Volunteer-based plant monitoring in the UK has focused mainly on distribution mapping; there has been less emphasis on the collection of data on plant communities and habitats. Abundance data provide ...different insights into ecological pattern and allow for more powerful inference when considering environmental change. Abundance monitoring for other groups of organisms is well-established in the UK, e.g. for birds and butterflies, and conservation agencies have long desired comparable schemes for plants. We describe a new citizen science scheme for the UK (the 'National Plant Monitoring Scheme'; NPMS), with the primary aim of monitoring the abundance of plants at small scales. Scheme development emphasised volunteer flexibility through scheme co-creation and feedback, whilst retaining a rigorous approach to design. Sampling frameworks, target habitats and species, field methods and power are all described. We also evaluate several outcomes of the scheme design process, including: (i) landscape-context bias in the first two years of the scheme; (ii) the ability of different sets of indicator species to capture the main ecological gradients of UK vegetation; and, (iii) species richness bias in returns relative to a professional survey. Survey rates have been promising (over 60% of squares released have been surveyed), although upland squares are under-represented. Ecological gradients present in an ordination of an independent, unbiased, national survey were well-represented by NPMS indicator species, although further filtering to an entry-level set of easily identifiable species degraded signal in an ordination axis representing succession and disturbance. Comparison with another professional survey indicated that different biases might be present at different levels of participation within the scheme. Understanding the strengths and limitations of the NPMS will guide development, increase trust in outputs, and direct efforts for maintaining volunteer interest, as well as providing a set of ideas for other countries to experiment with.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
RNA-based vaccines against SARS-CoV-2 have proven critical to limiting COVID-19 disease severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain ...uncertain. Here we identify and characterize antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 using multiple single-cell technologies for in depth analysis of longitudinal samples from a cohort of healthy participants. Mass cytometry and unbiased machine learning pinpoint an expanding, population of antigen-specific memory CD4
and CD8
T cells with characteristics of follicular or peripheral helper cells. B cell receptor sequencing suggest progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlate with eventual SARS-CoV-2 IgG, and a participant lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms identify an antigen-specific cellular basis of RNA vaccine-based immunity.
Invasive alien species (IAS) are considered one of the greatest threats to biodiversity, particularly through their interactions with other drivers of change. Horizon scanning, the systematic ...examination of future potential threats and opportunities, leading to prioritization of IAS threats is seen as an essential component of IAS management. Our aim was to consider IAS that were likely to impact on native biodiversity but were not yet established in the wild in Great Britain. To achieve this, we developed an approach which coupled consensus methods (which have previously been used for collaboratively identifying priorities in other contexts) with rapid risk assessment. The process involved two distinct phases: Preliminary consultation with experts within five groups (plants, terrestrial invertebrates, freshwater invertebrates, vertebrates and marine species) to derive ranked lists of potential IAS. Consensus‐building across expert groups to compile and rank the entire list of potential IAS. Five hundred and ninety‐one species not native to Great Britain were considered. Ninety‐three of these species were agreed to constitute at least a medium risk (based on score and consensus) with respect to them arriving, establishing and posing a threat to native biodiversity. The quagga mussel, Dreissena rostriformis bugensis, received maximum scores for risk of arrival, establishment and impact; following discussions the unanimous consensus was to rank it in the top position. A further 29 species were considered to constitute a high risk and were grouped according to their ranked risk. The remaining 63 species were considered as medium risk, and included in an unranked long list. The information collated through this novel extension of the consensus method for horizon scanning provides evidence for underpinning and prioritizing management both for the species and, perhaps more importantly, their pathways of arrival. Although our study focused on Great Britain, we suggest that the methods adopted are applicable globally.
The generation of variation is paramount for the action of natural selection. Although biologists are now moving beyond the idea that random mutation provides the sole source of variation for ...adaptive evolution, we still assume that variation occurs randomly. In this review, we discuss an alternative view for how phenotypic plasticity, which has become well accepted as a source of phenotypic variation within evolutionary biology, can generate nonrandom variation. Although phenotypic plasticity is often defined as a property of a genotype, we argue that it needs to be considered more explicitly as a property of developmental systems involving more than the genotype. We provide examples of where plasticity could be initiating developmental bias, either through direct active responses to similar stimuli across populations or as the result of programmed variation within developmental systems. Such biased variation can echo past adaptations that reflect the evolutionary history of a lineage but can also serve to initiate evolution when environments change. Such adaptive programs can remain latent for millions of years and allow development to harbor an array of complex adaptations that can initiate new bouts of evolution. Specifically, we address how ideas such as the flexible stem hypothesis and cryptic genetic variation overlap, how modularity among traits can direct the outcomes of plasticity, and how the structure of developmental signaling pathways is limited to a few outcomes. We highlight key questions throughout and conclude by providing suggestions for future research that can address how plasticity initiates and harbors developmental bias.
