Long term resilience decline in plant ecosystems across the Danian Dan-C2 hyperthermal event, Boltysh crater, Ukraine

Acknowledgements and Funding The authors are extremely grateful for the receipt of NERC award NE/ D005043/1, which funded the initial Boltysh impact crater study. R. Spicer and J. Leake are thanked for interesting discussions. C. Wellman, W. Gosling and M. Donovan are thanked for constructively critical reviews of the paper. Scientific editing by Quentin Crowley

Molecular cloning of a family of xenobiotic-inducible drosophilid cytochrome P450s: Evidence for involvement in host-plant allelochemical resistance

Cytochrome P450s constitute a superfamily of genes encoding mostly microsomal hemoproteins that play a dominant role in the metabolism of a wide variety of both endogenous and foreign compounds. In insects, xenobiotic metabolism (i.e., metabolism of insecticides and toxic natural plant compounds) is known to involve members of the CYP6 family of cytochrome P450s. Use of a 3′ RACE (rapid amplification of cDNA ends) strategy with a degenerate primer based on the conserved cytochrome P450 heme-binding decapeptide loop resulted in the amplification of four cDNA sequences representing another family of cytochrome P450 genes (CYP28) from two species of isoquinoline alkaloid-resistant Drosophila and the cosmopolitan species Drosophila hydei. The CYP28 family forms a monophyletic clade with strong regional homologies to the vertebrate CYP3 family and the insect CYP6 family (both of which are involved in xenobiotic metabolism) and to the insect CYP9 family (of unknown function). Induction of mRNA levels for three of the CYP28 cytochrome P450s by toxic host-plant allelochemicals (up to 11.5-fold) and phenobarbital (up to 49-fold) corroborates previous in vitro metabolism studies and suggests a potentially important role for the CYP28 family in determining patterns of insect–host-plant relationships through xenobiotic detoxification.

Molecular recognition of pathogen attack occurs inside of plant cells in plant disease resistance specified by the Arabidopsis genes RPS2 and RPM1

The Arabidopsis thaliana disease resistance genes RPS2 and RPM1 belong to a class of plant disease resistance genes that encode proteins that contain an N-terminal tripartite nucleotide binding site (NBS) and a C- terminal tandem array of leucine-rich repeats. RPS2 and RPM1 confer resistance to strains of the bacterial phytopathogen Pseudomonas syringae carrying the avirulence genes avrRpt2 and avrB, respectively. In these gene-for-gene relationships, it has been proposed that pathogen avirulence genes generate specific ligands that are recognized by cognate receptors encoded by the corresponding plant resistance genes. To test this hypothesis, it is crucial to know the site of the potential molecular recognition. Mutational analysis of RPS2 protein and in vitro translation/translocation studies indicated that RPS2 protein is localized in the plant cytoplasm. To determine whether avirulence gene products themselves are the ligands for resistance proteins, we expressed the avrRpt2 and avrB genes directly in plant cells using a novel quantitative transient expression assay, and found that expression of avrRpt2 and avrB elicited a resistance response in plants carrying the corresponding resistance genes. This observation indicates that no bacterial factors other than the avirulence gene products are required for the specific resistance response as long as the avirulence gene products are correctly localized. We propose that molecular recognition of P. syringae in RPS2- and RPM1-specified resistance occurs inside of plant cells.

Plant biology in the future

In the beginning of modern plant biology, plant biologists followed a simple model for their science. This model included important branches of plant biology known then. Of course, plants had to be identified and classified first. Thus, there was much work on taxonomy, genetics, and physiology. Ecology and evolution were approached implicitly, rather than explicitly, through paleobotany, taxonomy, morphology, and historical geography. However, the burgeoning explosion of knowledge and great advances in molecular biology, e.g., to the extent that genes for specific traits can be added (or deleted) at will, have created a revolution in the study of plants. Genomics in agriculture has made it possible to address many important issues in crop production by the identification and manipulation of genes in crop plants. The current model of plant study differs from the previous one in that it places greater emphasis on developmental controls and on evolution by differential fitness. In a rapidly changing environment, the current model also explicitly considers the phenotypic variation among individuals on which selection operates. These are calls for the unity of science. In fact, the proponents of “Complexity Theory” think there are common algorithms describing all levels of organization, from atoms all the way to the structure of the universe, and that when these are discovered, the issue of scaling will be greatly simplified! Plant biology must seriously contribute to, among other things, meeting the nutritional needs of the human population. This challenge constitutes a key part of the backdrop against which future evolution will occur. Genetic engineering technologies are and will continue to be an important component of agriculture; however, we must consider the evolutionary implications of these new technologies. Meeting these demands requires drastic changes in the undergraduate curriculum. Students of biology should be trained in molecular, cellular, organismal, and ecosystem biology, including all living organisms.

Rapid plant diversification: Planning for an evolutionary future

Systematic conservation planning is a branch of conservation biology that seeks to identify spatially explicit options for the preservation of biodiversity. Alternative systems of conservation areas are predictions about effective ways of promoting the persistence of biodiversity; therefore, they should consider not only biodiversity pattern but also the ecological and evolutionary processes that maintain and generate species. Most research and application, however, has focused on pattern representation only. This paper outlines the development of a conservation system designed to preserve biodiversity pattern and process in the context of a rapidly changing environment. The study area is the Cape Floristic Region (CFR), a biodiversity hotspot of global significance, located in southwestern Africa. This region has experienced rapid (post-Pliocene) ecological diversification of many plant lineages; there are numerous genera with large clusters of closely related species (flocks) that have subdivided habitats at a very fine scale. The challenge is to design conservation systems that will preserve both the pattern of large numbers of species and various natural processes, including the potential for lineage turnover. We outline an approach for designing a system of conservation areas to incorporate the spatial components of the evolutionary processes that maintain and generate biodiversity in the CFR. We discuss the difficulty of assessing the requirements for pattern versus process representation in the face of ongoing threats to biodiversity, the difficulty of testing the predictions of alternative conservation systems, and the widespread need in conservation planning to incorporate and set targets for the spatial components (or surrogates) of processes.

Genome projects and gene pools: New germplasm for plant breeding?

Crop gene pools have adapted to and sustained the demands of agricultural systems for thousands of years. Yet, very little is known about their content, distribution, architecture, or circuitry. The presumably shallow elite gene pools often continue to yield genetic gains while the exotic pools remain mostly untapped, uncharacterized, and underutilized. The concept and content of a crop’s gene pools are being changed by advancements in plant science and technology. In the first generation of plant genomics, DNA markers have refined some perceptions of genetic variation by providing a glimpse of a primary source, DNA polymorphism. The markers have provided new and more powerful ways of assessing genetic relationships, diversity, and merit by infusing genetic information for the first time in many scenarios or in a more comprehensive manner for others. As a result, crop gene pools may be supplemented through more rapid and directed methods from a greater variety of sources. Previously limited by the barriers of sexual reproduction, the native gene pools will soon be complemented by another gene pool (transgenes) and perhaps by other native exotic gene pools through comparative analyses of plants’ biological repertoire. Plant genomics will be an important force of change for crop improvement. The plant science community and crop gene pools may be united and enriched as never before. Also, the genomes and gene pools, the products of evolution and crop domestication, will be reduced and subjected to the vagaries and potential divisiveness of intellectual property considerations. Let the gains begin.

Use of plant roots for phytoremediation and molecular farming

Alternative agriculture, which expands the uses of plants well beyond food and fiber, is beginning to change plant biology. Two plant-based biotechnologies were recently developed that take advantage of the ability of plant roots to absorb or secrete various substances. They are (i) phytoextraction, the use of plants to remove pollutants from the environment and (ii) rhizosecretion, a subset of molecular farming, designed to produce and secrete valuable natural products and recombinant proteins from roots. Here we discuss recent advances in these technologies and assess their potential in soil remediation, drug discovery, and molecular farming.

Physical stress and diversity-productivity relationships: The role of positive interactions

If environmental stress provides conditions under which positive relationships between plant species richness and productivity become apparent, then species that seem functionally redundant under constant conditions may add to community functioning under variable conditions. Using naturally co-occurring mosses and liverworts, we constructed bryophyte communities to test relationships between species diversity (1, 2, 4, 8, 16, 24, or 32 species) and productivity under constant conditions and when exposed to experimental drought. We found no relationship between species richness and biomass under constant conditions. However, when communities were exposed to experimental drought, biomass increased with species richness. Responses of individual species demonstrated that facilitative interactions rather than sampling effects or niche complementarity best explained results—survivorship increased for almost all species, and those species least resistant to drought in monoculture had the greatest increase in biomass. Positive interactions may be an important but previously underemphasized mechanism linking high diversity to high productivity under stressful environmental conditions.

Auxin-Growth Relationships in Maize Coleoptiles and Pea Internodes and Control by Auxin of the Tissue Sensitivity to Auxin

Growth of a zone of maize (Zea mays L.) coleoptiles and pea (Pisum sativum L.) internodes was greatly suppressed when the organ was decapitated or ringed at an upper position with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) mixed with lanolin. The transport of apically applied 3H-labeled indole-3-acetic acid (IAA) was similarly inhibited by NPA. The growth suppressed by NPA or decapitation was restored by the IAA mixed with lanolin and applied directly to the zone, and the maximal capacity to respond to IAA did not change after NPA treatment, although it declined slightly after decapitation. The growth rate at IAA saturation was greater than the rate in intact, nontreated plants. It was concluded that growth is limited and controlled by auxin supplied from the apical region. In maize coleoptiles the sensitivity to IAA increased more than 3 times when the auxin level was reduced over a few hours with NPA treatment. This result, together with our previous result that the maximal capacity to respond to IAA declines in pea internodes when the IAA level is enhanced for a few hours, indicates that the IAA concentration-response relationship is subject to relatively slow adaptive regulation by IAA itself. The spontaneous growth recovery observed in decapitated maize coleoptiles was prevented by an NPA ring placed at an upper position of the stump, supporting the view that recovery is due to regenerated auxin-producing activity. The sensitivity increase also appeared to participate in an early recovery phase, causing a growth rate greater than in intact plants.

From seed germination to flowering, light controls plant development via the pigment phytochrome.

Plant growth and development are regulated by interactions between the environment and endogenous developmental programs. Of the various environmental factors controlling plant development, light plays an especially important role, in photosynthesis, in seasonal and diurnal time sensing, and as a cue for altering developmental pattern. Recently, several laboratories have devised a variety of genetic screens using Arabidopsis thaliana to dissect the signal transduction pathways of the various photoreceptor systems. Genetic analysis demonstrates that light responses are not simply endpoints of linear signal transduction pathways but are the result of the integration of information from a variety of photoreceptors through a complex network of interacting signaling components. These signaling components include the red/far-red light receptors, phytochromes, at least one blue light receptor, and negative regulatory genes (DET, COP, and FUS) that act downstream from the photoreceptors in the nucleus. In addition, a steroid hormone, brassinolide, also plays a role in light-regulated development and gene expression in Arabidopsis. These molecular and genetic data are allowing us to construct models of the mechanisms by which light controls development and gene expression in Arabidopsis. In the future, this knowledge can be used as a framework for understanding how all land plants respond to changes in their environment.

A natural experiment on plant acclimation: lifetime stomatal frequency response of an individual tree to annual atmospheric CO2 increase.

Carbon dioxide (CO2) has been increasing in atmospheric concentration since the Industrial Revolution. A decreasing number of stomata on leaves of land plants still provides the only morphological evidence that this man-made increase has already affected the biosphere. The current rate of CO2 responsiveness in individual long-lived species cannot be accurately determined from field studies or by controlled-environment experiments. However, the required long-term data sets can be obtained from continuous records of buried leaves from living trees in wetland ecosystems. Fine-resolution analysis of the lifetime leaf record of an individual birch (Betula pendula) indicates a gradual reduction of stomatal frequency as a phenotypic acclimation to CO2 increase. During the past four decades, CO2 increments of 1 part per million by volume resulted in a stomatal density decline of approximately 0.6%. It may be hypothesized that this plastic stomatal frequency response of deciduous tree species has evolved in conjunction with the overall Cenozoic reduction of atmospheric CO2 concentrations.

Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.

Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although exon shuffling in plants has been inferred from the analysis of intron phases of plant genes [Long, M., Rosenberg, C. & Gilbert, W. (1995) Proc. Natl. Acad. Sci. USA 92, 12495-12499] and from the comparison of two functionally unknown sunflower genes [Domon, C. & Steinmetz, A. (1994) Mol. Gen. Genet. 244, 312-317], clear cases of exon shuffling in plant genes remain to be uncovered. Here, we report an example of exon shuffling in two important nucleus-encoded plant genes: cytosolic glyceraldehyde-3-phosphate dehydrogenase (cytosolic GAPDH or GapC) and cytochrome c1 precursor. The intron-exon structures of the shuffled region indicate that the shuffling event took place at the DNA sequence level. In this case, we can establish a donor-recipient relationship for the exon shuffling. Three amino terminal exons of GapC have been donated to cytochrome c1, where, in a new protein environment, they serve as a source of the mitochondrial targeting function. This finding throws light upon an old important but unsolved question in gene evolution: the origin of presequences or transit peptides that generally exist in nucleus-encoded organelle genes.

Interazioni piante - insetti: ruolo delle formiche in un sistema multitrofico. Aspetti ecoetologici ed applicativi

Le formiche svolgono un importante ruolo all’interno degli ecosistemi ed alcune specie sono considerate keystone in quanto in grado di modificare la componente biotica e/o abiotica dell’ecosistema stesso. Sono animali ubiquitari che hanno colonizzato molteplici ambienti, compresi gli agroecosistemi. Negli agroecosistemi spesso svolgono un ruolo impattante determinando la diffusione o il regresso di specie di artropodi, alcune delle quali dannose alle colture. La presente ricerca tiene conto di un’ampia visione dei rapporti ecoetologici intercorrenti tra le formiche e la componente biotica di un ecosistema, utilizzando il concetto di rete multitrofica. In quest’ottica, si è pensato di costruire un sistema multitrofico costituito da una specie vegetale di interesse agrario (Cucumis sativus), dai suoi fitofagi naturali, divisi in fitomizi (afidi) (Aphis gossypii e Myzus persicae) e fitofagi masticatori (bruchi del lepidottero Mamestra brassicae), formiche (Formica pratensis) e predatori afidofagi (Aphidolets aphidimyza). Il sistema multitrofico è stato utilizzato sia per studiare l’aggressività delle formiche, sia per verificare l’esistenza di una comunicazione interspecifica tra le formiche e le piante (allelochimici). Gli studi sull’aggressività sono consistiti nel: • Verificare il livello di aggressività delle formiche nei confronti di un fitofago masticatore, competitore degli afidi nello sfruttare la pianta ospite. • Verificare se la presenza di afidi mutualisti fa variare il livello di aggressività delle formiche verso il competitore. • Verificare se esiste aggressività verso un predatore di afidi, i quali, secondo il paradigma della trofobiosi, dovrebbero essere difesi dalle formiche in cambio della melata. • Verificare se il predatore ha evoluto strategie volte ad eludere il controllo delle formiche sugli insetti che si approcciano alla colonia di afidi. Gli studi sui rapporti piante-formiche sono stati effettuati mediante olfattometro, osservando la risposta delle formiche alle sostanze volatili provenienti da piante infestate in modo differente con i fitofagi del sistema. Attraverso il trappolaggio e l’analisi gas-cromatografica delle sostanze prodotte dalle piante oggetto di studio abbiamo quindi individuato tipo e quantità di ogni composto volatile. Oltre alle piante di cetriolo, per questi esperimenti sono state utilizzate anche piante di patata (Solanum tuberosum). Dagli esperimenti sull’aggressività è risultato che le formiche manifestano un elevato potenziale predatorio, eradicando completamente la presenza dei bruchi sulle piante. Questo livello di aggressività tuttavia non cresce con la presenza degli afidi mutualisti che dovrebbero essere difesi dai competitori. Le formiche inoltre non sono in grado di sopprimere i predatori afidofagi che ipotizziamo riescano ad effettuare un camuffamento chimico, assumendo gli odori degli afidi dei quali si nutrono. I risultati degli esperimenti in olfattometro mostrano una chiara risposta positiva delle formiche verso gli odori di alcune delle piante infestate. Vi sono delle differenze nella risposta in funzione della specie di fitofago presente e della specie di pianta utilizzata. Nei trattamenti in cui erano presenti le piante di C. sativus, gli esperimenti in olfattometro hanno mostrato che le formiche rispondono in modo significativo agli odori emessi dalle piante in cui vi era la presenza del fitofago masticatore M. brassicae, solo o in associazione con A. gossypii. La presenza dei soli afidi, sia mutualisti (A. gossypii) sia non mutualisti (M. persicae), non ha invece indotto una risposta significativa nelle formiche rispetto agli odori delle piante non infestate. Nei trattamenti in cui erano presenti le piante di S. tuberosum la scelta delle formiche è stata significativa verso gli odori emessi dalle piante infestate con ciascuna delle singole specie di erbivori rispetto alle piante non infestate. Gli esperimenti sull’analisi delle sostanze volatili emesse dalle piante hanno confermato che gli organismi vegetali sono una vera centrale di produzione biochimica, infatti ben 91 composti volatili diversi sono stati individuati dall’analisi gas-cromatografica delle piante di cetriolo e 85 in quelle di patata. Dalle elaborazioni effettuate, rispettivamente 27 e 4 di essi sono prodotti esclusivamente dalle piante attaccate dai fitofagi. In generale, il cambiamento più consistente è dato dalla quantità di alcune sostanze volatili emesse dalle piante infestate rispetto a quelle integre che determina un cambiamento nei rapporti tra le sostanze che compongono i volatiles. E’ probabile che l’effetto attrattivo esercitato sulle formiche sia dato da un Blend di sostanze più che dai singoli composti presenti

The role of the social environment in non-suicidal self-injury among LGBTQ youth: A mixed methods study

Non-suicidal self-injury (NSSI), such as cutting and burning, is a widespread social problem among lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth. Extant research indicates that this population is more than twice as likely to engage in NSSI than heterosexual and cisgender (non-transgender) youth. Despite the scope of this social problem, it remains relatively unexamined in the literature. Research on other risk behaviors among LGBTQ youth indicates that experiencing homophobia and transphobia in key social contexts such as families, schools, and peer relationships contributes to health disparities among this group. Consequently, the aims of this study were to examine: (1) the relationship between LGBTQ youth's social environments and their NSSI behavior, and (2) whether/how specific aspects of the social environment contribute to an understanding of NSSI among LGBTQ youth. This study was conducted using an exploratory, sequential mixed methods design with two phases. The first phase of the study involved analysis of transcripts from interviews conducted with 44 LGBTQ youth recruited from a community-based organization. In this phase, five qualitative themes were identified: (1) Violence; (2) Misconceptions, Stigma, and Shame; (3) Negotiating LGBTQ Identity; (4) Invisibility and Isolation; and (5) Peer Relationships. Results from the qualitative phase were used to identify key variables and specify statistical models in the second, quantitative, phase of the study, using secondary data from a survey of 252 LGBTQ youth. The qualitative phase revealed how LGBTQ youth, themselves, described the role of the social environment in their NSSI behavior, while the quantitative phase was used to determine whether the qualitative findings could be used to predict engagement in NSSI among a larger sample of LGBTQ youth. The quantitative analyses found that certain social-environmental factors such as experiencing physical abuse at home, feeling unsafe at school, and greater openness about sexual orientation significantly predicted the likelihood of engaging in NSSI among LGBTQ youth. Furthermore, depression partially mediated the relationships between family physical abuse and NSSI and feeling unsafe at school and NSSI. The qualitative and quantitative results were compared in the interpretation phase to explore areas of convergence and incongruence. Overall, this study's findings indicate that social-environmental factors are salient to understanding NSSI among LGBTQ youth. The particular social contexts in which LGBTQ youth live significantly influence their engagement in this risk behavior. These findings can inform the development of culturally relevant NSSI interventions that address the social realities of LGBTQ youth's lives.

From The Holding Cell to the Holding Environment: Applying an Intersubjective Approach into Trauma Treatment with Women in the Correctional Setting

Abstract This paper investigates themes and parallels related to the traumatic experiences women face within the correctional setting and how these experiences influence women's behavior choices that increase their risk of recidivism. Intersubjective Systems Theory is used to conceptualize the distinct dynamics and impact of trauma with this particular population. Intersubjectivity also informs the changes needed to create an environment that would help women in correctional settings to heal, avoid recidivism, and foster successful community reintegration. Principles from Intersubjective Systems Theory are reviewed in this paper to demonstrate: (a) how developmental trauma impacts the lives of incarcerated women, (b) how these women's attempts at self-healing are often maladaptive and lead to arrests, (c) how the current climate in corrections leads to retraumatization and promotes later recidivism, and (d) what changes in the corrections system would promote optimal healing and better outcomes for incarcerated women. Improved outcomes are defined as healthy boundaries, empowerment in choice of relationships, improvement of social support and occupational skills, and reduction of relapse and recidivism.