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Microporous polymers feature shape-persistent free volume elements (FVEs), which are permeated by small molecules and ions when used as membranes for chemical separations, water purification, fuel cells and batteries 1 – 3 . Identifying FVEs that have analyte specificity remains a challenge, owing to difficulties in generating polymers with sufficient diversity to enable screening of their properties. Here we describe a diversity-oriented synthetic strategy for microporous polymer membranes to identify candidates featuring FVEs that serve as solvation cages for lithium ions (Li + ). This strategy includes diversification of bis(catechol) monomers by Mannich reactions to introduce Li + -coordinating functionality within FVEs, topology-enforcing polymerizations for networking FVEs into different pore architectures, and several on-polymer reactions for diversifying pore geometries and dielectric properties. The most promising candidate membranes featuring ion solvation cages exhibited both higher ionic conductivity and higher cation transference number than control membranes, in which FVEs were aspecific, indicating that conventional bounds for membrane permeability and selectivity for ion transport can be overcome 4 . These advantages are associated with enhanced Li + partitioning from the electrolyte when cages are present, higher diffusion barriers for anions within pores, and network-enforced restrictions on Li + coordination number compared to the bulk electrolyte, which reduces the effective mass of the working ion. Such membranes show promise as anode-stabilizing interlayers in high-voltage lithium metal batteries. A diversity-oriented synthesis approach that yields a library of architecturally broad microporous polymers is used to develop structurally diverse polymer membranes with ion specificity and to screen their properties.

Pyridinium electrolytes are promising candidates for flow-battery-based energy storage 1 – 4 . However, the mechanisms underlying both their charge–discharge processes and overall cycling stability remain poorly understood. Here we probe the redox behaviour of pyridinium electrolytes under representative flow battery conditions, offering insights into air tolerance of batteries containing these electrolytes while providing a universal physico-chemical descriptor of their reversibility. Leveraging a synthetic library of extended bispyridinium compounds, we track their performance over a wide range of potentials and identify the singlet–triplet free energy gap as a descriptor that successfully predicts the onset of previously unidentified capacity fade mechanisms. Using coupled operando nuclear magnetic resonance and electron paramagnetic resonance spectroscopies 5 , 6 , we explain the redox behaviour of these electrolytes and determine the presence of two distinct regimes (narrow and wide energy gaps) of electrochemical performance. In both regimes, we tie capacity fade to the formation of free radical species, and further show that π -dimerization plays a decisive role in suppressing reactivity between these radicals and trace impurities such as dissolved oxygen. Our findings stand in direct contrast to prevailing views surrounding the role of π -dimers in redox flow batteries 1 , 4 , 7 – 11 and enable us to efficiently mitigate capacity fade from oxygen even on prolonged (days) exposure to air. These insights pave the way to new electrolyte systems, in which reactivity of reduced species is controlled by their propensity for intra- and intermolecular pairing of free radicals, enabling operation in air. The redox behaviour of pyridinium electrolytes under representative flow battery conditions is investigated, offering insights into air tolerance of batteries containing these electrolytes while providing a universal physico-chemical descriptor of their reversibility.

Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information. Genes are made up of DNA and contain the instructions to make molecules called proteins. This information is stored as a genetic code consisting of four bases: adenine (A), cytosine (C), guanine (G) and thymine (T). The order of these bases and their different combinations serves as a blueprint for making thousands of different proteins and to assemble living cells. Converting the information in the genes into proteins requires several steps. First, the code from the DNA needs to be transcribed into RNA and then processed to make messenger RNA, or mRNA for short, which in turn is translated into proteins. Cells decode mRNAs by reading the bases as groups of three, also called codons. Most codons specify an amino acid – the building blocks of proteins – but certain codons also mark the start and end point of a protein. This ensures that the mRNA is read in the correct ‘frame’ and the desired proteins are made. Any cell contains thousands of different proteins and each protein has its own unique level. The mechanisms used to set the number of each different type of protein can operate at every point in the process. In many organisms, the number of times a gene is transcribed to make an mRNA, underpins differences in protein levels. Trypanosomes, for example, are parasites that cause a range of devastating diseases in humans and livestock. They lack the ability to set individual mRNA levels by regulating how often the gene is transcribed. This suggests that the expression of thousands of mRNAs is regulated by a common control mechanism later in the process ending in protein synthesis. However, until now, it was unclear what these mechanisms are. Most amino acids are encoded by more than one codon. The different codons for one amino acid are not equivalent and using a different codon can lead the mRNA to yield more or less protein. Evolution acts on these differences between codons, and the ‘codon choice’ in any one mRNA represents the outcome of natural selection. Now, Nascimento, Kelly et al. found that codon choice directs both the levels of mRNAs and the level of translation. For the experiments, a new metric that enables a prediction of the level of expression for each mRNA was created. This metric (known as the ‘gene expression codon adaptation index’ or geCAI for short) could relate the codon choice to mRNA levels. For example, mRNAs with a low index score had shorter half-lives, i.e., how long that mRNA remained in the cell before being broken down. Nascimento, Kelly et al. confirmed this by measuring mRNA levels in specific genes tagged with distinguishable markers and revealed that the codon choice indeed dictated the rate at which an mRNA would be broken down. A separate study by Jeacock, Faria and Horn looked more closely at how codon choice contributes to the control of the copy number of proteins. However, genes and mRNAs involved in development could deviate from the levels predicted by the geCAI metric, which suggests that other mechanisms may be in place to control the stability these mRNAs. The importance of codon choice in setting mRNA levels has now been demonstrated in several organisms, including yeast and trypanosomes, which suggests that this process is more widespread than previously realised.

Background Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts. Results We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids. Conclusions Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the ‘shopping bag’ hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.

ApolipoproteinL1 (APOL1) protects humans and some primates against several African trypanosomes. APOL1 genetic variants strongly associated with kidney disease in African Americans have additional trypanolytic activity against Trypanosoma brucei rhodesiense , the cause of acute African sleeping sickness. We combined genetic, physiological, and biochemical studies to explore coevolution between the APOL1 gene and trypanosomes. We analyzed the APOL1 sequence in modern and archaic humans and baboons along with geographic distribution in present day Africa to understand how the kidney risk variants evolved. Then, we tested Old World monkey, human, and engineered APOL1 variants for their ability to kill human infective trypanosomes in vivo to identify the molecular mechanism whereby human trypanolytic APOL1 variants evade T. brucei rhodesiense virulence factor serum resistance-associated protein (SRA). For one APOL1 kidney risk variant, a two-residue deletion of amino acids 388 and 389 causes a shift in a single lysine residue that mimics the Old World monkey sequence, which augments trypanolytic activity by preventing SRA binding. A second human APOL1 kidney risk allele, with an amino acid substitution that also restores sequence alignment with Old World monkeys, protected against T. brucei rhodesiense due in part to reduced SRA binding. Both APOL1 risk variants induced tissue injury in murine livers, the site of transgenic gene expression. Our study shows that both genetic variants of human APOL1 that protect against T. brucei rhodesiense have recapitulated molecular signatures found in Old World monkeys and raises the possibility that APOL1 variants have broader innate immune activity that extends beyond trypanosomes.

The exon junction complex (EJC) is a key player in metazoan mRNA quality control and is placed upstream of the exon-exon junction after splicing. Its inner core is composed of Magoh, Y14, eIF4AIII and BTZ and the outer core of proteins involved in mRNA splicing (CWC22), export (Yra1), translation (PYM) and nonsense mediated decay (NMD, UPF1/2/3). Trypanosoma brucei encodes only two genes with introns, but all mRNAs are processed by trans -splicing. The presence of three core EJC proteins and a potential BTZ homologue (Rbp25) in trypanosomes has been suggested to adapt of the EJC function to mark trans -spliced mRNAs. We analysed trypanosome EJC components and noticed major differences between eIF4AIII and Magoh/Y14: (i) whilst eIF4AIII is essential, knocking out both Magoh and Y14 elicits only a mild growth phenotype (ii) eIF4AIII localization is mostly nucleolar, while Magoh and Y14 are nucleolar and nucleoplasmic but excluded from the cytoplasm (iii) eIF4AIII associates with nucleolar proteins and the splicing factor CWC22, but not with Y14 or Magoh, while Magoh and Y14 associate with each other, but not with eIF4AIII, CWC22 or nucleolar proteins. Our data argue against the presence of a functional EJC in trypanosomes, but indicate that eIF4AIII adopted non-EJC related, essential functions, while Magoh and Y14 became redundant. Trypanosomes also possess homologues to the NMD proteins UPF1 and UPF2. Depletion of UPF1 causes only a minor reduction in growth and phylogenetic analyses show several independent losses of UPF1 and UPF2, as well as complete loss of UPF3 in the Kinetoplastida group, indicating that UPF1-dependent NMD is not essential. Regardless, we demonstrate that UPF1 depletion restores the mRNA levels of a PTC reporter. Altogether, we show that the almost intron-less trypanosomes are in the process of losing the canonical EJC/NMD pathways: Y14 and Magoh have become redundant and the still-functional UPF1-dependent NMD pathway is not essential.

