Search

The evolutionary spread of a trait that benefits individuals of one species in their interactions with a second species may be constrained by “ecological costs” if the trait also has detrimental effects on interactions with a third species in the environment. In particular, the identification of ecological costs may help explain why natural plant populations often display less-than-maximal resistance against natural enemies—even when the plant populations possess substantial genetic variation that could serve as raw material for evolving greater resistance. One such resistance trait that confers an obvious fitness advantage, yet is maintained in populations at intermediate levels, is the strategy of resistance-by-ducking displayed by certain species of goldenrods (Solidago). In a ducking individual, the stem temporarily nods near the apex during a time in spring that coincides with the oviposition season of several herbivores. I investigated whether the fitness benefits of ducking in terms of deterring apex-galling insects may be offset by ecological costs posed by a common sap-sucking specialist—the red goldenrod aphid, Uroleucon nigrotuberculatum. In a controlled outdoor experiment, ducking was associated with significantly lower antixenosis (i.e., reduced preference), antibiosis (reduced performance), and indirect resistance against aphids. Specifically, aphids colonized ducking plants at a higher rate than erect-stemmed plants; populations of aphids on bagged ducking plants increased more quickly than on bagged erect-stemmed plants; and aphid populations on erect-stemmed plants were wiped out more quickly by natural enemies than on ducking plants when bags were removed. To the extent that aphid damage reduces goldenrod’s fitness, these ecological costs may be responsible for limiting the ducking trait to intermediate levels in goldenrod populations. Because most plant species are attacked by multiple types of herbivores, ecological costs of resistance mechanisms are likely to be more widespread than is generally appreciated, though their subtlety may make them challenging to identify.

Background The urea breath test (UBT) is widely used for diagnosing Helicobacter pylori infection. In the Shenzhen Kuichong People’s Hospital, some UBT findings were contradictory to the histology outcomes, therefore this study aimed to assess and compare the diagnostic performance of both 13C- and 14C-UBT assays. Methods We recruited 484 H. pylori-treatment naïve patients, among which 217 and 267 were tested by the 13C-UBT or 14C-UBT, respectively. The cutoff value for H. pylori positivity based on manufacturer’s instruction was 4% delta over baseline (DOB) for the 13C-UBT, and 100 disintegrations per minute (DPM) for the 14C-UBT. Gastric biopsies of the antrum and corpus were obtained during endoscopy for histopathology. Results In patients who were tested using the 13C-UBT kit, histopathology was positive in 136 out of 164 UBT-positive patients (82.9% concordance), and negative in 46 out of 53 UBT-negative cases (86.8% concordance). For the 14C-UBT-tested patients, histopathology was positive for H. pylori in 186 out of 220 UBT-positive patients (84.5% concordance), and negative in 41 out of 47 UBT-negative cases (87.2% concordance). While the 13C-UBT and 14C-UBT each had a high sensitivity level of 95.1% and 96.9%, respectively, their specificity was low, at 62.2% and 54.7%, respectively. By using new optimal cutoff values and including an indeterminate range (3–10.3% DOB for 13C-UBT and 87–237 DPM for 14C-UBT), the specificity values can be improved to 76.7% and 76.9% for the 13C- and 14C-UBT, respectively. Conclusions The establishment of an indeterminate range is recommended to allow for repeated testing to confirm H. pylori infection, and thereby avoiding unnecessary antibiotic treatment. Trial registration: Chinese Clinical Trial Registry, ChiCTR2000041570. Registered 29 December 2020- Retrospectively registered, http://www.chictr.org.cn/edit.aspx?pid=66416&htm=4

While herbivores can have a wide range of impacts on their host plants, instances in which herbivore damage is truly beneficial are rare. Thus, it was surprising that damage by the potato stalk borer (PSB) was associated with increased fitness of its native host plant (horsenettle) in a recent field study, particularly because this insect can have such severe negative effects on potato crops. A controlled experiment with potted horsenettle was conducted to investigate the impact of damage by PSB to see if it has any negative impacts on the plants, or whether horsenettle truly overcompensates for its damage. Damage by PSB had negligible impact on sexual reproduction and potential future vegetative propagation through root production in this experiment. Additionally, PSB damage did not exacerbate the negative fitness impact of heavy leaf damage by the eggplant lace bug. The lack of positive impacts in the potted horsenettle study suggests that selection for decreased resistance to PSB in the field study was due to correlated selection for increased plant vigor, rather than to overcompensation. That is, when given options, PSB females may preferentially oviposit on larger, healthier plants that are likely to be better hosts for their larvae. An important implication of these results is that a wild weed’s high tolerance of a natural herbivore can compound the weed’s potential to serve as a reservoir from which the herbivore can switch to closely related agricultural plants that are not tolerant of its damage.

