Dietary generalism accelerates arrival and persistence of coral‐reef fishes in their novel ranges under climate change

Climate change is redistributing marine and terrestrial species globally. Life‐history traits mediate the ability of species to cope with novel environmental conditions, and can be used to gauge the potential redistribution of taxa facing the challenges of a changing climate. However, it is unclear whether the same traits are important across different stages of range shifts (arrival, population increase, persistence). To test which life‐history traits most mediate the process of range extension, we used a 16‐year dataset of 35 range‐extending coral‐reef fish species and quantified the importance of various traits on the arrival time (earliness) and degree of persistence (prevalence and patchiness) at higher latitudes. We show that traits predisposing species to shift their range more rapidly (large body size, broad latitudinal range, long dispersal duration) did not drive the early stages of redistribution. Instead, we found that as diet breadth increased, the initial arrival and establishment (prevalence and patchiness) of climate migrant species in temperate locations occurred earlier. While the initial incursion of range‐shifting species depends on traits associated with dispersal potential, subsequent establishment hinges more on a species’ ability to exploit novel food resources locally. These results highlight that generalist species that can best adapt to novel food sources might be most successful in a future ocean.     

Synthesis and antitumour evaluation of novel 2-phenylbenzimidazoles

A new series of fluorinated and non-fluorinated 2-phenylbenzimidazoles bearing oxygenated substituents on the phenyl ring has been synthesized. Synthesis of the new series was based on our previous discovery of 2-(3,4-dimethoxyphenyl)-5-fluorobenzothiazole (PMX 610) as a potent and selective antitumour agent in vitro (sub-nanomolar GI₅₀ in sensitive human cancer cell lines), but with poor aqueous solubility and lack of a definitive cellular target limiting further development. In this study we test the hypothesis that 2-phenylbenzimidazoles with similar substitution patterns to PMX 610 would retain potent antitumour activity but with potentially superior pharmaceutical properties. In general the new compounds were less active than the former benzothiazole series in vitro when tested against the breast cancer cell lines MCF-7 and MDA 468; however the two most active compounds in the present series (3j and 3k) exhibit low micromolar GI₅₀ values in both cell lines and provide the opportunity for further chemical derivatization with a view to target identification.     

