Transient intermediate in the formation of an amorphous metal-organic framework.

Amorphous metal-organic frameworks are rarely formed via direct synthesis. Our limited understanding of their atomic assembly in solution prevents full exploitation of their unique structural complexity. Here, we use in situ synchrotron X-ray absorption spectroscopy with sub-second time resolution to probe the formation of the amorphous Fe-BTC framework. Using a combination of spectral fingerprinting, linear combination analysis, and principal component analysis coupled with kinetic analyses, we reveal a multi-stage formation mechanism that, crucially, proceeds via the generation of a transient intermediate species.

Properties of Single-Component Metal-Organic Framework Crystal-Glass Composites.

The formation, and subsequent structural, thermal and adsorptive properties of single-component metal-organic framework crystal-glass composites (MOF-CGCs) are investigated. A series of novel materials exhibiting chemically identical glassy and crystalline phases within the same material were produced, where crystalline ZIF-62(Zn) was incorporated within an ag ZIF-62(Zn) matrix. X-ray diffraction showed that the crystalline phase was still present after heating to above the glass transition temperature of ag ZIF-62(Zn), and interfacial compatibility between the crystalline and glassy phases was investigated using a mixed-metal (ZIF-62(Co))0.5 (ag ZIF-62(Zn))0.5 analogue. CO2 gas adsorption measurements showed that the CO2 uptakes of the MOF-CGCs were between those of the crystalline and glassy phases.

Identifying the liquid and glassy states of coordination polymers and metal-organic frameworks.

The field of metal-organic frameworks (MOFs) is still heavily focused upon crystalline materials. However, solid-liquid transitions in both MOFs and their parent coordination polymer family are now receiving increasing attention due to the largely unknown properties of both the liquid phase and the glasses that may be formed upon melt-quenching. Here, we argue that the commonly reported concept of 'thermal stability' in the hybrid materials field is insufficient. We present several case studies of the use of differential scanning calorimetry alongside thermogravimetric analysis to prove, or disprove, the cooperative phenomena of melting in several MOF families.

Inducing Social Self-Sorting in Organic Cages To Tune The Shape of The Internal Cavity.

Many interesting target guest molecules have low symmetry, yet most methods for synthesising hosts result in highly symmetrical capsules. Methods of generating lower symmetry pores are thus required to maximise the binding affinity in host-guest complexes. Herein, we use mixtures of tetraaldehyde building blocks with cyclohexanediamine to access low-symmetry imine cages. Whether a low-energy cage is isolated can be correctly predicted from the thermodynamic preference observed in computational models. The stability of the observed structures depends on the geometrical match of the aldehyde building blocks. One bent aldehyde stands out as unable to assemble into high-symmetry cages-and the same aldehyde generates low-symmetry socially self-sorted cages when combined with a linear aldehyde. We exploit this finding to synthesise a family of low-symmetry cages containing heteroatoms, illustrating that pores of varying geometries and surface chemistries may be reliably accessed through computational prediction and self-sorting.

Biodiversity in marine invertebrate responses to acute warming revealed by a comparative multi-omics approach.

Understanding species' responses to environmental change underpins our abilities to make predictions on future biodiversity under any range of scenarios. In spite of the huge biodiversity in most ecosystems, a model species approach is often taken in environmental studies. To date, we still do not know how many species we need to study to input into models and inform on ecosystem-level responses to change. In this study, we tested current paradigms on factors setting thermal limits by investigating the acute warming response of six Antarctic marine invertebrates: a crustacean Paraceradocus miersi, a brachiopod Liothyrella uva, two bivalve molluscs, Laternula elliptica, Aequiyoldia eightsii, a gastropod mollusc Marseniopsis mollis and an echinoderm Cucumaria georgiana. Each species was warmed at the rate of 1 °C h-1 and taken to the same physiological end point (just prior to heat coma). Their molecular responses were evaluated using complementary metabolomics and transcriptomics approaches with the aim of discovering the underlying mechanisms of their resilience or sensitivity to warming. The responses were species-specific; only two showed accumulation of anaerobic end products and three exhibited the classical heat shock response with expression of HSP70 transcripts. These diverse cellular measures did not directly correlate with resilience to heat stress and suggested that each species may have a different critical point of failure. Thus, one unifying molecular mechanism underpinning response to warming could not be assigned, and no overarching paradigm was supported. This biodiversity in response makes future ecosystems predictions extremely challenging, as we clearly need to develop a macrophysiology-type approach to cellular evaluations of the environmental stress response, studying a range of well-rationalized members from different community levels and of different phylogenetic origins rather than extrapolating from one or two arbitrary model species.