Background Helicobacter pylori is a Gram-negative bacterium which mainly causes peptic ulcer disease in human, but is also the predominant cause of stomach cancer. It has been coevolving with human since 120,000 years and, according to Multi-locus sequence typing (MLST), H. pylori can be classified into seven major population types, namely, hpAfrica1, hpAfrica2, hpNEAfrica, hpEastAsia, hpAsia2, hpEurope and hpSahul. Helicobacter pylori harbours a large number of restriction-modification (R-M) systems. The methyltransferase (MTase) unit plays a significant role in gene regulation and also possibly modulates pathogenicity. The diversity in MTase can act as geomarkers to correlate strains with the phylogeographic origins. This paper describes the complete genome sequence and methylome of gastric pathogen H. pylori belonging to the population hpNEAfrica. Results In this paper, we present the complete genome sequence and the methylome profile of H. pylori hpNEAfrica strain HP14039, isolated from a patient who was born in Somalia and likely to be infected locally during early childhood prior to migration. The genome of HP14039 consists of 1,678,260 bp with 1574 coding genes and 38.7% GC content. The sequence analysis showed that this strain lacks the cag pathogenicity island. The vacA gene is of S2M2 type. We have also identified 15 methylation motifs, including WCANHNNNNTG and CTANNNNNNNTAYG that were not previously described. Conclusions We have described the complete genome of H. pylori strain HP14039. The information regarding phylo-geography, methylome and associated metadata would help scientific community to study more about hpNEAfrica population type. Electronic supplementary material The online version of this article (10.1186/s13099-019-0284-y) contains supplementary material, which is available to authorized users.

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

Background Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates. Results Population structure analysis of the 59 isolates together with 72 isolates from an international collection, revealed six population groups suggesting that N. gonorrhoeae is a weakly clonal species. Two distinct population groups, Aus1 and Aus2, represented 63% of WA isolates and were mostly composed of the remote community isolates that carried no chromosomal AMR genotypes. In contrast, the Western Australian metropolitan isolates were frequently multi-drug resistant and belonged to population groups found in the international database, suggesting international transmission of the isolates. Conclusions Our study suggests that the population structure of N. gonorrhoeae is distinct between the communities in remote and metropolitan WA. Given the high rate of AMR in metropolitan regions, ongoing surveillance is essential to ensure the enduring efficacy of the empiric gonorrhoea treatment in remote WA.

Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.

Interactions between plants and herbivores are considered “diffuse” if the ecological interactions between two species, or their evolutionary responses, differ depending on the presence of a third species. I looked for evidence of diffuse interactions among horsenettle (Solanum carolinense) and two common herbivores. Plants experimentally protected from lace bugs (Gargaphia solani) were twice as susceptible to attack from flea beetles (Epitrix fuscula) once transplanted into the field. Thus, the selective benefit to horsenettle of resistance against lace bugs in nature would likely be diminished by increased attack from flea beetles. Moreover, the relative rank among horsenettle genotypes for resistance against flea beetles was changed by prior exposure to lace bugs. Thus, the genetic expression of resistance to flea beetles would depend on the “lace bug environment.” By affecting selective pressures or response to selection, these sorts of diffuse interactions in a plant-herbivore community can slow the host plant’s evolution of resistance to its herbivores.

Interspecific competition (or facilitation) between herbivores sharing a host plant species can result in negative (or positive) correlations in damage levels, independent of a plant’s genetic covariance in resistance to the herbivores. Just like genetic correlations in resistance to herbivory, these “environmental correlations” in damage may affect the evolution of resistance in the host plant. In a field study of 960 ramets and 40 genets of the herbaceous plant Solanum carolinense, I looked for evidence of such environmental correlations in damage caused by 11 species of herbivores, including 10 insects and 1 mammal. There were 28 significant correlations in damage levels between species (21 negative and 7 positive) after plant genetic influences on resistance were statistically removed. Negative environmental correlations were more likely between species that fed upon the same type of plant organs than between those that fed on different types of organs, and the magnitudes of the correlations were inversely proportional to the abundance of the organ types. Taken together, these results offer strong evidence that competition is largely responsible for the pattern of environmental correlations in damage. Environmental correlations were just as common as genetic correlations in resistance, but the environmental correlations tended to be lower in magnitude, were more likely to be negative, and were more evenly spread out among the herbivore community than the genetic correlations. Damage levels by all 11 species were negatively correlated with damage by at least one other species. Thus the selective advantage a plant would receive from increased resistance any of these herbivores would be partially negated by increased damage by competing herbivores. As a result, competition has the potential to be an important constraint on the evolution of resistance in S. carolinense.

Evidence of poor correspondence between an insect herbivore's oviposition preferences and the performance of its offspring has generally been attributed either to maladaptive behavior of the insect mother or inadequate measurement by the researcher. In contrast, we hypothesize that many cases of "bad mothers" in herbivores may be a byproduct of the hierarchical way natural selection works on resistance in host plants. Epistatic selection on the components of resistance (i.e., antixenosis and antibiosis) may generate negative genetic correlations between the resistance components, which could counteract the efforts of herbivores to oviposit on the best hosts for the performance of their offspring. In common garden and greenhouse experiments, we measured aspects of antixenosis and antibiosis resistance in 26 genets of tall goldenrod, Solidago altissima, against two common herbivores: the gall-inducing fly Eurosta solidaginis and the spittlebug Philaenus spumarius. Goldenrod antixenosis and antibiosis were positively correlated against E. solidaginis and negatively correlated against P. spumarius. Analogously, population-wide preference-performance correlations were positive for the gall flies and negative for the spittlebugs. Several natural history differences between the two insects could make gall flies better mothers, including better synchrony of the phenologies of the flies and the host plant, the much narrower host range of the gall flies than the spittlebugs, and the more sedentary lifestyle of the gall fly larvae than the spittlebug nymphs. If these results are typical in nature, then negative genetic correlations in antixenosis and antibiosis in plants may often result in zero or negative population-wide correlations between preference and performance in herbivores, and thus may be an important reason why herbivorous insects often appear to be bad mothers.

Research into late embryogenesis abundant (LEA) proteins has been ongoing for more than 20 years but, although there is a strong association of LEA proteins with abiotic stress tolerance particularly dehydration and cold stress, for most of that time, their function has been entirely obscure. After their initial discovery in plant seeds, three major groups (numbered 1, 2 and 3) of LEA proteins have been described in a range of different plants and plant tissues. Homologues of groups 1 and 3 proteins have also been found in bacteria and in certain invertebrates. In this review, we present some new data, survey the biochemistry, biophysics and bioinformatics of the LEA proteins and highlight several possible functions. These include roles as antioxidants and as membrane and protein stabilisers during water stress, either by direct interaction or by acting as molecular shields. Along with other hydrophilic proteins and compatible solutes, LEA proteins might also serve as "space fillers" to prevent cellular collapse at low water activities. This multifunctional capacity of the LEA proteins is probably attributable in part to their structural plasticity, as they are largely lacking in secondary structure in the fully hydrated state, but can become more folded during water stress and/or through association with membrane surfaces. The challenge now facing researchers investigating these enigmatic proteins is to make sense of the various in vitro defined functions in the living cell: Are the LEA proteins truly multi-talented, or are they still just misunderstood?

While a plant’s capacity to tolerate damage by herbivores can be studied as a single trait, it is important to recognize that tolerance is generally a result of the combined action of several different traits. Here, we report on a pair of experiments to identify mechanisms for tolerating floral herbivory in Solanum carolinense, an andromonoecious perennial herb that regularly suffers from high levels of florivory. We measured the effect of actual and simulated florivory on host-plant fitness and assessed which plant traits exhibited plasticity in response to florivory. In addition, for each of nine plant genets, we calculated tolerance indices and determined which traits were genetically correlated with tolerance. Traits that served to help S. carolinense tolerate florivory in terms of sexual reproduction included initiating more inflorescences, aborting fewer buds prior to anthesis and fewer ovaries after fertilization, and increasing the ratio of perfect:male flowers. In addition, the greater the levels of florivory, the more the plants allocated to root growth, which may promote tolerance through greater potential future reproduction. The plant population contained significant genetic variation for tolerance itself and for nearly all of the putative tolerance mechanisms, which suggests that S. carolinense has the potential to evolve greater tolerance through a variety of different routes in response to natural selection.

Background The MexTAg transgenic mouse model of mesothelioma replicates many aspects of human mesothelioma, including induction by asbestos, pathogenicity and response to cytotoxic chemotherapy, despite high levels of the SV40 large T Antigen (TAg) in the mesothelial compartment. This model enables analysis of the molecular events associated with asbestos induced mesothelioma and is utilised here to investigate the molecular dynamics of tumours induced in these mice, using gene expression patterns as a read out. Methods Gene expression of MexTAg mesothelioma cell lines bearing a high or low number of copies of the TAg transgene were compared to wild type mouse mesotheliomas and normal mouse mesothelial cells using Affymetrix microarray. These data were then compared to a similar published human microarray study using the same platform. Results The main expression differences between transgenic mouse and wild type mouse mesotheliomas occurred for genes involved in cell cycle regulation and DNA replication, as would be expected from overexpression of the TAg oncogene. Quantitative PCR confirmed that E2F and E2F regulated genes were significantly more upregulated in MexTAg mesotheliomas and MexTAg mesothelial cells compared to wild type mesotheliomas. Like human mesothelioma, both MexTAg and wild type mesotheliomas had more genes underexpressed than overexpressed compared to normal mouse mesothelial cells. Most notably, the cdkn2 locus was deleted in the wild type mouse mesotheliomas, consistent with 80 % human mesotheliomas, however, this region was not deleted in MexTAg mesotheliomas. Regardless of the presence of TAg, all mouse mesotheliomas had a highly concordant set of deregulated genes compared to normal mesothelial cells that overlapped with the deregulated genes between human mesotheliomas and mesothelial cells. Conclusions This investigation demonstrates that the MexTAg mesotheliomas are comparable with wild type mouse mesotheliomas in their representation of human mesothelioma at the molecular level, with some key gene expression differences that are attributable to the TAg transgene expression. Of particular note, MexTAg mesothelioma development was not dependent on cdkn2 deletion. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1953-y) contains supplementary material, which is available to authorized users.

The frequency of coevolution as a process of strong mutual interaction between a single plant and herbivore species has been questioned in light of more commonly observed, complex relationships between a plant and a suite of herbivore species. Despite recognition of the possibility of diffuse coevolution, relatively few studies have examined ecological responses of plants to herbivores in complex associations. We studied the impact of two specialist herbivores, the horse nettle beetle, Leptinotarsa juncta, and the eggplant flea beetle, Epitrix fuscula, on reproduction of their host, Solanum carolinense. Our study involved field and controlled-environment experimental tests of the impact on sexual and potential asexual reproduction of attack by individuals of the two herbivore species, individually and in combination. Field tests demonstrated that under normal levels of phytophagous insect attack, horse nettle plants experienced a reduction in fruit production of more than 75% compared with plants from which insects were excluded. In controlled-environment experiments using enclosure-exclosure cages, the horse nettle's two principal herbivores, the flea beetle and the horse nettle beetle, caused decreases in sexual reproduction similar to those observed in the field, and a reduction in potential asexual reproduction, represented by root biomass. Attack by each herbivore reduced the numbers of fruits produced, and root growth, when feeding in isolation. When both species were feeding together, fruit production, but not root growth, was lower than when either beetle species fed alone. Ecological interactions between horse nettle and its two primary herbivores necessary for diffuse coevolution to occur were evident from an overall analysis of the statistical interactions between the two herbivores for combined assessment of fruit and vegetative traits. For either of these traits alone, the interactions necessary to promote diffuse coevolution apparently were lacking.

Background The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties.