Aspergillus fumigatus: saprophyte or pathogen?

Large-scale genome comparisons have shown that no gene sets are shared exclusively by both Aspergillus fumigatus and any other human pathogen sequenced to date, such as Candida or Cryptococcus species. By contrast, and in agreement with the environmental occurrence of this fungus in decaying vegetation, the enzymatic machinery required by a fungus to colonize plant substrates has been found in the A. fumigatus genome. In addition, the proteome of this fungus contains numerous efflux pumps, including >100 major facilitators that help the fungus to resist either natural aggressive molecules present in the environment or antifungal drugs in humans. Environment sensing, counteracting reactive oxidants, and retrieving essential nutriments from the environment are general metabolic traits that are associated with the growth of the saprotrophic mold A. fumigatus in an unfriendly environment such as its human host.     

What makes a nest-building male successful? Male behavior and female care in penduline tits

Why do females increase parental effort when caring for theoffspring of attractive males? First, attractive males may bepoor fathers so that their females are compelled to increasetheir own contribution in order to fledge some young (the partner-compensationhypothesis). Second, females mated to attractive males may bewilling to increase their parental effort to reap high indirectbenefits for their offspring, and in turn males can decreasetheir own contribution (the differential allocation hypothesis[DAH]). We investigated these hypotheses in the penduline titRemiz pendulinus, a small passerine bird that has sequentialpolygamy by both sexes and strict uniparental care either bythe male or the female. We focused on two sexually selectedmale traits: nest size and nest-building behavior. We show thatmale care is unrelated to nest-building behavior, whereas femalesare more likely to care for the offspring of those males thatspend more time nest building. Females also more likely carefor the offspring of males that build large nests. Consequently,the reproductive success of males increases with nest size andnest-building behavior. Our results are consistent with theDAH and suggest that nest-building behavior and nest size areunder postmating sexual selection in penduline tits.     

What makes a mitochondrion?

Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.     

What makes a species central in a cleaning mutualism network?

Mutualisms often form networks of interacting species, characterized by the existence of a central core of species that potentially drive the ecology and the evolution of the whole community. Centrality measures allow quantification of how central or peripheral a species is within a network, thus informing about the role of each species in network organization, dynamics, and stability. In the present study we addressed the question whether the structural position of species in the network (i.e. their topological importance) relates to their ecological traits. We studied interactions between cleaner and client reef fishes to identify central and peripheral species within a mutualistic network, and investigated five ecological correlates. We used three measures to estimate the level of centrality of a species for distinct structural patterns, such as the number of interactions and the structural proximity to other species. Through the use of a principal component analysis (PCA) we observed that the centrality measures were highly correlated (92.5%) in the studied network, which indicates that the same species plays a similar role for the different structural patterns. Three cleaner and ten client species had positive values of centrality, which suggests that these species are modulating ecological and evolutionary dynamics within the network. Higher centralities were related to higher abundances and feeding habits for client fishes, but not for cleaners. The high correlation between centrality measures in the present study is likely related to the nested structure of the cleaning network. The cleaner species’ set, by having central species that are not necessarily the most abundant ones, bears potentially more vulnerable points for network cohesiveness. Additionally, the present study generalizes previous findings for plant–animal mutualisms, as it shows that the structure of marine mutualisms is also related to a complex interplay between abundance and niche‐related features.     

What makes a successful biocontrol agent? A meta-analysis of biological control agent performance

We qualitatively reviewed the biocontrol literature in two major journals, Biological Control and Environmental Entomology, over the past 10 years by scoring 878 studies into 11 biocontrol-oriented questions. Quantitative meta-analyses were then used on data from 145 studies to examine the effects of different types of biocontrol agents (parasitoids, predators, and pathogens) on several attributes of weed and pest populations. Results for our qualitative review showed that most biocontrol studies were focused on lepidopteran pests, and that parasitoids were the most common biocontrol agents used. Our quantitative review showed that, for weeds, biocontrol agents significantly reduced weed biomass (−82.0%), flower (−98.9%), and seed production (−89.4%). For pests, our quantitative review showed that biocontrol agents significantly reduced pest abundance by 130% compared to control groups, increased parasitism (+139.0%) and increased overall pest mortality (+159.0%) compared to targets not exposed to biocontrol agents. Effects on pest mortality tended to be stronger for parasitoids than predators, although reductions caused in pest abundance were much stronger when predators were used as biocontrol agents. Addition of two or more biocontrol agents increased mortality by 12.97% and decreased pest abundance by 27.17% compared to single releases. Separate sets of meta-analyses demonstrated that the negative impacts of biocontrol on non-target species were much smaller than those for target species, although adverse effects of biocontrol on non-target organisms are based on small sample sizes and should be interpreted with caution. Our results also showed that biocontrol efficacy tended to be higher when agents were generalists than when they were specialists. Large fail–safe numbers found for most of the estimated effects indicate the robustness of the results found for the efficacy of biological control programs.     

What makes a specialized endophyte special?

Fungal plant symbionts can be highly specialized on a limited range of host genotypes and species. Understanding the genetic basis of this specialization, the mechanisms governing its establishment and the relationship between specialization and speciation is a major challenge for evolutionary biologists (Timms & Read, 1999 ). A deeper knowledge of evolutionary plant–microbe interactions could be exploited to improve agricultural management, by bringing fungal biodiversity and fungal biomass under greater and more durable human control. Previous studies on pathogens have shown that effectors, that is, small secreted proteins that modulate plant physiology to favour host colonization, play a key role in infection of novel hosts (e.g., Inoue et al., 2017 ) or in host specialization (e.g., Liao et al. ( 2016 )). Like pathogens, endophytes also manipulate the physiology of their hosts and colonize novel hosts to which they specialize (Hardoim et al., 2015 ). These biological characteristics of endophytes raise the question of similarities in the protein arsenal contributing to the specialization of pathogens and endophytes. In this issue of Molecular Ecology, Schirrmann et al. ( 2018 ) used a combination of divergence genome scans and tests for positive selection to investigate the genetic basis of specialization of two subspecies of the symbiont Epichloë typhina occurring on two different grass hosts. Their analyses suggest a key role of effectors as determinants of host specialization. This study paves the way towards the comparative analysis of the genomics of speciation among plant symbionts.     

What makes a fly enter diapause?

Diapause is a dormant state that insects may undergo as a response to changing environmental conditions. In flies, like many insects inhabiting temperate zones, diapause occurs generally during the winter months when ambient temperatures are cool and food sources scarce. Whilst the environmental factors involved in determining diapause have been known for a long time, the genes and molecular events controling its initiation are poorly understood. Here I outline the factors that initiate diapause and highlight recent studies that implicate insulin signaling in its control.     

What makes a binding site a binding site?

Organic probe molecules have recently been used to define hydrophobic binding sites on the surface of proteins. It appears that the presence of water on the surface of a protein plays a crucial role in the interaction between that protein and its binding site.     

Azole Resistance in Aspergillus fumigatus—Current Epidemiology and Future Perspectives

Azole resistance in Aspergillus fumigatus isolates is increasingly reported in different nosologic contexts with variable prevalence in different countries. Mutations in the target of triazoles are widely described in azole-resistant clinical isolates. The recovery of mutated/resistant isolates is described either in patients undergoing long-term azole treatment or after inhalation of environmentally acquired resistant isolates. Acquisition in patients during azole therapy highlights the capacity of this fungus to adapt to its environment, but it has a low impact in terms of public health, as interhuman transmission of A. fumigatus is uncommon. Environmentally acquired resistant isolates may propagate and affect populations at risk. The use of triazoles as first-line therapy or prophylaxis could lead to selection of resistant isolates in patients, because most isolates harbor azole cross-resistance. Although mold-active triazoles have provided major progress in the prophylaxis and treatment of Aspergillus infection, the increase of azole resistance could question their use in humans.     

What makes a plant species specialist in mixed broad-leaved deciduous forests?

Knowledge about relationships between specialization degree of species, i.e. the width of their realized niche and functional traits, may have important implications for the assessment of future population developments under environmental change. In this study, we used a recently introduced method to calculate ecological niche widths of plant species in mixed broad-leaved deciduous forests and to investigate the dependence between niche widths of plants and their functional traits and Ellenberg indicator values. The research is based on a dataset of 4556 phytosociological relevés of mixed broad-leaved deciduous forests in Slovenia. We calculated theta indices for 326 species, which ranks them along a continuous gradient of habitat specialization. For 272 species, we compiled 26 functional traits and Ellenberg indicator values. We found some significant correlations between theta indices of species and their functional traits and Ellenberg indicator values; habitat specialists thrive primarily on the highest altitudes, on colder, dry sites and achieve the age of first flowering later than generalists. They also have smaller seed diameter, lower leaf dry matter content, lower mean canopy height and bigger specific leaf area than generalists. Two species groups, chamaephytes and spring green species, are particularly characterized as specialist species. The added value of our work is in complementing the knowledge about the niche differentiating along different environmental gradients and species coexistence in mixed broad-leaved deciduous forests.     

Are adhesion molecules involved in stress-induced changes in lymphocyte distribution?

Acute psychological stress is associated with important changes in circulating cell populations and reductions in cell-mediated immune responses. However, the mechanisms underlying these phenomena are poorly understood. In this study, we investigated (i) acute and chronic restraint stress effects in Sprague-Dawley rats on peripheral lymphocyte subsets and (ii) adhesion molecule (beta2 integrins) expression and (iii) also determined whether glucocorticoids could underlie stress-related changes in cellular redistribution. We observed time-dependent changes in lymphocyte distribution including decreased (-21%) percentages of peripheral T helper cells and increased (88%) NK cell numbers following acute brief restraint. Acute stress was also found to overall upregulate beta2-integrin (CD11a and CD11b) expression on T cells and to raise (1049%) plasma corticosterone levels. However, this stress response was found habituated (-75% vs. acute) in the animals previously exposed to chronic restraint stress. Stress effects on circulating lymphocytes were not observed in animals previously exposed to chronic intermittent restraint stress or chronically stressed animals re-exposed to the same stressor. Our results indicate that 1) stress alters lymphocyte distribution, 2) that adhesion molecules may be involved in stress-induced alterations of T-cell distribution and 3) that these changes may be related to circulating glucocorticoids and subjected to adaptation with repeated stress exposure.     

What makes a gene name? Named entity recognition in the biomedical literature

The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources. Precise NER tools are a prerequisite for many applications working on text, such as information retrieval, information extraction or document classification. Over the past years, the problem has achieved considerable attention in the bioinformatics community and experience has shown that NER in the life sciences is a rather difficult problem. Several systems and algorithms have been devised and implemented. In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed.