Search

A study was made of the influence of hydralazine on the oral availability of a sustained release formulation of propranolol (Inderal LA). Sustained release propranolol 160 mg was given orally either alone or in combination with oral hydralazine 25 mg on separate occasions to six healthy volunteers. Blood and urine samples were collected post- dosing over 34 h. Peak concentrations of propranolol, time to peak and area under the plasma concentration-time curve (AUC) were not altered by co-administration of hydralazine with sustained release propranolol. Similarly, there was no change in recovery of 11C-labelled propranolol and metabolites in those individuals to whom tracer label was given. These results contrast with previous reports of marked interaction between the conventional formulation of propranolol and hydralazine or food. Interactions were confirmed between hydralazine and conventional propranolol in three subjects who had been studied previously with sustained release propranolol. Analysis of metabolite profiles in one of these subjects established that the major metabolites do change under hydralazine stimulus. These results indicate that substrate delivery rates may determine presystemic drug interactions, suggesting capacity limitations of hydroxylation processes or short-term flow redistribution following hydralazine, resulting in functional shunting past the hydroxylation enzymes. These results exclude global or lasting enzyme inhibition by hydralazine or simple flow-sensitivity of presystemic clearance. [ABSTRACT FROM AUTHOR]

Novel introductions of largemouth bass, Micropterus salmoides, often cause negative impacts on endemic populations of prey fishes and interspecific competitors. Although many studies have investigated trophic interactions between M. salmoides and smallmouth bass, Micropterus dolomieu, few have included chain pickerel, Esox niger, as a competitor despite similarities in their habitat use. We used stable isotope analysis to investigate the trophic ecology of a recently introduced population of M. salmoides in the Wolastoq|Saint John River. Specifically, we measured carbon (δ 13 C) and nitrogen (δ 15 N) isotopes to describe isotopic niches and infer resource use of introduced M. salmoides, M. dolomieu, E. niger, and native yellow perch, Perca flavescens, at various life stages. Our results showed that isotopic niche overlap occurred between M. salmoides and other study species, indicative of resource competition. However, resource use plasticity, as demonstrated by a wide variety of resources (marine, terrestrial, littoral, and pelagic) used by all study species, could potentially reduce interspecific competition. Our findings indicate that competition is highest between adult M. salmoides and E. niger, but the presence of a seasonal marine resource can provide important contributions to diets and potentially reduce competition. Further research should focus on monitoring of long-term trends to identify the dynamics of all study species as M. salmoides populations become further established and dispersed., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Compositionally biased regions (CBRs), ie, tracts that are dominated by a subset of residue types, are common features of eukaryotic proteins. These are often found bounded within or almost coterminous with intrinsically disordered or 'natively unfolded' parts. Here, it is investigated how the function of such intrinsically disordered compositionally biased regions (ID-CBRs) is directly linked to their compositional traits, focusing on the well-characterized yeast ( Saccharomyces cerevisiae ) proteome as a test case. The ID-CBRs that are clustered together using compositional distance are discovered to have clear functional linkages at various levels of diversity. The specific case of the Sup35p and Rnq1p proteins that underlie causally linked prion phenomena ([PSI+] and [RNQ+]) is highlighted. Their prion-forming ID-CBRs are typically clustered very close together indicating some compositional engendering for [RNQ+] seeding of [PSI+] prions. Delving further, ID-CBRs with distinct types of residue patterning such as 'blocking' or relative segregation of residues into homopeptides are found to have significant functional trends. Specific examples of such ID-CBR functional linkages that are discussed are: Q/N-rich ID-CBRs linked to transcriptional coactivation, S-rich to transcription-factor binding, R-rich to DNA-binding, S/E-rich to protein localization, and D-rich linked to chromatin remodelling. These data may be useful in informing experimental hypotheses for proteins containing such regions., Competing 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) 2024.)

