Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

Comparison of the sorghum, maize and rice genomes shows that gene duplication and functional innovation is common to evolution of most but not all genes in the C4 photosynthetic pathwa

Gliding Experiments of the Wright Brothers: Flight Research 1899-1908

Presentation showing glider experiments of the Wright Brothers from 1899-1908 are presented. The slides review the experiments that the Wright Brothers conducted prior to their first powered flight in 1903 to developing the first practical aircraft in 1905, Many pictures of the gliders and other devices are used to illustrate the gradual development and experimentation that preceeded the first powered flight

Gliding Experiments of the Wright Brothers: The Wrights and Flight Research 1899-1908

Presentation sharing aspects of the gliding experiments of the Wright brothers and their flight research from 1899-190

Simultaneous determination of natural and synthetic steroid estrogens and their conjugates in aqueous matrices by liquid chromatography / mass spectrometry

An analytical method for the simultaneous determination of nine free and conjugated steroid estrogens was developed with application to environmental aqueous matrices. Solid phase extraction (SPE) was employed for isolation and concentration, with detection by liquid chromatography/mass spectrometry (LC/MS) using electrospray ionisation (ESI) in the negative mode. Method recoveries for various aqueous matrices (wastewater, lake and drinking water) were determined, recoveries proving to be sample dependent. When spiked at 50 ng/l concentrations in sewage influent, recoveries ranged from 62-89 % with relative standard deviations (RSD) < 8.1 %. In comparison, drinking water spiked at the same concentrations had recoveries between 82-100 % with an RSD < 5%. Ion suppression is a known phenomenon when using ESI; hence its impact on method recovery was elucidated for raw sewage. Both ion suppression from matrix interferences and the extraction procedure has bearing on the overall method recovery. Analysis of municipal raw sewage identified several of the analytes of interest at ng/l concentrations, estriol (E3) being the most abundant. Only one conjugate, estrone 3-sulphate (E1-3S) was observe

A phase I trial of Flavopiridol in relapsed multiple myeloma

PURPOSE: Flavopiridol is primarily a cyclin-dependent kinase-9 inhibitor, and we performed a dose escalation trial to determine the maximum tolerated dose and safety and generate a pharmacokinetic (PK) profile. METHODS: Patients with a diagnosis of relapsed myeloma after at least two prior treatments were included. Flavopiridol was administered as a bolus and then continuous infusion weekly for 4 weeks in a 6-week cycle. RESULTS: Fifteen patients were treated at three dose levels (30 mg/m(2) bolus, 30 mg/m(2) CIV to 50 mg/m(2) bolus, and 50 mg/m(2) CIV). Cytopenias were significant, and elevated transaminases (grade 4 in 3 patients, grade 3 in 4 patients, and grade 2 in 3 patients) were noted but were transient. Diarrhea (grade 3 in 6 patients and grade 2 in 5 patients) did not lead to hospital admission. There were no confirmed partial responses although one patient with t(4;14) had a decrease in his monoclonal protein >50 % that did not persist. PK properties were similar to prior publications, and immunohistochemical staining for cyclin D1 and phospho-retinoblastoma did not predict response. CONCLUSIONS: Flavopiridol as a single agent given by bolus and then infusion caused significant diarrhea, cytopenias, and transaminase elevation but only achieved marginal responses in relapsed myelom

Analysis and functional classification of transcripts from the nematode Meloidogyne incognita

BACKGROUND: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita. RESULTS: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases. CONCLUSIONS: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract\ud \ud \ud \ud Background\ud \ud Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level.\ud \ud \ud \ud Results\ud \ud The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons.\ud \ud \ud \ud Conclusions\ud \ud The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.We acknowledge our colleagues at the University of Oklahomas Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GSFLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by startup funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR.We acknowledge our colleagues at the University of Oklahoma's Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GS-FLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by start-up funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR

Endoscopic and Nonendoscopic Approaches to Single-Level Lumbar Spine Decompression: Propensity Score-Matched Comparative Analysis and Frailty-Driven Predictive Model

Objective The endoscopic spine surgery (ESS) approach is associated with high levels of patient satisfaction, shorter recovery time, and reduced complications. The present study reports multicenter, international data, comparing ESS and non-ESS approaches for single-level lumbar decompression, and proposes a frailty-driven predictive model for nonhome discharge (NHD) disposition. Methods Cases of ESS and non-ESS lumbar spine decompression were queried from the American College of Surgeons National Surgical Quality Improvement Program database (2017–2020). Propensity score matching was performed on baseline characteristics frailty score (measured by risk analysis index [RAI] and modified frailty index-5 [mFI-5]). The primary outcome of interest was NHD disposition. A predictive model was built using logistic regression with RAI as the primary driver. Results Single-level nonfusion spine lumbar decompression surgery was performed in 38,686 patients. Frailty, as measured by RAI, was a reliable predictor of NHD with excellent discriminatory accuracy in receiver operating characteristic (ROC) curve analysis: C-statistic: 0.80 (95% confidence interval [CI], 0.65–0.94) in ESS cohort, C-statistic: 0.75 (95% CI, 0.73–0.76) overall cohort. After propensity score matching, there was a reduction in total operative time (89 minutes vs. 103 minutes, p = 0.049) and hospital length of stay (LOS) (0.82 days vs. 1.37 days, p < 0.001) in patients treated endoscopically. In ROC curve analysis, the frailty-driven predictive model performed with excellent diagnostic accuracy for the primary outcome of NHD (C-statistic: 0.87; 95% CI, 0.85–0.88). Conclusion After frailty-based propensity matching, ESS is associated with reduced operative time, shorter hospital LOS, and decreased NHD. The RAI frailty-driven model predicts NHD with excellent diagnostic accuracy and may be applied to preoperative decision-making with a user-friendly calculator: nsgyfrailtyoutcomeslab.shinyapps.io/lumbar_decompression_dischargedispo

An Integrated-Photonics Optical-Frequency Synthesizer

Integrated-photonics microchips now enable a range of advanced functionalities for high-coherence applications such as data transmission, highly optimized physical sensors, and harnessing quantum states, but with cost, efficiency, and portability much beyond tabletop experiments. Through high-volume semiconductor processing built around advanced materials there exists an opportunity for integrated devices to impact applications cutting across disciplines of basic science and technology. Here we show how to synthesize the absolute frequency of a lightwave signal, using integrated photonics to implement lasers, system interconnects, and nonlinear frequency comb generation. The laser frequency output of our synthesizer is programmed by a microwave clock across 4 THz near 1550 nm with 1 Hz resolution and traceability to the SI second. This is accomplished with a heterogeneously integrated III/V-Si tunable laser, which is guided by dual dissipative-Kerr-soliton frequency combs fabricated on silicon chips. Through out-of-loop measurements of the phase-coherent, microwave-to-optical link, we verify that the fractional-frequency instability of the integrated photonics synthesizer matches the $7.0*10^{-13}$ reference-clock instability for a 1 second acquisition, and constrain any synthesis error to $7.7*10^{-15}$ while stepping the synthesizer across the telecommunication C band. Any application of an optical frequency source would be enabled by the precision optical synthesis presented here. Building on the ubiquitous capability in the microwave domain, our results demonstrate a first path to synthesis with integrated photonics, leveraging low-cost, low-power, and compact features that will be critical for its widespread use.Comment: 10 pages, 6 figure