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Phosphorus (P) discharge from agricultural and urban drainage is known for causing downstream eutrophication worldwide. Agricultural best management practices that are designed to reduce P load out of farms target different P species from various sources such as fertilizers leaching and farm soil and canal sediment erosion, however, few studies have assessed the impact of floating aquatic vegetation (FAV) on canal sediment and farm drainage water quality. This study evaluated the impact of FAVs on canal sediment properties and P water quality in drainage canals in the Everglades Agricultural Area in south Florida, USA. Non-parametric statistical methods, correlation analysis, trend analysis and principal component analysis (PCA) were used to determine the relationship between FAV coverage with sediment properties and P water quality parameters. Results showed that FAV coverage was correlated with the highly recalcitrant and most stable form of P in the sediment layer (Residual P Pool). FAV coverage also correlated with the dissolved organic P (DOP) which was the smallest P pool (7 %) of total P concentration in drainage water, therefore FAV coverage had no correlation with farm P load. The trend analysis showed no trend in farm P loads, despite a decline in FAV coverage at farm canals over an 8-year period. Phosphorus content in the sediment surface layer was strongly associated with farm P load and had a significant correlation with particulate P (PP) and soluble reactive P (SRP) which constituted 47 % and 46 % of the total P concentration in the drainage water, respectively. Equilibrium P concentration assays also showed the potential to release SRP from the sediment layer. The P budget established for this study reveals that sediment stores the largest P mass (333 kg P), while FAVs store the smallest P mass (8 kg P) in a farm canal, highlighting the significant contribution of canal sediment to farm P discharges. Further research is required to evaluate the impact of sediment removal and canal maintenance practices that help reduce farm P discharges., Competing Interests: Declaration of competing interest The authors declare no known competing financial interests or personal relationships that could have influenced the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Veganism is the subject of an increasingly diverse body of social scientific research, yet it remains relatively understudied in geography. Meanwhile, contemporary cultural commentaries note how veganism has gone mainstream, with critics warning of veganism's corporate nature - expressed in the rise of what we term 'Big Veganism'. We argue that food geographers are well placed to examine these trends. We first review vegan studies work beyond geography that examines and critiques the mainstreaming of veganism. We focus on literature that explores multiple contested modes of veganism, veganism as praxis in place and the rise of corporate veganism as useful foundations for geographers to build on, particularly in light of currently unfolding developments in vegan cultures and practice. Taking this work forward, we identify four conceptual traditions from research in food geographies - following foodways , alternative food networks and the cultural and material politics of eating - to develop a 'vegan food geographies' programme that aims to advance critical geographic work on veganism and the emerging implications of its contemporary mainstreaming., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2022.)

Background: Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry-based proteomics using data-dependent acquisition has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility., Results: Here, we present a comprehensive P. falciparum-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites., Conclusion: A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

This article examines the role of place-specifically the place of Silicon Valley in California-in the emerging economic geographies of alternative proteins (APs), including cellular and plant-based substitutes. Drawing on original fieldwork data and existing economic geography debates on food, place, and innovation, I develop the concept of innovation terroir to examine the key role Silicon Valley has played in shaping the spatial trajectories and political possibilities of the AP sector. I first illustrate the power of Silicon Valley's place-myth in (re)producing the importance for AP founders to be physically in place within the region, in part to access its renowned industrial resources but also to provide a protective niche of credibility and credulity for these nascent ventures. Second, I outline that to be there in spatial terms has also involved an encountering with a specific culture of logics and practices of the tech-noindustrial region of Silicon Valley. To succeed at doing protein food in this region has required a choice by AP ventures to become culturally in place and thereby reimagine food through the Valley's image of high-tech entrepreneurial innovation; in short, it has required food to become software. This exploration of cultural emplacement builds directly on recent work in geography and related fields on alternative food economies, geographies of innovation, and the ontological politics of APs. It offers timely contributions for considering how AP development might be done otherwise and what it means to look to Silicon Valley for solutions to global food security and broader planetary challenges.

Plant-based milk alternatives-or mylks -have surged in popularity over the past ten years. We consider the politics and consumer subjectivities fostered by mylks as part of the broader trend towards 'plant-based' food. We demonstrate how mylk companies inherit and strategically deploy positive framings of milk as wholesome and convenient, as well as negative framings of dairy as environmentally damaging and cruel, to position plant-based as the 'better' alternative. By navigating this affective landscape, brands attempt to (re)make mylk as simultaneously palatable and disruptive to the status quo. We examine the politics of mylks through the concept of palatable disruption , where people are encouraged to care about the environment, health, and animal welfare enough to adopt mylks but to ultimately remain consumers of a commodity food. By encouraging consumers to reach for "plant-based" as a way to cope with environmental catastrophe and a life out of balance, mylks promote a neoliberal ethic: they individualize systemic problems and further entrench market mechanisms as solutions, thereby reinforcing the political economy of industrial agriculture. In conclusion, we reflect on the limits of the current plant-based trend for transitioning to more just and sustainable food production and consumption., (© The Author(s) 2020.)

Plasmodium species are evolutionarily distant from model eukaryotes, and as a consequence they exhibit many non-canonical cellular processes. In the post-genomic era, functional "omics" disciplines (transcriptomics, proteomics, and metabolomics) have accelerated our understanding of unique aspects of the biology of malaria parasites. Functional "omics" tools, in combination with genetic manipulations, have offered new opportunities to investigate the function of previously uncharacterized genes. Knowledge of basic parasite biology is fundamental to understanding drug modes of action, mechanisms of drug resistance, and relevance of vaccine candidates. This Perspective highlights recent "omics"-based discoveries in basic biology and gene function of the most virulent human malaria parasite, Plasmodium falciparum .

Cultured/clean/cell-based meat (CM) now has a near two decade history of laboratory research, commencing with the early NASA-funded work at Touro College and the bioarts practice of the Tissue Culture and Art project. Across this period the field, or as it is now more commonly termed, the "space," has developed significantly while promoting different visions for what CM is and can do, and the best mechanisms for delivery. Here we both analyse and critically engage with this near-twenty year period as a productive provocation to those engaged with CM, or considering becoming so. This paper is not a history of the field, and does not offer a comprehensive timeline. Instead it identifies significant activities, transitions, and moments in which key meanings and practices have taken form or exerted influence. We do this through analyzing two related themes: the CM "institutional context" and the CM "interpretative package." The former, the institutional context, refers to events and infrastructures that have come into being to support and shape the CM field, including university activities, conferences, third sector groups, various potential funding mechanisms, and the establishment of a start-up sector. The latter, the interpretative package, refers to the constellation of factors that shape or assert how CM should be understood, including the various names used to describe it, accounts of what it will achieve, and most recently, the emergent regulatory discussions that frame its legal standing. Across the paper we argue it is productive to think of the CM community in terms of a first and second wave. The first wave was more university-based and broadly covers the period from the millennium until around the 2013 cultured burger event. The second wave saw the increasing prevalence of a start-up culture and the circuits of venture capital interest that support it. Through this analysis we seek to provoke further reflection upon how the CM community has come to be as it is, and how this could develop in the future., Competing Interests: Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

This paper offers a critical examination of the narrative landscape that has emerged with a new movement of alternative proteins intended as substitutes for conventional meat, milk and other animal-based food products. The alternative protein approaches analysed include edible insects, plant-based proteins and cellular agriculture, the latter of which encompasses 'cultured' or 'clean' meat, milk and egg products produced in vitro via cell-science methods. We build on previous research that has analysed the promissory narratives specific to cultured/clean meat by examining the key promises that have worked across the broader alternative protein movement. In doing so, we develop a five-fold typology that outlines the distinct yet interconnected claims that have operated in alternative protein promotional discourses to date. The second part of the paper examines the counter-narratives that have emerged in response to alternative protein claims from different stakeholders linked to conventional livestock production. We offer a second typology of three counter-narratives that have so far characterised these responses. Through mapping this narrative landscape, we show how different types of 'goodness' have been ascribed by alternative protein and conventional livestock stakeholders to their respective approaches. Moreover, our analysis reveals a series of tensions underpinning these contested food futures, many of which have long histories in broader debates over what constitutes better (protein) food production and consumption. The paper's discussion contributes to ongoing research across the social sciences on the ontological politics of (good) food, and the key role of narratives in constructing and contesting visions of 'better' food futures., (© The Author(s) 2019.)

The malaria-causing blood stage of Plasmodium falciparum requires extracellular pantothenate for proliferation. The parasite converts pantothenate into coenzyme A (CoA) via five enzymes, the first being a pantothenate kinase (PfPanK). Multiple antiplasmodial pantothenate analogues, including pantothenol and CJ-15,801, kill the parasite by targeting CoA biosynthesis/utilisation. Their mechanism of action, however, remains unknown. Here, we show that parasites pressured with pantothenol or CJ-15,801 become resistant to these analogues. Whole-genome sequencing revealed mutations in one of two putative PanK genes (Pfpank1) in each resistant line. These mutations significantly alter PfPanK activity, with two conferring a fitness cost, consistent with Pfpank1 coding for a functional PanK that is essential for normal growth. The mutants exhibit a different sensitivity profile to recently-described, potent, antiplasmodial pantothenate analogues, with one line being hypersensitive. We provide evidence consistent with different pantothenate analogue classes having different mechanisms of action: some inhibit CoA biosynthesis while others inhibit CoA-utilising enzymes.

Transient regulation of Plasmodium numbers below the density that induces fever has been observed in chronic malaria infections in humans. This species transcending control cannot be explained by immunity alone. Using an in vitro system we have observed density dependent regulation of malaria population size as a mechanism to possibly explain these in vivo observations. Specifically, Plasmodium falciparum blood stages from a high but not low-density environment exhibited unique phenotypic changes during the late trophozoite (LT) and schizont stages of the intraerythrocytic cycle. These included in order of appearance: failure of schizonts to mature and merozoites to replicate, apoptotic-like morphological changes including shrinking, loss of mitochondrial membrane potential, and blebbing with eventual release of aberrant parasites from infected erythrocytes. This unique death phenotype was triggered in a stage-specific manner by sensing of a high-density culture environment. Conditions of glucose starvation, nutrient depletion, and high lactate could not induce the phenotype. A high-density culture environment induced rapid global changes in the parasite transcriptome including differential expression of genes involved in cell remodeling, clonal antigenic variation, metabolism, and cell death pathways including an apoptosis-associated metacaspase gene. This transcriptional profile was also characterized by concomitant expression of asexual and sexual stage-specific genes. The data show strong evidence to support our hypothesis that density sensing exists in P. falciparum. They indicate that an apoptotic-like mechanism may play a role in P. falciparum density regulation, which, as in yeast, has features quite distinguishable from mammalian apoptosis., Database: Gene expression data are available in the GEO databases under the accession number GSE91188., (© 2017 Federation of European Biochemical Societies.)

A detailed analysis of the metabolic state of human-stem-cell-derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high-resolution LC-MS-based untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable-isotope-labeled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes. Most metabolite species found to be enriched in reticulocytes were residual pools of metabolites produced by earlier erythropoietic processes, and their systematic depletion in mature erythrocytes aligns with the simplification process, which is also seen at the cellular and the structural level. Our work shows that high-resolution LC-MS-based untargeted metabolomics provides a global coverage of the biochemical species that are present in erythrocytes. However, the incorporation of stable isotope labeling provides a more accurate description of the active metabolic processes that occur in each developmental stage. To our knowledge, this is the first detailed characterization of the active metabolic pathways of the erythroid lineage, and it provides a rich database for understanding the physiology of the maturation of reticulocytes into mature erythrocytes.

Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide-range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of pro are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in Cα atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes., (© 2015 The Protein Society.)

RAW 264.7 cells rapidly induce cyclooxygenase-2 (COX-2) in response to lipopolysaccharide treatment. Part of the increased COX-2 expression occurred through post-transcriptional mechanisms mediated through specific regions of the 3'-untranslated region (UTR) of the message. The proximal region of the 3'-UTR of COX-2 contains a highly conserved AU-rich element that was able to confer lipopolysaccharide regulation of a chimeric reporter-gene. Electrophoretic mobility shift assays demonstrated that the RNA-binding proteins TIAR, AUF1, HuR, and TIA-1 all form an RNA-protein complex with the first 60 nucleotides of the 3'-UTR of COX-2. Biotinylated RNA probes were used to isolate additional proteins that bind the 3'-UTR of COX-2. We identified several RNA-binding proteins including TIAR, AUF1, CBF-A, RBM3, heterogeneous nuclear ribonucleoprotein (hnRNP) A3, and hnRNP A2/B1. We identified four alternatively spliced isoforms of AUF1 which migrated at multiple isoelectric points. Likewise, we identified alternatively spliced isoforms of CBF-A, hnRNP A3, and hnRNP A2/B1. Western analysis of two-dimensional gels identified multiple isoforms of TIA-1, TIAR, and AUF1 at pI values that spanned nearly 3 pH units. Thus, through a combination of alternative splicing and post-translational modification cells are able to increase greatly the repertoire of protein species expressed at a given time or in response to extracellular stimuli.