Passiflora plastome sequencing reveals widespread genomic rearrangements

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.     

Nuclear fast red‐based colorimetric sensors for sensitive and selective detection of Ag ions

The reduction of nuclear fast red (NFR) stain by sodium tetrahydroboron was catalyzed in the presence of silver ions (Ag⁺). The fluorescence properties of reduced NFR differed from that of NFR. The product showed fluorescence emission at 480 nm with excitation at 369 nm. Furthermore, the fluorescence intensity of the mixture increased strongly in the presence of Ag⁺ and Britton–Robinson buffer at pH 4.78. There was a good linear relationship between increased fluorescence intensity (ΔI) and Ag⁺ concentration in the range 5.0 × 10^?9 to 5.0 × 10^?8 M. The correlation coefficient was 0.998, and the detection limit (3σ/k) was 1.5 × 10^?9 M. The colour of the reaction system changed with variation in Ag⁺ concentration over a wide range. Based on the colour change, a visual semiquantitative detection method for recognition and sensing of Ag⁺ was developed for the range 1.0 × 10^?8 to 5.0 × 10^?4 M, with an indicator that was visible to the naked eye. Therefore, a sensitive, simple method for determination of Ag⁺ was developed. Optimum conditions for Ag⁺ detection, the effect of other ions and the analytical application of Ag⁺ detection of synthesized sample were investigated.     

Global patterns in fine root decomposition: climate,chemistry, mycorrhizal association and woodiness

Fine root decomposition constitutes a critical yet poorly understood flux of carbon and nutrients in terrestrial ecosystems. Here, we present the first large‐scale synthesis of species trait effects on the early stages of fine root decomposition at both global and local scales. Based on decomposition rates for 279 plant species across 105 studies and 176 sites, we found that mycorrhizal association and woodiness are the best categorical traits for predicting rates of fine root decomposition. Consistent positive effects of nitrogen and phosphorus concentrations and negative effects of lignin concentration emerged on decomposition rates within sites. Similar relationships were present across sites, along with positive effects of temperature and moisture. Calcium was not consistently related to decomposition rate at either scale. While the chemical drivers of fine root decomposition parallel those of leaf decomposition, our results indicate that the best plant functional groups for predicting fine root decomposition differ from those predicting leaf decomposition.     

Surface analysis of sheep menisci after meniscectomy via infrared attenuated total reflection spectroscopy

Menisci are very important fibrocartilaginous tissue, which maintain biomechanical functions and physiological stabilization of knee joint. Meniscectomy is known as a surgery to recover partial functions from acute meniscus tears. However, the late consequences of total or partial meniscectomy include signs of osteoarthritis and even ligament instability. Infrared attenuated total reflection (IR‐ATR) spectroscopy is a very useful technique, which can reveal molecular characteristics via the analysis of vibrational bands. The present study has employed IR‐ATR spectroscopy to investigate sheep menisci samples after meniscectomy in a label‐free fashion. Several differences of peak absorbance change and peak shift were observed between the native healthy samples and the meniscectomy samples in distinct IR wavenumber regions, such as amide I band, amide II band, C‐H bending band as well as the sugar band region. Combining the results from the collagen protein IR spectra, it can be speculated that six months after meniscectomy collagen fibrils on the incision lose its ordered arrangement and a decrease in the triple helical structure of collagen fibril is observed. In addition, the collagen fibrils and proteoglycan content might also be slight varied after meniscectomy.      

Application of Human‐Induced Pluripotent Stem Cells (hiPSCs) to Study Synaptopathy of Neurodevelopmental Disorders

Synapses are the basic structural and functional units for information processing and storage in the brain. Their diverse properties and functions ultimately underlie the complexity of human behavior. Proper development and maintenance of synapses are essential for normal functioning of the nervous system. Disruption in synaptogenesis and the consequent alteration in synaptic function have been strongly implicated to cause neurodevelopmental disorders such as autism spectrum disorders (ASDs) and schizophrenia (SCZ). The introduction of human‐induced pluripotent stem cells (hiPSCs) provides a new path to elucidate disease mechanisms and potential therapies. In this review, we will discuss the advantages and limitations of using hiPSC‐derived neurons to study synaptic disorders. Many mutations in genes encoding for proteins that regulate synaptogenesis have been identified in patients with ASDs and SCZ. We use Methyl‐CpG binding protein 2 (MECP2), SH3 and multiple ankyrin repeat domains 3 (SHANK3) and Disrupted in schizophrenia 1 (DISC1) as examples to illustrate the promise of using hiPSCs as cellular models to elucidate the mechanisms underlying disease‐related synaptopathy.     

Independent component analysis of Raman spectra: Application on paraffin-embedded skin biopsies

Raman spectra provide wealthy but complex information about the chemical constituents of biological samples. Digital processing techniques are usually needed to extract the spectra of chemical constituents and their associated concentration profiles. However, spectral signatures may admit transformations from those recorded on pure constituents and these techniques require a priori knowledge of spectra to be estimated. We propose in this study to analyse paraffin-embedded skin biopsies of malignant and benign tumors dedicated to oncology researches by Raman spectroscopy and advanced signal processing methods. We show that the commonly used principal component analysis (PCA) does not give physically interpretable estimators of spectra and associated concentration profiles. Based on a linear model and taking into account the statistical properties of spectra, independent component analysis (ICA) is used to better estimate the spectra of chemical constituents. The estimators of associated concentration profiles are no longer orthogonal and have only positive values, contrary to PCA. ICA allows to model the paraffin by three Raman spectra and provides good estimators of underlying spectra of the human skin, which is of great interest in oncology since the retrieval of spectral features of different types of skin tumors is sufficient for their discrimination.     

Classification of life cycle form spectrum of artificial community of Pinus svlvestris var. mongolica

The plant life cycle form and its spectrum features of different plants in the artificial community of Pinus svlvestris var. mongolica at the botanical garden of Northeast Forestry University were classified by PCA method. For canopy layer plants, the vegetative growth (V) accounted for 46%, the sexual growth (S) accounted for 35%, and the clonal growth (C) accounted for the rest 19%. For succession layer plants, V accounted for more than 50%, and C accounted for a little higher than S did. For herbaceous layer plants, V accounted for nearly 47%, which was only 4% higher than that of S, and C only accounted for 11%. These findings indicate that the plant life cycle forms of canopy layer plants and herbaceous layer plants were VS transition form with V form as the main form, while the succession layer plants were V form. At the viewpoint of artificial community, the life cycle form can be described as V_0.49S_0.33C_0.18, a typical VS transition form, indicating that most of the species studied in this community are in a healthy status with the V form. Moreover, the relatively high (33%) percentage in the S form indicates that the community also tends to sexual growth for offspring, although it will be steady within a period of time for the vegetative growth of bodies.     

A correlational study between serum asymmetric dimethylarginine level and impaired glucose tolerance patients associated with obesity

Asymmetric dimethylarginine (ADMA) plays a vital role in the regulation of insulin sensitivity and has been shown as a potential marker for various disease, including type 2 diabetes mellitus (DM2). However, the correlation between ADMA and impaired glucose tolerance (IGT) and obesity has not been studied. A total of 195 subjects were involved in our study. The characteristics of the subjects in the study cohort were measured and analyzed. We found that the serum ADMA and C-reactive protein levels were significantly increased in IGT and diabetic patients, whereas the levels of lipoprotein A and adiponectin were decreased, especially in diabetic patients with obesity. The serum ADMA level was positively correlated to a homeostatic model assessment for insulin resistance, and multivariate regression analysis further indicated that ADMA was an independent factor for DM patients with obesity. Our study expands the understanding of the complicated relationship between obesity, insulin resistance, IGT, and ADMA. In addition, we demonstrated that the serum ADMA level could serve as a diagnositic biomarker of the early signs for IGT patients with obesity.     

BI1 alleviates cardiac microvascular ischemia-reperfusion injury via modifying mitochondrial fission and inhibiting XO/ROS/F-actin pathways

Pathogenesis of cardiac microvascular ischemia-reperfusion (IR) injury is associated with excessive mitochondrial fission. However, the upstream mediator of mitochondrial fission remains obscure. Bax inhibitor 1 (BI1) is linked to multiple mitochondrial functions, and there have been no studies investigating the contribution of BI1 on mitochondrial fission in the setting of cardiac microvascular IR injury. This study was undertaken to establish the action of BI1 on the cardiac microvascular reperfusion injury and figure out whether BI1 sustained endothelial viability via inhibiting mitochondrial fission. Our observation indicated that BI1 was downregulated in reperfused hearts and overexpression of BI1 attenuated microvascular IR injury. Mechanistically, reperfusion injury elevated the levels of xanthine oxidase (XO), an effect that was followed by increased reactive oxygen species (ROS) production. Subsequently, oxidative stress mediated F-actin depolymerization and the latter promoted mitochondrial fission. Aberrant fission caused mitochondrial dysfunction and ultimately activated mitochondrial apoptosis in cardiac microvascular endothelial cells. By comparison, BI1 overexpression repressed XO expression and thus neutralized ROS, interrupting F-actin-mediated mitochondrial fission. The inhibitory effect of BI1 on mitochondrial fission sustained endothelial viability, reversed endothelial barrier integrity, attenuated the microvascular inflammation response, and maintained microcirculation patency. Altogether, we conclude that BI1 is essential in maintaining mitochondrial homeostasis and alleviating cardiac microvascular IR injury. Deregulated BI1 via the XO/ROS/F-actin pathways plays a causative role in the development of cardiac microvascular reperfusion injury.