Species divergence and environmental adaptation of Picea asperata complex at the whole genome level.

To study the interspecific differentiation characteristics of species originating from recent radiation, the genotyping-by-sequencing (GBS) technique was used to explore the kinship, population structure, gene flow, genetic variability, genotype-environment association and selective sweeps of Picea asperata complex with similar phenotypes from a genome-wide perspective. The following results were obtained: 14 populations of P. asperata complex could be divided into 5 clades; P. wilsonii and P. neoveitchii diverged earlier and were more distantly related to the remaining 6 spruce species. Various geological events have promoted the species differentiation of P. asperata complex. There were four instances of gene flow among P. koraiensis, P. meyeri, P. asperata, P. crassifolia and P. mongolica. The population of P. mongolica had the highest level of nucleotide diversity, and P. neoveitchii may have experienced a bottleneck recently. Genotype-environment association found that a total of 20,808 genes were related to the environmental variables, which enhanced the adaptability of spruce in different environments. Genes that were selectively swept in the P. asperata complex were primarily associated with plant stress resistance. Among them were some genes involved in plant growth and development, heat stress, circadian rhythms and flowering. In addition to the commonly selected genes, different spruce species also displayed unique genes subjected to selective sweeps that improved their adaptability to different habitats. Understanding the interspecific gene flow and adaptive evolution of Picea species is beneficial to further understanding the species relationships of spruce and can provide a basis for studying spruce introgression and functional genomics.

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level.

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

Effects of climate change on vegetation dynamics of the Qinghai-Tibet Plateau, a causality analysis using empirical dynamic modeling.

Given the vital role of the Qinghai-Tibet Plateau (QTP) as water tower in Asia and regulator for regional and even global climate, the relationship between climate change and vegetation dynamics on it has received considerable focused attention. Climate change may influence the vegetation growth on the plateau, but clear empirical evidence of such causal linkages is sparse. Herein, using datasets CRU-TS v4.04 and AVHHR NDVI from 1981 to 2019, we quantify causal effects of climate factors on vegetation dynamics with an empirical dynamical model (EDM) -- a nonlinear dynamical systems analysis approach based on state-space reconstruction rather than correlation. Results showed the following: (1) climate change promotes the growth of vegetation on the QTP, and specifically, this favorable influence of temperature is stronger than precipitation's; (2) the direction and strength of climate effects on vegetation varied over time, and the effects are seasonally different; (3) a significant increase in temperature and a slight increase in precipitation are beneficial to vegetation growth, specifically, NDVI will increase within 2% in the next 40 years with the climate trend of warming and humidity. Besides the above results, another interesting finding is that the two seasons in which precipitation strongly influence vegetation in the Three-River Source region (part of the QTP) are spring and winter. This study provides insights into the mechanisms by which climate change affects vegetation growth on the QTP, aiding in the modeling of vegetation dynamics in future scenarios.

Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis.

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

Repetitive Transcranial Magnetic Stimulation Reduces Neuronal Loss and Neuroinflammation in Parkinson?s Disease Through the miR-195a-5p/CREB Axis.

AIM: To elucidate the molecular mechanism underlying the repetitive transcranial magnetic stimulation (rTMS) -induced improvement in Parkinson's disease (PD). MATERIAL AND METHODS: We established a PD model by administering 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine to SAMP8 mice. The mice were then subjected to rTMS. Motor coordination and cognition were assessed using rotarod and Morris water maze tests, respectively. Nissl staining was performed to evaluate neuronal apoptosis. Furthermore, western blotting was employed to assess the expression of tyrosine hydroxylase and brain-derived neurotrophic factor. Additionally, the levels of tumor necrosis factor-α, interferon-γ, and interleukin-6 in the cerebrospinal fluid were evaluated using specific enzyme-linked immunosorbent assay kits. The expression of miR-195a-5p and cyclic AMP-response element-binding protein (CREB) was examined using quantitative real-time polymerase chain reaction and western blotting. Dual-luciferase reporter assay was performed using primary cortical rat neurons to validate the interaction between miR-195a-5p and CREB. RESULTS: rTMS improved cognition and motor coordination as well as reduced neuronal apoptosis/ and the levels of inflammatory factors in PD mice. It downregulated the expression of miR-195a-5p but upregulated that of CREB. In primary rat cortical neurons, miR-195a-5p directly targeted CREB, and we found that miR-195a-5p suppression enhanced cognitive and motor functions in PD mice. Moreover, miR-195a-5p downregulation decreased inflammatory response and neuronal loss in the PD mice. CONCLUSION: rTMS exerted its neuroprotective effects on PD mice by regulating the miR-195a-5p/CREB axis. This finding reveals a novel mechanism through which rTMS improves PD and indicates that miR-195a-5p is a potential therapeutic target for PD treatment.

Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa.

The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.

Characterization and analysis of the transcriptome response to drought in Larix kaempferi using PacBio full-length cDNA sequencing integrated with de novo RNA-seq reads.

MAIN CONCLUSION: A hypothetical model of drought tolerance mechanism of Larix kaempferi was established through SMRT-seq and Illumina HiSeq. Larix kaempferi is an important economic and ecological species and a major afforestation species in north-eastern China. To date, no information has been reliably derived regarding full-length cDNA sequencing information on L. kaempferi. By single-molecule long-read isoform sequencing (SMRT-seq), here we report a total of 26,153,342 subreads (21.24 Gb) and 330,371 circular consensus sequence (CCS) reads after the modification of site mismatch, and 35,414 unigenes were successfully collected. To gain deeper insights into the molecular mechanisms of L. kaempferi response to drought stress, we combined Illumina HiSeq with SMRT-seq to decode full-length transcripts. In this study, we report 27 differentially expressed genes (DEGs) involved in the perception and transmission of drought stress signals in L. kaempferi. A large number of DEGs responding to drought stress were detected in L. kaempferi, especially DEGs involved in the reactive oxygen species (ROS) scavenging, lignin biosynthesis, and sugar metabolism, and DEGs encoding drought stress proteins. We detected 73 transcription factors (TFs) under drought stress, including AP2/ERF, bZIP, TCP, and MYB. This study provides basic full sequence resources for L. kaempferi research and will help us to better understand the functions of drought-resistance genes in L. kaempferi.

Distribution of graphene oxide and TiO2-graphene oxide composite in A549 cells.

Graphene and its derivatives are increasingly applied in nanoelectronics, biosensing, drug delivery, and biomedical applications. However, the information about its cytotoxicity remains limited. Herein, the distribution and cytotoxicity of graphene oxide (GO) and TiO2-graphene oxide composite (TiO2-GO composite) were evaluated in A549 cells. Cell viability and cell ultrastructure were measured. Our results indicated that GO could enter A549 cells and located in the cytoplasm and nucleus without causing any cell damage. TiO2 nanoparticles and GO would be separated after TiO2-GO composite entered A549 cells. TiO2-GO composite could induce cytotoxicity similar to TiO2 nanoparticles, which was probably attributed to oxidative stress. These results should be considered in the development of biological applications of GO and TiO2-GO composite.

Effects of fullerene C60 nanoparticles on A549 cells.

Fullerene C60 nanoparticles (C60 NPs) have been widely applied in many fields due to their excellent physical and chemical properties. As production and applications of C60 NPs expand, public concern about the potential risk to human health has also risen. The toxicity of C60 NPs was evaluated by the CCK-8 assay using the cultured human epithelial cell line A549. Cellular uptake of the C60 NPs was observed by TEM imaging. In our findings, C60 NPs could readily enter A549 cells and showed no significant toxicity. Exposure of cultured A549 cells to C60 NPs led to an increase of intracellular reactive oxygen species (ROS) while glutathione reductase activity was probably activated to generate more GSH to maintain a cellular oxidation-reduction equilibrium. The A549 cells responded to the ROS increases through the inauguration of autophagic responses, aimed at restoring cellular health and equilibrium.

Cytotoxicity of silica nanoparticles on HaCaT cells.

Despite the widespread use of silica nanoparticles (SiO2 NPs) in biological and medical fields, their adverse effects have not been clearly elucidated. In this study, spherical SiO2 NPs with a 50 nm diameter were used to study their interaction with HaCaT cells. SiO2 NPs were found to be readily internalized into HaCaT cells and localized in the cytoplasm, lysosomes and autophagosomes. Decreased cell viability and damaged cell membrane integrity showed the cytotoxicity of SiO2 NPs. Significant glutathione depletion and reactive oxygen species generation, which reduced the cellular antioxidant level, could be the major factor of cytotoxicity induced by SiO2 NPs.

Mitochondrial injury induced by nanosized titanium dioxide in A549 cells and rats.

The nanosized titanium dioxide (nano-TiO2) is an important nanoscale compound applied in many different fields because of its superior performance. Here, an anatase nano-TiO2 showed cytotoxicity in a dosage-dependent manner, which was in accordance with changes of A549 cell ultrastructure, A549 cell viability and intracellular ATP level. The lungs of rats treated with single intratracheal instillation of nano-TiO2 were injured, which was demonstrated by changes of alveolar epithelial cell ultrastructure, lung tissue pathology and lung tissue MDA level. The results of this study indicated that nano-TiO2 should be related to the generation of intracellular reactive oxygen species (ROS), which injured mitochondria and prevented the synthesis of ATP. The cells were approaching to apoptosis eventually. In macroscopic view, the lungs inevitably suffered.