Functional characterization of a constitutively active kinase variant of Arabidopsis phototropin 1

Phototropins (phots) are plasma membrane-associated serine/threonine kinases that coordinate a range of processes linked to optimizing photosynthetic efficiency in plants. These photoreceptors contain two light-, oxygen- or voltage-sensing (LOV) domains within their N-terminus, with each binding one molecule of flavin mononucleotide (FMN) as a UV/blue light absorbing chromophore. Although phots contain two LOV domains, light-induced activation of the C-terminal kinase domain and subsequent receptor autophosphorylation is controlled primarily by the A′α-LOV2-Jα photosensory module. Mutations that disrupt interactions between the LOV2-core and its flanking helical segments can uncouple this mode of light regulation. Yet, the impact of these mutations on phot function in Arabidopsis has not been explored. Here, we report that histidine substitution of Arg-472 located within the A′α-helix of Arabidopsis phot1 to histidine results in constitutively activates kinas activity in vitro without affecting LOV2 photochemistry. Expression analysis of phot1 R472H in the phot-deficient mutant confirmed that it is autophosphorylated in darkness in vivo, but was unable to initiate phot1 signaling in the absence of light. Instead, we found that the phot1 R472H mutant is poorly functional under low-light conditions, but can restore phototropism, chloroplast accumulation, stomatal opening, and leaf positioning and expansion at higher light intensities. Our findings suggest that Arabidopsis can adapt to the elevated phosphorylation status of the phot1 R472H mutant by in part reducing its stability, whereas the activity the mutant under high-light conditions can be attributed to additional increases in LOV2-mediated photoreceptor autophosphorylation

Patterns of expansion and expression divergence in the plant polygalacturonase gene family

BACKGROUND: Polygalacturonases (PGs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, fruit softening and decay, xylem cell formation, and pollen tube growth, thus illustrating divergent roles for members of this gene family. A close look at phylogenetic relationships among Arabidopsis and rice PGs accompanied by analysis of expression data provides an opportunity to address key questions on the evolution and functions of duplicate genes. RESULTS: We found that both tandem and whole-genome duplications contribute significantly to the expansion of this gene family but are associated with substantial gene losses. In addition, there are at least 21 PGs in the common ancestor of Arabidopsis and rice. We have also determined the relationships between Arabidopsis and rice PGs and their expression patterns in Arabidopsis to provide insights into the functional divergence between members of this gene family. By evaluating expression in five Arabidopsis tissues and during five stages of abscission, we found overlapping but distinct expression patterns for most of the different PGs. CONCLUSION: Expression data suggest specialized roles or subfunctionalization for each PG gene member. PGs derived from whole genome duplication tend to have more similar expression patterns than those derived from tandem duplications. Our findings suggest that PG duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate

Relationship of ACL Injury and Posterior Tibial Slope With Patient Age, Sex, and Race.

BackgroundPosterior tibial slope (PTS) has been proposed as a potential risk factor for anterior cruciate ligament (ACL) injury; however, studies that have examined this relationship have provided inconclusive and sometimes contradictory results. Further characterization of this relationship may enable the medical community to identify individuals at greater risk for ACL injury and possibly characterize an anatomic target during surgical reconstruction.PurposeThe primary goal was to investigate the relationship between PTS and ACL injury. The secondary goal was to determine whether there are any patient factors, such as age, race, or sex, that correlate with ACL injury and PTS.Study designCross-sectional study; Level of evidence, 3.MethodsMedical records of 221 patients who underwent magnetic resonance imaging (MRI) of the knee between January 2003 and December 2009 were reviewed. Patients were separated into 2 groups: a study group of those subjects who had undergone surgery for ACL injury (n = 107) and a control group of patients diagnosed with patellofemoral syndrome (n = 114). Demographic data were collected, and MRI images from both groups were analyzed using imaging software to obtain medial and lateral tibial slope measurements. Data were then analyzed using analysis of variance (ANOVA) comparison and a multivariable regression model to determine which, if any, patient factors were related to probability of having an ACL injury.ResultsANOVA comparison demonstrated that the study group had significantly greater values for lateral PTS (6° ± 4°; P < .001) and medial PTS (7° ± 4°; P = .002) compared with controls (5° ± 3° and 5° ± 4°, respectively). After stepwise elimination of nonsignificant variables, the final multivariable logistic regression model determined that age (odds ratio [OR], 0.94; P < .001) and lateral PTS (OR, 1.12; P = .002) had statistically significant relationships with ACL injury. Medial PTS, race, and sex were not demonstrated to be significant predictors of ACL injury in this final model.ConclusionThis study demonstrates a relationship between increased lateral PTS and ACL injury, which corroborates the findings of previously published studies. The findings presented in this article may help identify patients who are at greater risk of ACL injury and could potentially benefit from treatments aimed at modification of PTS

Can Phytoremediation-Induced Changes in the Microbiome Improve Saline/Sodic Soil and Plant Health?

Increasing soil salinity and/or sodicity is an expanding problem in the Northern Great Plains (NGP) of North America. This study investigated the impact of phytoremediation on the soil microbiome and if changes, in turn, had positive or negative effects on plant establishment. Amplicon sequencing and gas chromatograph/mass spectrometer analysis compared root metabolites and microbial composition of bulk vs. rhizosphere soils between two soil types (productive and saline/sodic). Beta-diversity analysis indicated that bacterial and fungal communities from both the bulk and rhizosphere soils from each soil type clustered separately, indicating dissimilar microbial composition. Plant species also influenced both root-associated bacterial and fungal communities with separate clustering of operational taxonomic units (OTUs) identified. Canonical correlation analysis (CCA) found a clear association between specific soil characteristics and soil types. Bacterial and fungal OTUs from productive soil were correlated with greater %Ca Sat, %H Sat, and potassium (ppm), especially for OTUs differentially enriched in productive soil. Both bacterial and fungal OTUs from saline/sodic soil are associated with increased Ca (ppm), soil pH, %Na Sat and CEC. Metabolite analysis showed that kochia (Bassia scoparia) roots from the saline/sodic soil had a 4.4-fold decrease in pantothenate accumulation (p = 0.004). Moreover, two endophytic bacterial isolates, a Bacillus spp. and a previously uncultured halophile, isolated from creeping foxtail (Alopecurus arundinaceus) grown in saline/sodic soil and used as buckwheat (Fagopyrum esculentum) seed inoculants, significantly increased seed germination by \u3e30% and vigor index by 0.2 under osmotic stress (0.2 M NaCl) (p \u3c 0.05). This study revealed the importance of soil, root-associated, and endophytic microbiomes. Using native microbes as seed inoculants may help in establishment and growth of species used for phytoremediation of saline/sodic soil

Plants Reduced Nitrous Oxide Emissions from a Northern Great Plains Saline/Sodic Soil

The slowly establishing salt-tolerant perennial grasses reduced nitrous oxide (N2 O- N) emissions from saline/sodic soil compared to barren areas. Other salt-tolerant species may accelerate vegetative establishment and reduce N 2 O-N emissions. In a greenhouse study, barley (Hordeum vulgare L.), Florida broadleaf mustard (Brassica juncea L.), and Kernza intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] were grown for 63 days to compare shoot biomass and chemical composition, N 2 O-N emissions, and the soil microbiome between saline/sodic and productive (non-salt impacted) soils. Emissions were measured six times daily from 1 to 22 and 42 to 63 days after planting (DAP). Shoot and soil micro- bial biomass and communities were quantified 63 DAP. N2 O-N emissions were 87% greater from no-plant saline/sodic than no-plant productive soil (p \u3c 0.05). N2 O-N emissions were reduced from planted treatments soon after plant emergence. N2 O- N emissions reductions from saline/sodic soil during the first 22 DAP were 84%, 76%, and 61% for barley, mustard, and Kernza, respectively. Barley had the greatest shoot biomass and impact on the soil microbial community, increasing the fungi to bacteria ratio from 0.063 to 0.094 in the productive soil and from 0.056 to 0.076 in the saline/sodic soil. Plant-induced changes to the soil microbiome, and decreased soil inorganic N and water, contributed to N 2 O-N emission reductions. Archived field samples from grass-established saline/sodic soil areas had a fourfold increase in nos-Z gene copy number compared to no-plant controls, which may, in part, explain decreased N2 O-N emissions. Establishing these vigorous species may aid in restoring multiple ecosystem services to saline/sodic areas

The effect of gut microbiota elimination in Drosophila melanogaster: a how‐to guide for host–microbiota studies

In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behavior, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low‐dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analyzed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low‐dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioral research. Our study raises the important issue that the efficacy of and impacts on the host of these methods require investigation in a case‐by‐case manner, rather than assuming homogeneity across species and laboratories

Efficacy and acceptability of pharmacological and non-pharmacological interventions for non-specific chronic low back pain:a protocol for a systematic review and network meta-analysis

Background: Despite the enormous financial and humanistic burden of chronic low back pain (CLBP), there is little consensus on what constitutes the best treatment options from a multitude of competing interventions. The objective of this network meta-analysis (NMA) is to determine the relative efficacy and acceptability of primary care treatments for non-specific CLBP, with the overarching aim of providing a comprehensive evidence base for informing treatment decisions. Methods: We will perform a systematic search to identify randomised controlled trials of interventions endorsed in primary care guidelines for the treatment of non-specific CLBP in adults. Information sources searched will include major bibliographic databases (MEDLINE, Embase, CENTRAL, CINAHL, PsycINFO and LILACS) and clinical trial registries. Our primary outcomes will be patient-reported pain ratings and treatment acceptability (all-cause discontinuation), and secondary outcomes will be functional ability, quality of life and patient/physician ratings of overall improvement. A hierarchical Bayesian class-based NMA will be performed to determine the relative effects of different classes of pharmacological (NSAIDs, opioids, paracetamol, anti-depressants, muscle relaxants) and non- pharmacological (exercise, patient education, manual therapies, psychological therapy, multidisciplinary approaches, massage, acupuncture, mindfulness) interventions and individual treatments within a class (e.g. NSAIDs: diclofenac, ibuprofen, naproxen). We will conduct risk of bias assessments and threshold analysis to assess the robustness of the findings to potential bias. We will compute the effect of different interventions relative to placebo/no treatment for both short- and long-term efficacy and acceptability. Discussion: While many factors are important in selecting an appropriate intervention for an individual patient, evidence for the analgesic effects and acceptability of a treatment are key factors in guiding this selection. Thus, this NMA will provide an important source of evidence to inform treatment decisions and future clinical guidelines

Real Time Animation of Virtual Humans: A Trade-off Between Naturalness and Control

Virtual humans are employed in many interactive applications using 3D virtual environments, including (serious) games. The motion of such virtual humans should look realistic (or ‘natural’) and allow interaction with the surroundings and other (virtual) humans. Current animation techniques differ in the trade-off they offer between motion naturalness and the control that can be exerted over the motion. We show mechanisms to parametrize, combine (on different body parts) and concatenate motions generated by different animation techniques. We discuss several aspects of motion naturalness and show how it can be evaluated. We conclude by showing the promise of combinations of different animation paradigms to enhance both naturalness and control

Resonant Photonic Biosensors with Polarization-Based Multiparametric Discrimination in Each Channel

In this paper, we describe guided-mode resonance biochemical sensor technology. We briefly discuss sensor fabrication and show measured binding dynamics for example biomaterials in use in our laboratories. We then turn our attention to a particularly powerful attribute of this technology not possessed by competing methods. This attribute is the facile generation of multiple resonance peaks at an identical physical location on the sensor surface. These peaks respond uniquely to the biomolecular event, thereby enriching the data set available for event quantification. The peaks result from individual, polarization-dependent resonant leaky modes that are the foundation of this technology. Thus, by modeling the binding event and fitting to a rigorous electromagnetic formalism, we can determine individual attributes of the biolayer and its surroundings and avoid a separate reference site for background monitoring. Examples provide dual-polarization quantification of biotin binding to a silane-coated sensor as well as binding of the cancer biomarker protein calreticulin to its monoclonal IgG capture antibody. Finally, we present dual-polarization resonance response for poly (allylamine hydrochloride) binding to the sensor with corresponding results of backfitting to a simple model; this differentiates the contributions from biolayer adhesion and background changes

Uniform deposition of protein incorporated mineral layer on three-dimensional porous polymer scaffolds

Inorganic–organic hybrid materials designed to facilitate bone tissue regeneration use a calcium phosphate mineral layer to encourage cell adhesion, proliferation, and osteogenic differentiation. Mineral formed on porous materials is often discontinuous through the thickness of the scaffold. This study aimed to uniformly coat the pores of three-dimensional (3D) porous, polymer scaffolds with a bone-like mineral layer in addition to uniformly incorporating a model protein within this mineral layer. A filtration system designed to induce simulated body fluid flow through the interstices of 3D polylactic- co -glycolic acid scaffolds (10-mm diameter × 2-mm thickness) illustrated that a uniform, continuous mineral layer can be precipitated on the pore surfaces of a 3D porous structure within 5 days. MicroCT analysis showed increased mineral volume percent (MV%) (7.86 ± 3.25 MV%, p = 0.029) and continuous mineralization of filtered scaffolds compared with two static control groups (floating, 0.16 ± 0.26 MV% and submerged, 0.20 ± 0.01 MV%). Furthermore, the system was effective in coprecipitating a model protein, bone sialoprotein (BSA), within the mineral layer. A 10-fold increase in BSA incorporation was seen when coprecipitated filtered scaffolds (1308 ± 464 Μg) were compared to a submerged static control group (139 ± 45 Μg), p < 0.001. Confocal microscopy visually confirmed uniform coprecipitation of BSA throughout the thickness of the filtration scaffolds. The designed system enables 3D mineralization through the thickness of porous materials, and provides the option of including coprecipitated biomolecular cues within the mineral layer. This approach of providing a 3D conductive and osteoinductive environment could be conducive to bone tissue regeneration. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2008Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57926/1/30877_ftp.pd