With relatively few known specific transcription factors to control the abundance of specific mRNAs, Plasmodium parasites may rely more on the regulation of transcript stability and turnover to ...provide sufficient gene regulation. Plasmodium transmission stages impose translational repression on specific transcripts in part to accomplish this. However, few proteins are known to participate in this process, and those that are characterized primarily affect female gametocytes. We have identified and characterized Plasmodium yoelii (Py) CCR4-1, a putative deadenylase, which plays a role in the development and activation of male gametocytes, regulates the abundance of specific mRNAs in gametocytes, and ultimately increases the efficiency of host-to-vector transmission. We find that when pyccr4-1 is deleted or its protein made catalytically inactive, there is a loss in the initial coordination of male gametocyte maturation and a reduction of parasite infectivity of the mosquito. Expression of only the N-terminal CAF1 domain of the essential CAF1 deadenylase leads to a similar phenotype. Comparative RNA-seq revealed that PyCCR4-1 affects transcripts important for transmission-related functions that are associated with male or female gametocytes, some of which directly associate with the immunoprecipitated complex. Finally, circular RT-PCR of one of the bound, dysregulated transcripts showed that deletion of the pyccr4-1 gene does not result in gross changes to its UTR or poly(A) tail length. We conclude that the two putative deadenylases of the CAF1/CCR4/NOT complex play critical and intertwined roles in gametocyte maturation and transmission.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ponds can provide important refuges for aquatic biota on developed floodplains and are increasingly being constructed in an effort to enhance native biodiversity and ecosystem services in degraded ...landscapes. This study examined 34 constructed ponds to investigate the influence of design features on community composition, native biodiversity, and the biomass or abundance of common fish and waterbirds on the lower Waikato River floodplain, northern New Zealand.
Inundation frequency appeared to be a key factor affecting biomass of the native shortfin eel Anguilla australis and three invasive fish species (common carp Cyprinus carpio, brown bullhead Ameiurus nebulosus, and goldfish Carassius auratus), suggesting that colonisation occurred during flooding by adjacent waterbodies. Linear models indicated that shortfin eel abundance and total eel biomass were positively associated with the biomass of potential fish prey, the area occupied by islands and cover by trees in the riparian zone.
Native waterbird species richness was strongly related to water area, edge length (including islands) and area:perimeter ratio, with little increase in richness for ponds >1 ha in area, perimeters longer than 800 m, and ratios over 20. The protected grey teal (Anas gracilis), and the recreationally hunted species phenotypically assigned as mallard (Anas platyrhynchos + hybrids) and grey duck (Anas superciliosa + hybrids) appeared most strongly influenced, respectively, by perimeter length, water depth, and biomass of potential macroinvertebrate food supplies, suggesting variable effects of pond design attributes among waterfowl species.
Overall, these results indicate that constructed ponds can be designed to promote native waterbird diversity, enhance eel fishery and waterfowl gamebird services, and also limit the proliferation of some non‐native invasive fish species in degraded floodplain landscapes. A hierarchy of constructed pond design attributes was identified, involving landscape position and connectivity, pond morphology and complexity, and riparian maturity and buffering, which were associated with direct (habitat) and indirect (food supply, physicochemistry) effects on biodiversity and provisioning services.
Abstract
Little is known about the effects of woody plant encroachment—a recent but pervasive phenomenon—on the hydraulic properties of bedrock substrates. Recent work using stream solute ...concentrations paired with weathering models suggests that woody plant encroachment accelerates limestone weathering. In this field study, we evaluate this hypothesis by examining bedrock in the Edwards Plateau, an extensive karst landscape in Central Texas. We compared a site that has been heavily encroached by woody plants (mainly
Quercus fusiformis
and
Juniperus ashei
), with an adjacent site that has been maintained free of encroachment for the past eight decades. Both sites share the same bedrock, as confirmed by trenching, and originally had very few trees, which enabled us to evaluate how encroachment impacted the evolution of hydraulic properties over a period of no more than 80 years. Using in situ permeability tests in boreholes drilled into the weathered bedrock, we found that the mean saturated hydraulic conductivity of the bedrock was higher—by an order of magnitude—beneath woody plants than in the areas where woody plants have been continuously suppressed. Additionally, woody plant encroachment was associated with greater regolith thickness, greater plant rooting depths, significantly lower rock hardness, and a 24–44% increase in limestone matrix porosity. These findings are strong indicators that woody plant encroachment enhances bedrock weathering, thereby amplifying its permeability—a cycle of mutual reinforcement with the potential for substantial changes within a few decades. Given the importance of shallow bedrock for ecohydrological and biogeochemical processes, the broader impacts of woody plant encroachment on weathering rates and permeability warrant further investigation.
