The effect of circular soil biosolarization treatment on the physiology, metabolomics, and microbiome of tomato plants under certain abiotic stresses.

Soil biosolarization (SBS) is an alternative technique for soil pest control to standard techniques such as soil fumigation and soil solarization (SS). By using both solar heating and fermentation of organic amendments, faster and more effective control of soilborne pathogens can be achieved. A circular economy may be created by using the residues of a given crop as organic amendments to biosolarize fields that produce that crop, which is termed circular soil biosolarization (CSBS). In this study, CSBS was employed by biosolarizing soil with amended tomato pomace (TP) residues and examining its impact on tomato cropping under conditions of abiotic stresses, specifically high salinity and nitrogen deficiency. The results showed that in the absence of abiotic stress, CSBS can benefit plant physiological performance, growth and yield relative to SS. Moreover, CSBS significantly mitigated the impacts of abiotic stress conditions. The results also showed that CSBS impacted the soil microbiome and plant metabolome. Mycoplana and Kaistobacter genera were found to be positively correlated with benefits to tomato plants health under abiotic stress conditions. Conversely, the relative abundance of the orders RB41, MND1, and the family Ellin6075 and were negatively correlated with tomato plants health. Moreover, several metabolites were significantly affected in plants grown in SS- and CSBS-treated soils under abiotic stress conditions. The metabolite xylonic acid isomer was found to be significantly negatively correlated with tomato plants health performance across all treatments. These findings improve understanding of the interactions between CSBS, soil ecology, and crop physiology under abiotic stress conditions.

Telling it like it was: dignity therapy and moral reckoning in palliative care.

This article offers a conceptual analysis of self-respect and self-esteem that informs the ethics of psychotherapy in palliative care. It is focused on Chochinov's Dignity Therapy, an internationally recognized treatment offered to dying patients who express a need to bolster their sense of self-worth. Although Dignity Therapy aims to help such patients affirm their value through summarized life stories that are shared with their survivors, it is not grounded in a robust theory of self-respect. There is reason to be skeptical about deathbed narratives, and Dignity Therapy can unintentionally encourage distorted representations at odds with the self-respect it aims to affirm. Dignity therapy can also encourage distortions of self-esteem that are in conflict with self-respect. Although Chochinov does not address it, the distinction between self-respect and self-esteem is relevant to deathbed accounts. Dillon's feminist revisioning of self-respect can inform the practice of Dignity Therapy by encouraging honest life stories through a reckoning with one's moral complexity, especially in moral generativity cases where patients seek forgiveness, relate atonement, or present their lives as examples to be followed. Her concept of self-esteem allows for therapeutic benefits that are less demanding, but no less significant, than those derived from a moral reckoning. Appropriate affirmations of self-esteem can provide much-needed solace when self-respect is damaged beyond adequate repair. Dillon's account of self-respect and self-esteem enables a richer understanding of the kinds of personal evaluation and disclosure that Dignity Therapy accommodates. As such, their place in Dignity Therapy needs more critical evaluation than it has received.

Changes of Fusarium oxysporum f.sp. lactucae levels and soil microbial community during soil biosolarization using chitin as soil amendment.

Regulatory pressure along with environmental and human health concerns drive the development of soil fumigation alternatives such as soil biosolarization (SBS). SBS involves tarping soil that is at field capacity with a transparent film following amendment with certain organic materials. Heating via the greenhouse effect results in an increase of the soil temperature. The organic amendments can promote microbial activity that can enhance pest inactivation by depleting oxygen, producing biopesticidal fermentation products, and competing with pests. The properties of the organic amendments can heavily influence the type and magnitude of these effects. This study evaluated the viability of chitin as a novel SBS soil amendment to influence soil fungal and bacterial microbial communities, including control of the plant pathogen Fusarium oxysporum f.sp. lactucae (FOL). Changes to FOL and the broader soil microbiota were monitored in response to biosolarization using 0.1% (by dry weight) amendment with chitin (Rootguard). FOL suppression was only observed in chitin amended soils that were incubated at room temperature, not under solarized conditions. Conversely, it decreased solarization efficacy in the upper (0-10 cm) soil layer. The presence of chitin also showed increase in FOL under anaerobic and fluctuating temperature regime conditions. Biosolarization with chitin amendment did exhibit an impact on the overall soil microbial community. The fungal genus Mortierella and the bacterial family Chitinophagaceae were consistently enriched in biosolarized soils with chitin amendment. This study showed low potential FOL suppression due chitin amendment at the studied levels. However, chitin amendment showed a higher impact on the fungal community than the bacterial community. The impact of these microbial changes on crop protection and yields need to be studied in the long-term.

Effects of Short-Term Biosolarization Using Mature Compost and Industrial Tomato Waste Amendments on the Generation and Persistence of Biocidal Soil Conditions and Subsequent Tomato Growth.

Conventional solarization and biosolarization with mature compost and tomato processing residue amendments were compared with respect to generation of pesticidal conditions and tomato ( Solanum lycopersicum L.) plant growth in treated soils. Soil oxygen depletion was examined as a response that has previously not been measured across multiple depths during biosolarization. For biosolarized soil, volatile fatty acids were found to accumulate concurrent with oxygen depletion, and the magnitude of these changes varied by soil depth. Two consecutive years of experimentation showed varying dissipation of volatile fatty acids from biosolarized soils post-treatment. When residual volatile fatty acids were detected in the biosolarized soil, fruit yield did not significantly differ from plants grown in solarized soil. However, when there was no residual volatile fatty acids in the soil at the time of planting, plants grown in biosolarized soil showed a significantly greater vegetation amount, fruit quantity, and fruit ripening than those of plants grown in solarized soil.

Effect of management of organic wastes on inactivation of Brassica nigra and Fusarium oxysporum f.sp. lactucae using soil biosolarization.

BACKGROUND: Soil biosolarization is a promising alternative to conventional fumigation. Volatile fatty acids (VFAs) produced in the soil through fermentation of amended organic matter can affect pest inactivation during biosolarization. The objective was to determine how soil amended with organic wastes that were partially stabilized through either composting or anaerobic digestion affected the inactivation of Brassica nigra (BN; a weed) and Fusarium oxysporum f. sp. lactucae (FOL; a phytopathogenic fungus). RESULTS: The mortality of BN seeds in the biosolarized soil was 12% higher than in the solarized soil, although this difference was not significant. However, a significant correlation between BN mortality and VFA accumulation was observed. The number of FOL colony-forming units (CFU) in solarized samples at 5 cm was 34 CFU g-1 of soil, whereas in the biosolarized samples levels were below the limit of quantification. At 15 cm, these levels were 100 CFU g-1 for solarized samples and < 50 CFU g-1 of soil for the biosolarized samples. Amendment addition positively affected the organic matter and potassium content after the solarization process. CONCLUSION: The organic waste stabilization method can impact downstream biosolarization performance and final pest inactivation levels. This study suggests that organic waste management practices can be leveraged to improve pest control and soil quality. © 2018 Society of Chemical Industry.

Climate Study of the Learning Environment for Faculty, Staff, and Students at a U.S. Dental School: Foundation for Culture Change.

The aim of this study was to assess the culture and climate for diversity and inclusion and the humanistic learning environment for students, faculty, and staff at the University of Michigan School of Dentistry. From July 2014 to June 2015, two committees of 16 faculty members, staff members, and students, in partnership with trained program evaluators, used a participatory program evaluation (PPE) process to conduct the assessment using key informant interviews, surveys, and focus groups. The topics addressed were humanistic environment, learning environment, diversity and inclusion, microaggressions and bullying, and activities and space. All staff members, all faculty members (both full- and part-time), and all students in all four years were invited to participate in the parallel but distinctive versions of the survey from November 10 to 25, 2014. Response rates for each group were as follows: 50% (318/642) for students, 68% (217/320) for staff, and 40% (147/366) for faculty; numbers responding to individual items varied. Among the respondents, the majority (76% faculty, 67% staff, 80% students) agreed that the environment fostered learning and personal growth and that a humanistic environment was important (97% faculty, 95% staff, 94% students). Many reported having experienced/witnessed a micro-aggression or bullying. Many also reported having "ever had" dissatisfaction with the learning environment (44% faculty, 39% staff, 68% students). The students sought better relationships with the faculty; the staff and faculty members sought opportunities for professional development and mentoring. Recommendations included cultural sensitivity training, courses for interpersonal skills, leadership and team-building efforts, addressing microaggressions and bullying, creating opportunities for collaboration, and increasing diversity of faculty, staff, and students. These recommendations were incorporated into the school's strategic plan. In this study, a utilization-focused PPE process using mixed methods was effective for evaluating the dental school's climate for diversity and inclusion, as well as the learning environment for faculty, staff, and students.

Assessment of Two Solid Anaerobic Digestate Soil Amendments for Effects on Soil Quality and Biosolarization Efficacy.

Anaerobic digestion is an organic waste bioconversion process that produces biofuel and digestates. Digestates have potential to be applied as soil amendment to improve properties for crop production including phytonutrient content and pest load. Our objective was to assess the impact of solid anaerobic digestates on weed seed inactivation and soil quality upon soil biosolarization (a pest control technique that combines solar heating and amendment-induced microbial activity). Two solid digestates from thermophilic (TD) and mesophilic (MD) digesters were tested. The solarized TD-amended samples presented significantly higher mortality of Brassica nigra (71%, P = 0.032) than its equivalent incubated at room temperature. However, biosolarization with digestate amendment led to decreased weed seed mortality in certain treatments. The plant-available water, total C, and extractable P and K were significantly increased (P < 0.05) in the incubated amended soils. The results confirm the potential of digestates as beneficial soil amendments. Further studies are needed to elucidate the impacts of digestate stability on biosolarization efficacy and soil properties.

Weed seed inactivation in soil mesocosms via biosolarization with mature compost and tomato processing waste amendments.

BACKGROUND: Biosolarization is a fumigation alternative that combines passive solar heating with amendment-driven soil microbial activity to temporarily create antagonistic soil conditions, such as elevated temperature and acidity, that can inactivate weed seeds and other pest propagules. The aim of this study was to use a mesocosm-based field trial to assess soil heating, pH, volatile fatty acid accumulation and weed seed inactivation during biosolarization. RESULTS: Biosolarization for 8 days using 2% mature green waste compost and 2 or 5% tomato processing residues in the soil resulted in accumulation of volatile fatty acids in the soil, particularly acetic acid, and >95% inactivation of Brassica nigra and Solanum nigrum seeds. Inactivation kinetics data showed that near complete weed seed inactivation in soil was achieved within the first 5 days of biosolarization. This was significantly greater than the inactivation achieved in control soils that were solar heated without amendment or were amended but not solar heated. CONCLUSION: The composition and concentration of organic matter amendments in soil significantly affected volatile fatty acid accumulation at various soil depths during biosolarization. Combining solar heating with organic matter amendment resulted in accelerated weed seed inactivation compared with either approach alone. © 2016 Society of Chemical Industry.

Beyond thermoregulation: metabolic function of cetacean blubber in migrating bowhead and beluga whales.

The processes of lipid deposition and utilization, via the gene leptin (Lep), are poorly understood in taxa with varying degrees of adipose storage. This study examines how these systems may have adapted in marine aquatic environments inhabited by cetaceans. Bowhead (Balaena mysticetus) and beluga whales (Delphinapterus leucas) are ideal study animals-they possess large subcutaneous adipose stores (blubber) and undergo bi-annual migrations concurrent with variations in food availability. To answer long-standing questions regarding how (or if) energy and lipid utilization adapted to aquatic stressors, we quantified variations in gene transcripts critical to lipid metabolism related to season, age, and blubber depth. We predicted leptin tertiary structure conservation and assessed inter-specific variations in Lep transcript numbers between bowheads and other mammals. Our study is the first to identify seasonal and age-related variations in Lep and lipolysis in these cetaceans. While Lep transcripts and protein oscillate with season in adult bowheads reminiscent of hibernating mammals, transcript levels reach up to 10 times higher in bowheads than any other mammal. Data from immature bowheads are consistent with the hypothesis that short baleen inhibits efficient feeding. Lipolysis transcripts also indicate young Fall bowheads and those sampled during Spring months limit energy utilization. These novel data from rarely examined species expand the existing knowledge and offer unique insight into how the regulation of Lep and lipolysis has adapted to permit seasonal deposition and maintain vital blubber stores.

Assessment of tomato and wine processing solid wastes as soil amendments for biosolarization.

Pomaces from tomato paste and wine production are the most abundant fruit processing residues in California. These residues were examined as soil amendments for solarization to promote conditions conducive to soil disinfestation (biosolarization). Simulated biosolarization studies were performed in both aerobic and anaerobic soil environments and soil temperature elevation, pH, and evolution of CO2, H2 and CH4 gases were measured as metrics of soil microbial activity. Tomato pomace amendment induced conditions associated with soil pest inactivation, including elevation of soil temperature by up to 2°C for a duration of 4days under aerobic conditions and a reduction of soil pH from 6.5 to 4.68 under anaerobic conditions. White wine grape pomace amendment showed similar trends but to a lesser extent. Red wine grape pomace was generally less suitable for biosolarization due to significantly lower soil temperature elevations, reduced acidification relative to the other pomaces and induction of methanogenesis in the soil.

A field test of a model for the stability of androdioecy in the freshwater shrimp, Eulimnadia texana.

The evolution of hermaphroditism from dioecy is a poorly studied transition. Androdioecy (the coexistence of males and hermaphrodites) has been suggested as an intermediate step in this evolutionary transition or could be a stable reproductive mode. Freshwater crustaceans in the genus Eulimnadia have reproduced via androdioecy for 24+ million years and thus are excellent organisms to test models of the stability of androdioecy. Two related models that allow for the stable maintenance of males and hermaphrodites rely on the counterbalancing of three life history parameters. We tested these models in the field over three field seasons and compared the results to previous laboratory estimates of these three parameters. Male and hermaphroditic ratios within years were not well predicted using either the simpler original model or a version of this model updated to account for differences between hermaphroditic types ('monogenic' and 'amphigenic' hermaphrodites). Using parameter estimates of the previous year to predict the next year's sex ratios revealed a much better fit to the original relative to the updated version of the model. Therefore, counter to expectations, accounting for differences between the two hermaphroditic types did not improve the fit of these models. At the moment, we lack strong evidence that the long-term maintenance of androdioecy in these crustaceans is the result of a balancing of life history parameters; other factors, such as metapopulation dynamics or evolutionary constraints, may better explain the 24+ million year maintenance of androdioecy in clam shrimp.

Leptin and leptin receptor: analysis of a structure to function relationship in interaction and evolution from humans to fish.

Leptin is a circulating protein which regulates dietary intake through binding the leptin receptor. Numerous labs have used known structures and mutagenesis to study this binding process in common animal models (human, mouse and rat). Understanding this binding process in other vertebrate species will allow for a better understanding of leptin and leptin receptor function. The binding site between leptin and leptin receptor is highly conserved in mammals as confirmed through sequence alignments mapped onto structures of both leptin and leptin receptor. More variation in this interaction is found in lizard and frog sequences. Using our models, we show that the avian leptin sequences have far less variation in the binding site than does the leptin receptor. This analysis further suggests that avian leptins are artifactual. In fish, gene duplication events have led to the expression of multiple leptin proteins. These multiple leptin proteins have variation in the regions interacting with leptin receptor. In zebrafish and the Japanese rice fish, we propose that leptin A has a higher binding energy than does B. Differing binding energies are evidence of either divergent functions, different binding confirmations, or other protein partners of leptin B.

Sex chromosome evolution in the clam shrimp, Eulimnadia texana.

Chromosomes that determine sex are predicted to evolve differently than autosomes: a lack of recombination on one of the two sex chromosomes is predicted to allow an accumulation of deleterious alleles that eventually leads to reduced functionality and potential physical degradation of the nonrecombining chromosome. Because these changes should occur at an elevated evolutionary rate, it is difficult to find appropriate species in which to test these evolutionary predictions. The unique genetic sex-determining mechanism of the crustacean Eulimnadia texana prevents major chromosome degeneration because of expression of both 'proto-sex' (i.e. early stage of development) chromosomes in homozygous form (ZZ and WW). Herein, we exploit this unique genetic system to examine the predicted accumulation of deleterious alleles by comparing both homogametic sexual types to their heterogametic counterpart. We report differences in crossing over in a sex-linked region in the ZW hermaphrodites (approximately 3%) relative to the ZZ males (approximately 21%), indicative of cross-over suppression in the ZW hermaphrodites. Additionally, we report that both ZZ and WW genotypes have reduced fitness relative to ZW hermaphrodites, which is consistent with the prediction of harboured recessive mutations embedded on both the Z and the W chromosomes. These results suggest that the proto-sex chromosomes in E. texana accumulate recessive deleterious alleles. We hypothesize that recessive deleterious alleles of large effect cannot accumulate because of expression in both ZZ and WW individuals, keeping both chromosomes from losing significant function.

The effects of EPA, DHA, and aspirin ingestion on plasma lysophospholipids and autotaxin.

Lysophophatidylcholine (LPC) and lysophosphatidic acid (LPA) are potent lysolipid mediators increasingly linked with atherosclerosis and inflammation. A current model proposing that plasma LPA is produced when LPC is hydrolyzed by the enzyme autotaxin has not been rigorously investigated in human subjects. We conducted a clinical trial of eicosapentaenoic acid/docosahexaenoic acid (EPA/DHA) and aspirin ingestion in normal volunteers. Fasting blood samples were drawn at baseline and after 4-week supplementation with EPA/DHA (3.4 g/d) with and without aspirin (650 mg). Plasma LPC and LPA species and autotaxin activity were measured. EPA-LPC and DHA-LPC concentrations increased significantly with EPA/DHA supplementation whereas EPA- and DHA-LPA did not. Autotaxin activity was unaffected by any treatment, and aspirin had no effect on any endpoint. Taken together, our data demonstrate that plasma LPC, but not LPA, species can be dynamically regulated by dietary supplementation, and argue against a simple model of LPA generation via LPC hydrolysis.

The antidepressant debate and the balanced placebo trial design: an ethical analysis.

There is ongoing debate about whether randomized, placebo-controlled trials under a double-blind have reliably established the pharmacological efficacy of antidepressants. Numerous meta-analyses of antidepressant efficacy trials, e.g., Kirsch et al. [Kirsch, I., Moore, T. J., Scoboria, A., & Nicholls, S. (2002). The emperor's new drugs: An analysis of antidepressant medication data submitted to the U.S. food and drug administration. Prevention and Treatment, 5, Article 23. (Retrieved July 19, 2007 from http://journals.apa.org/prevention/volume5)], have shown a modest drug-placebo difference but methodological problems with standard trial design preclude a definitive conclusion that this difference results from specific biological effects of antidepressants or the nonspecific factors that have not been adequately excluded. Standard trial design assumes the additivity thesis of pharmacological efficacy, being the assumption that the specific or "true" magnitude of the pharmacological effect is limited to the difference between the drug and placebo responses in a standard trial. If the drug effects are as small as these meta-analyses suggest, then their clinical effectiveness is questionable. If the drug effects are actually larger but masked by placebo effects, then the additivity thesis is not valid and we risk false negative results with standard trial design. Kirsch et al. propose an alternative, four arm balanced placebo trial design (BPTD) that can accurately test the additivity thesis. The BPTD uses antidepressants, active placebos and the intentional deception of research subjects. My focal question is whether the BPTD is ethically defensible. I will explore two objections that can be raised against it: 1) lying to BPTD research subjects violates their autonomy and exploits their illness and 2) the BPTD may not enable us to test the additivity thesis with accuracy, i.e., it may contribute to the masking of drug effects that it aims to avoid. I argue that these objections support the conclusion that the BPTD is ethically indefensible.

Cloning and expression analysis of cadherin7 in the central nervous system of the embryonic zebrafish.

Cadherin cell adhesion molecules exhibit unique expression patterns during development of the vertebrate central nervous system. In this study, we obtained a full-length cDNA of a novel zebrafish cadherin using reverse transcriptase-polymerase chain reaction (RT-PCR) and 5' and 3' rapid amplification of cDNA ends (RACE). The deduced amino acid sequence of this molecule is most similar to the published amino acid sequences of chicken and mammalian cadherin7 (Cdh7), a member of the type II cadherin subfamily. cadherin7 message (cdh7) expression in embryonic zebrafish was studied using in situ hybridization and RT-PCR methods. cdh7 expression begins at about 12h postfertilization (hpf) in a small patch in the anterior neural keel, and along the midline of the posterior neural keel. By 24 hpf, cdh7 expression in the brain shows a distinct segmental pattern that reflects the neuromeric organization of the brain, while its expression domain in the spinal cord is continuous, but confined to the middle region of the spinal cord. As development proceeds, cdh7 expression is detected in more regions of the brain, including the major visual structures in the fore- and midbrains, while its expression domain in the hindbrain becomes more restricted, and its expression in the spinal cord becomes undetectable. cdh7 expression becomes reduced in 3-day old embryos. Our results show that cdh7 expression in the zebrafish developing central nervous system is both spatially and temporally regulated.

The deepest divergences in land plants inferred from phylogenomic evidence.

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.

Divergent RNA editing frequencies in hornwort mitochondrial nad5 sequences.

Hornwort mitochondrial genomes have some of the highest rates of RNA editing among plants. Comparison of eleven partial mitochondrial nad5 genomic and cDNA sequences from diverse taxa of hornworts reveal 125 edited sites in only 1107 nt. No single sample exhibits more than half of these sites. Ten of the 11 hornwort taxa have between 35 and 54 edited sties each; whereas, the eleventh taxon, Leiosporoceros, which represents a potential sister taxa to all other hornworts, has only eight sites. Comparison of multiple cDNA sequences from several individuals reveals the presence of many immature transcripts showing the heterogonous nature of the progression of editing. Phylogenetic analyses of hornwort genomic and cDNAs sequences reveal that 65 of the 94 phylogenetically informative sites within the hornwort clade are edited positions.

Pervasive RNA editing among hornwort rbcL transcripts except Leiosporoceros.

RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven taxonomically diverse hornwort rbcL sequences combined with a survey of 13 additional DNA sequences for potential edited sites demonstrate the presence of 62 edited sites and predict a minimum of 10 additional sites. These 72 total edited sites represent 43 C-to-U and 28 U-to-C nucleotide conversions, with 1 site exhibiting editing in both directions. With one exception, all taxa are heavily edited, with each having from 20 to 34 edited sites. However, a single sample, Leiosporoceros, is shown to lack edited sites. Phylogenetic reconstruction of hornworts results in ambiguous resolution of Leiosporoceros depending on whether edited sites are maintained or eliminated from the analyses. Depending on the inferred relationship of Leiosporoceros to the hornworts, at least two explanations for the origin and maintenance of pervasive editing in hornworts are possible. The absence of edited sites in Leiosporoceros could represent either the absence or a low level of editing ability in the common ancestor of hornworts, as represented by Leiosporoceros, or the loss of editing sites in this lineage after the primary diversification events in the group.