Stand spatial structure and microbial diversity are key drivers of soil multifunctionality during secondary succession in degraded karst forests.

Studying the relationship between biodiversity and ecosystem multifunctionality (the ability of ecosystems to provide multiple ecosystem functions) (BEMF) is a current hotspot in ecology research. Previous studies on BEMF emphasized the role of plant and microbial diversity but rarely mention stand spatial structure. To investigate the effect of stand spatial structure on BEMF, this study established 30 forest dynamic plots in three natural restoration stages (shrubbery, secondary growth forest, and old-growth forest) in Maolan National Nature Reserve, Guizhou province, China. A positive response in soil multifunctionality (SMF), plant species diversity, stand spatial structure, and fungal ß diversity (p < 0.05) followed natural restoration. However, bacterial ß diversity showed a negative response (p < 0.05), while microbial α diversity remained unchanged (p > 0.05). These results based on a structural equation model showed that plant species diversity had no direct or indirect effect on SMF, soil microbial diversity was the only direct driver of SMF, and stand spatial structure indirectly affected SMF through soil microbial diversity. The random forest model showed that soil microbial ß diversity and the Shannon-Wiener index of the diameter at breast height for woody plant species were the optimal variables to characterize SMF and soil microbial diversity, respectively. These results suggested that natural restoration promoted SMF, and microbial diversity had a direct positive effect on SMF. In the meantime, stand spatial structure had a significant indirect effect on SMF, while plant species diversity did not. Future work on degraded karst forest restoration should direct more attention to the role of the stand spatial structure and emphasize the importance of biodiversity.

Variations in species diversity patterns and community assembly rules among vegetation types in the karst landscape.

The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.

How do species richness and its component dependence vary along the natural restoration in extremely heterogeneous forest ecosystems?

Giant habitat heterogeneity is an important factor contributing to the high species richness (SR) in karst forests. Yet, the driving factor behind the alterations in SR patterns during natural restoration remains unclear. In this study, we established the forest dynamics plots along the natural restoration sequence (including shrub-tree mixed forest stage (SC), secondary forest stage (SG) and old-growth forest sage (OG)) in degraded karst forests to compare the SR and the dependence on its components (including total community abundance, species abundance distribution (SAD), and conspecific spatial aggregation (CSA)) among stages of natural restoration. By evaluating the degree of contribution of the components to local SR and rarefied SR, we found that the SG exhibited the highest local SR, while the rarefied SR remained increasing along the restoration sequence after controlling the sample size. At SC-SG stage, SAD and CSA contributed negatively to the differences in SR, while abundance made a positive contribution to SR differences. At SG-OG, abundance contributed positively to the difference in SR at all scales, while SAD contributed negatively at small scales. No significant contribution of CSA was found at observed scales. In addition, local SR varied more significantly with PIE than with abundance. Our research emphasizes the importance of eliminating the influence of abundance on species richness in forest ecology and management, as well as the significance of separately evaluating the components that shape the diversity patterns.

Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation.

The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.

Abdominal Massage to Improve Motor Dysfunction in Rats with Cerebral Palsy.

Cerebral palsy (CP) is a disease with a high disability rate and morbidity. The clinical symptoms of cerebral palsy are motor dysfunction and abnormal posture development, often accompanied by cognitive impairment. Massage, a traditional Chinese Medicine therapy, can coordinate Zang and Fu, regulate Qi and blood, make the viscera work more smoothly, and calm Yin and Yang. Furthermore, it has been an effective method for CP in clinical. This paper summarizes a set of simple and standardized manipulations of massage for young rats with CP, which is easy to follow. The procedure follows: first, massage of four limb acupoints, including Quchi (LI11) and Zusanli (ST36); second, massage of the abdomen acupoints Zhongwan (RN12), Tianshu (ST25), Guanyuan (CV4), and Qihai (CV6); and finally, massage of the abdomen of the rats. This set of massage methods considerably improved the motor function of young rats with CP and is simple, standardized, and easy to follow. We adapted this set of manipulation methods in animal models to promote the internationalization and standardization of massage.

Copper-Catalyzed Annulation of O-Acyl Oximes with Cyclic 1,3-Diones for the Synthesis of 7,8-Dihydroindolizin-5(6H)-ones and Cyclohexanone-Fused Furans.

A copper-catalyzed annulation of O-acyl oximes with cyclic 1,3-diones has been developed for the concise synthesis of 7,8-dihydroindolizin-5(6H)-ones and cyclohexanone-fused furans through the substituent-controlled selective radical coupling process. 2-Alkyl cyclic 1,3-diones undergo C-C radical coupling, while 2-unsubstituted cyclic 1,3-diones undergo C-O radical coupling.