Proteins can contain tracts dominated by a subset of amino acids and that have a functional significance. These are often termed 'low-complexity regions' (LCRs) or 'compositionally-biased regions' (CBRs). However, a wide spectrum of compositional bias is possible, and program parameters used to annotate these regions are often arbitrarily chosen. Also, investigators are sometimes interested in longer regions, or sometimes very short ones. Here, two programs for annotating LCRs/CBRs, namely SEG and fLPS, are investigated in detail across the whole expanse of their parameter spaces. In doing so, boundary behaviours are resolved that are used to derive an optimized systematic strategy for annotating LCRs/CBRs. Sets of parameters that progressively annotate or 'cover' more of protein sequence space and are optimized for a given target length have been derived. This progressive annotation can be applied to discern the biological relevance of CBRs, e.g., in parsing domains for experimental constructs and in generating hypotheses. It is also useful for picking out candidate regions of interest of a given target length and bias signature, and for assessing the parameter dependence of annotations. This latter application is demonstrated for a set of human intrinsically-disordered proteins associated with cancer., (© 2024. The Author(s).)

Foraging is a behavioural process and, therefore, individual behaviour and diet are theorized to covary. However, few comparisons of individual behaviour type and diet exist in the wild. We tested whether behaviour type and diet covary in a protected population of Atlantic cod, Gadus morhua. Working in a no-take marine reserve, we could collect data on natural behavioural variation and diet choice with minimal anthropogenic disturbance. We inferred behaviour using acoustic telemetry and diet from stable isotope compositions (expressed as δ 13 C and δ 15 N values). We further investigated whether behaviour and diet could have survival costs. We found cod with shorter diel vertical migration distances fed at higher trophic levels. Cod δ 13 C and δ 15 N values scaled positively with body size. Neither behaviour nor diet predicted survival, indicating phenotypic diversity is maintained without survival costs for cod in a protected ecosystem. The links between diet and diel vertical migration highlight that future work is needed to understand whether the shifts in this behaviour during environmental change (e.g. fishing or climate), could lead to trophic cascades., (© 2023 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Prions are proteinaceous particles that can propagate an alternative conformation to further copies of the same protein. They have been described in mammals, fungi, bacteria and archaea. Furthermore, across diverse organisms from bacteria to eukaryotes, prion-like proteins that have similar sequence characters are evident. Such prion-like proteins have been linked to pathomechanisms of amyotrophic lateral sclerosis (ALS) in humans, in particular TDP43, FUS, TAF15, EWSR1 and hnRNPA2. Because of the desire to study human disease-linked proteins in model organisms, and to gain insights into the functionally important parts of these proteins and how they have changed across hundreds of millions of years of evolution, we analyzed how the sequence traits of these five proteins have evolved across eukaryotes, including plants and metazoa. We discover that the RNA-binding domain architecture of these proteins is deeply conserved since their emergence. Prion-like regions are also deeply and widely conserved since the origination of the protein families for FUS, TAF15 and EWSR1, and since the last common ancestor of metazoa for TDP43 and hnRNPA2. Prion-like composition is uncommon or weak in any plant orthologs observed, however in TDP43 many plant proteins have equivalent regions rich in other amino acids (namely glycine and tyrosine and/or serine) that may be linked to stress granule recruitment. Deeply conserved low-complexity domains are identified that likely have functional significance., Competing Interests: The authors declare that they have no competing interests., (© 2022 Luo and Harrison.)

Immunoglobulin superfamily, member 1 (IGSF1) is a transmembrane glycoprotein with high expression in the mammalian pituitary gland. Mutations in the IGSF1 gene cause congenital central hypothyroidism in humans. The IGSF1 protein is co-translationally cleaved into N- and C-terminal domains (NTD and CTD), the latter of which is trafficked to the plasma membrane and appears to be the functional portion of the molecule. Though the IGSF1-NTD is retained in the endoplasmic reticulum and has no apparent function, it has a high degree of sequence identity with the IGSF1-CTD and is conserved across mammalian species. Based upon phylogenetic analyses, we propose that the ancestral IGSF1 gene encoded the IGSF1-CTD, which was duplicated and integrated immediately upstream of itself, yielding a larger protein encompassing the IGSF1-NTD and IGSF1-CTD. The selective pressures favoring the initial gene duplication and subsequent retention of a conserved IGSF1-NTD are unresolved., Competing Interests: The authors have declared that no competing interests exist.

Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias ( i.e., those termed 'low-complexity'), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized 'dark matter' of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A 'thorough' option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper., Competing Interests: The author declares there are no competing interests., (©2021 Harrison.)

Homopeptides (runs of one amino-acid type) are evolutionarily important since they are prone to expand/contract during DNA replication, recombination and repair. To gain insight into the genomic/proteomic traits driving their variation, we analyzed how homopeptides and homocodons (which are pure codon repeats) vary across 405 Dikarya, and probed their linkage to genome GC/AT bias and other factors. We find that amino-acid homopeptide frequencies vary diversely between clades, with the AT-rich Saccharomycotina trending distinctly. As organisms evolve, homocodon and homopeptide numbers are majorly coupled to GC/AT-bias, exhibiting a bi-furcated correlation with degree of AT- or GC-bias. Mid-GC/AT genomes tend to have markedly fewer simply because they are mid-GC/AT. Despite these trends, homopeptides tend to be GC-biased relative to other parts of coding sequences, even in AT-rich organisms, indicating they absorb AT bias less or are inherently more GC-rich. The most frequent and most variable homopeptide amino acids favour intrinsic disorder, and there are an opposing correlation and anti-correlation versus homopeptide levels for intrinsic disorder and structured-domain content respectively. Specific homopeptides show unique behaviours that we suggest are linked to inherent slippage probabilities during DNA replication and recombination, such as poly-glutamine, which is an evolutionarily very variable homopeptide with a codon repertoire unbiased for GC/AT, and poly-lysine whose homocodons are overwhelmingly made from the codon AAG.

The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.

The proteome of the malaria parasite Plasmodium falciparum is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum . Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (<5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (<10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (≥10 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include "vesicle-mediated transport", and "DNA-directed 5'-3' RNA polymerase activity", with various categories linked to "binding" evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near/in IDRs. The implications of these findings are discussed., Competing Interests: The authors declare that they have no competing interests., (© 2020 Wang et al.)

Prions are self-propagating alternative states of protein domains. They are linked to both diseases and functional protein roles in eukaryotes. Prion-forming domains in Saccharomyces cerevisiae are typically domains with high intrinsic protein disorder ( i.e., that remain unfolded in the cell during at least some part of their functioning), that are converted to self-replicating amyloid forms. S. cerevisiae is a member of the fungal class Saccharomycetes , during the evolution of which a large population of prion-like domains has appeared. It is still unclear what principles might govern the molecular evolution of prion-forming domains, and intrinsically disordered domains generally. Here, it is discovered that in a set of such prion-forming domains some evolve in the fungal class Saccharomycetes in such a way as to absorb general mutation biases across millions of years, whereas others do not, indicating a spectrum of selection pressures on composition and sequence. Thus, if the bias-absorbing prion formers are conserving a prion-forming capability, then this capability is not interfered with by the absorption of bias changes over the duration of evolutionary epochs. Evidence is discovered for selective constraint against the occurrence of lysine residues (which likely disrupt prion formation) in S. cerevisiae prion-forming domains as they evolve across Saccharomycetes . These results provide a case study of the absorption of mutational trends by compositionally biased domains, and suggest methodology for assessing selection pressures on the composition of intrinsically disordered regions., Competing Interests: The author declares there are no competing interests., (©2020 Harrison.)

Memory, on multiple timescales, is critical to our ability to discover the structure of our surroundings, and efficiently interact with the environment. We combined behavioural manipulation and modelling to investigate the dynamics of memory formation for rarely reoccurring acoustic patterns. In a series of experiments, participants detected the emergence of regularly repeating patterns within rapid tone-pip sequences. Unbeknownst to them, a few patterns reoccurred every ~3 min. All sequences consisted of the same 20 frequencies and were distinguishable only by the order of tone-pips. Despite this, reoccurring patterns were associated with a rapidly growing detection-time advantage over novel patterns. This effect was implicit, robust to interference, and persisted for 7 weeks. The results implicate an interplay between short (a few seconds) and long-term (over many minutes) integration in memory formation and demonstrate the remarkable sensitivity of the human auditory system to sporadically reoccurring structure within the acoustic environment., Competing Interests: RB, PH, MH, CB, SP, MP, MC No competing interests declared, (© 2020, Bianco et al.)

Pub1 protein is an important RNA-binding protein functional in stress granule assembly in budding yeast Saccharomyces cerevisiae and, as its co-ortholog Tia1, in humans. It is unique among proteins in evidencing prion-like aggregation in both its yeast and human forms. Previously, we noted that Pub1/Tia1 was the only protein linked to human disease that has prion-like character and and has demonstrated such aggregation in both species. Thus, we were motivated to probe further into the evolution of the Pub1/Tia1 family (and its close relative Nam8 and its orthologs) to gain a picture of how such a protein has evolved over deep evolutionary time since the last common ancestor of eukaryotes. Here, we discover that the prion-like composition of this protein family is deeply conserved across eukaryotes, as is the prion-like composition of its close relative Nam8/Ngr1. A sizeable minority of protein orthologs have multiple prion-like domains within their sequences (6-20% depending on criteria). The number of RNA-binding RRM domains is conserved at three copies over >86% of the Pub1 family (>71% of the Nam8 family), but proteins with just one or two RRM domains occur frequently in some clades, indicating that these are not due to annotation errors. Overall, our results indicate that a basic scaffold comprising three RNA-binding domains and at least one prion-like region has been largely conserved since the last common ancestor of eukaryotes, providing further evidence that prion-like aggregation may be a very ancient and conserved phenomenon for certain specific proteins., Competing Interests: The authors declare that they have no competing interests., (© 2020 Su and Harrison.)

Prions in eukaryotes have been linked to diseases, evolutionary capacitance, large-scale genetic control, and long-term memory formation. Prion formation and propagation have been studied extensively in the budding yeast Saccharomyces cerevisiae . Here, we have analysed the conservation of sequence and of prion-like composition for prion-forming proteins and for other prion-like proteins from S. cerevisiae , across three evolutionary levels. We discover that prion-like status is well-conserved for about half the set of prion-formers at the Saccharomycetes level, and that prion-forming domains evolve more quickly as sequences than other prion-like domains do. Such increased mutation rates may be linked to the acquisition of functional roles for prion-forming domains during the evolutionary epoch of Saccharomycetes . Domain scores for prion-like composition in S. cerevisiae are strongly correlated with scores for such composition weighted evolutionarily over the dozens of fungal species examined, indicating conservation of such prion-like status. Examples of notable prion-like proteins that are highly conserved both in sequence and prion-like composition are discussed.

Prions in eukaryotes have been linked to diseases, evolutionary capacitance, large-scale genetic control and long-term memory formation. In bacteria, constructed prion-forming proteins have been described, such as the prion-forming protein recently described for Clostridium botulinum transcription terminator Rho. Here, I analyzed the evolution of the Rho prion-forming domain across bacteria, and discovered that its conservation is sporadic both in the Clostridium genus and in bacteria generally. Nonetheless, it has an apparent evolutionary reach into eight or more different bacterial phyla. Motivated by these results, I investigated whether this pattern of wide-ranging evolutionary sporadicity is typical of bacterial prion-like domains. A measure of coverage of a domain (C) within its evolutionary range was derived, which is effectively a weighted fraction of the number of species in which the domain is found. I observe that occurrence across multiple phyla is not uncommon for bacterial prion-like protein domain families, but that they tend to sample of a low fraction of species within their evolutionary range, like Rho. The Rho prion-like domain family is one of the top three most widely distributed prion-like protein domain families in terms of number of phyla. There are >60 prion-like protein domain families that have at least the evolutionary coverage of Rho, and are found in multiple phyla. The implications of these findings for evolution and for experimental investigations into prion-forming proteins are discussed., Competing Interests: The author has declared that no competing interests exist.

