Capturing a rhodopsin receptor signalling cascade across a native membrane.

G protein-coupled receptors (GPCRs) are cell-surface receptors that respond to various stimuli to induce signalling pathways across cell membranes. Recent progress has yielded atomic structures of key intermediates1,2 and roles for lipids in signalling3,4. However, capturing signalling events of a wild-type receptor in real time, across a native membrane to its downstream effectors, has remained elusive. Here we probe the archetypal class A GPCR, rhodopsin, directly from fragments of native disc membranes using mass spectrometry. We monitor real-time photoconversion of dark-adapted rhodopsin to opsin, delineating retinal isomerization and hydrolysis steps, and further showing that the reaction is significantly slower in its native membrane than in detergent micelles. Considering the lipids ejected with rhodopsin, we demonstrate that opsin can be regenerated in membranes through photoisomerized retinal-lipid conjugates, and we provide evidence for increased association of rhodopsin with unsaturated long-chain phosphatidylcholine during signalling. Capturing the secondary steps of the signalling cascade, we monitor light activation of transducin (Gt) through loss of GDP to generate an intermediate apo-trimeric G protein, and observe Gαt•GTP subunits interacting with PDE6 to hydrolyse cyclic GMP. We also show how rhodopsin-targeting compounds either stimulate or dampen signalling through rhodopsin-opsin and transducin signalling pathways. Our results not only reveal the effect of native lipids on rhodopsin signalling and regeneration but also enable us to propose a paradigm for GPCR drug discovery in native membrane environments.

Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome.

BACKGROUND: Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS: We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS: These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.

Factors affecting local alveolar bone thickness in unilateral maxillary canine-lateral incisor transposition.

INTRODUCTION: This study aimed to use 3-dimensional data to investigate the factors affecting local alveolar bone thickness in unilateral maxillary canine-lateral incisor transposition. METHODS: Pretreatment cone-beam computed tomography data of 34 patients with unilateral maxillary canine-lateral transposition were imported into Dolphin Imaging software (version 11.8; Dolphin Imaging and Management Solutions, Chatsworth, Calif) for 3-dimensional reconstruction. The age, gender, and type of transposition at the beginning of treatment were recorded. The thickness and height of the transposed canine, the labiopalatal and distomedial distance from the transposed canine to the apex of the lateral incisor, the inclination of the transposed lateral incisor, the apical height of the lateral incisor, and the alveolar bone thickness in the apical plane were measured. Multiple linear regression analyses were applied to investigate the factors affecting alveolar bone thickness in the apical plane of the transposed lateral incisor. Two sample t test were applied to assess the difference of alveolar bone thickness in patients of different ages. RESULTS: The 10 boys and 24 girls had a mean age of 12.26 ± 2.34 years. In all 34 participants, the apical alveolar bone thickness of transposed lateral incisors was significantly higher than that of the unaffected side (P <0.05). Based on multiple regression analyses, factors associated with a wider alveolar bone thickness were as follows: age (ß = -0.237; P = 0.008), the labiopalatal distance from the transposed canine to the apex of the lateral incisor (ß = 0.675; P <0.001), and the inclination of the transposed lateral incisor (ß = 0.048; P = 0.032). Patients aged <11 years had significantly thicker alveolar bone than that of patients aged >11 years (P <0.05). CONCLUSIONS: Patients with younger age, greater lateral incisor inclination, and greater labiopalatal distance between canine and lateral incisor had more alveolar bone thickness. Early treatment permits tooth movement within the thicker alveolar bone.

Multiple Calcium Channel Types with Unique Expression Patterns Mediate Retinal Signaling at Bipolar Cell Ribbon Synapses.

Retinal bipolar cells (BCs) compose the canonical vertical excitatory pathway that conveys photoreceptor output to inner retinal neurons. Although synaptic transmission from BC terminals is thought to rely almost exclusively on Ca2+ influx through voltage-gated Ca2+ (CaV) channels mediating L-type currents, the molecular identity of CaV channels in BCs is uncertain. Therefore, we combined molecular and functional analyses to determine the expression profiles of CaV α1, ß, and α2δ subunits in mouse rod bipolar (RB) cells, BCs from which the dynamics of synaptic transmission are relatively well-characterized. We found significant heterogeneity in CaV subunit expression within the RB population from mice of either sex, and significantly, we discovered that transmission from RB synapses was mediated by Ca2+ influx through P/Q-type (CaV2.1) and N-type (CaV2.2) conductances as well as the previously-described L-type (CaV1) and T-type (CaV3) conductances. Furthermore, we found both CaV1.3 and CaV1.4 proteins located near presynaptic ribbon-type active zones in RB axon terminals, indicating that the L-type conductance is mediated by multiple CaV1 subtypes. Similarly, CaV3 α1, ß, and α2δ subunits also appear to obey a "multisubtype" rule, i.e., we observed a combination of multiple subtypes, rather than a single subtype as previously thought, for each CaV subunit in individual cells.SIGNIFICANCE STATEMENT Bipolar cells (BCs) transmit photoreceptor output to inner retinal neurons. Although synaptic transmission from BC terminals is thought to rely almost exclusively on Ca2+ influx through L-type voltage-gated Ca2+ (CaV) channels, the molecular identity of CaV channels in BCs is uncertain. Here, we report unexpectedly high molecular diversity of CaV subunits in BCs. Transmission from rod bipolar (RB) cell synapses can be mediated by Ca2+ influx through P/Q-type (CaV2.1) and N-type (CaV2.2) conductances as well as the previously-described L-type (CaV1) and T-type (CaV3) conductances. Furthermore, CaV1, CaV3, ß, and α2δ subunits appear to obey a "multisubtype" rule, i.e., a combination of multiple subtypes for each subunit in individual cells, rather than a single subtype as previously thought.

Effect of smoking on thrombotic antiphospholipid syndrome: a 10-year prospective cohort study.

OBJECTIVES: Cigarette smoking is an established risk factor for autoimmune diseases. However, whether smoking plays a clear role in thrombotic antiphospholipid syndrome (TAPS) has not been determined. We aimed to investigate the effects of smoking on clinical characteristics and prognosis of TAPS. METHODS: This was a prospective cohort study from 2013 to 2022. During the study period, 297 patients were diagnosed with TAPS, including 82 smokers and 215 non-smokers. After propensity score matching, 57 smokers and 57 non-smokers matched by age and sex were analysed. RESULTS: Overall, smokers with TAPS had more cardiovascular risk factors (CVRFs) than non-smokers, including hypertension (36.59% vs. 14.42%, P<0.001), obesity (15.85% vs. 7.44%, P=0.029), dyslipidaemia (64.63% vs. 48.37%, P=0.012), and hyperhomocysteinaemia (62.20% vs. 36.28%, P<0.001). Arterial thrombotic events were more common in smokers at diagnosis (62.20% vs. 46.05%, P=0.013), especially myocardial infarction, visceral thrombosis, and peripheral vascular thrombosis. After matching, smokers showed balanced CVRFs with non-smokers at baseline, but retained a higher prevalence of arterial thrombosis (59.65% vs. 33.33%, P=0.005), mainly distributed in cerebral vascular, cardiovascular, and retinal vascular territories. During follow-up, smokers presented a tendency for more recurrent arterial thrombosis and less recurrent venous thrombosis. Smokers had significantly poorer outcomes for organ damage with higher DIAPS (median, 2.00 vs. 1.00, P=0.008), especially in the cardiovascular (26.32% vs. 3.51%, P=0.001), gastrointestinal (15.79% vs. 1.75%, P=0.016), and ophthalmologic (10.53% vs. 00.00%, P=0.027) systems. CONCLUSION: Smoking is related to increased arterial events and poor prognosis in TAPS patients. Patients with TAPS should be fully encouraged to avoid smoking.

Broadband spectral combining of three pulse-shaped fiber amplifiers with 42fs compressed pulse duration.

We demonstrate ultra-broadband spectral combining of ultrashort pulses from Yb-doped fiber amplifiers, with coherently spectrally synthesized pulse shaping, to achieve tens-of-fs pulses. This method can fully compensate for gain narrowing and high order dispersion over broad bandwidth. We produce 42fs pulses by spectrally synthesizing three chirped-pulse fiber amplifiers and two programmable pulse shapers across an 80nm overall bandwidth. To the best of our knowledge, this is the shortest pulse duration achieved from a spectrally combined fiber system at one-micron wavelength. This work provides a path toward high-energy, tens-of-fs fiber chirped-pulse amplification systems.

Morphometric evaluation of alveolar bone after orthodontic treatment of multiple impacted teeth in the unilateral maxillary anterior region.

INTRODUCTION: This study aimed to investigate the height and thickness of alveolar bone by cone-beam computed tomography imaging after orthodontic treatment in the unilateral maxillary anterior region and speculate on reasons for the difference in alveolar bone morphology. METHODS: This study selected 11 patients (3 males and 8 females; mean age, 9.42 ± 1.45 years). Cone-beam computed tomography was performed for these 11 patients before and after treatment using Dolphin Imaging software (Dolphin Imaging and Management Solutions, Chatsworth, Calif). Labial and palatal alveolar bone thickness (BT) at root apices and different levels along the roots and loss of alveolar bone height was measured for each impacted tooth and its contralateral homonymous tooth. RESULTS: After orthodontic therapy, all 3 impacted anterior teeth had different degrees of loss of labial alveolar bone height compared with the normal side (central incisor: -1.5 mm, P <0.005; lateral incisor: -1.06 mm, P <0.01; canine: -0.59 mm, P < 0.01). The lateral incisors also showed palatal alveolar bone height loss compared with the unaffected side (-0.8 mm, P <0.005). Alveolar BT at root apices of impacted canines was 1.14 mm thicker than the normal side (P <0.005). Central and lateral incisors were similar to the normal side. The thickness of the alveolar bone at 8, 10, and 12 mm of the impacted canine position was still larger than that on the healthy side, whereas the difference in average thickness between the healthy and affected side had been significantly reduced compared with pretreatment measurements. CONCLUSIONS: There is satisfactory retention of alveolar bone height in canines after orthodontic treatment; however, alveolar bone loss is slightly worse at central and lateral incisors. Retention of alveolar BT was normal for impacted anterior teeth, whereas excess apical alveolar BT at the canines, although still present, was substantially less significant than had been observed before treatment.

Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase.

Myeloperoxidase (MPO) plays essential roles in neutrophil-mediated immunity via the generation of reactive oxidation products. Complex carbohydrates decorate MPO at discrete sites, but their functional relevance remains elusive. To this end, we have characterised the structure-biosynthesis-activity relationship of neutrophil MPO (nMPO). Mass spectrometry demonstrated that nMPO carries both characteristic under-processed and hyper-truncated glycans. Occlusion of the Asn355/Asn391-glycosylation sites and the Asn323-/Asn483-glycans, located in the MPO dimerisation zone, was found to affect the local glycan processing, thereby providing a molecular basis of the site-specific nMPO glycosylation. Native mass spectrometry, mass photometry and glycopeptide profiling revealed significant molecular complexity of diprotomeric nMPO arising from heterogeneous glycosylation, oxidation, chlorination and polypeptide truncation variants and a previously unreported low-abundance monoprotomer. Longitudinal profiling of maturing, mature, granule-separated and pathogen-stimulated neutrophils demonstrated that nMPO is dynamically expressed during granulopoiesis, unevenly distributed across granules and degranulated upon activation. We also show that proMPO-to-MPO maturation occurs during early/mid-stage granulopoiesis. While similar global MPO glycosylation was observed across conditions, the conserved Asn355-/Asn391-sites displayed elevated glycan hyper-truncation, which correlated with higher enzyme activities of MPO in distinct granule populations. Enzymatic trimming of the Asn355-/Asn391-glycans recapitulated the activity gain and showed that nMPO carrying hyper-truncated glycans at these positions exhibits increased thermal stability, polypeptide accessibility and ceruloplasmin-mediated inhibition potential relative to native nMPO. Finally, molecular modelling revealed that hyper-truncated Asn355-glycans positioned in the MPO-ceruloplasmin interface are critical for uninterrupted inhibition. Here, through an innovative and comprehensive approach, we report novel functional roles of MPO glycans, providing new insight into neutrophil-mediated immunity.

NaViA: a program for the visual analysis of complex mass spectra.

MOTIVATION: Native mass spectrometry is now a well-established method for the investigation of protein complexes, specifically their subunit stoichiometry and ligand binding properties. Recent advances allowing the analysis of complex mixtures lead to an increasing diversity and complexity in the spectra obtained. These spectra can be time-consuming to tackle through manual assignment and challenging for automated approaches. RESULTS: Native Mass Spectrometry Visual Analyser is a web-based tool to augment the manual process of peak assignment. In addition to matching masses to the stoichiometry of its component subunits, it allows raw data processing, assignment and annotation and permits mass spectra to be shared with their respective interpretation. AVAILABILITY AND IMPLEMENTATION: NaViA is open-source and can be accessed online under https://navia.ms. The source code and documentation can be accessed at https://github.com/d-que/navia, under the BSD 2-Clause licence. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Surface astigmatism correction using segmented freeform surfaces for a progressive addition lens.

The undesired distribution of irregular surface astigmatism (SA) on the freeform surface has been the major concern of progressive addition lens (PAL) design. Herein, we proposed a segmented freeform surface (SFS) construction method, which relies on the lines of curvature to rule the surface segmentation and then eliminates the difference between principal curvatures to correct the SA. Based on ray tracing and numerical simulation results, the SFS-PAL design has superior performance in image quality within a dynamic field of view over the conventional freeform PAL. To verify the feasibility and the real performance of the new design, we used the diamond turning method with a fast tool servo to realize the rapid prototyping, and then used injection molding for the mass production of the high-quality SFS-PALs.

Gradually or immediately? The effects of ad type and fresh start mindset on health persuasion.

As a necessary means of encouraging individuals to adopt healthy behaviors, improving the persuasiveness of ads related to health has been a major topic of common concern in both academic and practical circles. However, scant attention has been given to how consumers' fresh start mindset (FSM) may influence the effect of ad types on health persuasion. Based on the construal level theory (CLT), the current research investigates the interplay of ad type (progression ad vs. before/after ad) and FSM (weak vs. strong) on the persuasiveness of health ads and the mechanisms underlying it. Across three studies, we demonstrated that progression ads are more effective when consumers have a weak FSM, whereas a before/after ad will be more persuasive when consumers hold a strong FSM. More importantly, consumers' perceived feasibility and desirability drive the interactive effect of ad type and FSM, such that perceived feasibility mediates the positive effect of progression ads on persuasion among consumers with a weaker FSM, while perceived desirability mediates the positive effect of before/after ads on persuasion among consumers with a stronger FSM. Our findings extend the existing literature streams on the fresh start effect, message persuasion, and construal level theory and provide practical insights for health product manufacturers and policymakers concerned about public health.

Native Mass Spectrometry Meets Glycomics: Resolving Structural Detail and Occupancy of Glycans on Intact Glycoproteins.

Glycoproteins are inherently heterogeneous and therefore resolving structures in their entirety remains a major challenge in structural biology. Native mass spectrometry has transformed our ability to study glycoproteins, and despite advances in high-resolution instrumentation, there are comparatively a few studies demonstrating its potential with data largely limited to an overall measure of monosaccharide composition for all glycans across glycosylation sites for a given protein. Clearly, these readouts lack glycan topology information, namely, monosaccharide linkage and glycan branching. To address this deficiency, we developed a new approach that joins native mass spectrometry with glycan exoglycosidase sequencing, the combination of which provides remarkable glycoprotein structural details. We show how N-glycan branching, terminal fucosylation, LacNAc extensions, and N- and O-glycan occupancy (i.e., total number of glycans) can be directly characterized on intact glycoproteins with minimal sample preparation. Taken together, native exoglycosidase sequencing mass spectrometry (NES-MS) notably improves our ability to characterize protein glycosylation, addressing a significant need in structural biology that will enable new routes to understand glycoprotein function.