Integrated bioinformatics-based identification of diagnostic markers in Alzheimer disease.

Alzheimer disease (AD) is a progressive neurodegenerative disease resulting from the accumulation of extracellular amyloid beta (Aß) and intracellular neurofibrillary tangles. There are currently no objective diagnostic measures for AD. The aim of this study was to identify potential diagnostic markers for AD and evaluate the role of immune cell infiltration in disease pathogenesis. AD expression profiling data for human hippocampus tissue (GSE48350 and GSE5281) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using R software and the Human Protein Atlas database was used to screen AD-related DEGs. We performed functional enrichment analysis and established a protein-protein interaction (PPI) network to identify disease-related hub DEGs. The fraction of infiltrating immune cells in samples was determined with the Microenvironment Cell Populations-counter method. The random forest algorithm was used to develop a prediction model and receiver operating characteristic (ROC) curve analysis was performed to validate the diagnostic utility of the candidate AD markers. The correlation between expression of the diagnostic markers and immune cell infiltration was also analyzed. A total of 107 AD-related DEGs were screened in this study, including 28 that were upregulated and 79 that were downregulated. The DEGs were enriched in the Gene Ontology terms GABAergic synapse, Morphine addiction, Nicotine addiction, Phagosome, and Synaptic vesicle cycle. We identified 10 disease-related hub genes and 20 candidate diagnostic genes. Synaptophysin (SYP) and regulator of G protein signaling 4 (RGS4) (area under the ROC curve = 0.909) were verified as potential diagnostic markers for AD in the GSE28146 validation dataset. Natural killer cells, B lineage cells, monocytic lineage cells, endothelial cells, and fibroblasts were found to be involved in AD; additionally, the expression levels of both SYP and RGS4 were negatively correlated with the infiltration of these immune cell types. These results suggest that SYP and RGS4 are potential diagnostic markers for AD and that immune cell infiltration plays an important role in AD development and progression.

Evaluation of using a porous medium approach to simulate flat-sheet membrane bioreactors.

The porous medium approach has been applied by others to study the global hydrodynamics in hollow-fiber (HF) membrane bioreactors (MBR). This study explores the usability of the porous medium approach for flat-sheet (FS) MBR and introduces a CFD-based numerical calibration of the porous parameters. Two key modeling strategies are suggested to ensure the pressure prediction accuracy: (1) use SST k - ω turbulence model incorporated with an intermittency transition model (SSIT); (2) considerate two-phase flow during the calibration. The results showed that SSIT significantly improved the pressure prediction of the flow between two sheets. Also, unlike HF MBR, the gas phase was observed to be non-negligible during the calibration for FS MBR. The numerically calibrated porous parameters were then applied in a three-dimensional simplified model (SPM), where multiple membrane sheets were treated as one porous zone. The SPM was compared with a realistic model (RM), where all membrane sheets were simulated directly. A similar pressure distribution was observed in both models; however, local flow characteristics (i.e., the acceleration of the flow entering the module zone) were not reflected in the SPM. Hence, it is recommended to use the porous medium approach for global hydrodynamics investigation when the local flow characteristics are not of interest.

Modulation of hippocampal dopamine and synapse-related proteins by electroacupuncture improves memory deficit caused by sleep deprivation.

BACKGROUND: Sleep is crucial for proper functioning of the brain, whereas lack of sleep is very common in modern society and can cause memory impairment. Hence, it is of great significance to find effective methods to intervene in the pathogenesis of memory impairment. OBJECTIVE: We designed this study to explore the mechanism underlying the therapeutic effects of electroacupuncture (EA) on the deficits caused by sleep deprivation (SD). METHODS: In this study, we first utilized the modified multiple platform method (MMPM) to establish a rat model of SD, which was followed by use of the Y-maze and Morris water maze (MWM) to assess the performance of rats following EA treatment. RESULTS: We found that EA at GV20 and ST36 significantly decreased the number of error reactions, increased the number of active avoidance responses in the Y-maze and shortened the latency of finding the platform in the MWM test in SD + EA versus untreated SD groups. Moreover, EA treatment partially restored SD-induced reductions in hippocampal dopamine (DA) content and significantly increased the levels of phosphorylated (p) synapsin I, calcium/calmodulin-dependent protein kinase (CaMK) II, and tyrosine hydroxylase, which are related to the synthesis and release of DA. CONCLUSIONS: In summary, we it appears that EA at GV20 and ST36 may improve SD-induced memory deficits by restoring the quantity of DA in the hippocampus, which is related to activation of CaMK II, synapsin I, and tyrosine hydroxylase. EA may have potential as an alternative therapy for SD and could improve learning and memory deficits among those suffering from sleep deficiency, although this needs verification by prospective clinical studies.

Corrigendum to "Tuina Massage Improves Cognitive Functions of Hypoxic-Ischemic Neonatal Rats by Regulating Genome-Wide DNA Hydroxymethylation Levels".

[This corrects the article DOI: 10.1155/2019/1282085.].

Tuina Massage Improves Cognitive Functions of Hypoxic-Ischemic Neonatal Rats by Regulating Genome-Wide DNA Hydroxymethylation Levels.

In addition to abnormalities of motor and posture, children with cerebral palsy (CP) often have intellectual disability. As a complementary and alternative traditional Chinese medicine (TCM) therapy, Chinese Tuina massage, also called Tuina in China, has been widely applied in clinical treatment for CP in China for a long time. However, the molecular basis for this still remains largely unknown. Recently, DNA hydroxymethylation has been shown to be sensitive to environment and plays critical roles in some neurological disorders, whereas the research focusing on the relationship between 5 hmC and Tuina therapy for cerebral palsy is deficient. In our study, we first observed that Tuina improved learning and memory functions of hypoxic-ischemic (HI) rat pups. Meanwhile, 5 hmC level of the temporal lobe cortex in the HI neonatal rat model is decreased significantly compared to that of the rats in control and Tuina groups. Then, we used the hMeDIP-Seq method to explore whether and how DNA hydroxymethylation is involved in Tuina therapy for cerebral palsy. Genomic annotation of DhMRs of HI group's hypo-hydroxymethylation to genes revealed enrichment in multiple neurodevelopmental signaling pathways. Moreover, we found the depletion of 5 hmC modifications in genes associated with neuronal development was accompanied by reduced mRNA levels of these genes. Taken together, our results indicate that Tuina may regulate the expression of neurodevelopment-related genes by changing the status of DNA hydroxymethylation, thereby improving learning and memory functions of cerebral palsy.

Genome-Wide Alteration of 5-Hydroxymethylcytosine in Hypoxic-Ischemic Neonatal Rat Model of Cerebral Palsy.

Cerebral palsy (CP) is a neurodevelopmental disorder usually occurring early in life and persisting through the whole life. Several risk factors, including perinatal hypoxia-ischemia (HI), may contribute to occurrence of CP in preterm infants. DNA hydroxymethylation has been shown to play an important role in neurodevelopment and neurodegenerative disorders. However, the effect of DNA hydroxymethylation in CP remains unknown. The aim of this study is to explore whether and how DNA hydroxymethylation is involved in CP pathogenesis. We observed that overall 5-hydroxymethylcytosine (5hmC) abundance in the cortex of the temporal lobe of rat pups was decreased significantly after hypoxic-ischemic injury, and the reduced expression of Tet1 and Tet2 enzymes might be responsible for this change. Identified differential hydroxymethylation regions (DhMRs) were richly involved in multiple signaling pathways related to neuronal development and function. Furthermore, we found that reduced 5hmC modification on the DhMRs-related genes were accompanied by decrease of their mRNA expression levels. These results suggest that 5hmC modifications are involved in the CP pathogenesis and may potentially serve as a new therapeutic target.

Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis).

BACKGROUND: The SQUAMOSA promoter binding protein-like (SPL) proteins are plant-specific transcription factors (TFs) that function in a variety of developmental processes including growth, flower development, and signal transduction. SPL proteins are encoded by a gene family, and these genes have been characterized in two model grass species, Zea mays and Oryza sativa. The SPL gene family has not been well studied in moso bamboo (Phyllostachys edulis), a woody grass species. RESULTS: We identified 32 putative PeSPL genes in the P. edulis genome. Phylogenetic analysis arranged the PeSPL protein sequences in eight groups. Similarly, phylogenetic analysis of the SBP-like and SBP proteins from rice and maize clustered them into eight groups analogous to those from P. edulis. Furthermore, the deduced PeSPL proteins in each group contained very similar conserved sequence motifs. Our analyses indicate that the PeSPL genes experienced a large-scale duplication event ~15 million years ago (MYA), and that divergence between the PeSPL and OsSPL genes occurred 34 MYA. The stress-response expression profiles and tissue-specificity of the putative PeSPL gene promoter regions showed that SPL genes in moso bamboo have potential biological functions in stress resistance as well as in growth and development. We therefore examined PeSPL gene expression in response to different plant hormone and drought (polyethylene glycol-6000; PEG) treatments to mimic biotic and abiotic stresses. Expression of three (PeSPL10, -12, -17), six (PeSPL1, -10, -12, -17, -20, -31), and nine (PeSPL5, -8, -9, -14, -15, -19, -20, -31, -32) genes remained relatively stable after treating with salicylic acid (SA), gibberellic acid (GA), and PEG, respectively, while the expression patterns of other genes changed. In addition, analysis of tissue-specific expression of the moso bamboo SPL genes during development showed differences in their spatiotemporal expression patterns, and many were expressed at high levels in flowers and leaves. CONCLUSIONS: The PeSPL genes play important roles in plant growth and development, including responses to stresses, and most of the genes are expressed in different tissues. Our study provides a comprehensive understanding of the PeSPL gene family and may enable future studies on the function and evolution of SPL genes in moso bamboo.

