Genome-Wide Analysis and Expression Profiling of HD-ZIP III Genes in Three Brassica Species

Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, a total of 10, 9 and 16 HD-ZIP III genes were identified from B. rapa, B. oleracea and B. napus, respectively. The phylogenetic analysis showed that HD-ZIP III proteins were grouped into three clades: PHB/PHV, REV and CNA/HB8. Genes in the same group tended to have similar exon–intron structures. Various phytohormone-responsive elements and stress-responsive elements were detected in the promoter regions of HD-ZIP III genes. Gene expression levels in different tissues, as well as under different stress conditions, were investigated using public transcription profiling data. The HD-ZIP III genes were constitutively expressed among all the tested tissues and were highly accumulated in root and stem. In B. rapa, only one BrREV gene especially responded to heat stress, BrPHB and BrREV members were downregulated upon cold stress and most HD-ZIP III genes exhibited divergent responses to drought stress. In addition, we investigated the genetic variation at known miR165/166 complementary sites of the identified HD-ZIP III genes and found one single nucleotide polymorphism (SNP) in PHB members and two SNPs in REV members, which were further confirmed using Sanger sequencing. Taken together, these results provide information for the genome-wide characterization of HD-ZIP III genes and their stress response diversity in Brassica species.

Global Characterization of XRN 5′-3′ Exoribonucleases and Their Responses to Environmental Stresses in Plants

The XRN family of 5′-3′ Exoribonucleases is functionally conserved in eukaryotic organisms. However, the molecular evolution of XRN proteins in plants and their functions in plant response to environment stresses remain largely unexplored. In this study, we identified 23 XRN proteins in 6 representative plant species. Polygenetic analysis revealed that XRN2 was Arabidopsis-specific among these species, and additional branches outside the clades of XRN3 and XRN4 proteins, which we named as XRN5, were found in rice, maize, and soybean. However, XRN5 in soybean lost their entire 5′-3′ XRN Exoribonuclease domain. Protein conserved sequence analysis showed that XRN3/XRN2 contained potential bipartite nuclear-localization signals (NLS) while all the XRN4 proteins lost their second KR/RR motif of NLS, potentially leading to their cytoplasm localization. SIXRN3-2 contained one mutation in this second KR/RR motif, which may change their sub-cellular localization. The promoter cis-element analysis indicated that these XRN genes responded to multiple stresses and plant hormones diversely at transcriptional level. Finally, transcriptomic analysis suggested that OsXRN3 and ZmXRN3-1 were induced by low temperature, SIXRN4 and ZmXRN4 was inhibited by heat shock, and OsXRN5 and GmXRN5-2 were repressed by drought. However, in general, the expression patterns revealed the response diversity of XRNs to environment stimuli in different plant species. Taken together, this study characterized 23 XRNs with NLS variation that contributed to their sub-cellular localization and provided an overview of the XRNs response diversity to multiple environmental stresses, suggesting that XRNs could be used as potential gene editing candidates for precise stress-tolerant crop breeding.

Diverse Response Diversity in Pollinators: Implications to the Resilience of Pollination Services in Buckwheat

Response diversity to environmental change among species is important for the maintenance of ecosystem services, but response diversity to changes in multiple environmental parameters is largely unexplored. Here, we examined how insect visitations to buckwheat flowers differ among species groups in response to changes in multiple weather variables and landscape structures.We found differences in responses to changes in weather conditions among insect taxonomic groups visiting buckwheat flowers. Specifically, beetles, butterflies, and wasps were more active in sunny and/or high-temperature conditions, whereas ants and flies showed the opposite pattern. Furthermore, responses to weather conditions differed between large and small insects, which agreed with the expectation that optimal temperature for insect activity has a positive association with body size. Response diversity per se was also diverse. For instance, large insects were responsive to temperatures more than small insects while smaller insects were responsive to sunshine duration more than large insects. Responses to spatial variables also differed; large insects were more abundant in fields with surrounding forests and mosaic habitats, whereas small insects were not. We suggest that the “diversity” in “response diversity,” which is a higher-order response diversity, should be a focus of future studies of the biodiversity–ecosystem service relationships.

Tropicalization of temperate reef fish communities depends on urchin herbivory and thermal response diversity

Global declines in structurally complex habitats are reshaping both land and seascapes in directions that affect biological communities’ responses to warming. Here, we test whether widespread loss of kelp habitats through sea urchin overgrazing systematically changes warming sensitivity of fish communities. Community thermal affinity shifts related to habitat were assessed by simulating and comparing fish communities from 2,271 surveys across 15 ecoregions. We find that fishes in kelp and urchin barrens differ in realized thermal affinities and range sizes, but only in regions where species pools have high variability in species’ thermal affinities. Barrens on warm-temperate reefs host relatively more warm-affinity fish species than neighbouring kelp beds, highlighting acceleration of tropicalization processes facilitated by urchin herbivory. By contrast, proportionally more cool-affinity fishes colonize barrens at high temperate latitudes, contributing to community lags with ocean warming in these regions. Our findings implicate urchins as drivers of ecological change, in part by affecting biological resilience to warming.

