skip to main content

Search for: All records

Creators/Authors contains: "Rose, A."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract Aims and background

    The resurrection plantMyrothamnus flabellifoliatolerates complete desiccation and is a great model for studying how plants cope with extreme drought. Root-associated microbes play a major role in stress tolerance and are an attractive target for enhancing drought tolerance in staple crops. However, how these dynamics play out under the most extreme water limitation remains underexplored. This study aimed to identify bacterial and fungal communities that tolerate extreme drought stress in the bulk soil, rhizosphere, and endosphere ofM. flabellifolia.


    High-throughput amplicon sequencing was used to characterise the microbial communities associated withM. flabellifolia.


    The bacterial phyla that were most abundant across all compartments wereAcidobacteriota, Actinobacteriota, Chloroflexota, Planctomycetota,andPseudomonadota, while the most abundant fungal phyla wereAscomycotaandBasidiomycota. Although the bulk soil hosted multiple beneficial root-associated microbes, the rhizosphere compartment showed the highest functional diversity of bacteria and fungi. In contrast, the endosphere exhibited a low abundance and diversity of microbes. These findings share consistent with the theory thatM. flabellifoliarecruits soil microbes from the bulk to the rhizosphere and finally to the endosphere. It is possible that these microbes could promote drought tolerance in associated plant tissues.


    We find that compartments act as the major driver of microbial diversity, but the soil physicochemical factorsmore »also influence microbial composition. These results suggest that the root-associated microbiome ofM. flabellifoliais highly structured and may aid in plant function.

    « less

    We investigate the role of dense environments in suppressing star formation by studying $\rm \log _{10}(M_\star /M_\odot) \gt 9.7$ star-forming galaxies in nine clusters from the Local Cluster Survey (0.0137 < z < 0.0433) and a large comparison field sample drawn from the Sloan Digital Sky Survey. We compare the star formation rate (SFR) with stellar mass relation as a function of environment and morphology. After carefully controlling for mass, we find that in all environments, the degree of SFR suppression increases with increasing bulge-to-total (B/T) ratio. In addition, the SFRs of cluster and infall galaxies at a fixed mass are more suppressed than their field counterparts at all values of B/T. These results suggest a quenching mechanism that is linked to bulge growth that operates in all environments and an additional mechanism that further reduces the SFRs of galaxies in dense environments. We limit the sample to B/T ≤ 0.3 galaxies to control for the trends with morphology and find that the excess population of cluster galaxies with suppressed SFRs persists. We model the time-scale associated with the decline of SFRs in dense environments and find that the observed SFRs of the cluster core galaxies are consistent withmore »a range of models including a mechanism that acts slowly and continuously over a long (2–5 Gyr) time-scale, and a more rapid (<1 Gyr) quenching event that occurs after a delay period of 1–6 Gyr. Quenching may therefore start immediately after galaxies enter clusters.

    « less
  3. The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. Here, we analyzed ~300,000 papers published over the past two decades to quantify disparities across nations, genders, and taxonomy in the plant science literature. Our analyses reveal striking geographical biases—affluent nations dominate the publishing landscape and vast areas of the globe have virtually no footprint in the literature. Authors in Northern America are cited nearly twice as many times as authors based in Sub-Saharan Africa and Latin America, despite publishing in journals with similar impact factors. Gender imbalances are similarly stark and show remarkably little improvement over time. Some of the most affluent nations have extremely male biased publication records, despite supposed improvements in gender equality. In addition, we find that most studies focus on economically important crop and model species, and a wealth of biodiversity is underrepresented in the literature. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences.
    Free, publicly-accessible full text available March 7, 2024
  4. Abstract

    Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are “variants of uncertain significance” (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFoldthat is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPEmore »targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.

    « less
  5. Abstract The brain is composed of networks of interacting brain regions that support higher-order cognition. Among these, a core network of regions has been associated with recollection and other forms of episodic construction. Past research has focused largely on the roles of individual brain regions in recollection or on their mutual engagement as part of an integrated network. However, the relationship between these region- and network-level contributions remains poorly understood. Here, we applied multilevel structural equation modeling to examine the functional organization of the posterior medial (PM) network and its relationship to episodic memory outcomes. We evaluated two aspects of functional heterogeneity in the PM network: first, the organization of individual regions into subnetworks, and second, the presence of regionally specific contributions while accounting for network-level effects. Our results suggest that the PM network is composed of ventral and dorsal subnetworks, with the ventral subnetwork making a unique contribution to recollection, especially to recollection of spatial information, and that memory-related activity in individual regions is well accounted for by these network-level effects. These findings highlight the importance of considering the functions of individual brain regions within the context of their affiliated networks.
  6. Many desiccation-tolerant plants are widely distributed and exposed to substantial environmental variation across their native range. These environmental differences generate site-specific selective pressures that could drive natural variation in desiccation tolerance across populations. If identified, such natural variation can be used to target tolerance-enhancing characteristics and identify trait associations within a common genetic background. Here, we tested for natural variation in desiccation tolerance across wild populations of the South African resurrection plant Myrothamnus flabellifolia. We surveyed a suite of functional traits related to desiccation tolerance, leaf economics, and reproductive allocation in M. flabellifolia to test for trait associations and tradeoffs. Despite considerable environmental variation across the study area, M. flabellifolia plants were extremely desiccation tolerant at all sites, suggesting that tolerance is either maintained by selection or fixed in these populations. However, we detected notable associations between environmental variation, population characteristics, and fitness traits. Relative to mesic sites, plants in xeric sites were more abundant and larger, but were slower growing and less reproductive. The negative association between growth and reproduction with plant size and abundance pointed towards a potential growth–abundance tradeoff. The finding that M. flabellifolia is more common in xeric sites despite reductions in growth rate and reproductionmore »suggests that these plants thrive in extreme aridity.« less
  7. Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta–Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were Craterostigma plantagineum (17.5%), Haberlea rhodopensis (13.7%), Xerophyta viscosa (reclassified as X. schlechteri) (11.9%), Myrothamnus flabellifolia (8.5%), and Boea hygrometrica (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species,more »but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.« less
  8. Abstract

    The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism—both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.

  9. Abstract Virgo is the nearest galaxy cluster; it is thus ideal for studies of galaxy evolution in dense environments in the local universe. It is embedded in a complex filamentary network of galaxies and groups, which represents the skeleton of the large-scale Laniakea supercluster. Here we assemble a comprehensive catalog of galaxies extending up to ∼12 virial radii in projection from Virgo to revisit the cosmic-web structure around it. This work is the foundation of a series of papers that will investigate the multiwavelength properties of galaxies in the cosmic web around Virgo. We match spectroscopically confirmed sources from several databases and surveys including HyperLeda, NASA Sloan Atlas, NASA/IPAC Extragalactic Database, and ALFALFA. The sample consists of ∼7000 galaxies. By exploiting a tomographic approach, we identify 13 filaments, spanning several megaparsecs in length. Long >17 h –1 Mpc filaments, tend to be thin (<1 h –1 Mpc in radius) and with a low-density contrast (<5), while shorter filaments show a larger scatter in their structural properties. Overall, we find that filaments are a transitioning environment between the field and cluster in terms of local densities, galaxy morphologies, and fraction of barred galaxies. Denser filaments have a higher fraction of early-typemore »galaxies, suggesting that the morphology–density relation is already in place in the filaments, before galaxies fall into the cluster itself. We release the full catalog of galaxies around Virgo and their associated properties.« less