• The major obstacle for bioenergy production from switchgrass biomass is the low saccharification efficiency caused by cell wall recalcitrance. Saccharification efficiency is negatively correlated ...with both lignin content and cell wall ester‐linked p‐coumarate: ferulate (p‐CA : FA) ratio. In this study, we cloned and functionally characterized an R2R3‐MYB transcription factor from switchgrass and evaluated its potential for developing lignocellulosic feedstocks. • The switchgrass PvMYB4 cDNAs were cloned and expressed in Escherichia coli, yeast, tobacco and switchgrass for functional characterization. Analyses included determination of phylogenetic relations, in situ hybridization, electrophoretic mobility shift assays to determine binding sites in target promoters, and protoplast transactivation assays to demonstrate domains active on target promoters. • PvMYB4 binds to the AC‐I, AC‐II and AC‐III elements of monolignol pathway genes and down‐regulates these genes in vivo. Ectopic overexpression of PvMYB4 in transgenic switchgrass resulted in reduced lignin content and ester‐linked p‐CA : FA ratio, reduced plant stature, increased tillering and an approx. threefold increase in sugar release efficiency from cell wall residues. • We describe an alternative strategy for reducing recalcitrance in switchgrass by manipulating the expression of a key transcription factor instead of a lignin biosynthetic gene. PvMYB4‐OX transgenic switchgrass lines can be used as potential germplasm for improvement of lignocellulosic feedstocks and provide a platform for further understanding gene regulatory networks underlying switchgrass cell wall recalcitrance.
Abstract
Efficiently entangling pairs of qubits is essential to fully harness the power of quantum computing. Here, we devise an exact protocol that simultaneously entangles arbitrary pairs of qubits ...on a trapped-ion quantum computer. The protocol requires classical computational resources polynomial in the system size, and very little overhead in the quantum control compared to a single-pair case. We demonstrate an exponential improvement in both classical and quantum resources over the current state of the art. We implement the protocol on a software-defined trapped-ion quantum computer, where we reconfigure the quantum computer architecture on demand. Our protocol may also be extended to a wide variety of other quantum computing platforms.
Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of ...appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.
In the first approach, a multiple regression analysis model was developed to derive DeltaDeltaCt from estimation of interaction of gene and treatment effects. In the second approach, an ANCOVA (analysis of covariance) model was proposed, and the DeltaDeltaCt can be derived from analysis of effects of variables. The other two models involve calculation DeltaCt followed by a two group t-test and non-parametric analogous Wilcoxon test. SAS programs were developed for all four models and data output for analysis of a sample set are presented. In addition, a data quality control model was developed and implemented using SAS.
Practical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of ...comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ~200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
It is necessary to overcome recalcitrance of the biomass to saccharification (sugar release) to make switchgrass (Panicum virgatum) economically viable as a feedstock for liquid biofuels. Lignin ...content correlates negatively with sugar release efficiency in switchgrass, but selecting the right gene candidates for engineering lignin biosynthesis in this tetraploid outcrossing species is not straightforward. To assist this endeavor, we have used an inducible switchgrass cell suspension system for studying lignin biosynthesis in response to exogenous brassinolide. By applying a combination of protein sequence phylogeny with whole-genome microarray analyses of induced cell cultures and developing stem internode sections, we have generated a list of candidate monolignol biosynthetic genes for switchgrass. Several genes that were strongly supported through our bioinformatics analysis as involved in lignin biosynthesis were confirmed by gene silencing studies, in which lignin levels were reduced as a result of targeting a single gene. However, candidate genes encoding enzymes involved in the early steps of the currently accepted monolignol biosynthesis pathway in dicots may have functionally redundant paralogues in switchgrass and therefore require further evaluation. This work provides a blueprint and resources for the systematic genome-wide study of the monolignol pathway in switchgrass, as well as other C4 monocot species.
We tested the null hypothesis that no factors are independently associated with the development of symptomatic neuroma after traumatic digital amputation.
We performed a retrospective review of 1,083 ...patients who underwent revision amputation for traumatic digital amputation; we excluded those undergoing replantation or revascularization. Patients who developed a painful neuroma during follow-up were identified with a minimum follow-up of 1 week and a median of 3.3 months. We calculated the rate of developing a painful neuroma as a proportion of the total number of patients and performed multivariable logistic regression analysis to identify factors independently associated with its development.
Of 1,083 patients, 71 (6.6%) developed a symptomatic neuroma. Mean time to diagnosis was 6.4 months. A total of 47 patients (66%) underwent surgery for painful neuroma. Mean time to surgical intervention was 11 months. Index finger injury and avulsion injury mechanism were significantly associated with a higher risk for symptomatic neuroma.
Approximately 1 in 15 patients will develop a symptomatic neuroma after traumatic digital amputation and more than half of these patients will undergo revision surgery for neuroma, with a mean time to operative intervention of 11 months.
Prognostic II.
Purpose To examine the relationship between patient-rated physician empathy and patient satisfaction after a single new hand surgery office visit. Methods Directly after the office visit, 112 ...consecutive new patients rated their overall satisfaction with the provider and completed the Consultation and Relational Empathy Measure, the Newest Vital Sign health literacy test, a sociodemographic survey, and 3 Patient-Reported Outcomes Measurement Information System-based questionnaires: Pain Interference, Upper-Extremity Function, and Depression. We also measured the waiting time in the office to see the physician, the duration of the visit, and the time from booking until appointment. Multivariable logistic and linear regression models were used to identify factors independently associated with patient satisfaction. Results Patient-rated physician empathy correlated strongly with the degree of overall satisfaction with the provider. After controlling for confounding effects, greater empathy was independently associated with patient satisfaction, and it alone accounted for 65% of the variation in satisfaction scores. Older patient age was also associated with satisfaction. There were no differences between satisfied and dissatisfied patients with regard to waiting time in the office, duration of the appointment, time from booking until appointment, and health literacy. Conclusions Physician empathy was the strongest driver of patient satisfaction in the hand surgery office setting. As patient satisfaction plays a growing role in reimbursement, targeted educational programs to enhance empathic communication skills in hand surgeons merit consideration. Type of study/level of evidence Prognostic II.
In capitellar osteochondritis dissecans (OCD), unstable lesions generally demonstrate signs of subchondral sclerosis. We postulate that OCD lesions have abnormal subchondral bone density. We aimed to ...quantify the subchondral bone thickness around OCD lesions using conventional computed tomography (CT) imaging.
This retrospective study included 15 patients with capitellar OCD (OCD group) and 12 patients with an unaffected radio-capitellar joint (control group). We constructed 3-dimensional humerus models using CT data and quantified the bone density with colored contour mapping to determine the subchondral bone thickness. We measured the thickness relative to the condylar height at the centroid and lateral, medial, superior, and inferior edge points of the OCD lesion, and compared the findings between the groups. We then correlated the CT measurements with the magnetic resonance imaging measurements.
Subchondral bone thickness at the centroid and lateral, medial, superior, and inferior edges in the OCD group was significantly higher than that in the control group. Correlation analyses revealed that the magnetic resonance imaging measurements highly correlated with the CT subchondral bone measurements.
We found that there is a zone of increased subchondral bone thickness around OCD lesions that should be considered during drilling, microfracture, or other reconstruction methods. We observed a high correlation with low errors between the measurements taken from conventional CT images and the measurements from magnetic resonance imaging, suggesting that both modalities are useful in clinical decision making.
Diagnostic IV.
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