African trypanosomes replicate within infected mammals where they are exposed to the complement system. This system centres around complement C3, which is present in a soluble form in serum but becomes covalently deposited onto the surfaces of pathogens after proteolytic cleavage to C3b. Membrane-associated C3b triggers different complement-mediated effectors which promote pathogen clearance. To counter complement-mediated clearance, African trypanosomes have a cell surface receptor, ISG65, which binds to C3b and which decreases the rate of trypanosome clearance in an infection model. However, the mechanism by which ISG65 reduces C3b function has not been determined. We reveal through cryogenic electron microscopy that ISG65 has two distinct binding sites for C3b, only one of which is available in C3 and C3d. We show that ISG65 does not block the formation of C3b or the function of the C3 convertase which catalyses the surface deposition of C3b. However, we show that ISG65 forms a specific conjugate with C3b, perhaps acting as a decoy. ISG65 also occludes the binding sites for complement receptors 2 and 3, which may disrupt recruitment of immune cells, including B cells, phagocytes, and granulocytes. This suggests that ISG65 protects trypanosomes by combining multiple approaches to dampen the complement cascade.

Background Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group. Results We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis . Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy. Conclusions The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.

Variations on the statement \"the variant surface glycoprotein (VSG) coat that covers the external face of the mammalian bloodstream form of Trypanosoma brucei acts a physical barrier\" appear regularly in research articles and reviews. The concept of the impenetrable VSG coat is an attractive one, as it provides a clear model for understanding how a trypanosome population persists; each successive VSG protects the plasma membrane and is immunologically distinct from previous VSGs. What is the evidence that the VSG coat is an impenetrable barrier, and how do antibodies and other extracellular proteins interact with it? In this review, the nature of the extracellular surface of the bloodstream form trypanosome is described, and past experiments that investigated binding of antibodies and lectins to trypanosomes are analysed using knowledge of VSG sequence and structure that was unavailable when the experiments were performed. Epitopes for some VSG monoclonal antibodies are mapped as far as possible from previous experimental data, onto models of VSG structures. The binding of lectins to some, but not to other, VSGs is revisited with more recent knowledge of the location and nature of N-linked oligosaccharides. The conclusions are: (i) Much of the variation observed in earlier experiments can be explained by the identity of the individual VSGs. (ii) Much of an individual VSG is accessible to antibodies, and the barrier that prevents access to the cell surface is probably at the base of the VSG N-terminal domain, approximately 5 nm from the plasma membrane. This second conclusion highlights a gap in our understanding of how the VSG coat works, as several plasma membrane proteins with large extracellular domains are very unlikely to be hidden from host antibodies by VSG.

Persistent pathogens have evolved to avoid elimination by the mammalian immune system including mechanisms to evade complement. Infections with African trypanosomes can persist for years and cause human and animal disease throughout sub-Saharan Africa. It is not known how trypanosomes limit the action of the alternative complement pathway. Here we identify an African trypanosome receptor for mammalian factor H, a negative regulator of the alternative pathway. Structural studies show how the receptor binds ligand, leaving inhibitory domains of factor H free to inactivate complement C3b deposited on the trypanosome surface. Receptor expression is highest in developmental stages transmitted to the tsetse fly vector and those exposed to blood meals in the tsetse gut. Receptor gene deletion reduced tsetse infection, identifying this receptor as a virulence factor for transmission. This demonstrates how a pathogen evolved a molecular mechanism to increase transmission to an insect vector by exploitation of a mammalian complement regulator. African trypanosome infections can persist for years, but immune evasion mechanisms are not fully understood. Here, Macleod et al . identify a trypanosome receptor for mammalian factor H, a negative regulator of the alternative complement pathway, that increases parasite transmission to tsetse flies.