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Pain and inflammation contribute immeasurably to reduced quality of life, yet modern analgesic and anti-inflammatory therapeutics can cause dependence and side effects. Here, we screened 1444 plant extracts, prepared primarily from native species in California and the United States Virgin Islands, against two voltage-gated K+ channels - T-cell expressed Kv1.3 and nociceptive-neuron expressed Kv7.2/7.3. A subset of extracts both inhibits Kv1.3 and activates Kv7.2/7.3 at hyperpolarized potentials, effects predicted to be anti-inflammatory and analgesic, respectively. Among the top dual hits are witch hazel and fireweed; polymodal modulation of multiple K+ channel types by hydrolysable tannins contributes to their dual anti-inflammatory, analgesic actions. In silico docking and mutagenesis data suggest pore-proximal extracellular linker sequence divergence underlies opposite effects of hydrolysable tannins on different Kv1 isoforms. The findings provide molecular insights into the enduring, widespread medicinal use of witch hazel and fireweed and demonstrate a screening strategy for discovering dual anti-inflammatory, analgesic small molecules.

In this review and synthesis, we argue that California is an important test case for the nation and world because terrestrial biodiversity is very high, present and anticipated threats to biodiversity from climate change and other interacting stressors are severe, and innovative approaches to protecting biodiversity in the context of climate change are being developed and tested. We first review salient dimensions of Californias terrestrial physical, biological, and human diversity. Next, we examine four facets of the threat to their sustainability of these dimensions posed by climate change: direct impacts, illustrated by a new analysis of shifting diversity hotspots for plants; interactive effects involving invasive species, land-use change, and other stressors; the impacts of changing fire regimes; and the impacts of land-based renewable energy development. We examine recent policy responses in each of these areas, representing attempts to better protect biodiversity while advancing climate adaptation and mitigation. We conclude that Californias ambitious 30 × 30 Initiative and its efforts to harmonize biodiversity conservation with renewable energy development are important areas of progress. Adapting traditional suppression-oriented fire policies to the reality of new fire regimes is an area in which much progress remains to be made.

Plant-systemic neonicotinoid (NN) insecticides can exert non-target impacts on organisms like beneficial insects and soil microbes. NNs can affect plant microbiomes, but we know little about their effects on microbial communities that mediate plant-insect interactions, including nectar-inhabiting microbes (NIMs). Here we employed two approaches to assess the impacts of NN exposure on several NIM taxa. First, we assayed the in vitro effects of six NN compounds on NIM growth using plate assays. Second, we inoculated a standardised NIM community into the nectar of NN-treated canola (Brassica napus) and assessed microbial survival and growth after 24 h. With few exceptions, in vitro NN exposure tended to decrease bacterial growth metrics. However, the magnitude of the decrease and the NN concentrations at which effects were observed varied substantially across bacteria. Yeasts showed no consistent in vitro response to NNs. In nectar, we saw no effects of NN treatment on NIM community metrics. Rather, NIM abundance and diversity responded to inherent plant qualities like nectar volume. In conclusion, we found no evidence that NIMs respond to field-relevant NN levels in nectar within 24 h, but our study suggests that context, specifically assay methods, time and plant traits, is important in assaying the effects of NNs on microbial communities.

Building on previous studies, this essay discusses the use of embryological images and analogies in Anaximander, Empedocles, Democritus, and Lucretius. It pursues their intertextual connections arguing that in ancient philosophy embryology was not only relevant for conceiving the early formation of the cosmos as has been claimed so far, but that it also shaped the conception of the primeval rise of animal life and the living processes of plants. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a toxic metal primarily found as a by-product of zinc production. Cd was a proven carcinogen, and exposure to this metal has been linked to various adverse health effects, which were first reported in the mid-19th century and thoroughly investigated by the 20th century. The toxicokinetics and dynamics of Cd reveal its propensity for long biological retention and predominant storage in soft tissues. Until the 1950s, Cd pollution was caused by industrial activities, whereas nowadays, the main source is phosphate fertilizers, which strongly contaminate soil and water and affect human health and ecosystems. Cd enters the human body mainly through ingestion and inhalation, with food and tobacco smoke being the primary sources. It accumulates in various organs, particularly the kidney and liver, and is known to cause severe health problems, including renal dysfunction, bone diseases, cardiovascular problems, and many others. On a cellular level, Cd disrupts numerous biological processes, inducing oxidative stress generation and DNA damage. This comprehensive review explores Cd pollution, accumulation, distribution, and biological impacts on bacteria, fungi, edible mushrooms, plants, animals, and humans on a molecular level. Molecular aspects of carcinogenesis, apoptosis, autophagy, specific gene expression, stress protein synthesis, and ROS formation caused by Cd were discussed as well. This paper also summarizes how Cd is removed from contaminated environments and the human body. [ABSTRACT FROM AUTHOR]

Understanding the circumstances under which insect herbivores will adopt a novel host plant is a longstanding question in basic and applied ecology. While geographic variation in host use can arise through differences in both herbivore preference and plant characteristics, there is a tendency to attribute geographic variation in host use to regional differences in herbivore preference alone. This is especially true for herbivores specialized to one or a few plant species. We compared how geographic variation in herbivore preference and host plant origin shape regional differences in host plant use by the specialized herbivore, Euphydryas phaeton. In parts of its range, E. phaeton uses only a native host, Chelone glabra, while in others, it also uses an introduced host, Plantago lanceolata. We offered female butterflies from each region the non-native host plant sourced from both regions and compared their oviposition behavior. The non-native host was almost universally rejected by butterflies in the region where only the native plant is used. In the region where butterflies use both hosts, females accepted non-native plants from their natal region twice as often as non-native plants from the other region where they are not used. Acceptance differed substantially among individual butterflies within regions but not among plants within regions. Thus, both individual preference and regional differences in both the insect and non-native host contributed to the geographic variation in different ways. These results highlight that, in addition to herbivore preference, regional differences in perceived plant suitability may be an important driver of diet breadth.

AbstractThe biomolecular condensates (BCs) formed by proteins through phase separation provide the necessary space and raw materials for the orderly progression of cellular activities, and on this basis, various membraneless organelles (MLOs) are formed. The occurrence of eukaryotic phase separation is driven by multivalent interactions from intrinsically disordered regions (IDRs) and/or specific protein/nucleic acid binding domains and is regulated by various environmental factors. In plant and animal cells, the MLOs involved in gene expression regulation, stress response, and mitotic control display similar functions and mechanisms. In contrast, the phase separation related to reproductive development and immune regulation differs significantly between the two kingdoms owing to their distinct cell structures and nutritional patterns. In addition, animals and plants each exhibit unique protein phase separation activities, such as neural regulation and light signal response. By comparing the similarities and differences in the formation mechanism and functional regulation of known protein phase separation, we elucidated its importance in the evolution, differentiation, and environmental adaptation of both animals and plants. The significance of studying protein phase separation for enhancing biological quality of life has been further emphasized. [ABSTRACT FROM AUTHOR]

A star-filled sky has long been a source of awe and inspiration, and its loss adversely affects human, nonhuman, and environmental health. In one generation, this majestic nighttime overstory has been lost due to national and international overuse of light-emitting diodes lighting. This article canvasses ill health effects of excessive light at night. Blue wavelengths of light are damaging to many forms of life, and glare from unshielded light compromises road safety and infiltrates bedrooms, suppressing melatonin production, undermining sleep quality and duration, and exacerbating susceptibility to many kinds of illness. [ABSTRACT FROM AUTHOR]

The article tries to present and systematize the Late Antique miracles with the participation of plants and animals. The main source material is drawn from the collections of miracles such as the works of Gregory of Tours and Gregory the Great. The distinction will be made between the miracles that happened during the lifetime of a saint or after their death and between the miracles in which the plants and animals are objects or subjects of a miracle, or both at the same time. [ABSTRACT FROM AUTHOR]

The evergreen plant rosemary (Salvia rosmarinus) has been employed medicinally for centuries as a memory aid, analgesic, spasmolytic, vasorelaxant and antihypertensive, with recent preclinical and clinical evidence rationalizing some applications. Voltage-gated potassium (Kv) channels in the KCNQ (Kv7) subfamily are highly influential in the nervous system, muscle and epithelia. KCNQ4 and KCNQ5 regulate vascular smooth muscle excitability and contractility and are implicated as antihypertensive drug targets. Here, we found that rosemary extract potentiates homomeric and heteromeric KCNQ4 and KCNQ5 activity, resulting in membrane hyperpolarization. Two rosemary diterpenes, carnosol and carnosic acid, underlie the effects and, like rosemary, are efficacious KCNQ-dependent vasorelaxants, quantified by myography in rat mesenteric arteries. Sex- and estrous cycle stage-dependence of the vasorelaxation matches sex- and estrous cycle stage-dependent KCNQ expression. The results uncover a molecular mechanism underlying rosemary vasorelaxant effects and identify new chemical spaces for KCNQ-dependent vasorelaxants.

Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.

Root-knot nematodes (Meloidogyne spp.) are highly evolved obligate parasites threatening global food security. These parasites have a remarkable ability to establish elaborate feeding sites in roots, which are their only source of nutrients throughout their life cycle. A wide range of nematode effectors have been implicated in modulation of host pathways for defense suppression and/or feeding site development. Plants produce a diverse array of peptide hormones including PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY)-family peptides, which promote root growth via cell expansion and proliferation. A sulfated PSY-like peptide RaxX (required for activation of XA21 mediated immunity X) produced by the biotrophic bacterial pathogen (Xanthomonas oryzae pv. oryzae) has been previously shown to contribute to bacterial virulence. Here, we report the identification of genes from root-knot nematodes predicted to encode PSY-like peptides (MigPSYs) with high sequence similarity to both bacterial RaxX and plant PSYs. Synthetic sulfated peptides corresponding to predicted MigPSYs stimulate root growth in Arabidopsis. MigPSY transcript levels are highest early in the infection cycle. Downregulation of MigPSY gene expression reduces root galling and egg production, suggesting that the MigPSYs serve as nematode virulence factors. Together, these results indicate that nematodes and bacteria exploit similar sulfated peptides to hijack plant developmental signaling pathways to facilitate parasitism.

