistant superbugs, such as MRSA and vancomycin-resistant enterococci, died when exposed to this new compound, lugdunin. Antimicrobial resistance is a major global threat, with Europe facing “Antimicrobial Armageddon” by 2025. Leading scientists predict a million deaths from untreatable infections if more new antibiotics aren’t found. So academics hunting for new drugs in unusual places such as human “snot” are on the right track. Here are ten more surprising places scientists are looking for antibiotics, from ants and cow stomachs to medieval libraries and snake blood

The integration of nanoscale imaging and quantitation of nanomechanical properties in microbiology

Recent developments in nanotechnology enable the imaging, quantification and manipulation of materials at the near-atomic level. The number of applications of atomic force microscopy (AFM) in the life sciences is increasing, now allowing the integrated study of topological and quantitative nanoscale mechanical characterization of living cells and their interactions with their environments, which was inconceivable until recently