Molecular snapshot of an intracellular freezing event in an Antarctic nematode.

The Antarctic nematode, Panagrolaimus sp. DAW1 (formerly called Panagrolaimus davidi), is the best documented example of an organism able to survive intracellular ice formation in all of its compartments. Not only is it able to survive such extreme physiological disruption, but it is able to produce progeny once thawed from such a state. In addition, under slower rates, or less extreme degrees, of cooling, its body remains unfrozen and the vapour pressure difference between the supercooled body fluids and the surrounding ice leads to a process termed cryoprotective dehydration. In contrast to a fairly large body of work in building up our molecular understanding of cryoprotective dehydration, no comparable work has been undertaken on intracellular freezing. This paper describes an experiment subjecting cultures of Panagrolaimus sp. DAW1 to a range of temperatures including a rapid descent to -10 °C, in a medium just prior to, and after, freezing. Through deep sequencing of RNA libraries we have gained a snapshot of which genes are highly abundant when P. sp. DAW1 is undergoing an intracellular freezing event. The onset of freezing correlated with a high production of genes involved in cuticle formation and subsequently, after 24 h in a frozen state, protease production. In addition to the mapping of RNA sequencing, we have focused on a select set of genes arising both from the expression profiles, as well as implicated from other cold tolerance studies, to undertake qPCR. Among the most abundantly represented transcripts in the RNA mapping is the zinc-metalloenzyme, neprilysin, which also shows a particularly strong upregulated signal through qPCR once the nematodes have frozen.

High-throughput sequencing reveals inbreeding depression in a natural population.

Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49%. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged.

Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.

BACKGROUND: The capacity of marine species to survive chronic heat stress underpins their ability to survive warming oceans as a result of climate change. In this study RNA-Seq and 2-DE proteomics were employed to decipher the molecular response of the sub-tidal bivalve Pecten maximus, to elevated temperatures. RESULTS: Individuals were maintained at three different temperatures (15, 21 and 25 °C) for 56 days, representing control conditions, maximum environmental temperature and extreme warming, with individuals sampled at seven time points. The scallops thrived at 21 °C, but suffered a reduction in condition at 25 °C. RNA-Seq analyses produced 26,064 assembled contigs, of which 531 were differentially expressed, with putative annotation assigned to 177 transcripts. The proteomic approach identified 24 differentially expressed proteins, with nine identified by mass spectrometry. Network analysis of these results indicated a pivotal role for GAPDH and AP-1 signalling pathways. Data also suggested a remodelling of the cell structure, as revealed by the differential expression of genes involved in the cytoskeleton and cell membrane and a reduction in DNA repair. They also indicated the diversion of energetic metabolism towards the mobilization of lipid energy reserves to fuel the increased metabolic rate at the higher temperature. CONCLUSIONS: This work provides preliminary insights into the response of P. maximus to chronic heat stress and provides a basis for future studies examining the tipping points and energetic trade-offs of scallop culture in warming oceans.

Variability among individuals is generated at the gene expression level.