Most flowering plants require animal pollination and are visited by multiple pollinator species. Historically, the effects of pollinators on plant fitness have been compared using the number of pollen grains they deposit, and the number of seeds or fruits produced following a visit to a virgin flower. While useful, these methods fail to consider differences in pollen quality and the fitness of zygotes resulting from pollination by different floral visitors. Here we show that, for three common native self-compatible plants in Southern California, super-abundant, non-native honeybees (Apis mellifera L.) visit more flowers on an individual before moving to the next plant compared with the suite of native insect visitors. This probably increases the transfer of self-pollen. Offspring produced after honeybee pollination have similar fitness to those resulting from hand self-pollination and both are far less fit than those produced after pollination by native insects or by cross-pollination. Because honeybees often forage methodically, visiting many flowers on each plant, low offspring fitness may commonly result from honeybee pollination of self-compatible plants. To our knowledge, this is the first study to directly compare the fitness of offspring resulting from honeybee pollination to that of other floral visitors.

Community diversity can reduce the prevalence and spread of disease, but certain species may play a disproportionate role in diluting or amplifying pathogens. Flowers act as both sources of nutrition and sites of pathogen transmission, but the effects of specific plant species in shaping bee disease dynamics are not well understood. We evaluated whether plantings of sunflower (Helianthus annuus), whose pollen reduces infection by some pathogens when fed to bees in captivity, lowered pathogen levels and increased reproduction in free-foraging bumblebee colonies (Bombus impatiens). Sunflower abundance reduced the prevalence of a common gut pathogen, Crithidia bombi, and reduced infection intensity, with an order of magnitude lower infection intensity at high sunflower sites compared with sites with little to no sunflower. Sunflower abundance was also positively associated with greater queen production in colonies. Sunflower did not affect prevalence of other detected pathogens. This work demonstrates that a single plant species can drive disease dynamics in foraging B. impatiens, and that sunflower plantings can be used as a tool for mitigating a prevalent pathogen while also increasing reproduction of an agriculturally important bee species.

Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.

The production of vaccines in plant cells, termed plant-made pharmaceuticals or molecular farming, is a promising technology for scalable production. Compared to mammalian cell lines, like Chinese Hamster Ovary (CHO) or bacterial cells, plants can be grown with less cost on a large scale to make vaccines antigens and therapeutics affordable and accessible worldwide. An innovative application of this alternative system is the production of vaccines in edible tissues that can be consumed orally to deliver protein antigen without any further processing. In this project, we report stable expression of amino acid sequences corresponding to the TM-1 gene of Mycoplasma gallisepticum as a candidate vaccine antigen against Chronic Respiratory Disease (CRD) in chickens using wheat seed's tissues as a production host. Molecular and immunoblotting analysis confirmed the ubiquitous expression of a recombinant 41.8-kDa protein with an expression level of 1.03 mg/g dry weight in the endosperm tissues. When orally delivered, the plant-made vaccine was effective in terms of developing antibody response in animal model i.e., chicken without any detectable weight loss. Two doses of orally delivered plant-made TM-1 vaccine candidate elicited the immune response and protective effect against MG virus challenge at the level comparable to commercially available inactivated vaccine against CRD. Our study demonstrates that plant-made vaccines are not only safe but also scalable and cost-effective with prolonged stability at room temperature.

This article was motivated by the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) announcement that on 17 December 2021 it rescinded Federal Orders of 2 May 2007 that regulated (what was believed to be) a new outbreak of the light brown apple moth (LBAM, Epiphyas postvittana (Walker)) in the mainland United States. Our article follows from, and builds on, a 2013 article published by Carey and Harder that outlined major concerns about the LBAM eradication program including the need, cost, safety, practicality, and feasibility of the program and the public opposition to it. The program began with an emergency order based on USDA claims of billions of dollars in potential crop losses and the need to circumvent safety review processes to urgently prevent the pest's establishment. The program ended with the realization by government decision-makers, 14 years after initiating the program, that LBAM posed no quarantine-level threat in the first place and with no evidence of any economic damage done by the insect. This article summarizes the mistakes made in devising and carrying out what has ultimately proven to be one of the most oversold, overhyped, misguided, ill-advised, unnecessary, and costly programs in the recent history of insect eradication programs in California. Termination of the LBAM program by USDA-APHIS presents an opportunity to review the program to identify lessons learned and provide recommendations to help avoid similar mistakes in future invasive species response programs. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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This article is an adapted version of the 2023 David Buchan Memorial Lecture. Humans, animals, and plants talk to each other in songs, stories, legends, and other forms of creative expressions encompassed in the term folklore. This distinguishing feature of folklore is mostly perceived as merely fantastic, or even unrealistic. This article re-evaluates it from perspectives based in current human–animal studies and new scientific understanding of the non-human beings, and finds that folk narrative texts present an ecological consciousness in which humans and non-human animals communicate, fight, and cooperate with each other. This multi-species world, based on inter-species communication, has played a role in the making of human–animal relationships in different cultures and can also play a role in healing what the author calls our agonized ecology. [ABSTRACT FROM AUTHOR]

Since its discovery in 2016, the Polerovirus Barley virus G has been reported in at least nine countries and multiple species of monocot plants. All of these reports have used PCR and/or sequencing based assays to identify BVG, however none have investigated the biology of BVG. In this study we detail the generation of the first infectious cDNA clone of BVG from archived RNA, thereby producing a valuable experimental tool and system for studying BVG biology. Using this system we identified two compatible aphid vectors and confirmed the susceptibility of several monocot plants, and the dicotyledonous plant host Nicotiana benthamiana, to BVG.

Climate change may disrupt plant-pollinator mutualisms by generating phenological asynchronies and by altering traits that shape interaction costs and benefits. Our knowledge is limited to studies that manipulate only one partner or focus on either phenological or trait-based mismatches. We assembled communities of three annual plants and a solitary bee prior to flowering and emergence to test how springtime warming affects phenologies, traits, interactions and reproductive output. Warming advanced community-level flowering onset, peak and end but did not alter bee emergence. Warmed plant communities produced fewer and smaller flowers with less, more-concentrated nectar, reducing attractiveness, and warmed bees were more generalized in their foraging, reducing their effectiveness. Plant-bee interactions were less frequent, shorter and peaked earlier under warming. As a result, warmed plants produced fewer, lighter seeds, indicating pollinator-mediated fitness costs. Climate change will perturb plant-pollinator mutualisms, causing wide-ranging effects on partner species and diminishing the ecosystem service they provide.

A critical function of animal coloration is avoiding attack, either by warning predators or reducing detectability. Evolution of these divergent strategies may depend on prey palatability and apparency to predators: conspicuous coloration may be favoured if species are distasteful, or habitats make hiding difficult; by contrast, camouflage may be effective if prey lack defences or environments are visually complex. For insect herbivores, host plants provide both chemical defence and the background against which they are detected or obscured; thus, plant traits may be key to coloration in these foundational terrestrial organisms. We use 1808 species of larval Lepidoptera to explore macroevolution of protective coloration strategy. We find that colour and pattern evolve jointly in caterpillars, similar to an array of species across the animal kingdom, while individual elements of coloration evolve closely with diet ecology. Consistent with key tenets of plant defence and plant-herbivore coevolutionary theory, conspicuous colours are associated with herbaceous host plants-thought to be defended by toxins-while camouflage colours and patterns are associated with woody plants and grasses. Contrary to theory, dietary specialization is not associated with conspicuous coloration. Our results add valuable insights into the evolutionary forces shaping colour and pattern in nature.

Although plants and animals both assess their environment and respond to stimuli, this reaction is considered a behavior in animals and a response in plants. Responses in plants are seen within various timescales- from the nanosecond stimuli is presented to a lifelong progression. Within this study, we bridge the gap between animal behavioral studies and plant response. Sensitive plants (Mimosa pudica L.) are an ideal subject for this due to the rapid closure of their primary leaflets when touched. We designed a multimodal, or stress combination, experiment to test two hypotheses with sensitive plants: if they could be distracted and if they would alter their risk assessment when exposed to external stimuli (wind and sound). To evaluate the distraction hypothesis, we measured an individuals latency to close, hypothesizing that if the plants were distracted, they would take longer to close. To evaluate the uncertain risk hypothesis, we quantified the latency to reopen, hypothesizing that if the plants were uncertain, they would take longer to reopen. We also quantified the number of pinnae closed on the selected stem to test for changes in risk assessment across treatments. We expected the unimodal treatments would distract or alter risk assessment, and the multimodal treatment would elicit an enhanced response. Multimodal stimuli had a significant effect on the number of pinnae closed before the tap, but we found no evidence that plants were distracted by any stimulus tested. We found that temperature had a significant effect on the latency to close, and that plants modified their risk assessment when exposed to experimental wind stimuli. By manipulating environmental stimuli, we found that sensitive plants trade-off energy and perceived risk much in the way that is commonly found in animals. Framing the study of plants responses to environmental stimuli as behavioral questions may generate new insights.

Prometryn is a methylthio-s-triazine herbicide used to control the growth of annual broadleaf and grass weeds in many cultivated plants. Significant traces of prometryn are documented in the environment, mainly in waters, soil, and plants used for human and domestic consumption. Previous studies have shown that triazine herbicides have carcinogenic potential in humans. However, there is limited information about the effects of prometryn on the cardiac system in the literature, or the mechanisms and signaling pathways underlying any potential cytotoxic effects are not known. It is important to understand the possible effects of exogenous compounds such as prometryn on the heart. To determine the mechanisms and signaling pathways affected by prometryn (185 mg/kg every 48 h for seven days), we performed proteomic profiling of male mice heart with quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) using ten-plex tandem mass tag (TMT) labeling. The data suggest that several major pathways, including energy metabolism, protein degradation, fatty acid metabolism, calcium signaling, and antioxidant defense system were altered in the hearts of prometryn-treated mice. Proteasome and immunoproteasome activity assays and expression levels showed proteasome dysfunction in the hearts of prometryn-treated mice. The results suggest that prometryn induced changes in mitochondrial function and various signaling pathways within the heart, particularly affecting stress-related responses.

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.

Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments where human management and disturbance is minimized. We know little about what species are rare, how many species are rare, and what management practices promote rare species in urban environments. Here, we identified which plants and species of birds and bees that control pests and pollinate crops are rare in urban gardens and assessed how social, biophysical factors, and cross-taxonomic comparisons influence rare species richness. We found overwhelming numbers of rare species, with more than 50% of plants observed classified as rare. Our results highlight the importance of women, older individuals, and gardeners who live closer to garden sites in increasing the number of rare plants within urban areas. Fewer rare plants were found in older gardens and gardens with more bare soil. There were more rare bird species in larger gardens and more rare bee species for which canopy cover was higher. We also found that in some cases, rarity begets rarity, with positive correlations found between the number of rare plants and bee species and between bee and bird species. Overall, our results suggest that urban gardens include a high number of species existing at low frequency and that social and biophysical factors promoting rare, planned biodiversity can cascade down to promote rare, associated biodiversity.

The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.

Fossilized leaves provide the longest running record of hyperdiverse plant-insect herbivore associations. Reconstructions of these relationships over deep time indicate strong links between environmental conditions, herbivore diversity, and feeding damage on leaves. However, herbivory has not been compared between the past and the modern era, which is characterized by intense anthropogenic environmental change. Here, we present estimates for damage frequencies and diversities on fossil leaves from the Late Cretaceous (66.8 Ma) through the Pleistocene (2.06 Ma) and compare these estimates with Recent (post-1955) leaves collected via paleobotanical methods from modern ecosystems: Harvard Forest, United States; the Smithsonian Environmental Research Center, United States; and La Selva, Costa Rica. Total damage frequency, measured as the percentage of leaves with any herbivore damage, within modern ecosystems is greater than any fossil locality within this record. This pattern is driven by increased frequencies across nearly all functional feeding groups within the Recent. Diversities of total, specialized, and mining damage types are elevated within the Recent compared with fossil floras. Our results demonstrate that plants in the modern era are experiencing unprecedented levels of insect damage, despite widespread insect declines. Human influence, such as the rate of global climate warming, influencing insect feeding and timing of life cycle processes along with urbanization and the introduction of invasive plant and insect species may drive elevated herbivory. This research suggests that the strength of human influence on plant-insect interactions is not controlled by climate change alone but rather, the way in which humans interact with terrestrial landscape.

Transcriptomic studies are an important tool for understanding the molecular pathways underlying host plant use by agricultural pests, including vectors of damaging plant pathogens. Thus far, bulk RNA-Seq has been the main approach for non-model insects. This method relies on pooling large numbers of whole organisms or hundreds of individually dissected organs. The latter approach is logistically challenging, may introduce artifacts of handling and storage, and is not compatible with biological replication. Here, we tested an approach to generate transcriptomes of individual salivary glands and other low-input body tissues from whiteflies (Bemisia tabaci MEAM1), which are major vectors of plant viruses. By comparing our outputs to published bulk RNA-Seq datasets for whole whitefly bodies and pools of salivary glands, we demonstrate that this approach recovers similar numbers of transcripts relative to bulk RNA-Seq in a tissue-specific manner, and for some metrics, exceeds performance of bulk tissue RNA-Seq. Libraries generated from individual salivary glands also yielded additional novel transcripts not identified in pooled salivary gland datasets, and had hundreds of enriched transcripts when compared with whole head tissues. Overall, our study demonstrates that it is feasible to produce high quality, replicated transcriptomes of whitefly salivary glands and other low-input tissues. We anticipate that our approach will expand hypothesis-driven research on salivary glands of whiteflies and other Hemiptera, thus enabling novel control strategies to disrupt feeding and virus transmission.

In the last two decades, there has been a blossoming literature aiming to counter the neglect of plant capacities. In their recent paper, Miguel Segundo-Ortin and Paco Calvo begin by providing an overview of the literature to then question the mistaken assumptions that led to plants being immediately rejected as candidates for sentience. However, it appears that many responses to their arguments are based on the implicit conviction that because animals have far more sophisticated cognition and agency than plants, and that plants should not have the same moral status as animals, plants should not have any moral status. Put in simpler terms: it is not as bad to eat plants than to eat, say, pigs. While there are still uncertainties around comparative moral and policy implications between animals and plants, given a gradualist account of quasi-sentience and partial moral status, both of which we claim are a matter of degree, we may not have to abolish our convictions by declaring that plants have no sentience or moral status at all. Indeed, we can hold two things at the same time: that animals and plants have moral status, but animals have prima facie more moral status than plants. [ABSTRACT FROM AUTHOR]

Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.

Animal biologists have recently focused on individual variation in behavioral traits and have found that individuals of many species have personalities. These are defined as consistent intraspecific differences in behaviors that are repeatable across different situations and stable over time. When animals sense danger, some individuals will alert neighbors with alarm calls and both calling and responding vary consistently among individuals. Plants, including sagebrush, emit volatile cues when they are attacked by herbivores and neighbors perceive these cues and reduce their own damage. We experimentally transferred volatiles between pairs of sagebrush plants to evaluate whether individuals showed consistent variation in their effectiveness as emitters and as receivers of cues, measured in terms of reduced herbivore damage. We found that 64% of the variance in chewing damage to branches over the growing season was attributable to the identity of the individual receiving the cues. This variation could have been caused by inherent differences in the plants as well as by differences in the environments where they grew and their histories. We found that 5% of the variance in chewing damage was attributable to the identity of the emitter that provided the cue. This fraction of variation was statistically significant and could not be attributed to the environmental conditions of the receiver. Effective receivers were also relatively effective emitters, indicating consistency across different situations. Pairs of receivers and emitters that were effective communicators in 2018 were again relatively effective in 2019, indicating consistency over time. These results suggest that plants have repeatable individual personalities with respect to alarm calls.