Compositionally biased regions (BRs) occur when a few amino-acid types are enriched in a protein segment. There are possibly BR types in the known protein universe that have not been characterized experimentally. The UniProt protein database has been surveyed for evidence of such compositionally ''dark matter''. A ''dark biased region'' (DBR) is defined as a biased region with low probability of being an individual structural domain or intrinsically disordered region. The bias annotation program fLPS is used to generate a list of >13 million BRs, which is then thoroughly filtered for structure and intrinsic disorder. About a third of BRs (31%) has both substantial intrinsic disorder and structure. After filtering, there are ≈0.9 million DBRs (≈7% of the original BRs in ≈1.4% of proteins). These DBRs are hugely enriched in eukaryotes and hugely depleted in bacteria. They tend to be more hydrophobic than other protein regions, but are made of less extreme combinations of hydrophobic/hydrophilic residues. Given varying assumptions, It has been estimated that how many DBRs there might be for the high bias levels examined (with p-values < 1 × 10 -06 ), deriving a reasonable range of 0.7-7.2% of proteins having such DBRs. Hypotheses are examined about what such DBRs might be, that is, that they are from un- or undersampled domain/region categories or are unappreciated categories somewhat like existing ones., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture., Competing Interests: The authors have declared that no competing interests exist.

Primary ubiquinone (UQ) deficiency is an important subset of mitochondrial disease that is caused by mutations in UQ biosynthesis genes. To guide therapeutic efforts we sought to estimate the number of individuals who are born with pathogenic variants likely to cause this disorder. We used the NCBI ClinVar database and literature reviews to identify pathogenic genetic variants that have been shown to cause primary UQ deficiency, and used the gnomAD database of full genome or exome sequences to estimate the frequency of both homozygous and compound heterozygotes within seven genetically-defined populations. We used known population sizes to estimate the number of afflicted individuals in these populations and in the mixed population of the USA. We then performed the same analysis on predicted pathogenic loss-of-function and missense variants that we identified in gnomAD. When including only known pathogenic variants, our analysis predicts 1,665 affected individuals worldwide and 192 in the USA. Adding predicted pathogenic variants, our estimate grows to 123,789 worldwide and 1,462 in the USA. This analysis predicts that there are many undiagnosed cases of primary UQ deficiency, and that a large proportion of these will be in developing regions of the world.

Background: Proteins often contain regions that are compositionally biased (CB), i.e., they are made from a small subset of amino-acid residue types. These CB regions can be functionally important, e.g., the prion-forming and prion-like regions that are rich in asparagine and glutamine residues., Results: Here I report a new program fLPS that can rapidly annotate CB regions. It discovers both single-residue and multiple-residue biases. It works through a process of probability minimization. First, contigs are constructed for each amino-acid type out of sequence windows with a low degree of bias; second, these contigs are searched exhaustively for low-probability subsequences (LPSs); third, such LPSs are iteratively assessed for merger into possible multiple-residue biases. At each of these stages, efficiency measures are taken to avoid or delay probability calculations unless/until they are necessary. On a current desktop workstation, the fLPS algorithm can annotate the biased regions of the yeast proteome (>5700 sequences) in <1 s, and of the whole current TrEMBL database (>65 million sequences) in as little as ~1 h, which is >2 times faster than the commonly used program SEG, using default parameters. fLPS discovers both shorter CB regions (of the sort that are often termed 'low-complexity sequence'), and milder biases that may only be detectable over long tracts of sequence., Conclusions: fLPS can readily handle very large protein data sets, such as might come from metagenomics projects. It is useful in searching for proteins with similar CB regions, and for making functional inferences about CB regions for a protein of interest. The fLPS package is available from: http://biology.mcgill.ca/faculty/harrison/flps.html , or https://github.com/pmharrison/flps , or is a supplement to this article.

The variations in migration that comprise partial diel migrations, putatively occur entirely as a consequence of behavioural flexibility. However, seasonal partial migrations are increasingly recognised to be mediated by a combination of reversible plasticity in response to environmental variation and individual variation due to genetic and environmental effects. Here, we test the hypothesis that while partial diel migration heterogeneity occurs primarily due to short-term within-individual flexibility in behaviour, long-term individual differences in migratory behaviour also underpin this migration variation. Specifically, we use a hierarchical behavioural reaction norm approach to partition within- and among-individual variation in depth use and diel plasticity in depth use, across short- and long-term time-scales, in a group of 47 burbot (Lota lota) tagged with depth-sensing acoustic telemetry transmitters. We found that within-individual variation at the among-dates-within-seasons and among-seasons scale, explained the dominant proportion of phenotypic variation. However, individuals also repeatedly differed in their expression of migration behaviour over the 2 year study duration. These results reveal that diel migration variation occurs primarily due to short-term within-individual flexibility in depth use and diel migration behaviour. However, repeatable individual differences also played a key role in mediating partial diel migration. These findings represent a significant advancement of our understanding of the mechanisms generating the important, yet poorly understood phenomena of partial diel migration. Moreover, given the pervasive occurrence of diel migrations across aquatic taxa, these findings indicate that individual differences have an important, yet previously unacknowledged role in structuring the temporal and vertical dynamics of aquatic ecosystems., (© 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.)

Despite many similarities and intuitive links between individual dietary specialization and behavioral inter-individual variation, these phenomena have been studied in isolation, and empirical data confirming relationships between these intraspecific variance sources are lacking. Here we use stable isotope analysis and acoustic telemetry to test the hypothesis that individual specialization in trophic (δ 15 N) and littoral/pelagic prey reliance (δ 13 C) covary with inter-individual variation in movement in a group of 34 free-swimming burbot (Lota lota). By performing stable isotope analysis on tissues with differing isotopic turnover rates (anal fin and dorsal muscle), in 24 lethally sampled burbot, we demonstrate that individual specialization in trophic niche (δ 15 N) and littoral/pelagic prey reliance (δ 13 C) occurred within the population. By performing stable isotope analysis on anal fins of a group of telemetry tagged burbot, we were able to show that interactions between trophic niche and littoral/pelagic prey reliance, explained a significant proportion of the subsequent between-individual variance in mean movement rates. These findings demonstrate an empirical connection between behavioral inter-individual variation and dietary specialization, thus providing a substantial expansion of our understanding of the wider ecological consequences of these interesting phenomena., (© 2016 by the Ecological Society of America.)

Background: Prions are proteinaceous particles that propagate alternative protein conformations/states to further copies of the same proteins, and are transmitted from cell-to-cell, and organism-to-organism. Prions are usually made of the beta-sheet rich assemblies termed amyloid. The original prion protein PrP causes devastating neurodegenerative disorders in humans and other mammals. In the yeast Saccharomyces cerevisiae, many prion-forming proteins have been observed; a prominent feature of these proteins is an intrinsically disordered domain rich in glutamine (Q) and asparagine (N) residues. Several human proteins that are yeast-prion-like, in particular those with poly-glutamine (poly-Q) expansions, have been experimentally implicated in human neurodegenerative diseases., Results: Here, we have constructed a comprehensive list of human yeast-prion-like proteins that are linked to human neurological disease. Surprisingly, different methods to annotate yeast-prion-like proteins in humans have limited intersection. However, independent of annotation method, we find that human yeast-prion-like proteins as a group have a statistically significant genetic linkage to neurological disease, that is caused specifically by linkage to neurodegenerative diseases. This is despite: (i) no especially high expression of yeast-prion-like proteins in the central nervous system, or (ii) no general enrichment of intrinsically disordered proteins in neurological/neurodegenerative diseases. Cytoskeletal proteins are significantly overrepresented in the set of human yeast-prion-like neurological proteins. Whether involved in neurological pathomechanisms or not, yeast-prion-like proteins in humans have very limited conservation outside of Deuterostomia (< ~10 %) with only a handful having prion-like character in both human and S. cerevisiae. The only such protein with a disease linkage is PUB1/TIA1, which functions as a stress granule component. Thus, the yeast-prion-like character of proteins linked to neurodegenerative diseases has not been conserved over the deep evolutionary time since the last common ancestor of yeasts and humans., Conclusion: Our results provide a comprehensive picture of yeast-prion-like proteins in humans and contribute to the strategic basis for experimental investigation of the link between yeast-prion-like protein character and neurological disease., Reviewers: Reviewed by Istvan Simon and Alexander Schleiffer. For the full reviews, please go to the Reviewers' comments section.