Landscape complexity promotes resilience of biological pest control to climate change

Increased climate variability as a result of anthropogenic climate change can threaten the functioning of ecosystem services. However, diverse responses to climate change among species (response diversity) can provide ecosystems with resilience to this growing threat. Measuring and managing response diversity and resilience to global change are key ecological challenges. Here, we develop a novel index of climate resilience of ecosystem services, exemplified by the thermal resilience of predator communities providing biological pest control. Field assays revealed substantial differences in the temperature-dependent activity of predator species and indices of thermal resilience varied among predator communities occupying different fields. Predator assemblages with higher thermal resilience provided more stable pest control in microcosms where the temperature was experimentally varied, confirming that the index of thermal resilience developed here is linked to predator function. Importantly, complex landscapes containing a high number of non-crop habitat patches were more likely to contain predator communities with high thermal resilience. Thus, the conservation and restoration of non-crop habitats in agricultural landscapes—practices known to strengthen natural pest suppression under current conditions—will also confer resilience in ecosystem service provisioning to climate change.

Different individual-level responses of great black-backed gulls (Larus marinus) to shifting local prey availability

To grow, survive and reproduce under anthropogenic-induced changes, individuals must respond quickly and favourably to the surrounding environment. A species that feeds on a wide variety of prey types (i.e. generalist diet) may be comprised of generalist individuals, specialist individuals that feed on different prey types, or a combination of the two. If individuals within a population respond differently to an environmental change, population-level responses may not be detectable. By tracking foraging movements of eight great black-backed gulls ( Larus marinus ), a generalist species, we compared group-level and individual-level responses to an increase in prey biomass (capelin; Mallotus villosus ) during the breeding season in coastal Newfoundland, Canada. As hypothesized, shifts in prey availability resulted in significantly different individual responses in foraging behaviour and space use, which was not detectable when data from individuals were combined. Some individuals maintained similar foraging areas, foraging trip characteristics (e.g., trip length, duration) and habitat use with increased capelin availability, while others shifted foraging areas and habitats resulting in either increased or decreased trip characteristics. We show that individual specialization can be non-contextual in some gulls, whereby these individuals continuously use the same feeding strategy despite significant change in prey availability conditions. Findings also indicate high response diversity among individuals to shifting prey conditions that a population- or group-level study would not have detected, emphasizing the importance of examining individual-level strategies for future diet and foraging studies on generalist species.

Drug Response Diversity: A Hidden Bacterium?

Interindividual heterogeneity in response to treatment is a real public health problem. It is a factor that can be responsible not only for ineffectiveness or fatal toxicity but also for hospitalization due to iatrogenic effects, thus increasing the cost of patient care. Several research teams have been interested in what may be at the origin of these phenomena, particularly at the genetic level and the basal activity of organs dedicated to the inactivation and elimination of drug molecules. Today, a new branch is being set up, explaining the enigmatic part that could not be explained before. Pharmacomicrobiomics attempts to investigate the interactions between bacteria, especially those in the gut, and drug response. In this review, we provide a state of the art on what this field has brought as new information and discuss the challenges that lie ahead to see the real application in clinical practice.

Diversity of vaccination-induced immune responses can prevent the spread of vaccine escape mutants

Pathogens that are resistant against drug treatment are widely observed. In contrast, pathogens that escape the immune response elicited upon vaccination are rare. Previous studies showed that the prophylactic character of vaccines, the multiplicity of epitopes to which the immune system responds within a host, and their diversity between hosts delay the evolution and emergence of escape mutants in a vaccinated population. By extending previous mathematical models, we find that, depending on the cost of the escape mutations, there even exist critical levels of immune response diversity that completely prevent vaccine escape. Furthermore, to quantify the potential for vaccine escape below these critical levels, we propose a concept of escape depth which measures the fraction of escape mutants that can spread in a vaccinated population. Determining this escape depth for a vaccine could help to predict its sustainability in the face of pathogen evolution.

Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response

The heterogeneity of breast cancer plays a major role in drug response and resistance and has been extensively characterized at the genomic level. Here, a single-cell breast cancer mass cytometry (BCMC) panel is optimized to identify cell phenotypes and their oncogenic signalling states in a biobank of patient-derived tumour xenograft (PDTX) models representing the diversity of human breast cancer. The BCMC panel identifies 13 cellular phenotypes (11 human and 2 murine), associated with both breast cancer subtypes and specific genomic features. Pre-treatment cellular phenotypic composition is a determinant of response to anticancer therapies. Single-cell profiling also reveals drug-induced cellular phenotypic dynamics, unravelling previously unnoticed intra-tumour response diversity. The comprehensive view of the landscapes of cellular phenotypic heterogeneity in PDTXs uncovered by the BCMC panel, which is mirrored in primary human tumours, has profound implications for understanding and predicting therapy response and resistance.