N-terminal Protein Processing: A Comparative Proteogenomic Analysis

N-terminal methionine excision (NME) and N-terminal acetylation (NTA) are two of the most common protein post-translational modifications. NME is a universally conserved activity and a highly specific mechanism across all life forms. NTA is very common in eukaryotes but occurs rarely in prokaryotes. By analyzing data sets from yeast, mammals and bacteria (including 112 million spectra from 57 bacterial species), the largest comparative proteogenomics study to date, it is shown that previous assumptions/perceptions about the specificity and purposes of NME are not entirely correct. Although NME, through the universal enzymatic specificity of the methionine aminopeptidases, results in the removal of the initiator Met in proteins when the second residue is Gly, Ala, Ser, Cys, Thr, Pro, or Val, the comparative genomic analyses suggest that this specificity may vary modestly in some organisms. In addition, the functional role of NME may be primarily to expose Ala and Ser rather than all seven of these residues. Although any of this group provide “stabilizing” N termini in the N-end rule, and de facto leave the remaining 13 amino acid types that are classed as “destabilizing” (in higher eukaryotes) protected by the initiator Met, the conservation of NME-substrate proteins through evolution suggests that the other five are not crucially important for proteins with these residues in the second position. They are apparently merely inconsequential players (their function is not affected by NME) that become exposed because their side chains are smaller or comparable to those of Ala and Ser. The importance of exposing mainly two amino acids at the N terminus, i.e. Ala and Ser, is unclear but may be related to NTA or other post-translational modifications. In this regard, these analyses also reveal that NTA is more prevalent in some prokaryotes than previously appreciated.Although methionine is used to initiate protein synthesis for essentially all proteins, it is subsequently removed in a large percentage of cases, either by cleavage of an N-terminal “signal ” peptide (as part of cellular translocation mechanisms or precursor activations) or by the action of specific methionine aminopeptidases (MetAPs). Approximately two-thirds of the proteins in any proteome are potential substrates for the latter N-terminal methionine excision (NME),¹ and MetAPs appear in all organisms from bacteria to eukaryotes (1). The second, or P2, amino acid in protein substrates is crucially important for NME because MetAP specificity mainly depends on the nature of this residue, a selectivity that is conserved across all species (1–5). These enzymes generally excise the N-terminal Met when the second residue is Gly, Ala, Ser, Thr, Cys, Pro, or Val (3, 6, 7), which are the amino acids smallest in size (based on radius of gyration of the side chain (8)). NME is a necessary process for proper cell functioning; it is included in the minimal genome set of eubacteria (9). Eukaryotes contain two MetAPs derived from a version in bacteria (MetAP1), and another found in archea (MetAP2) (11). Just as the deletion of MetAP eubacteria is lethal, the deletion of both MetAPs in yeast is also lethal (10).In 1988, Arfin and Bradshaw (2) observed that the specificity of NME coincided with that of the N-end rule (NER) (12, 13), a ubiquitin-dependent protein degradation process that is based on the recognition of N-terminal residues. The stabilizing residues for the NER include Gly, Ala, Ser, Cys, Thr, Pro, and Val and, with the exception of Met, the destabilizing residues are all found to be in the class of P2-residues that are not substrates for the MetAPs. This suggested that NME acts to release Met from proteins whose stability is unaffected by the NER creating at the same time a second class of proteins, who have the potential for regulated turnover downstream of the cotranslational processing, when, and if, the N-terminal Met is subsequently removed by a mechanism other than the cotranslational action of the MetAPs. However, despite extensive studies, this type of programmed protein turnover (requiring downstream removal of Met) has not been demonstrated to occur. An implication of this correlation is that exposing of the stabilizing residues may also contribute to increasing their lifetime.The stabilizing residues exposed by the action of the MetAPs can be further modified. The most extensive of these reactions is N-terminal acetylation (NTA), which can occur on as much as 70–80% of the mass of the soluble protein in eukaryotes. Although the specificity of the N-acetyltransferase (NAT) responsible is not as rigid as the MetAPs, the principal substrates in the stabilizing class are usually the four smallest residues (Gly, Ala, Ser, and Thr) (6, 14). A second class of NATs can also modify the retained Met when the adjacent residues are Asp, Glu or Asn (15). The functional importance of this modification (in either case) is not known although it has been suggested that it may exert a protective effect against spurious aminopeptidase cleavages. Recently, Hwang et al. (16) have extended the NER to include Nα-acetylated termini as also destabilizing thus providing another possible function for this modification. In contrast, to date, very few instances of Nα-acetylation have been observed in bacteria. Other modifications can also occur in both eukaryotes and prokaryotes although they are generally much more limited in scope.The specificity of the MetAPs suggest an apparent connection between NME and protein degradation. However, this connection has never been examined using high-throughput mass spectrometric data or a comparative genomics approach; thus it remains unclear whether exposing these stabilizing residues contributes to increasing protein half-life and thus represents a primary purpose of NME. (The connection between NME and NER in bacteria, which has an NER with a somewhat different profile (17), is even more obscure.) Recent studies provide some examples where disruption of NME via a single-residue substitution in the P2 position causes protein degradation (18–20); however, some of these experimental results are in conflict with the NER (13). Giglione et al. (20) have shown that NME triggers degradation of D2 protein in Caenorhabditis reinhardtii in the PSII complex after replacing the second (stabilizing) Thr residue by another amino acid to prevent NME. This replacement results in early degradation of D2 and instability of the PSII complex. From this, Giglione et al. (20) postulated that NME determines protein life-span via currently unknown machinery. However, because Bachmair et al. (12) classified Met as a stabilizing residue, it is not entirely clear why substituting one stabilizing residue (Met) by another one (Gly, Ala, Ser, Cys, Thr, Pro, or Val) should affect protein stability and the substitution may have other deleterious effects that are manifested in different ways.The logic for analyzing NME and NER is shown in Fig. 1. NME exposes 7 different residues as new N termini of proteins. The natural conclusion that has become a dogma of NME is that these seven residues are exposed for a functional reason. The broad scope of NME suggests a universal reason that surpasses any particular protein''s role. In turn the comparative genomics postulate (function suggests conservation) leads to the conclusion that the seven residues should be evolutionarily conserved at position P2 of proteins. However, because only two out of the seven residues are conserved, we argue that one of the two assumptions in Fig. 1A must be incorrect and put forth the alternative logic depicted in Fig. 1B, which matches our analysis across dozens of species. According to this logic, NME accomplishes the goal of exposing Ala and Ser by exposing all residues with side chains smaller or comparable in size to Ala and Ser (G, T, V, P, and C). These residues are thus inconsequential players that are not functionally important (and are not evolutionarily conserved) at P2.Open in a separate windowFig. 1.Two alternative cases for NME function. A, NME exposes seven residues to be new N termini of proteins. Because this is presumably for some functional reason, the conventional assumption is that all seven residues must have functional importance as N termini. By the comparative genomics postulate (as defined in the text), evolutionary conservation of all seven at P2 should be observed. If all of these residues are not conserved, one of the two assumptions must be incorrect; either not all seven residues are important or the comparative genomics postulate is invalid. B, Given that the comparative genomics postulate holds, and only two of the seven residues are of functional importance as N termini, then the other five residues are inconsequential players and only these two residues should be evolutionarily conserved.In this report, we examine the connection between the specificity of NME and stabilizing residues of NER. In doing so, data sets from bacteria (including 112 million mass spectrometric spectra from 57 species), yeast, and mammals, were analyzed for N-terminal peptides both with respect to the excision (or not) of initiator Met residues and the distribution of P2-residues. The results reveal a strong preference of Ala and Ser as P2-residues. However, this process does not appear to be linked to the NER other than being generally compatible with it. These studies also demonstrate a much greater than expected number of Nα-acetylation events in some bacteria.     

Targeted Lipidomics in Drosophila melanogaster Identifies Novel 2-Monoacylglycerols and N-acyl Amides

Lipid metabolism is critical to coordinate organ development and physiology in response to tissue-autonomous signals and environmental cues. Changes to the availability and signaling of lipid mediators can limit competitiveness, adaptation to environmental stressors, and augment pathological processes. Two classes of lipids, the N-acyl amides and the 2-acyl glycerols, have emerged as important signaling molecules in a wide range of species with important signaling properties, though most of what is known about their cellular functions is from mammalian models. Therefore, expanding available knowledge on the repertoire of these lipids in invertebrates will provide additional avenues of research aimed at elucidating biosynthetic, metabolic, and signaling properties of these molecules. Drosophila melanogaster is a commonly used organism to study intercellular communication, including the functions of bioactive lipids. However, limited information is available on the molecular identity of lipids with putative biological activities in Drosophila. Here, we used a targeted lipidomics approach to identify putative signaling lipids in third instar Drosophila larvae, possessing particularly large lipid mass in their fat body. We identified 2-linoleoyl glycerol, 2-oleoyl glycerol, and 45 N-acyl amides in larval tissues, and validated our findings by the comparative analysis of Oregon-RS, Canton-S and w1118 strains. Data here suggest that Drosophila represent another model system to use for the study of 2-acyl glycerol and N-acyl amide signaling.     

Measuring variation in potato roots in both field and glasshouse: the search for useful yield predictors and a simple screen for root traits

Aims

Potatoes have an inadequate rooting system for efficient acquisition of water and minerals and use disproportionate amounts of irrigation and fertilizer. This research determines whether significant variation in rooting characteristics of potato exists, which characters correlate with final yield and whether a simple screen for rooting traits could be developed.

Methods

Twenty-eight genotypes of Solanum tuberosum groups Tuberosum and Phureja were grown in the field; eight replicate blocks to final harvest, while entire root systems were excavated from four blocks. Root classes were categorised and measured. The same measurements were made on these genotypes in the glasshouse, 2 weeks post emergence.

Results

In the field, total root length varied from 40 m to 112 m per plant. Final yield was correlated negatively with basal root specific root length and weakly but positively with total root weight. Solanum tuberosum group Phureja genotypes had more numerous roots and proportionally more basal than stolon roots compared with Solanum tuberosum, group Tuberosum genotypes. There were significant correlations between glasshouse and field measurements.

Conclusions

Our data demonstrate that variability in rooting traits amongst commercially available potato genotypes exists and a robust glasshouse screen has been developed. By measuring potato roots as described in this study, it is now possible to assess rooting traits of large populations of potato genotypes.     

AMP-activated protein kinase and ATP-citrate lyase are two distinct molecular targets for ETC-1002, a novel small molecule regulator of lipid and carbohydrate metabolism

ETC-1002 (8-hydroxy-2,2,14,14-tetramethylpentadecanedioic acid) is a novel investigational drug being developed for the treatment of dyslipidemia and other cardio-metabolic risk factors. The hypolipidemic, anti-atherosclerotic, anti-obesity, and glucose-lowering properties of ETC-1002, characterized in preclinical disease models, are believed to be due to dual inhibition of sterol and fatty acid synthesis and enhanced mitochondrial long-chain fatty acid β-oxidation. However, the molecular mechanism(s) mediating these activities remained undefined. Studies described here show that ETC-1002 free acid activates AMP-activated protein kinase in a Ca²⁺/calmodulin-dependent kinase β-independent and liver kinase β 1-dependent manner, without detectable changes in adenylate energy charge. Furthermore, ETC-1002 is shown to rapidly form a CoA thioester in liver, which directly inhibits ATP-citrate lyase. These distinct molecular mechanisms are complementary in their beneficial effects on lipid and carbohydrate metabolism in vitro and in vivo. Consistent with these mechanisms, ETC-1002 treatment reduced circulating proatherogenic lipoproteins, hepatic lipids, and body weight in a hamster model of hyperlipidemia, and it reduced body weight and improved glycemic control in a mouse model of diet-induced obesity. ETC-1002 offers promise as a novel therapeutic approach to improve multiple risk factors associated with metabolic syndrome and benefit patients with cardiovascular disease.     

Repeated oral administration of capsaicin increases anxiety-like behaviours with prolonged stress-response in rats

This study was conducted to examine the psycho-emotional effects of repeated oral exposure to capsaicin, the principal active component of chili peppers. Each rat received 1 mL of 0.02% capsaicin into its oral cavity daily, and was subjected to behavioural tests following 10 daily administrations of capsaicin. Stereotypy counts and rostral grooming were significantly increased, and caudal grooming decreased, in capsaicin-treated rats during the ambulatory activity test. In elevated plus maze test, not only the time spent in open arms but also the percent arm entry into open arms was reduced in capsaicin-treated rats compared with control rats. In forced swim test, although swimming duration was decreased, struggling increased in the capsaicin group, immobility duration did not differ between the groups. Repeated oral capsaicin did not affect the basal levels of plasma corticosterone; however, the stress-induced elevation of plasma corticosterone was prolonged in capsaicin treated rats. Oral capsaicin exposure significantly increased c-Fos expression not only in the nucleus tractus of solitarius but also in the paraventricular nucleus. Results suggest that repeated oral exposure to capsaicin increases anxiety-like behaviours in rats, and dysfunction of the hypothalamic-pituitary-adrenal axis may play a role in its pathophysiology.     

Temperature-related sex allocation shifts in a recovering keystone species,Pinus palustris

Summary

In the light of all that has been discovered about the mechanism of evolution it has become tempting to follow Darwin's lead and to “see no limit to this power“. Yet a careful examination of situations in which evolution is known to be occurring in some species, shows complete absence of evolution in others. This not because these species have not had the opportunity; in many situations there may even be uncolonised bare space.

The explanation must lie in the supply of appropriate variation. A tacit assumption of evolution by natural selection is that the necessary variation is always available. Yet there is no a priori justification for this. Evidence from populations in nature, particularly of species which are potential colonists of old metal mine workings and similar metal contaminated habitats, shows that the species that successfully colonise these habitats, by the evolution of metal tolerant populations, possess within their normal populations the necessary variation. But those species which fail to colonise these habitats, despite the opportunity, do not possess this variation. This applies also at the level of the population, in the replicated evolutionary situations occurring under electricity pylons.

Such evidence, together with arguments from theory, suggests that the failures of evolution have been as important as its successes in moulding the living world as we see it today, and that the reasons for failure must be sought at the molecular level in limitations to the origin of new variation.     

Effect of weight loss and exercise on angiogenic factors in the circulation and in adipose tissue in obese subjects

Background:

Vascular growth is a prerequisite for adipose tissue (AT) development and expansion. Some AT cytokines and hormones have effects on vascular development, like vascular endothelial growth factor (VEGF‐A), angiopoietin (ANG‐1), ANG‐2 and angiopoietin‐like protein‐4 (ANGPTL‐4).

Methods:

In this study, the independent and combined effects of diet‐induced weight loss and exercise on AT gene expression and proteins levels of those angiogenic factors were investigated. Seventy‐nine obese males and females were randomized to: 1. Exercise‐only (EXO; 12‐weeks exercise without diet‐restriction), 2. Hypocaloric diet (DIO; 8‐weeks very low energy diet (VLED) + 4‐weeks weight maintenance diet) and 3. Hypocaloric diet and exercise (DEX; 8‐weeks VLED + 4‐weeks weight maintenance diet combined with exercise throughout the 12 weeks). Blood samples and fat biopsies were taken before and after the intervention.

Results:

Weight loss was 3.5 kg in the EXO group and 12.3 kg in the DIO and DEX groups. VEGF‐A protein was non‐significantly reduced in the weight loss groups. ANG‐1 protein levels were significantly reduced 22‐25% after all three interventions (P < 0.01). The ANG‐1/ANG‐2 ratio was also decreased in all three groups (P < 0.05) by 27‐38%. ANGPTL‐4 was increased in the EXO group (15%, P < 0.05) and 9% (P < 0.05) in the DIO group. VEGF‐A, ANG‐1, and ANGPTL‐4 were all expressed in human AT, but only ANGPTL‐4 was influenced by the interventions.

Conclusions:

Our data show that serum VEGF‐A, ANG‐1, ANG‐2, and ANGPTL‐4 levels are influenced by weight changes, indicating the involvement of these factors in the obese state. Moreover, it was found that weight loss generally was associated with a reduced angiogenic activity in the circulation.     

Evaporative Cooler Use Influences Temporal Indoor Relative Humidity but Not Dust Mite Allergen Levels in Homes in a Semi-Arid Climate

Concerns about energy consumption and climate change make residential evaporative coolers a popular alternative to central air conditioning in arid and semi-arid climates. However, evaporative coolers have been shown to significantly increase indoor relative humidity and dust mite allergen levels in some studies, while showing no association in other studies. Improved measurement of temporal fluctuations in indoor relative humidity may help identify factors that promote mite growth in homes in dry climates. Dust samples and continuous indoor relative humidity measurements were collected from homes with central air conditioning and homes with evaporative coolers in Utah. Samples were collected over two seasons, winter/spring (Jan–Apr) and summer (July–Sept), 2014. Dust samples were analyzed for Der p 1 and Der f 1 using a two-site monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) analysis. Housing characteristics including age of home, occupant density, and age of mattresses, furniture, and carpeting were also measured. Positive Der p 1 or Der f 1 samples were found in 25.0% of the homes and there was no difference in mean allergen levels by type of air conditioning. Indoor relative humidity was significantly higher in homes with evaporative coolers compared to those with central air conditioning during the summer. Homes with evaporative coolers also spent significantly more time during summer above 55.0% and 65.0% relative humidity compared to central air homes, but not above 75.0%. Findings from this study suggest that increased humidity from evaporative coolers may not be sufficient to exceed the critical equilibrium humidity or maintain humidity excursions for sufficient duration in relatively larger single-family homes in semi-arid climates to support mite growth and reproduction.