Thermal Stability of Protic Ionic Liquids.

While protic ionic liquids (ILs) have found great success as solvents for a broad range of applications, little is known about their degradation when exposed to temperatures above ambient for extended periods of time. Here, we report the thermal stability of six protic ILs, namely, ethylammonium nitrate, ethylammonium formate, ethylammonium acetate, ethanolammonium nitrate, ethanolammonium formate, and ethanolammonium acetate. The effect of heating each ionic liquid to 60 °C for 1 h or 1 week (sealed or open to the atmosphere) was evaluated by considering the changes to water content, pH, mass, thermal phase transitions, and molecular structure after each treatment. Heating each of the six ILs when sealed led to measurable shifts in their water content and 10 wt % pH, but there was no significant change in their mass, thermal phase transitions according to differential scanning calorimetry (DSC), or molecular structure using proton nuclear magnetic resonance (1H NMR) spectra, indicating that the samples were largely unchanged. The samples that were heated open to the atmosphere also displayed no significant changes after 1 h but displayed significant changes after 1 week.

Reconstructing colonization dynamics to establish how human activities transformed island biodiversity.

Drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, hampering assessments of subsequent modification of island biodiversity. We developed and tested a new statistical-simulation approach for reconstructing the pattern and pace of human migration across islands at high spatiotemporal resolutions. Using Polynesian colonisation of New Zealand as an example, we show that process-explicit models, informed by archaeological records and spatiotemporal reconstructions of past climates and environments, can provide new and important insights into the patterns and mechanisms of arrival and establishment of people on islands. We find that colonisation of New Zealand required there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding rapidly over both North and South Islands. These verified spatiotemporal reconstructions of colonisation dynamics provide new opportunities to explore more extensively the potential ecological impacts of human colonisation on New Zealand's native biota and ecosystems.

Biophysical Characterization and Cryopreservation of Mammalian Cells Using Ionic Liquids.

Ionic liquids (ILs) are a diverse class of solvents which can be selected for task-specific properties, making them attractive alternatives to traditional solvents. To tailor ILs for specific biological applications, it is necessary to understand the structure-property relationships of ILs and their interactions with cells. Here, a selection of carboxylate anion-based ILs were investigated as cryoprotectants, which are compounds added to cells before freezing to mitigate lethal freezing damage. The cytotoxicity, cell permeability, thermal behavior, and cryoprotective efficacy of the ILs were assessed with two model mammalian cell lines. We found that the biophysical interactions, including permeability of the ILs, were influenced by considering the IL pair together, rather than as single species acting independently. All of the ILs tested had high cytotoxicity, but ethylammonium acetate demonstrated good cryoprotective efficacy for both cell types tested. These results demonstrate that despite toxicity, ILs may be suitable for certain biological applications. It also demonstrates that more research is required to understand the contribution of ion pairs to structure-property relationships and that knowing the behavior of a single ionic species will not necessarily predict its behavior as part of an IL.

Lyotropic liquid crystal phases of monoolein in protic ionic liquids.

Monoolein-based liquid crystal phases are established media that are researched for various biological applications, including drug delivery. While water is the most common solvent for self-assembly, some ionic liquids (ILs) can support lipidic self-assembly. However, currently, there is limited knowledge of IL-lipid phase behavior in ILs. In this study, the lyotropic liquid crystal phase behavior of monoolein was investigated in six protic ILs known to support amphiphile self-assembly, namely ethylammonium nitrate, ethanolammonium nitrate, ethylammonium formate, ethanolammonium formate, ethylammonium acetate, and ethanolammonium acetate. These ILs were selected to identify specific ion effects on monoolein self-assembly, specifically increasing the alkyl chain length of the cation or anion, the presence of a hydroxyl group in the cation, and varying the anion. The lyotropic liquid crystal phases with 20-80 wt. % of monoolein were characterized over a temperature range from 25 to 65 °C using synchrotron small angle x-ray scattering and cross-polarized optical microscopy. These results were used to construct partial phase diagrams of monoolein in each of the six protic ILs, with inverse hexagonal, bicontinuous cubic, and lamellar phases observed. Protic ILs containing the ethylammonium cation led to monoolein forming lamellar and bicontinuous cubic phases, while those containing the ethanolammonium cation formed inverse hexagonal and bicontinuous cubic phases. Protic ILs containing formate and acetate anions favored bicontinuous cubic phases across a broader range of protic IL concentrations than those containing the nitrate anion.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

Millennial processes of population decline, range contraction and near extinction of the European bison.