In this study, animal-borne telemetry with temperature sensors was coupled with extensive habitat temperature monitoring in a dimictic reservoir, to test the following hypotheses: behavioural thermoregulation occurs throughout the year and temperature selection varies on a diel and seasonal basis, in a winter-specialist diel-migrating fish. Burbot Lota lota demonstrated nightly behavioural thermoregulation throughout the year, with a large seasonal shift between selection for very cold temperatures (<2° C) optimal for reproduction during the spawning period and selection for warmer temperatures (12-14° C) optimal for hunting and feeding during non-reproductive periods. During daylight hours, while L. lota avoided habitats warmer than optimal for reproduction and feeding during the spawning and non-reproductive periods, respectively, active selection was limited to selection for 4-6° C habitat during the prespawning period. Although behavioural thermoregulation explained the night-time migration, behavioural thermoregulation only partially explained daytime behaviour, indicating that diel migration is best explained by a combination of factors. Thus, thermal-habitat selection was a good predictor of night-time habitat occupancy in a diel-migrating species. Together, these results show that thermal-habitat selection by fishes may be important throughout the year and a more seasonally plastic behaviour than previously recognized., (© 2016 The Fisheries Society of the British Isles.)

Key Points: The presynaptic protein α-synuclein forms aggregates during Parkinson's disease. Accumulating evidence suggests that the small soluble oligomers of α-synuclein are more toxic than the larger aggregates appearing later in the disease. The link between oligomer toxicity and structure still remains unclear. In the present study, we have produced two structurally-defined oligomers that have a similar morphology but differ in secondary structure. These oligomers were introduced into neocortical pyramidal cells during whole-cell recording and, using a combination of experimentation and modelling, electrophysiological parameters were extracted. Both oligomeric species had similar effects on neuronal properties reducing input resistance, time constant and increasing capacitance. The net effect was a marked reduction in neuronal excitability that could impact on network activity., Abstract: The presynaptic protein α-synuclein (αSyn) aggregates during Parkinson's disease (PD) to form large proteinaceous amyloid plaques, the spread of which throughout the brain clinically defines the severity of the disease. During early stages of aggregation, αSyn forms soluble annular oligomers that show greater toxicity than much larger fibrils. These oligomers produce toxicity via a number of possible mechanisms, including the production of pore-forming complexes that permeabilize membranes. In the present study, two well-defined species of soluble αSyn oligomers were produced by different protocols: by polymerization of monomer and by sonication of fibrils. The two oligomeric species produced were morphologically similar, with both having an annular structure and consisting of approximately the same number of monomer subunits, although they differed in their secondary structure. Oligomeric and monomeric αSyn were injected directly into the soma of pyramidal neurons in mouse neocortical brain slices during whole-cell patch clamp recording. Using a combined experimental and modelling approach, neuronal parameters were extracted to measure, for the first time in the neocortex, specific changes in neuronal electrophysiology. Both species of oligomer had similar effects: (i) a significant reduction in input resistance and the membrane time constant and (ii) an increase in the current required to trigger an action potential with a resultant reduction in the firing rate. Differences in oligomer secondary structure appeared to produce only subtle differences in the activity of the oligomers. Monomeric αSyn had no effect on neuronal parameters, even at high concentrations. The oligomer-induced fall in neuronal excitability has the potential to impact both network activity and cognitive processing., (© 2016 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.)