Summary
Transmission of the malaria parasite occurs in an unpredictable moment, when a mosquito takes a blood meal. Plasmodium has therefore evolved strategies to prepare for transmission, including ...translationally repressing and protecting mRNAs needed to establish the infection. However, mechanisms underlying these critical controls are not well understood, including whether Plasmodium changes its translationally repressive complexes and mRNA targets in different stages. Efforts to understand this have been stymied by severe technical limitations due to substantial mosquito contamination of samples. Here using P. yoelii, for the first time we provide a proteomic comparison of a protein complex across asexual blood, sexual and sporozoite stages, along with a transcriptomic comparison of the mRNAs that are affected in these stages. We find that the Apicomplexan‐specific ALBA4 RNA‐binding protein acts to regulate development of the parasite's transmission stages, and that ALBA4 associates with both stage‐specific and stage‐independent partners to produce opposing mRNA fates. These efforts expand our understanding and ability to interrogate both sexual and sporozoite transmission stages and the molecular preparations they evolved to perpetuate their infectious cycle.
The apicomplexan‐specific RNA‐binding protein ALBA4 is important to both transmission stages in Plasmodium yoelii parasites. Comparative RNA‐seq and IP/mass spectrometry reveals that it may accomplish this through stage‐specific and stage‐independent protein interactions, ultimately producing opposing effects upon mRNAs in different stages. This work is the first to compare the proteomics and related transcriptomics of a protein complex across asexual blood, sexual blood and sporozoite stages in a malaria parasite.
E-cadherin, the primary epithelial adherens junction protein, has been implicated as playing a critical role in nucleating formation of adherens junctions, tight junctions, and desmosomes. In ...addition to its role in maintaining structural tissue integrity, E-cadherin has also been suggested as an important modulator of cell signaling via interactions with its cytoplasmic binding partners, catenins, as well as with growth factor receptors. Therefore, we proposed that loss of E-cadherin from the developing mouse intestinal epithelium would disrupt intestinal epithelial morphogenesis and function. To test this hypothesis, we used a conditional knockout approach to eliminate E-cadherin specifically in the intestinal epithelium during embryonic development. We found that E-cadherin conditional knockout mice failed to survive, dying within the first 24 hours of birth. Examination of intestinal architecture at E18.5 demonstrated severe disruption to intestinal morphogenesis in animals lacking E-cadherin in the epithelium of the small intestine. We observed changes in epithelial cell shape as well as in the morphology of villi. Although junctional complexes were evident, junctions were abnormal, and barrier function was compromised in E-cadherin mutant intestine. We also identified changes in the epithelial cell populations present in E-cadherin conditional knockout animals. The number of proliferating cells was increased, whereas the number of enterocytes was decreased. Although Wnt/β-catenin target mRNAs were more abundant in mutants compared with controls, the amount of nuclear activated β-catenin protein was dramatically lower in mutants compared with controls. In summary, our data demonstrate that E-cadherin is essential for intestinal epithelial morphogenesis and homeostasis during embryonic development.
► E-cadherin loss in the developing intestinal epithelium caused neonatal lethality. ► Intestinal epithelial architecture was severely disrupted in E-cadherin mutants. ► Barrier function was compromised in E-cadherin mutants. ► Mutant intestine contained more proliferating cells but fewer enterocytes. ► β-catenin target gene expression was increased, but β-catenin was less abundant in mutants.
Infection with COVID-19 pneumonia may necessitate intubation and mechanical ventilation. Viral inflammation and pressure necrosis may lead to scarring, stenosis, and in severe cases, fistula ...formation. Nonmalignant tracheoesophageal fistulas (TEF) represent a surgical challenge and may necessitate locoregional tissue transfer and tracheal resection to prevent recurrence and maintain airway patency. We present a case of TEF in a 63-year-old female secondary to prolonged mechanical ventilation in the setting of COVID pneumonia, detailing the clinical findings and surgical repair. Primary closure of the esophageal defect with pectoralis major muscle flap onlay and tracheal resection, with median sternotomy for access, provided successful intervention, allowing for subsequent tracheostomy decannulation and return to a complete oral diet. This case offers further evidence of the increased risk of airway complications in COVID-19 infection and provides otolaryngologists with an example of a rare surgical approach useful in management.
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