European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

De novo assembly and annotation of the singing mouse genome.

BACKGROUND: Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. RESULTS: Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. CONCLUSIONS: These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

Small angle X-ray scattering investigation of ionic liquid effect on the aggregation behavior of globular proteins.

Globular proteins are well-folded model proteins, where ions can substantially influence their structure and aggregation. Ionic liquids (ILs) are salts in the liquid state with versatile ion combinations. Understanding the IL effect on protein behavior remains a major challenge. Here, we employed small angle X-ray scattering to investigate the effect of aqueous ILs on the structure and aggregation of globular proteins, namely, hen egg white lysozyme (Lys), human lysozyme (HLys), myoglobin (Mb), ß-lactoglobulin (ßLg), trypsin (Tryp) and superfolder green fluorescent protein (sfGFP). The ILs contain ammonium-based cations paired with the mesylate, acetate or nitrate anion. Results showed that only Lys was monomeric, whereas the other proteins formed small or large aggregates in buffer. Solutions with over 17 mol% IL resulted in significant changes in the protein structure and aggregation. The Lys structure was expanded at 1 mol% but compact at 17 mol% with structural changes in loop regions. HLys formed small aggregates, with the IL effect similar to Lys. Mb and ßLg mostly had distinct monomer and dimer distributions depending on IL type and IL concentration. Complex aggregation was noted for Tryp and sfGFP. While the anion had the largest ion effect, changing the cation also induced the structural expansion and protein aggregation.

Pediatric Eye Care Treatment Rates and Community Compliance to a Spectacle Provision Program in an Underserved School District in San Diego, CA.

Significance: The need for early identification and treatment of young children's refractive error needs has become a public health concern. The UCSD Eyemobile for Children (EyeMobile) provides vision screenings and comprehensive eye exams on the Eyemobile among a population of underserved, predominantly Hispanic preschool and elementary school children. The program also provides spectacles for children who fail eye exams due to refractive error. Methods: We performed a retrospective cross-sectional analysis of all children screened from 2011 to 2017 by the Eyemobile across 10 San Diego elementary schools. We examined demographics, distance and near visual acuity, autorefraction, stereopsis, and color vision. To measure compliance to our spectacle program, we checked if children who were prescribed spectacles were wearing them, as instructed, at the following year's screening. Differences between compliance measures with respect to school, age, ethnicity, and gender were determined using chi-square analysis, while all other measures were fit to a binary logistic regression to determine statistically significant factors. Results: A total of 12,176 elementary school children were screened between 2011 and 2017. Of these children, 5269 (43.3%) were referred for a comprehensive eye examination. Across six years, 3163 (60.0%) of the children referred completed their eye examinations. There was a significant increase (p < 0.001) in exam completion in the successive years. Exam completion was significantly higher in ten-year-olds (p = 0.0278) and in 3 of the 10 schools (p < 0.0001, p = 0.0027, and p = 0.0309). A total of 1089 (8.9% of screened) children were prescribed spectacles. Of the 409 children that were recorded with the compliance method, 342 (83.6%) were found to be fully compliant and wearing their spectacles as prescribed. Conclusion: The Eyemobile program demonstrated high levels of compliance for both eye examination completion and prescribed spectacle wear in underserved populations in the San Diego region, compared to similar national programs.

Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing.