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.

Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].

Modulation of gait inter-limb coordination in children with unilateral spastic cerebral palsy after intensive upper extremity intervention.

Motor function difficulties associated with unilateral spastic cerebral palsy (USCP) impact gait inter-limb coordination between the upper and lower extremities. Two motor learning based, upper extremity treatments, Constraint Induced Movement Therapy (CIMT) and Hand Arm Bimanual Therapy (HABIT), have resulted in improvements in coordination and function between the arms in children with USCP. However, no study has investigated whether coordination between the upper and lower extremities improves after either intervention during a functional task, such as walking. Gait analysis was performed before and after participation in intensive (3 weeks, 90 h total) CIMT and HABIT interventions to determine if intensive upper extremity treatment can improve inter-limb coordination between the upper and lower extremities of children (n = 20, 6-17 years old) with USCP. While upper extremity clinical evaluations indicated hand function improvements, there were no changes in lower extremity parameters for either treatment. However, we found that 10 out of 11 children with a 2:1 arm swing-to-stride ratio at pre-test improved to a 1:1 ratio at post-test. Temporal synchronicity of contralateral limbs, swing displacement of the more affected arm, and arm swing side symmetry unexpectedly decreased. Positive changes in coordination were observed in children who demonstrated poor coordination during walking at pre-test, yet the changes were not robust. Principle component analysis did not indicate changes in limb coupling. While more coordinated, gross-motor training of the upper and lower extremity may reveal greater changes, lower extremity gait patterns were not improved in high functioning children with USCP.

Cross-Entropy Method for Content Placement and User Association in Cache-Enabled Coordinated Ultra-Dense Networks.

Due to the high splitting-gain of dense small cells, Ultra-Dense Network (UDN) is regarded as a promising networking technology to achieve high data rate and low latency in 5G mobile communications. In UDNs, each User Equipment (UE) may receive signals from multiple Base Stations (BSs), which impose severe interference in the networks and in turn motivates the possibility of using Coordinated Multi-Point (CoMP) transmissions to further enhance network capacity. In CoMP-based Ultra-Dense Networks, a great challenge is to tradeoff between the gain of network throughput and the worsening backhaul latency. Caching popular files on BSs has been identified as a promising method to reduce the backhaul traffic load. In this paper, we investigated content placement strategies and user association algorithms for the proactive caching ultra dense networks. The problem has been formulated to maximize network throughput of cell edge UEs under the consideration of backhaul load, which is a constrained non-convex combinatorial optimization problem. To decrease the complexity, the problem is decomposed into two suboptimal problems. We first solved the content placement algorithm based on the cross-entropy (CE) method to minimize the backhaul load of the network. Then, a user association algorithm based on the CE method was employed to pursue larger network throughput of cell edge UEs. Simulation were conducted to validate the performance of the proposed cross-entropy based schemes in terms of network throughput and backhaul load. The simulation results show that the proposed cross-entropy based content placement scheme significantly outperform the conventional random and Most Popular Content placement schemes, with with 50% and 20% backhaul load decrease respectively. Furthermore, the proposed cross-entropy based user association scheme can achieve 30% and 23% throughput gain, compared with the conventional N-best, No-CoMP, and Threshold based user association schemes.

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver.

Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.

Whole-Genome Comparison Reveals Divergent IR Borders and Mutation Hotspots in Chloroplast Genomes of Herbaceous Bamboos (Bambusoideae: Olyreae).

Herbaceous bamboos (Olyreae) are a separate lineage with idiosyncratic traits, e.g., unisexual flowers and annual or seasonal flowering lifestyle, in the grass family. To elucidate the evolution of herbaceous bamboos we produced two complete chloroplast (cp) genomes from two monotypic genera i.e., Froesiochloa and Rehia via the genome-skimming approach. The assembled F. boutelouoides and R. nervata cp genomes were 135,905 and 136,700 base-pair (bp), respectively. Further whole-genome comparative analyses revealed that the cp genes order was perfectly collinear, but the inverted repeats (IRs) borders, i.e., the junctions between IRs and single copy regions, were highly divergent in Olyreae. The IRs expansions/contractions occurred frequently in Olyreae, which have caused gene content and genome size variations, e.g., the copy number reduction of rps19 and trnH(GUG) genes in Froesiochloa. Subsequent nucleotide mutation analyses uncovered a greatly heterogeneous divergence pattern among different cpDNA regions in Olyreae cp genomes. On average, non-coding loci evolved at a rate of circa 1.9 times faster than coding loci, from which 20 rapidly evolving loci were determined as potential genetic markers for further studies on Olyreae. In addition, the phylogenomic analyses from 67 grass plastomes strongly supported the phylogenetic positions of Froesiochloa and Rehia in the Olyreae.

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.

High-energy pulse stacking via regenerative pulse-burst amplification.

Here we present a coherent pulse stacking approach for upscaling the energy of a solid-state femtosecond chirped pulse amplifier. We demonstrate pulse splitting into four replicas, amplification in a burst-mode regenerative Yb:CaF2 amplifier, designed to overcome intracavity optical damage by colliding pulse replicas, and coherent combining into a single millijoule level pulse. The thresholds of pulse-burst-induced damage of optical elements are experimentally investigated. The scheme allows achieving an enhancement factor of 2.62 using a single-stage stacker cavity and, potentially, much higher enhancement factors using cascaded stacking.

L-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti.

UNLABELLED: Sinorhizobium meliloti forms N2-fixing root nodules on alfalfa, and as a free-living bacterium, it can grow on a very broad range of substrates, including l-proline and several related compounds, such as proline betaine, trans-4-hydroxy-l-proline (trans-4-l-Hyp), and cis-4-hydroxy-d-proline (cis-4-d-Hyp). Fourteen hyp genes are induced upon growth of S. meliloti on trans-4-l-Hyp, and of those, hypMNPQ encodes an ABC-type trans-4-l-Hyp transporter and hypRE encodes an epimerase that converts trans-4-l-Hyp to cis-4-d-Hyp in the bacterial cytoplasm. Here, we present evidence that the HypO, HypD, and HypH proteins catalyze the remaining steps in which cis-4-d-Hyp is converted to α-ketoglutarate. The HypO protein functions as a d-amino acid dehydrogenase, converting cis-4-d-Hyp to Δ(1)-pyrroline-4-hydroxy-2-carboxylate, which is deaminated by HypD to α-ketoglutarate semialdehyde and then converted to α-ketoglutarate by HypH. The crystal structure of HypD revealed it to be a member of the N-acetylneuraminate lyase subfamily of the (α/ß)8 protein family and is consistent with the known enzymatic mechanism for other members of the group. It was also shown that S. meliloti can catabolize d-proline as both a carbon and a nitrogen source, that d-proline can complement l-proline auxotrophy, and that the catabolism of d-proline is dependent on the hyp cluster. Transport of d-proline involves the HypMNPQ transporter, following which d-proline is converted to Δ(1)-pyrroline-2-carboxylate (P2C) largely via HypO. The P2C is converted to l-proline through the NADPH-dependent reduction of P2C by the previously uncharacterized HypS protein. Thus, overall, we have now completed detailed genetic and/or biochemical characterization of 9 of the 14 hyp genes. IMPORTANCE: Hydroxyproline is abundant in proteins in animal and plant tissues and serves as a carbon and a nitrogen source for bacteria in diverse environments, including the rhizosphere, compost, and the mammalian gut. While the main biochemical features of bacterial hydroxyproline catabolism were elucidated in the 1960s, the genetic and molecular details have only recently been determined. Elucidating the genetics of hydroxyproline catabolism will aid in the annotation of these genes in other genomes and metagenomic libraries. This will facilitate an improved understanding of the importance of this pathway and may assist in determining the prevalence of hydroxyproline in a particular environment.