Selection acts on individuals, specifically on their differences. To understand adaptation and responses to change therefore requires knowledge of how variation is generated and distributed across traits. Variation occurs on different biological scales, from genetic through physiological to morphological, yet it is unclear which of these carries the most variability. For example, if individual variation is mainly generated by differences in gene expression, variability should decrease progressively from coding genes to morphological traits, whereas if post-translational and epigenetic effects increase variation, the opposite should occur. To test these predictions, we compared levels of variation among individuals in various measures of gene expression, physiology (including activity), and morphology in two abundant and geographically widespread Antarctic molluscs, the clam Laternula elliptica and the limpet Nacella concinna. Direct comparisons among traits as diverse as heat shock protein QPCR assays, whole transcription profiles, respiration rates, burying rate, shell length, and ash-free dry mass were made possible through the novel application of an established metric, the Wentworth Scale. In principle, this approach could be extended to analyses of populations, communities, or even entire ecosystems. We found consistently greater variation in gene expression than morphology, with physiological measures falling in between. This suggests that variability is generated at the gene expression level. These findings have important implications for refining current biological models and predictions of how biodiversity may respond to climate change.

Adult acclimation to combined temperature and pH stressors significantly enhances reproductive outcomes compared to short-term exposures.

This study examined the effects of long-term culture under altered conditions on the Antarctic sea urchin, Sterechinus neumayeri. Sterechinus neumayeri was cultured under the combined environmental stressors of lowered pH (-0.3 and -0.5 pH units) and increased temperature (+2 °C) for 2 years. This time-scale covered two full reproductive cycles in this species and analyses included studies on both adult metabolism and larval development. Adults took at least 6-8 months to acclimate to the altered conditions, but beyond this, there was no detectable effect of temperature or pH. Animals were spawned after 6 and 17 months exposure to altered conditions, with markedly different outcomes. At 6 months, the percentage hatching and larval survival rates were greatest in the animals kept at 0 °C under current pH conditions, whilst those under lowered pH and +2 °C performed significantly less well. After 17 months, performance was not significantly different across treatments, including controls. However, under the altered conditions urchins produced larger eggs compared with control animals. These data show that under long-term culture adult S. neumayeri appear to acclimate their metabolic and reproductive physiology to the combined stressors of altered pH and increased temperature, with relatively little measureable effect. They also emphasize the importance of long-term studies in evaluating effects of altered pH, particularly in slow developing marine species with long gonad maturation times, as the effects of altered conditions cannot be accurately evaluated unless gonads have fully matured under the new conditions.

Interaction strengths in balanced carbon cycles and the absence of a relation between ecosystem complexity and stability.

The strength of interactions is crucial to the stability of ecological networks. However, the patterns of interaction strengths in mathematical models of ecosystems have not yet been based upon independent observations of balanced material fluxes. Here we analyse two Antarctic ecosystems for which the interaction strengths are obtained: (1) directly, from independently measured material fluxes, (2) for the complete ecosystem and (3) with a close match between species and 'trophic groups'. We analyse the role of recycling, predation and competition and find that ecosystem stability can be estimated by the strengths of the shortest positive and negative predator-prey feedbacks in the network. We show the generality of our explanation with another 21 observed food webs, comparing random-type parameterisations of interaction strengths with empirical ones. Our results show how functional relationships dominate over average-network topology. They make clear that the classic complexity-instability paradox is essentially an artificial interaction-strength result.

Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis.

Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCRαß clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.

Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal.

BACKGROUND: Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals (Arctocephalus gazella) that died of natural causes at Bird Island, South Georgia. RESULTS: After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog (Canis lupus familiaris) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. CONCLUSIONS: Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern.

Formation of a meltable purinate metal-organic framework and its glass analogue.

The chemistries that can be incorporated within melt-quenched zeolitic imidazolate framework (ZIF) glasses are currently limited. Here we describe the preparation of a previously unknown purine-containing ZIF which we name ZIF-UC-7. We find that it melts and forms a glass at one of the lowest temperatures reported for 3D hybrid frameworks.

Physiological plasticity, long term resistance or acclimation to temperature, in the Antarctic bivalve, Laternula elliptica.