Objectives: Smoking is the commonest cause of oral cavity squamous cell carcinoma (OC-SCC), but the etiology of OC-SCC in nonsmokers is unknown. Our primary goal was to use metagenomic shotgun sequencing (MSS) to define the taxonomic composition and functional potential of oral metagenome in nonsmokers with OC-SCC. Methods: We conducted a case-control study with 42 OC-SCC case and 45 control nonsmokers. MSS was performed on DNA extracted from mouthwash samples. Taxonomic analysis and pathway analysis were done using MetaPhlAn2 and HUMAnN2, respectively. Statistical difference was determined using the Mann-Whitney test controlling false discovery rate. Results: There was no significant difference in age, sex, race, or alcohol consumption between OC-SCC and control patients. There was a significant difference in beta diversity between OC-SCC and controls. At the phylum level, Bacteroidetes and Synergistetes were overly represented in OC-SCC while Actinobacteria and Firmicutes were overly represented in controls. At the genus level, Fusobacterium was overly represented in OC-SCC compared with controls, while Corynebacterium, Streptococcus, Actinomyces, Cryptobacterium, and Selenomonas were overly represented in controls. Bacterial pathway analysis identified overrepresentation in OC-SCC of pathways related to metabolism of flavin, biotin, thiamin, heme, sugars, fatty acids, peptidoglycans, and tRNA and overrepresentation of nucleotides and essential amino acids in controls. Conclusions: The oral microbiome in nonsmoker patients with OC-SCC is significantly different from that of nonsmoker control patients in taxonomic compositions and functional potentials. Our study's MSS findings matched with previous 16S-based methods in taxonomic differentiation but varied greatly in functional differentiation of microbiomes in OC-SCC and controls.

Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.

Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.

Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia.

Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process-explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species-specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process-explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process-explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.

Faster ocean warming threatens richest areas of marine biodiversity.

The vulnerability of marine biodiversity to accelerated rates of climatic change is poorly understood. By developing a new method for identifying extreme oceanic warming events during Earth's most recent deglaciation, and comparing these to 21st century projections, we show that future rates of ocean warming will disproportionately affect the most speciose marine communities, potentially threatening biodiversity in more than 70% of current-day global hotspots of marine species richness. The persistence of these richest areas of marine biodiversity will require many species to move well beyond the biogeographic realm where they are endemic, at rates of redistribution not previously seen. Our approach for quantifying exposure of biodiversity to past and future rates of oceanic warming provides new context and scalable information for deriving and strengthening conservation actions to safeguard marine biodiversity under climate change.

Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma.

The incidence of esophageal adenocarcinoma (EA) has drastically increased in the United States since 1970s for unclear reasons. We hypothesized that the widespread usage of antibiotics has increased the procarcinogenic potential of the orodigestive microbiota along the sequence of gastroesophageal reflux (GR), Barrett's esophagus (BE) and EA phenotypes. This case control study included normal controls (NC) and three disease phenotypes GR, BE and EA. Microbiota in the mouth, esophagus, and stomach, and rectum were analyzed using 16S rRNA gene sequencing. Overall, we discovered 44 significant pairwise differences in abundance of microbial taxa between the four phenotypes, with 12 differences in the mouth, 21 in the esophagus, two in the stomach, and nine in the rectum. Along the GR→BE→EA sequence, oral and esophageal microbiota were more diversified, the dominant genus Streptococcus was progressively depleted while six other genera Atopobium, Actinomyces, Veillonella, Ralstonia, Burkholderia and Lautropia progressively enriched. In NC, Streptococcus appeared to control populations of other genera in the foregut via numerous negative and positive connections, while in disease states, the rich network was markedly simplified. Inferred gene functional content showed a progressive enrichment through the stages of EA development in genes encoding antibiotic resistance, ligands of Toll-like and NOD-like receptors, nitrate-nitrite-nitric oxide pathway and acetaldehyde metabolism. The orodigestive microbiota is in a progressive dysbiotic state along the GR-BE-EA sequence. The increasing dysbiosis and antibiotic and procarcinogenic genes in the disease states warrants further study to define their roles in EA pathogenesis.

