Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

<p>Abstract</p> <p>Background</p> <p>As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.</p> <p>Results</p> <p>We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the <it>Poaceae </it>family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and <it>Arabidopsis</it>. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine <it>Arabidopsis </it>mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.</p> <p>Conclusion</p> <p>The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.</p

Prevalence and characteristics of pain in moderate-to-severe obstructive sleep apnea patients and effect of CPAP treatment

Abstract Pain problems are common in patients with obstructive sleep apnea (OSA), but few studies have thoroughly evaluated pain in these patients. The objective of this study was to examine the prevalence and characteristics of pain in moderate-to-severe OSA patients and the effect of continuous positive airway pressure (CPAP) treatment. Moderate-to-severe OSA patients and healthy controls (HC) completed the Short Form McGill Pain Questionnaire (SF-MPQ) and a portion of the Brief Pain Inventory (BPI) Short Form to assess pain characteristics. The Epworth Sleepiness Scale (ESS), the Short Form-36 (SF-36), and the Hospital Anxiety and Depression Scale (HADS) were used to measure daytime sleepiness, health-related quality of life (HRQoL), and psychological status, respectively. The OSA patients with pain were divided into a CPAP-treated group and a CPAP-untreated group based on their adherence to CPAP. The subjects' pain intensity was reassessed after 3 months. The prevalence of pain was 57.5% in OSA versus 27.1% in HC (p < 0.001). Head (39.0%) accounted for the highest proportion of overall pain locations in subjects with OSA, with 28.8% of OSA patients experiencing headaches. Pain in OSA was associated with impaired HRQoL and psychological problems. Patients with very severe OSA had an increased risk for pain problems (OR: 7.000, p = 0.041). Associated factors for pain intensity in OSA included age, ESS ≥ 9.0, and lowest pulse oximetry (LSpO2) < 80.0%. Pain intensity in OSA decreased significantly after CPAP treatment (p < 0.001). Pain was prevalent among patients with moderate-to-severe OSA and was associated with depression, anxiety, and a lower HRQoL. Patients with very severe OSA had an increased risk for pain problems. The intensity of pain in OSA can be predicted by age, ESS ≥ 9.0, and LSpO2 < 80.0%, and it can be alleviated through CPAP treatment

Notch signaling in lung diseases: focus on Notch1 and Notch3

Notch signaling is an evolutionarily conserved cell–cell communication mechanism that plays a key role in lung homeostasis, injury and repair. The loss of regulation of Notch signaling, especially Notch1 and Notch3, has recently been linked to the pathogenesis of important lung diseases, in particular, chronic obstructive pulmonary disease (COPD), asthma, pulmonary fibrosis, pulmonary arterial hypertension (PAH), lung cancer and lung lesions in some congenital diseases. This review focuses on recent advances related to the mechanisms and the consequences of aberrant or absent Notch1/3 activity in the initiation and progression of lung diseases. Our increasing understanding of this signaling pathway offers great hope that manipulating Notch signaling may represent a promising alternative complementary therapeutic strategy in the future

Herbaceous Encroachment from Mountain Birch Forests to Alpine Tundra Plant Communities Through Above- and Belowground Competition

Alpine plant communities are highly sensitive to global warming. One of the consequences of the warming is encroachment by herbaceous plants from forests at low elevations into alpine ecosystems. In the Changbai Mountains, narrowleaf small reed (Deyeuxia angustifolia (Kom.) Y. L. Chang) from mountain birch forests encroached upward into alpine tundra, gradually replacing native tundra shrubs such as Rhododendron (Rhododendron aureum Georgi). How encroaching plants affect native plant communities is not fully understood. In this study, we analyzed above- and belowground biomass of alpine plant communities at five encroachment levels to investigate how biomass allocation changed at species and community scales. Our research showed that native plants are forced to change their morphology to cope with competition, at both above- and belowground levels, from encroaching plants. We found that (1) R. aureum increased the shoot height and leaf area in order to compete with D. angustifolia; (2) above- and belowground biomass of D. angustifolia increased while above- and belowground biomass of R. aureum decreased with increasing levels of encroachment; and (3) D. angustifolia encroachment reduced the total biomass of alpine tundra. Encroachment by herbaceous plants has a long-term negative impact on the ability of tundra plants to sequester carbon in the alpine tundra of the Changbai Mountains

Predicting Wetland Distribution Changes under Climate Change and Human Activities in a Mid- and High-Latitude Region

Wetlands in the mid- and high-latitudes are particularly vulnerable to environmental changes and have declined dramatically in recent decades. Climate change and human activities are arguably the most important factors driving wetland distribution changes which will have important implications for wetland ecological functions and services. We analyzed the importance of driving variables for wetland distribution and investigated the relative importance of climatic factors and human activity factors in driving historical wetland distribution changes. We predicted wetland distribution changes under climate change and human activities over the 21st century using the Random Forest model in a mid- and high-latitude region of Northeast China. Climate change scenarios included three Representative Concentration Pathways (RCPs) based on five general circulation models (GCMs) downloaded from the Coupled Model Intercomparison Project, Phase 5 (CMIP5). The three scenarios (RCP 2.6, RCP 4.5, and RCP 8.5) predicted radiative forcing to peak at 2.6, 4.5, and 8.5 W/m2 by the 2100s, respectively. Our results showed that the variables with high importance scores were agricultural population proportion, warmness index, distance to water body, coldness index, and annual mean precipitation; climatic variables were given higher importance scores than human activity variables on average. Average predicted wetland area among three emission scenarios were 340,000 ha, 123,000 ha, and 113,000 ha for the 2040s, 2070s, and 2100s, respectively. Average change percent in predicted wetland area among three periods was greatest under the RCP 8.5 emission scenario followed by RCP 4.5 and RCP 2.6 emission scenarios, which were 78%, 64%, and 55%, respectively. Losses in predicted wetland distribution were generally around agricultural lands and expanded continually from the north to the whole region over time, while the gains were mostly associated with grasslands and water in the most southern region. In conclusion, climatic factors had larger effects than human activity factors on historical wetland distribution changes and wetland distributions were predicted to decline remarkably over time under climate change scenarios. Our findings have important implications for wetland resource management and restoration because predictions of future wetland changes are needed for wetlands management planning

De Novo Sequencing of Complex Mixtures of Heparan Sulfate Oligosaccharides

Here, we describe the first sequencing method of a complex mixture of heparan sulfate tetrasaccharides by LC-MS/MS. Heparin and heparan sulfate (HS) are linear polysaccharides that are modified in a complex manner by N- and O-sulfation, N-acetylation, and epimerization of the uronic acid. Heparin and HS are involved in various essential cellular communication processes. The structural analysis of these glycosaminoglycans is challenging due to the lability of their sulfate groups, the high heterogeneity of modifications, and the epimerization of the uronic acids. While advances in liquid chromatography (LC) and mass spectrometry (MS) have enabled compositional profiling of HS oligosaccharide mixtures, online separation and detailed structural analysis of isomeric and epimeric HS mixtures has not been achieved. Here, we report the development and evaluation of a chemical derivatization and tandem mass spectrometry method that can separate and identify isomeric and epimeric structures from complex mixtures. A series of well-defined synthetic HS tetrasaccharides varying in sulfation patterns and uronic acid epimerization were analyzed by chemical derivatization and LC-MS/MS. These synthetic compounds made it possible to establish relationships between HS structure, chromatographic behavior and MS/MS fragmentation characteristics. Using the analytical characteristics determined through the analysis of the synthetic HS tetrasaccharide standards, an HS tetrasacharide mixture derived from natural sources was successfully sequenced. This method represents the first sequencing of complex mixtures of HS oligosaccharides, an essential milestone in the analysis of structure-function relationships of these carbohydrates