Genome-wide identification and analysis of the Populus trichocarpa TIFY gene family.

The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome. Numerous abiotic stress cis-elements were widely found in the promoter regions. Analysis of the Ka/Ks ratios indicated that the paralogs of the PtTIFY family principally underwent purifying selection. Microarray data and qRT-PCR analysis revealed that 24 PtTIFY genes were differentially expressed in various tissues. Quantitative real-time RT-PCR analysis of TIFY genes expression in response to salt, JA hormones and low-temperature stress revealed their stress-responses profiles. The results of this study provided valuable information for further exploration of the TIFY gene family in Populus trichocarpa.

Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants.

Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica. Strong purifying selection acted as a critical role in almost all of the paralogous and orthologous genes. The structure of LOX genes in Carica and Populus are relatively stable, whereas Vitis and Arabidopsis have a difference. By searching conserved motifs of LOX genes, we found that each sub-family shared similar components. Research on intraspecies gene collinearity show that recent duplication holds an important position in Populus and Arabidopsis. Gene collinearity analysis within and between these four rosid plants revealed that all LOX genes in each modern rosid were the offspring from different ancestral genes. This study traces the evolution of LOX genes which have been differentially retained and expanded in rosid plants. Our results presented here may aid in the selection of special genes retained in the rosid plants for further analysis of biological function.

Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis).

Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

Behavior-constrained support vector machines for fMRI data analysis.

Statistical learning methods are emerging as a valuable tool for decoding information from neural imaging data. The noisy signal and the limited number of training patterns that are typically recorded from functional brain imaging experiments pose a challenge for the application of statistical learning methods in the analysis of brain data. To overcome this difficulty, we propose using prior knowledge based on the behavioral performance of human observers to enhance the training of support vector machines (SVMs). We collect behavioral responses from human observers performing a categorization task during functional magnetic resonance imaging scanning. We use the psychometric function generated based on the observers behavioral choices as a distance constraint for training an SVM. We call this method behavior-constrained SVM (BCSVM). Our findings confirm that BCSVM outperforms SVM consistently.

A three-compartment model of the hemodynamic response and oxygen delivery to brain.

We describe a mathematical model linking changes in cerebral blood flow, blood volume and the blood oxygenation state in response to stimulation. The model has three compartments to take into account the fact that the cerebral blood flow and volume as measured concurrently using laser Doppler flowmetry and optical imaging spectroscopy have contributions from the arterial, capillary as well as the venous compartments of the vasculature. It is an extension to previous one-compartment hemodynamic models which assume that the measured blood volume changes are from the venous compartment only. An important assumption of the model is that the tissue oxygen concentration is a time varying state variable of the system and is driven by the changes in metabolic demand resulting from changes in neural activity. The model takes into account the pre-capillary oxygen diffusion by flexibly allowing the saturation of the arterial compartment to be less than unity. Simulations are used to explore the sensitivity of the model and to optimise the parameters for experimental data. We conclude that the three-compartment model was better than the one-compartment model at capturing the hemodynamics of the response to changes in neural activation following stimulation.

Sequential Bayesian decoding with a population of neurons.

Population coding is a simplified model of distributed information processing in the brain. This study investigates the performance and implementation of a sequential Bayesian decoding (SBD) paradigm in the framework of population coding. In the first step of decoding, when no prior knowledge is available, maximum likelihood inference is used; the result forms the prior knowledge of stimulus for the second step of decoding. Estimates are propagated sequentially to apply maximum a posteriori (MAP) decoding in which prior knowledge for any step is taken from estimates from the previous step. Not only do we analyze the performance of SBD, obtaining the optimal form of prior knowledge that achieves the best estimation result, but we also investigate its possible biological realization, in the sense that all operations are performed by the dynamics of a recurrent network. In order to achieve MAP, a crucial point is to identify a mechanism that propagates prior knowledge. We find that this could be achieved by short-term adaptation of network weights according to the Hebbian learning rule. Simulation results on both constant and time-varying stimulus support the analysis.