Urbanization is associated with increases in impervious land cover, which alters the distribution of resources available to wildlife and concentrates activity in unbuilt spaces such as parks and gardens. How resource shifts alter the dynamics of parasite and pathogen transmission has not been addressed for many important species in urban systems. We focus on urban gardens, resource-rich "islands" within the urban matrix, to examine how the availability of floral resources at local and landscape scales influences the prevalence of six RNA viruses and three parasites in honey bees and bumble bees. Because parasites and pathogens are transmitted at flowers between visitors, we expected that floral abundance would concentrate bees within gardens, amplifying infection rates in pollinators, unless increases in floral resources would enhance bee diversity enough to dilute transmission. We found that garden size and flowering perennial plant abundance had a positive, direct effect on parasite and pathogen richness in bumble bees, suggesting that resource provisioning amplifies transmission. We also found that parasitism rates in honey bees were positively associated with parasites and pathogens in bumble bees, suggesting spillover between species. Encouragingly, we found evidence that management may mitigate parasitism through indirect effects: garden size had a positive impact on bee diversity, which in turn was negatively associated with parasite and pathogen richness in bumble bees. Unexpectedly, we observed that that parasite and pathogen richness in honey bees had no significant predictors, highlighting the complexity of comparing transmission dynamics between species. Although floral resources provide bees with food, we suggest more research on the tradeoffs between resource provisioning and disease transmission to implement conservation plantings in changing landscapes.

Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.

DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As is evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation, also control tissue-specific methylation patterns, with the most striking pattern observed in ovules where CLSY3 and CLSY4 control DNA methylation at loci with a highly conserved DNA motif. On a more global scale, we demonstrate that specific clsy mutants are sufficient to shift the epigenetic landscape between tissues. Together, these findings reveal substantial epigenetic diversity between tissues and assign these changes to specific CLSY proteins, elucidating how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript diversification in eukaryotes, which is increasingly recognized as an important layer for eukaryotic gene expression. Recent studies based on single-cell RNA-seq (scRNA-seq) have revealed cell-to-cell heterogeneity in APA usage and APA dynamics across different cell types in various tissues, biological processes and diseases. However, currently available APA databases were all collected from bulk 3-seq and/or RNA-seq data, and no existing database has provided APA information at single-cell resolution. Here, we present a user-friendly database called scAPAdb (http://www.bmibig.cn/scAPAdb), which provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level. Currently, scAPAdb collects APA information from > 360 scRNA-seq experiments, covering six species including human, mouse and several other plant species. scAPAdb also provides batch download of data, and users can query the database through a variety of keywords such as gene identifier, gene function and accession number. scAPAdb would be a valuable and extendable resource for the study of cell-to-cell heterogeneity in APA isoform usages and APA-mediated gene regulation at the single-cell level under diverse cell types, tissues and species.

BACKGROUND: Foeniculum vulgare, F. vulgare, commonly known as fennel, is believed to be one of the worlds oldest medicinal herbs and has been exploited by people for centuries as a nutritional aid for digestive disorders. In many southeast Asian countries, it is ingested as an after-meal snack, mukhvas, due to its breath-freshening and digestive aid properties. F. vulgare is used in some countries, such as Iran, as a complementary and alternative treatment for inflammatory bowel disease (IBD). METHODS: This study investigated the effects of fennel seed extract on intestinal epithelium barrier function and the Signal Transducer and Activator of Transcription (STAT) pathway. This pathway is active in inflammatory bowel disease. To study the protective effects of fennel seed extract in vitro, monolayers derived from the T84 colonic cell line were challenged with interferon-gamma (IFN-γ) and monitored with and without fennel seed extract. To complement our in vitro studies, the dextran sodium sulfate induced murine colitis model was employed to ascertain whether the protective effect of fennel seed extract can be recapitulated in vivo. RESULTS: Fennel seed extract was shown to exert a protective effect on transepithelial electrical resistance (TEER) in both T84 and murine models and showed increases in tight junction-associated mRNA in T84 cell monolayers. Both models demonstrated significant decreases in phosphorylated STAT1 (pSTAT1), indicating reduced activation of the STAT pathway. Additionally, mice treated with fennel seed showed significantly lower ulcer indices than control mice. CONCLUSIONS: We conclude barrier function of the gastrointestinal tract is improved by fennel seed extract, suggesting the potential utility of this agent as an alternative or adjunctive therapy in IBD.

The nuclear basket (NB) is an essential structure of the nuclear pore complex (NPC) and serves as a dynamic and multifunctional platform that participates in various critical nuclear processes, including cargo transport, molecular docking, and gene expression regulation. However, the underlying molecular mechanisms are not completely understood, particularly in plants. Here, we identified a guanylate-binding protein (GBP)-like GTPase (GBPL3) as a novel NPC basket component in Arabidopsis. Using fluorescence and immunoelectron microscopy, we found that GBPL3 localizes to the nuclear rim and is enriched in the nuclear pore. Proximity labeling proteomics and protein-protein interaction assays revealed that GBPL3 is predominantly distributed at the NPC basket, where it physically associates with NB nucleoporins and recruits chromatin remodelers, transcription apparatus and regulators, and the RNA splicing and processing machinery, suggesting a conserved function of the NB in transcription regulation as reported in yeasts and animals. Moreover, we found that GBPL3 physically interacts with the nucleoskeleton via disordered coiled-coil regions. Simultaneous loss of GBPL3 and one of the 4 Arabidopsis nucleoskeleton genes CRWNs led to distinct development- and stress-related phenotypes, ranging from seedling lethality to lesion development, and aberrant transcription of stress-related genes. Our results indicate that GBPL3 is a bona fide component of the plant NPC and physically and functionally connects the NB with the nucleoskeleton, which is required for the coordination of gene expression during plant development and stress responses.

There is widespread evidence of plant viruses manipulating behavior of their insect vectors as a strategy to maximize infection of plants. Often, plant viruses and their insect vectors have multiple potential host plant species, and these may not overlap entirely. Moreover, insect vectors may not prefer plant species to which plant viruses are well-adapted. In such cases, can plant viruses manipulate their insect vectors to preferentially feed and oviposit on plant species, which are suitable for viral propagation but less suitable for themselves? To address this question, we conducted dual- and no-choice feeding studies (number and duration of probing events) and oviposition studies with non-viruliferous and viruliferous [carrying beet curly top virus (BCTV)] beet leafhoppers [Circulifer tenellus (Baker)] on three plant species: barley (Hordeum vulgare L.), ribwort plantain (Plantago lanceolata L.), and tomato (Solanum lycopersicum L.). Barley is not a host of BCTV, whereas ribwort plantain and tomato are susceptible to BCTV infection and develop a symptomless infection and severe curly top symptoms, respectively. Ribwort plantain plants can be used to maintain beet leafhopper colonies for multiple generations (suitable), whereas tomato plants cannot be used to maintain beet leafhopper colonies (unsuitable). Based on dual- and no-choice experiments, we demonstrated that BCTV appears to manipulate probing preference and behavior by beet leafhoppers, whereas there was no significant difference in oviposition preference. Simulation modeling predicted that BCTV infection rates would to be higher in tomato fields with barley compared with ribwort plantain as a trap crop. Simulation model results supported the hypothesis that manipulation of probing preference and behavior may increase BCTV infection in tomato fields. Results presented were based on the BCTV-beet leafhopper pathosystem, but the approach taken (combination of experimental studies with complementary simulation modeling) is widely applicable and relevant to other insect-vectored plant pathogen systems involving multiple plant species.

Modeling oviposition as a function of female insect age, temperature, and host plant suitability may provide valuable insight into insect population growth of polyphagous insect pests at a landscape level. In this study, we quantified oviposition by beet leafhoppers, Circulifer (= Neoaliturus) tenellus (Baker) (Hemiptera: Cicadellidae), on four common non-agricultural host plant species [Erodium cicutarium (L.) L'Hér. (Geraniaceae), Kochia scoparia (L.) Schrader (Amaranthaceae), Plantago ovata Forsskál (Plantaginaceae), and Salsola tragus L. (Amaranthaceae)] at two constant temperature conditions. Additionally, temperature-based oviposition models for each host plant species were validated, under semi-field and greenhouse conditions. We found that K. scoparia was the most suitable host plant, and optimal temperature for oviposition was estimated to be 30.6°C. Accordingly, beet leafhoppers appear to be well-adapted to high-temperature conditions, so increasing temperatures due to climate change may favor population growth in non-agricultural areas. Maximum total fecundity (Rm) was used as an indicator of relative suitability of host plants. S. tragus has been considered an important non-agricultural host plant, however, we found that S. tragus and E. cicutarium have lower Rm compared to K. scoparia and P. ovata. The combination of detailed experimental oviposition bioassays, modeling, and model validation is considered widely relevant and applicable to host plant assessments and modeling of population dynamics of other polyphagous insect pests.

I analyze Wisława Szymborska’s work as an example of affective translation used to build the autonomy of nonhuman subjects. The article focuses on the construction of plants’ autonomy (especially in the works “The Silence of Plants” and “A Note”) by perceiving their absolute separateness. I interpret the image of a non-listening, silent nature as affective due to its total otherness which gives rise to a fascination with an impenetrable way of being in the world that is completely different from human existence. [ABSTRACT FROM AUTHOR]

The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results using k-mers have shown the advantage of this approach in identification and phylogenetic placement of eukaryotic species. Here, we revisit the basic question of estimating genomic parameters such as genome length, coverage, and repeat structure, focusing specifically on estimating the k-mer repeat spectrum. We show using a mix of theoretical and empirical analysis that there are fundamental limitations to estimating the k-mer spectra due to ill-conditioned systems, and that has implications for other genomic parameters. We get around this problem using a novel constrained optimization approach (Spline Linear Programming), where the constraints are learned empirically. On reads simulated at 1X coverage from 66 genomes, our method, REPeat SPECTra Estimation (RESPECT), had 2.2% error in length estimation compared to 27% error previously achieved. In shotgun sequenced read samples with contaminants, RESPECT length estimates had median error 4%, in contrast to other methods that had median error 80%. Together, the results suggest that low-pass genomic sequencing can yield reliable estimates of the length and repeat content of the genome. The RESPECT software will be publicly available at https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_shahab-2Dsarmashghi_RESPECT.git&d=DwIGAw&c=-35OiAkTchMrZOngvJPOeA&r=ZozViWvD1E8PorCkfwYKYQMVKFoEcqLFm4Tg49XnPcA&m=f-xS8GMHKckknkc7Xpp8FJYw_ltUwz5frOw1a5pJ81EpdTOK8xhbYmrN4ZxniM96&s=717o8hLR1JmHFpRPSWG6xdUQTikyUjicjkipjFsKG4w&e=.

The community of plant-feeding insects (herbivores) that specialize on milkweeds (Apocynaceae) form a remarkable example of convergent evolution across levels of biological organization1. In response to toxic cardiac glycosides produced by these plants, the monarch butterfly (Danaus plexippus) and other specialist herbivores have evolved parallel substitutions in the alpha subunit (ATPA) of the Na+/K+-ATPase. These substitutions render the pump insensitive to cardiac glycosides2,3, allowing the monarch and other specialists, from aphids to beetles, to sequester cardiac glycosides, which in turn provide defense against attacks by enemies from the third trophic level4. The evolution of 'target-site-insensitivity' substitutions in these herbivores poses a fundamental biological question: have predators and parasitoids that feed on cardiac-glycoside-sequestering insects also evolved Na+/K+-ATPases that are similarly insensitive to cardiac glycosides (as predicted by Whiteman and Mooney)5? In other words, can plant toxins cause evolutionary cascades that reach the third trophic level? Here we show that at least four enemies of the monarch and other milkweed herbivores have indeed evolved amino-acid substitutions associated with target-site insensitivity to cardiac glycosides. These attackers represent four major animal clades, implicating cardiac glycosides as keystone molecules6 and establishing ATPalpha, which encodes ATPA, as a keystone gene with effects that reverberate within ecological communities7.

Plant-to-plant volatile-mediated communication and subsequent induced resistance to insect herbivores is common. Less clear is the adaptive significance of these interactions; what selective mechanisms favour plant communication and what conditions allow individuals to benefit by both emitting and responding to cues? We explored the predictions of two non-exclusive hypotheses to explain why plants might emit cues, the kin selection hypothesis (KSH) and the mutual benefit hypothesis (MBH). We examined 15 populations of sagebrush that experience a range of naturally occurring herbivory along a 300 km latitudinal transect. As predicted by the KSH, we found several uncommon chemotypes with some chemotypes occurring only within a single population. Consistent with the MBH, chemotypic diversity was negatively correlated with herbivore pressure; sites with higher levels of herbivory were associated with a few common cues broadly recognized by most individuals. These cues varied among different populations. Our results are similar to those reported for anti-predator signalling in vertebrates.

The fight against infectious diseases often focuses on epidemics and pandemics, which demand urgent resources and command attention from the health authorities and media. However, the vast majority of deaths caused by infectious diseases occur in endemic zones, particularly in developing countries, placing a disproportionate burden on underfunded health systems and often requiring international interventions. The provision of vaccines and other biologics is hampered not only by the high cost and limited scalability of traditional manufacturing platforms based on microbial and animal cells, but also by challenges caused by distribution and storage, particularly in regions without a complete cold chain. In this review article, we consider the potential of molecular farming to address the challenges of endemic and re-emerging diseases, focusing on edible plants for the development of oral drugs. Key recent developments in this field include successful clinical trials based on orally delivered dried leaves of Artemisia annua against malarial parasite strains resistant to artemisinin combination therapy, the ability to produce clinical-grade protein drugs in leaves to treat infectious diseases and the long-term storage of protein drugs in dried leaves at ambient temperatures. Recent FDA approval of the first orally delivered protein drug encapsulated in plant cells to treat peanut allergy has opened the door for the development of affordable oral drugs that can be manufactured and distributed in remote areas without cold storage infrastructure and that eliminate the need for expensive purification steps and sterile delivery by injection.

Extracellular vesicles (EVs) have recently been isolated from different plants. Plant-derived EVs have been proposed as potent therapeutics and drug-delivery nanoplatforms for delivering biomolecules, including proteins, RNAs, DNAs, and lipids. Herein, Petasites japonicus-derived EVs (PJ-EVs) were isolated through a series of centrifugation steps and characterized using dynamic light scattering and transmission electron microscopy. Immunomodulatory effects of PJ-EVs were assessed using dendritic cells (DCs). PJ-EVs exhibited a spherical morphology with an average size of 122.6 nm. They induced the maturation of DCs via an increase in the expression of surface molecules (CD80, CD86, MHC-I, and MHC-II), production of Th1-polarizing cytokines (TNF-α and IL-12p70), and antigen-presenting ability; however, they reduced the antigen-uptake ability. Furthermore, maturation of DCs induced by PJ-EVs was dependent on the activation and phosphorylation of MAPK and NF-κB signal pathways. Notably, PJ-EV-treated DCs strongly induced the proliferation and differentiation of naïve T cells toward Th1-type T cells and cytotoxic CD8+ T cells along with robust secretion of IFN-γ and IL-2. In conclusion, our study indicates that PJ-EVs can be potent immunostimulatory candidates with an ability of strongly inducing the maturation of DCs.

Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production worldwide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although additional transgenes have confirmed insecticidal activity, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of both endogenous maize genes and heterologous genes from other organisms for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defence signalling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) scorpion and spider toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with a subset of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors are a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.

All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.

BackgroundMicrobiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome.ResultsIn this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions.ConclusionsStandardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.