Machine learning investigation of viscosity and ionic conductivity of protic ionic liquids in water mixtures.

Ionic liquids (ILs) are well classified as designer solvents based on the ease of tailoring their properties through modifying the chemical structure of the cation and anion. However, while many structure-property relationships have been developed, these generally only identify the most dominant trends. Here, we have used machine learning on existing experimental data to construct robust models to produce meaningful predictions across a broad range of cation and anion chemical structures. Specifically, we used previously collated experimental data for the viscosity and conductivity of protic ILs [T. L. Greaves and C. J. Drummond, Chem. Rev. 115, 11379-11448 (2015)] as the inputs for multiple linear regression and neural network models. These were then used to predict the properties of all 1827 possible cation-anion combinations (excluding the input combinations). These models included the effect of water content of up to 5 wt. %. A selection of ten new protic ILs was then prepared, which validated the usefulness of the models. Overall, this work shows that relatively sparse data can be used productively to predict physicochemical properties of vast arrays of ILs.

Electrochemical Stability of Zinc and Copper Surfaces in Protic Ionic Liquids.

Ionic liquids are versatile solvents that can be tailored through modification of the cation and anion species. Relatively little is known about the corrosive properties of protic ionic liquids. In this study, we have explored the corrosion of both zinc and copper within a series of protic ionic liquids consisting of alkylammonium or alkanolammonium cations paired with nitrate or carboxylate anions along with three aprotic imidazolium ionic liquids for comparison. Electrochemical studies revealed that the presence of either carboxylate anions or alkanolammonium cations tend to induce a cathodic shift in the corrosion potential. The effect in copper was similar in magnitude for both cations and anions, while the anion effect was slightly more pronounced than that of the cation in the case of zinc. For copper, the presence of carboxylate anions or alkanolammonium cations led to a notable decrease in corrosion current, whereas an increase was typically observed for zinc. The ionic liquid-metal surface interactions were further explored for select protic ionic liquids on copper using X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) to characterize the interface. From these studies, the oxide species formed on the surface were identified, and copper speciation at the surface linked to ionic liquid and potential dependent surface passivation. Density functional theory and ab initio molecular dynamics simulations revealed that the ethanolammonium cation was more strongly bound to the copper surface than the ethylammonium counterpart. In addition, the nitrate anion was more tightly bound than the formate anion. These likely lead to competing effects on the process of corrosion: the tightly bound cations act as a source of passivation, whereas the tightly bound anions facilitate the electrodissolution of the copper.

C9orf72 dipeptides disrupt the nucleocytoplasmic transport machinery and cause TDP-43 mislocalisation to the cytoplasm.

A repeat expansion in C9orf72 is the major cause of both frontotemporal dementia and amyotrophic lateral sclerosis, accounting for approximately 1 in 12 cases of either disease. The expansion is translated to produce five dipeptide repeat proteins (DPRs) which aggregate in patient brain and are toxic in numerous models, though the mechanisms underlying this toxicity are poorly understood. Recent studies highlight nucleocytoplasmic transport impairments as a potential mechanism underlying neurodegeneration in C9orf72-linked disease, although the contribution of DPRs to this remains unclear. We expressed DPRs in HeLa cells, in the absence of repeat RNA. Crucially, we expressed DPRs at repeat-lengths found in patients (> 1000 units), ensuring our findings were relevant to disease. Immunofluorescence imaging was used to investigate the impact of each DPR on the nucleus, nucleocytoplasmic transport machinery and TDP-43 localisation. DPRs impaired the structural integrity of the nucleus, causing nuclear membrane disruption and misshapen nuclei. Ran and RanGAP, two proteins required for nucleocytoplasmic transport, were also mislocalised in DPR-expressing cells. Furthermore, DPRs triggered mislocalisation of TDP-43 to the cytoplasm, and this occurred in the same cells as Ran and RanGAP mislocalisation, suggesting a potential link between DPRs, nucleocytoplasmic transport impairments and TDP-43 pathology.

Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties.

Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.

Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation.

Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.