Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China.

Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei's gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources.

The alteration of cognitive function networks in remitted patients with major depressive disorder: an independent component analysis.

INTRODUCTION: Dysfunctional connectivity of resting-state functional networks has been observed in patients with major depressive disorder (MDD), particularly in cognitive function networks including the central executive network (CEN), default mode network (DMN) and salience network (SN). Findings from studies examining how aberrant functional connectivity (FC) changed after antidepressant treatment, however, have been inconsistent. Thus, the purpose of the present study was to explore potential mechanisms of altered cognitive function networks during resting-state between remitted major depressive disorder (rMDD) patients and healthy controls (HCs) and furthermore, the relationship between dysfunctional connectivity patterns in rMDD and clinical symptoms. METHODOLOGY: In this study, 19 HCs and 19 rMDD patients were recruited for resting-state functional magnetic resonance imaging (fMRI) scanning. FC was evaluated with independent component analysis for CEN, DMN and SN. Two sample t tests were conducted to compare differences between rMDD and HCs. A Pearson correlation analysis was also performed to examine the relationship between connectivity of networks and cognitive function scores and clinical symptoms. RESULTS: Compared to healthy controls, remitted patients showed lower connectivity in CEN, mostly in the superior frontal gyrus (SFG), middle frontal gyrus (MFG), inferior parietal lobule (IPL) and part of the supramarginal gyrus (SMG). Conversely, the bilateral insula, part of the SMG (a key node of the CEN) and dorsal anterior cingulate cortex (dACC) of the DMN showed higher connectivity in rMDD patients. Pearson correlation results demonstrated that connectivity of the right IPL in CEN was positively correlated with cognitive function scores, and connectivity of the left insula was negatively correlated with BDI scores. CONCLUSIONS: Though rMDD patients reached the standard of clinal remission, unique impairments of FC in cognitive function networks remained. Aberrant FC between cognitive function networks responsible for executive control was observed in rMDD and may be associated with residual clinical symptoms.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships.

BACKGROUND: Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana. RESULTS: The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value. CONCLUSION: Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.

Connectivity patterns of cognitive control network in first episode medication-naive depression and remitted depression.

BACKGROUND: Cognitive dysfunctions, such as impaired cognitive control, are frequently observed in patients with major depressive disorder (MDD). Although the cognitive control network (CCN) is widely considered a core feature of major depressive disorder (MDD), the relationship between cognitive dysfunction and symptom dimensions remains unclear. This study investigated differences in resting-state functional connectivity of the cognitive control network (CCN) between first-episode medication-naive MDD patients and remitted MDD. METHODS: We collected resting-state functional MRI (rs-fMRI) data from 22 first-episode medication-naive major depressive disorder (fMDD) patients, 20 patients previously diagnosed with MDD in the remitted phase of depression (rMDD), and 20 healthy controls (HC). The CCN was derived from fMRI images using independent component analysis (ICA), a data-driven image analysis method. RESULTS: Changes in functional connectivity (FC) within the CCN was mainly attenuated in the right dorsolateral prefrontal cortex and the left inferior parietal lobule, while strengthened in the right dorsal anterior cingulate cortex and the right insula in both fMDD and rMDD groups. Compared with the fMDD group, the rMDD group had decreased FC in the bilateral insula and the right dorsolateral prefrontal cortex. Further analysis explored that the FC in the bilateral insula, the right dorsal anterior cingulate cortex and the right inferior parietal lobule were correlated positively cognitive disturbance factor scores in both patients groups. CONCLUSIONS: These findings are in agreement with the previous findings that the cognitive control network are impaired in MDD. Furthermore, our results suggest that the alteration of CCN might underpin the cognitive disturbance and the distinct patterns of the CCN between fMDD and rMDD patients may be an important target for effective cognitive remediation in MDD.

Hippocampus-driving progressive structural alterations in medication-naïve major depressive disorder.

BACKGROUND: Major depressive disorder (MDD) is associated with abnormalities in brain structure. However, structural abnormality findings have been inconsistent and how structural changes lead to progressive morphometric alterations in depressed brain regions remains unclear. METHODS: High-resolution T1-weighted magnetic resonance images of first-episode medication-naïve MDD patients (20 men, 36 women) and healthy control participants (33 men, 23 women) were evaluated. Voxel-based morphometry analysis was conducted based on T1-weighted images. The causal network of structural covariance analysis (CaSCN) was accomplished by applying Granger causality analysis to the sequenced T1-weighted images in order to assess causal effect of structural changes. RESULTS: When comparing MDD patients and healthy controls, gray matter was greater in the bilateral amygdala, the bilateral hippocampus, the left parahippocampus, and the right fusiform, while it was lessened in the bilateral brainstem, the bilateral pallidum, and the bilateral thalamus. Selecting the hippocampus as the seed region to run further CaSCN analysis revealed that the hippocampus is a prominent node that exerts a causal effect on the amygdala and regions of the default mode network. LIMITATIONS: Our sample size was small and the subjects groups' ages were not well matched. We also recognize that the hippocampus is not necessarily the original source of brain network alteration in MDD. CONCLUSIONS: The CaSCN clarified the causal relationship between progressive gray matter alterations in the hippocampus and in other regions. Our work provided evidence of a network spread mechanism in terms of the causal influence of hippocampal alteration on progressive brain structural alterations in MDD.

Development of Species-Specific SCAR Markers, Based on a SCoT Analysis, to Authenticate Physalis (Solanaceae) Species.

Physalis is an important genus in the Solanaceae family. It includes many species of significant medicinal value, edible value, and ornamental value. However, many Physalis species are easily confused because of their similar morphological traits, which hinder the utilization and protection of Physalis resources. Therefore, it is necessary to create fast, sensitive, and reliable methods for the Physalis species authentication. Intended for that, in this study, species-specific sequence-characterized amplified region (SCAR) markers were developed for accurate identification of the closely related Physalis species P. angulata, P. minima, P. pubescens, and P. alkekengi var. franchetii, based on a simple and novel marker system, start codon targeted (SCoT) marker. A total of 34 selected SCoT primers yielded 289 reliable SCoT loci, of which 265 were polymorphic. Four species-specific SCoT fragments (SCoT3-1404, SCoT3-1589, SCoT5-550, and SCoT36-520) from Physalis species were successfully identified, cloned, and sequenced. Based on these selected specific DNA fragments, four SCAR primers pairs were developed and named ST3KZ, ST3MSJ, ST5SJ, and ST36XSJ. PCR analysis of each of these primer pairs clearly demonstrated a specific amplified band in all samples of the target Physalis species, but no amplification was observed in other Physalis species. Therefore, the species-specific SCAR primer pairs developed in this study could be used as powerful tools that can rapidly, effectively, and reliably identify and differentiate Physalis species.

[Application of DNA molecular marker technologies in study of medicinal Physalis species].

As traditional Chinese medicinal herbs, Physalis plants have a variety of pharmacological activities, such as anti-inflammatory, anti-oxidant, and anti-cancer effects, and have been used for the treatment of malaria, rheumatism, hepatitis, asthma, and cancer. In addition to the medicinal value, many Physalis species are also the high-grade nutrition health care fruits, can be made canned and candied etc. In the study, the application progress of DNA molecular marker technologies in medicinal Physalis plants in recent years was reviewed, in order to provide an important molecular technical basis for the identification, classification and rational development and protection of medicinal Physalis resources.

Development of SCoT-Based SCAR Marker for Rapid Authentication of Taxus Media.

Taxus media is an important species in the family Taxaceae with high medicinal and commercial value. Overexploitation and illegal trade have led T. media to a severe threat of extinction. In addition, T. media and other Taxus species have similar morphological traits and are easily misidentified, particularly during the seedling stage. The purpose of this study is to develop a species-specific marker for T. media. Through a screening of 36 start codon targeted (SCoT) polymorphism primers, among 15 individuals of 4 Taxus species (T. media, T. chinensis, T. cuspidate and T. fuana), a clear species-specific DNA fragment (amplified by primer SCoT3) for T. media was identified. After isolation and sequencing, a DNA sequence with 530 bp was obtained. Based on this DNA fragment, a primer pair for the sequence-characterized amplified region marker was designed and named MHSF/MHSR. PCR analysis with primer pair MHSF/MHSR revealed a clear amplified band for all individuals of T. media but not for T. chinensis, T. cuspidate and T. fuana. Therefore, this marker can be used as a quick, efficient and reliable tool to identify T. media among other related Taxus species. The results of this study will lay an important foundation for the protection and management of T. media as a natural resource.

Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA-trnH intergenic region.

Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA-trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA-trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA-trnH region were 100%. MEGA V6.0 was utilized to align the psbA-trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA-trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA-trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA-trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.

Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway.

BACKGROUND: Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown. RESULTS: In our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified. A gene ontology analysis showed that these proteins are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Moreover, two types of conserved succinylation motifs, '***Ksuc******K**' and '****EKsuc***', were identified. Our data showed that lysine succinylation occurred on five key enzymes in the glycolysis pathway. The numbers of average succinylation sites on these five enzymes in plants were lower than those in bacteria and mammals. Interestingly, two active site amino acids residues, K103 and K225, could be succinylated in fructose-bisphosphate aldolase, indicating a potential function of lysine succinylation in the regulation of glycolytic enzyme activities. Furthermore, the protein-protein interaction network for the succinylated proteins showed that several functional terms, such as glycolysis, TCA cycle, oxidative phosphorylation and ribosome, are consisted. CONCLUSIONS: Our results provide the first comprehensive view of the succinylome of D. officinale and may accelerate future biological investigations of succinylation in the synthesis of polysaccharides, which are major active ingredients.

Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study.

Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.