To further investigate the previously reported limited acclimation capacities of Antarctic marine stenotherms, the Antarctic mud clam, Laternula elliptica (King and Broderip, 1830-1831), was incubated at 3.0°C for 89days. The thermal windows of a suite of biochemical and physiological metrics that characterise tissue aerobic status, were then measured in response to acute temperature elevation (2-2.5°C increase per week). To test if acclimation had occurred at the higher temperature, results were compared with published data, from the preceding year, for L. elliptica which had been incubated at ambient temperature (0.0°C) and then subjected to the same acute temperature treatments. Incubation to 3.0°C led to a temperature induced increase of tissue aerobic status (reduced intracellular cCO(2) with increased O(2) consumption, PLA (phospho-L-arginine) and ATP). At the highest acute temperature (7.5°C) the increase in anaerobic pathways (summed acetate/succinate and propionate) was less after 3.0°C than 0.0°C incubation. No other metric shifted its reaction norm in response to acute temperature elevation and so whole animal acclimation had not occurred, even after 3months at 3.0°C. Combined with the constant mortality throughout the 3.0°C incubation period, these data suggest that the recorded physiological changes were either the early stages of acclimation or, more likely, time limited resistance mechanisms.

Practical Implementation of Genetics: New Concepts in Immunogenomics to Predict, Prevent, and Diagnose Drug Hypersensitivity.

Delayed drug hypersensitivities are CD8+ T cell-mediated reactions associated with up to 50% mortality. Human leukocyte antigen (HLA) alleles are known to predispose disease and are specific to drug, reaction, and patient ethnicity. Pretreatment screening is recommended for a handful of the strongest associations to identify and prevent drug use in high-risk patients. However, an incomplete predictive value implicates other HLA-imposed risk factors, and low carriage of many identified HLA-risk alleles combined with the high cost of sequence-based typing has limited economic viability for similar recommendation of screening across drugs and health care systems. For mitigation, an expanding armory of low-cost polymerase chain reaction-based screens is being developed, and HLA-imposed risk factors are being discovered. These include (1) polymorphic variants of metabolic and endoplasmic reticulum aminopeptidase enzymes toward multiallelic screening with increased predictivity; (2) regulation by immune checkpoint inhibitors, enabling detolerized animal models of human disease; and (3) immunodominant T cell receptors (TCR) on clonally expanded CD8+ T cells. For the latter, HLA risk-restricted TCR provides immunogenomic strategies and samples from a single patient to identify novel HLA-risk associations in underserved minority populations, tissue-relevant effector biomarkers toward earlier diagnosis and treatment, and HLA-TCR-presented immunogenic structures to aid future drug development.

Mechanochemically synthesised dicyanamide hybrid organic-inorganic perovskites, and their melt-quenched glasses.

Here we present efficient and scalable mechanochemical formation of hybrid organic-inorganic perovskites of the form [TPrA][M(dca)3] (M = Mn2+, Co2+) and the subsequent formation of their bulk melt-quenched glasses. In situ X-ray diffraction reveals direct, facile, and almost instantaneouos formation of both crystalline materials, while slow cooling limits recrystallisation in glasses. The glasses show good stability to acidic and basic aqueous solutions and display higher carbon dioxide uptakes than their crystalline precursors.

Investigating the chemical sensitivity of melting in zeolitic imidazolate frameworks.

The number of zeolitic imidazolate frameworks (ZIFs) that form melt-quenched glasses remains limited, with most displaying the cag network topology. Here, we expand our studies to zni topology ZIFs, starting with ZIF-zni [Zn(Im)2] before changing its linker chemistry, by incorporating 2-methylimidazolate and 5-aminobenzimidazolate. ZIF-zni was found to melt and form a glass, with Tm = 576 °C and Tg = 322 °C, although it was not possible to prepare the glass without zinc oxide impurities. The addition of 2-methylimidazolate to the structure gave ZIF-61 [Zn(Im)1.35(mIm)0.65], which decomposed without passing through the liquid state. However, incorporating small quantities of 5-aminobenzimidazolate resulted in a ZIF [Zn(Im)1.995(abIm)0.005] with a lower melting temperature (Tm = 569 °C) than pure ZIF-zni, and no evidence of zinc oxide growth. This demonstrates the sensitivity of melting behaviour in ZIFs towards linker chemistry, with only a 0.25% variation capable of eliciting a 7 °C change in melting temperature. This study highlights the chemical sensitivity of melting in ZIFs and serves as a promising strategy for tuning their melting behaviour.