Primary sclerosing cholangitis (PSC) remains a rare but significant disease, which affects mainly young males in association with inflammatory bowel disease. There have been few advances in the understanding of the pathogenesis of the condition and no therapeutics with proven mortality benefit aside from liver transplantation. There remain areas of controversy in the management of PSC which include the differentiation from other cholangiopathies, in particular immunoglobulin G4 related sclerosing cholangitis, the management of dominant biliary strictures, and the role of ursodeoxycholic acid. In addition, the timing of liver transplantation in PSC remains difficult to predict with standard liver severity scores. In this review, we address these controversies and highlight the latest evidence base in the management of PSC.

Background: Prions are transmissible, propagating alternative states of proteins, and are usually made from the fibrillar, beta-sheet-rich assemblies termed amyloid. Prions in the budding yeast Saccharomyces cerevisiae propagate heritable phenotypes, uncover hidden genetic variation, function in large-scale gene regulation, and can act like diseases. Almost all these amyloid prions have asparagine/glutamine-rich (N/Q-rich) domains. Other proteins, that we term here 'prionogenic amyloid formers' (PAFs), have been shown to form amyloid in vivo, and to have N/Q-rich domains that can propagate heritable states in yeast cells. Also, there are >200 other S.cerevisiae proteins with prion-like N/Q-rich sequence composition. Furthermore, human proteins with such N/Q-rich composition have been linked to the pathomechanisms of neurodegenerative amyloid diseases., Results: Here, we exploit the increasing abundance of complete fungal genomes to examine the ancestry of prions/PAFs and other N/Q-rich proteins across the fungal kingdom. We find distinct evolutionary behavior for Q-rich and N-rich prions/PAFs; those of ancient ancestry (outside the budding yeasts, Saccharomycetes) are Q-rich, whereas N-rich cases arose early in Saccharomycetes evolution. This emergence of N-rich prion/PAFs is linked to a large-scale emergence of N-rich proteins during Saccharomycetes evolution, with Saccharomycetes showing a distinctive trend for population sizes of prion-like proteins that sets them apart from all the other fungi. Conversely, some clades, e.g. Eurotiales, have much fewer N/Q-rich proteins, and in some cases likely lose them en masse, perhaps due to greater amyloid intolerance, although they contain relatively more non-N/Q-rich predicted prions. We find that recent mutational tendencies arising during Saccharomycetes evolution (i.e., increased numbers of N residues and a tendency to form more poly-N tracts), contributed to the expansion/development of the prion phenomenon. Variation in these mutational tendencies in Saccharomycetes is correlated with the population sizes of prion-like proteins, thus implying that selection pressures on N/Q-rich protein sequences against amyloidogenesis are not generally maintained in budding yeasts., Conclusions: These results help to delineate further the limits and origins of N/Q-rich prions, and provide insight as a case study of the evolution of compositionally-defined protein domains.

Nonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space. It is still unknown how the NRPS tailoring domains are structurally accommodated into megaenzymes or how they have adapted to function in nonribosomal peptide synthesis. Here we present a series of crystal structures of the initiation module of an antibiotic-producing NRPS, linear gramicidin synthetase. This module includes the specialized tailoring formylation domain, and states are captured that represent every major step of the assembly-line synthesis in the initiation module. The transitions between conformations are large in scale, with both the peptidyl carrier protein domain and the adenylation subdomain undergoing huge movements to transport substrate between distal active sites. The structures highlight the great versatility of NRPSs, as small domains repurpose and recycle their limited interfaces to interact with their various binding partners. Understanding tailoring domains is important if NRPSs are to be utilized in the production of novel therapeutics.

Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that 'fold on binding' to another molecule. Here, we perform bioinformatical parsing of human 'folding-on-binding' (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions ('Disordered-around-FB'), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding.