S-RNase Alleles Associated With Self-Compatibility in the Tomato Clade: Structure, Origins, and Expression Plasticity.

The self-incompatibility (SI) system in the Solanaceae is comprised of cytotoxic pistil S-RNases which are countered by S-locus F-box (SLF) resistance factors found in pollen. Under this barrier-resistance architecture, mating system transitions from SI to self-compatibility (SC) typically result from loss-of-function mutations in genes encoding pistil SI factors such as S-RNase. However, the nature of these mutations is often not well characterized. Here we use a combination of S-RNase sequence analysis, transcript profiling, protein expression and reproductive phenotyping to better understand different mechanisms that result in loss of S-RNase function. Our analysis focuses on 12 S-RNase alleles identified in SC species and populations across the tomato clade. In six cases, the reason for gene dysfunction due to mutations is evident. The six other alleles potentially encode functional S-RNase proteins but are typically transcriptionally silenced. We identified three S-RNase alleles which are transcriptionally silenced under some conditions but actively expressed in others. In one case, expression of the S-RNase is associated with SI. In another case, S-RNase expression does not lead to SI, but instead confers a reproductive barrier against pollen tubes from other tomato species. In the third case, expression of S-RNase does not affect self, interspecific or inter-population reproductive barriers. Our results indicate that S-RNase expression is more dynamic than previously thought, and that changes in expression can impact different reproductive barriers within or between natural populations.

Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species.

Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites-a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4-6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone-a geographical landmark in the Andes with high endemism and isolated microhabitats-was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.

Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage.

Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and "RRR" genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. "Control" genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain.

Exploratory Disposal and Reuse Feasibility Analysis of Winter Maintenance Wash Water.

The Ohio Department of Transportation has more than 60 facilities without sewer access generating approximately 19 million gallons of winter maintenance wash water. Off-site disposal is costly, creating the need for sustainable management strategies. The objective of this study was to conduct an exploratory feasibility analysis to assess wash water disposal and potential reuse as brine. Based on a comprehensive literature review and relevant environmental chemistry, a sampling protocol consisting of 31 water quality constituents was utilized for monthly sampling at three geographically distinct Ohio Department of Transportation garages during the winter of 2012. Results were compared to local disposal and reuse guidance limits. Three constituents, including a maximum copper concentration of 858 ppb, exceeded disposal limits, and many constituents also failed to meet reuse limits. Some concentrations were orders of magnitude higher than reuse limits and suggest pre-treatment would be necessary if wash water were reused as brine. These water quality results, in conjunction with copper chemical equilibrium modeling, show pH and dissolved carbon both significantly impact the total dissolved copper concentration and should be measured to assess reuse potential. The sampling protocol and specific obstacles highlighted in this paper aid in the future development of sustainable wash water management strategies.

Visualization of film-forming polymer particles with a liquid cell technique in a transmission electron microscope.

One of the long-standing challenges in studying structure-property relationships in latex films is to directly characterize the size and morphology of the corresponding polymer particles, especially the particles with low film formation temperatures. Here we present an in situ transmission electron microscopy (TEM) study that allows characterization of film-forming latex particles in solution. Liquid cell TEM provides the opportunity to image latexes with a range of particle sizes and glass transition temperatures. Together with a staining technique, it can also be used as a tool to characterize the internal structure of particles in solution.

A PARAFAC-based long-term assessment of DOM in a multi-coagulant drinking water treatment scheme.

A parallel factor (PARAFAC) analysis approach was used to study the character and composition of dissolved organic matter (DOM) in a multicoagulant (two aluminum-based coagulants) full scale drinking water treatment plant. A three year, long-term assessment was conducted based on deconstruction of the excitation-emission matrices (EEM) of over 1000 water samples collected before and after parallel coagulation treatment basins. Two humic moieties and a protein-like group were identified in the raw and treated waters. Apportionment of fluorophores was established using a novel approach based on the overall fluorescence intensity (OFI) of PARAFAC components. Uncorrected matrix correlation (UMC) revealed minimal changes of the fluorescence moieties after treatment (UMC > 0.98), and a comparable effect of both coagulants on the structure (UMC > 0.99) and distribution of these groups. Coagulation increased the proportion of the protein-like fluorophore and preferentially removed a humic-like group irrespective of the coagulant. Preference for this moiety was supported by a coagulant-affinity factor derived from the association between PARAFAC components after treatment. The suitability of a PARAFAC-based approach for coagulant evaluation/selection was demonstrated when compared to a dissolved organic carbon (DOC)-based criterion. This paper contributes to the understanding of the behavior of PARAFAC components in water treatment processes and presents several approaches for the future monitoring and control of coagulation at full scale treatment facilities.

Assessment of dissolved organic matter fluorescence PARAFAC components before and after coagulation-filtration in a full scale water treatment plant.

Fluorescence monitoring of the raw and treated water after coagulation-filtration in a drinking water treatment plant in Northeast Ohio was conducted during a period of 32 months. Principal fluorophore groups present in the dissolved organic matter (DOM) of the raw, treated, raw-treated combined water and differential fluorescence data sets comprising over 680 samples were determined through Parallel Factor (PARAFAC) analysis. Four components (two humic-like and two with protein nature) were identified in each model and their degree of similarity was evaluated using the Uncorrected Matrix Correlation (UMC), a measure of spectral overlapping. Results show that spectral characteristics of the components in the independent models are comparable (average UMC > 0.98), indicating that from a PARAFAC perspective, components in the raw water are not experiencing major transformations beyond removal through the treatment process and new fluorescent components are not being formed. Coagulation assessment based on PARAFAC application to the differential excitation-emission matrices (ΔEEM), representing the portion of fluorescence removed after treatment, is introduced in this paper along with the volumetric evaluation of the components present in a sample as an alternative approach to determine their relative contribution. Volumetric analysis revealed a predominance of humic components, constituting about 80% in the raw and treated water. Results of the ΔEEM model indicated that the most amenable component to be removed by coagulation (removal ≈ 50%) at full scale operation is a humic-like fluorophore with predominance in the raw water, while removal of the protein-like components was about 30%. Results also show that the PARAFAC sample loadings exhibit a higher association with the total EEM signal in the raw and treated water samples when compared with alternative analysis techniques. These results support the analysis of the PARAFAC components present in the raw and treated samples as a viable measure for assessment of the coagulation process in a drinking water treatment plant.

Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox.

Applying the principles of literature-based discovery (LBD), we elucidate the paradox that obesity is beneficial in critical care despite contributing to disease generally. Our approach enhances a previous extension to LBD, called "discovery browsing," and is implemented using Semantic MEDLINE, which summarizes the results of a PubMed search into an interactive graph of semantic predications. The methodology allows a user to construct argumentation underpinning an answer to a biomedical question by engaging the user in an iterative process between system output and user knowledge. Components of the Semantic MEDLINE output graph identified as "interesting" by the user both contribute to subsequent searches and are constructed into a logical chain of relationships constituting an explanatory network in answer to the initial question. Based on this methodology we suggest that phthalates leached from plastic in critical care interventions activate PPAR gamma, which is anti-inflammatory and abundant in obese patients.

A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men.

STUDY OBJECTIVES: Sleep quality commonly diminishes with age, and, further, aging men often exhibit a wider range of sleep pathologies than women. We used a freely available, web-based discovery technique (Semantic MEDLINE) supported by semantic relationships to automatically extract information from MEDLINE titles and abstracts. DESIGN: We assumed that testosterone is associated with sleep (the A-C relationship in the paradigm) and looked for a mechanism to explain this association (B explanatory link) as a potential or partial mechanism underpinning the etiology of eroded sleep quality in aging men. MEASUREMENTS AND RESULTS: Review of full-text papers in critical nodes discovered in this manner resulted in the proposal that testosterone enhances sleep by inhibiting cortisol. Using this discovery method, we posit, and could confirm as a novel hypothesis, cortisol as part of a mechanistic link elucidating the observed correlation between decreased testosterone in aging men and diminished sleep quality. CONCLUSIONS: This approach is publically available and useful not only in this manner but also to generate from the literature alternative explanatory models for observed experimental results.

Graph-based methods for discovery browsing with semantic predications.

We present an extension to literature-based discovery that goes beyond making discoveries to a principled way of navigating through selected aspects of some biomedical domain. The method is a type of "discovery browsing" that guides the user through the research literature on a specified phenomenon. Poorly understood relationships may be explored through novel points of view, and potentially interesting relationships need not be known ahead of time. In a process of "cooperative reciprocity" the user iteratively focuses system output, thus controlling the large number of relationships often generated in literature-based discovery systems. The underlying technology exploits SemRep semantic predications represented as a graph of interconnected nodes (predication arguments) and edges (predicates). The system suggests paths in this graph, which represent chains of relationships. The methodology is illustrated with depressive disorder and focuses on the interaction of inflammation, circadian phenomena, and the neurotransmitter norepinephrine. Insight provided may contribute to enhanced understanding of the pathophysiology, treatment, and prevention of this disorder.

Degree centrality for semantic abstraction summarization of therapeutic studies.

Automatic summarization has been proposed to help manage the results of biomedical information retrieval systems. Semantic MEDLINE, for example, summarizes semantic predications representing assertions in MEDLINE citations. Results are presented as a graph which maintains links to the original citations. Graphs summarizing more than 500 citations are hard to read and navigate, however. We exploit graph theory for focusing these large graphs. The method is based on degree centrality, which measures connectedness in a graph. Four categories of clinical concepts related to treatment of disease were identified and presented as a summary of input text. A baseline was created using term frequency of occurrence. The system was evaluated on summaries for treatment of five diseases compared to a reference standard produced manually by two physicians. The results showed that recall for system results was 72%, precision was 73%, and F-score was 0.72. The system F-score was considerably higher than that for the baseline (0.47).

Assessment and policy for commercial driver license referrals.

This report describes experiences, subsequent action, and policy recommendations regarding sleep disorders assessment of veterans in relation to a commercial driver medical examiner referral. A series of 6 veterans were seen in our sleep clinic, presenting with an order from a commercial driver medical examiner (CDME) for polysomnography and/or Multiple Sleep Latency Testing (PSG/MSLT). We searched the literature for an evidence-based justification for handling this referral, and we concluded that there is neither federal policy nor current evidence to suggest that any current diagnostic test, including PSG/MSLT and/or MWT, is capable of predicting which individual drivers are at risk for fall-asleep crashes. The best indicator of risk is self-reported sleepiness, regardless of cause. Thus, we concluded that an administrative request for a "PSGIMSLT" is not a rational use of VA resources. Procedures and a policy for the Cleveland VA system were developed to respond to the request for evaluation, recognizing that sleep problems and disorders other than sleep apnea may be present in this population. An educational component was an important feature of this response. We suspect that this approach may be appropriate for managed care systems in general.

Graduate medical training, learning, relationships, and sleep loss.

An extensive literature exists regarding the potential effect of sleep loss on human performance and the recent regulatory changes that now limit the duty hours of resident-physicians. Recent studies and reviews emphasize the effects of sleepiness on medical errors of commission and to a lesser extent omission. This review focuses on an emerging literature on the effects of sleep loss on personal, social and professional growth and development of residents. As with the early literature on sleep loss and resident performance, this literature is largely at an observational level, but there is sufficient evidence from other professions to indicate that sleep loss will affect post-graduate career and life skills. A multi-dimensional approach is needed to counter the adverse outcomes of sleep loss and fatigue and might consist of education on healthy sleep habits, family outreach, personal alertness strategies, and reversal of bias if sleepiness is personally disclosed. The multi-dimensional approach might include not only resident physicians, but also residency program directors and attending physicians at their institutions.

Interference screw divergence in femoral tunnel fixation during endoscopic anterior cruciate ligament reconstruction using hamstring grafts.

PURPOSE: To compare the divergence angles between bioabsorbable interference screws inserted into the femoral tunnel with the screwdriver placed through the anteromedial portal to those inserted with the screwdriver placed through the tibial tunnel and to examine the effect of the femoral tunnel interference screws' divergence angles on fixation strength of hamstring grafts after anterior cruciate ligament (ACL) reconstruction using hamstring grafts. TYPE OF STUDY: Cadaveric biomechanical pullout study. METHODS: ACL reconstruction was performed in 8 pairs of fresh-frozen human cadaveric knees using hamstring grafts fixed within the femoral tunnels using bioabsorbable interference screws. Within matched pairs, 1 screw was placed into the femoral tunnel using a screwdriver placed through the tibial tunnel (group 1), and in the other knee it was placed into the femoral tunnel using a screwdriver placed through the anteromedial portal (group 2). Radiographs were taken to measure the degree of divergence between the interference screw and the femoral tunnel. After disarticulation, pullout strength was then measured using a cyclic-loading model. RESULTS: In group 2, there was significantly more divergence between the screw and the femoral tunnel compared with group 1, particularly in the sagittal plane (average 14.4 degrees compared with 3.4 degrees, P =.00014). With the number of specimens available for comparison, no significant difference was detected between the 2 groups with regard to 3 mm and 5 mm of pullout when cyclically loaded (P =.77 and.74, respectively). CONCLUSIONS: The increased technical difficulty, combined with the potential risks of tibial tunnel widening and graft damage, with placement of the screwdriver through the tibial tunnel for the purpose of decreasing femoral interference screw divergence in ACL reconstruction using hamstring grafts may not be justified.