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Desertification in degraded grasslands is manifested through the development of bare sandy patches, which eventually lead to habitat fragmentation. The ability of these bare sandy patches to regenerate naturally through in-situ soil seed banks is not well understood. To fill this knowledge gap, we randomly selected 24 bare sandy patches with areas ranging from 19 to 898 m2 in a desertified grassland of the Horqin sandy land, Northern China to determine whether soil seed bank can be used for natural regeneration of bare sandy patches. Species composition and density of soil seed bank as well as aboveground vegetation composition, abundance and coverage were investigated. We then determined their relationships with in-situ habitat characteristics. Our observations showed that the studied area had low soil seed bank density and species richness, as well as depauperate soil seed bank communities. Consequently, local soil seed bank was not able to provide sufficient seed source for natural regeneration. This was indicated by the relationships between aboveground vegetation, soil seed bank and the in-situ habitat characteristics. For bare patches with an area between 300 m2 and 900 m2, increase the soil seed bank density and species richness should be the main restoration measures. For bare patches with a small area of less than 50 m2, restoration of vegetation density should be the main measure. Our data highlighted that different extents of desertification, indicated by different bare patches, are requiring distinct restoration measures.

Comprising ca. 200 species

Secondary diaspore dispersal by wind, that is, wind‐driven movement along the ground surface (GS), is important for the structure and dynamics of plant populations and communities. However, how wind velocity (WV), GS, and diaspore morphology influence diaspore secondary dispersal by wind are unclear. We used a wind tunnel and video camera to measure the threshold of WV (TWV) and diaspore velocities (DV) of secondary diaspore dispersal. Diaspores of seven Calligonum species with different appendages (wings, bristles, membranous balloon, and wings + thorns) were used to determine the TWV and DV under variable wind speed (4, 6, 8, and 10 m s‐¹) and four GSs (cement, sand, loam, and gravel). GS and diaspore morphological traits explained 37.1 and 18% of diaspore TWV, respectively. Meanwhile, WV, GS, and diaspore morphological traits explained 62.4, 13.6, and 3.2% of DV, respectively. An increasing trend was shown for TWV, and a decreasing trend was shown for DV in the order of cement, sand, loam, and gravel surfaces. Spherical and light diaspores had low TWV and high DV, whereas winged and heavy diaspores had high TWV and low DV. Our results indicated that adaptive features of diaspore appendages might be the result of selection for primary dispersal or secondary dispersal. The mechanism of diaspore secondary dispersal is important for understanding the recovery of degraded sand dunes and providing theoretical support for restoration practices.

At present, the effect of multiple antibiotics on aerobic composting process and its mechanism are not clear. So in this study, broiler manure containing different doses of Doxycycline (DOX) and Gatifloxacin (GAT) were used as raw materials and mixed with rice hull for aerobic composting, and the effects of the combination of multiple antibiotics on the process parameters of broiler manure composting and the succession of bacterial and fungal community structures were systematically analyzed. Our results showed that at the initial period of composting, the combination of multiple antibiotics led to a delayed temperature and pH increase (T1: 57.0 °C, T2: 48.3 °C, T3: 45.5 °C on Day 3 for temperature and T1: 7.44, T2: 7.1, T3: 6.88 on Day 5 for pH), and a slow total nitrogen decrease (T1: 1.56%, T2: 1.82%, T3: 1.74% on Day 5). Although these effects decreased gradually with the degradation of antibiotics, the relative abundance of Actinobacteriota (T1: 13.29%, T2: 10.57%, T3: 8.99%) and Bacteroidota (T1:27.52%, T2:40.03%, T3:39.81%)) were still influenced by multiple antibiotic residuals until the end of composting period. Higher levels of antibiotics had more lasting effects on the bacterial community (T3 T2). However, the combination of these two antibiotics did not significantly promote or inhibit the succession of the fungal community structure. The heatmaps showed that composting stage had a greater effect on the microbial community structures than antibiotics. The results provided a theoretical reference for composting broiler manure containing DOX and GAT.

The emergence of drug resistance is one of the main obstacles to the treatment of lung cancer patients with EGFR inhibitors. Here, to further understand the mechanism of EGFR inhibitors in lung cancer and offer novel therapeutic targets for anti-EGFR-inhibitor resistance via the deep mining of pharmacogenomics data, we associated DNA methylation with drug sensitivities for uncovering the methylation sites related to EGFR inhibitor sensitivity genes. Specifically, we first introduced a grouped regularized regression model (Group Least Absolute Shrinkage and Selection Operator, group lasso) to detect the genes that were closely related to EGFR inhibitor effectiveness. Then, we applied the classical regression model (lasso) to identify the methylation sites associated with the above drug sensitivity genes. The new model was validated on the well-known cancer genomics resource: CTRP. GeneHancer and Encyclopedia of DNA Elements (ENCODE) database searches indicated that the predicted methylation sites related to EGFR inhibitor sensitivity genes were related to regulatory elements. Moreover, the correlation analysis on sensitivity genes and predicted methylation sites suggested that the methylation sites located in the promoter region were more correlated with the expression of EGFR inhibitor sensitivity genes than those located in the enhancer region and the TFBS. Meanwhile, we performed differential expression analysis of genes and predicted methylation sites and found that changes in the methylation level of some sites may affect the expression of the corresponding EGFR inhibitor-responsive genes. Therefore, we supposed that the effectiveness of EGFR inhibitors in lung cancer may be improved by methylation modification in their sensitivity genes.

Affected by soil moisture and groundwater table, Mongolian pine roots displayed an hourglass-type distribution characteristic, the high roots density distributed in the shallow and deep layers on sand soil. Mongolian pine (Pinussylvestris var.mongolica) is widely planted in arid and semiarid sandy land and serves as an important wind control and sand fixation species. In order to understand the effects of soil moisture and groundwater table on root distribution characteristics of Mongolian pine, we examined root distribution characteristics and determined the soil moisture and groundwater table under Mongolian pine plantations. The results indicated that the vertical distribution of Mongolian pine roots displayed an hourglass-type characteristic that indicated high density in the shallow (5–35 cm) and deep (85–145 cm) layers, but a low density in the middle layer (35–85 cm). Fine roots, which have a strong relationship with water utilization, displayed typical hourglass-type distribution characteristics. The proportion of fine roots in shallow soil layers (5–35 cm), middle layers (35–85 cm) and deep layers (85–145 cm) was 44.67%, 11.8% and 43.53%, respectively. Corresponding to root distribution characteristic, the shallow (0–40 cm) layer and the deep (90–150 cm) layer have a high soil water content than the middle layer. From May to October, the depth of groundwater table in the Mongolian pine plantation showed an increasing trend, from 185 to 291 cm, and the average groundwater table depth was 251 cm. The average height of capillary fringe above the groundwater table was 75.27 cm. Rainfall and groundwater have effects on the soil water content in a Mongolian pine plantation, and that determines the root distribution characteristics of Mongolian pine. The deep root system of Mongolian pine was effectively supplemented by groundwater, which is a necessary condition to maintain Mongolian pine survival and growth in the western Horqin Sandy Land.

Currently the amount of data available on the effect of sand dune stabilization on species conservation in inter-dune lowland is very limited, especially for the sand dune systems in semi-arid regions. In this study, we determined whether the characteristics of above-ground vegetation, soil seed bank and their relationships with environmental factors changed with sand dune stabilization in the inter-dune lowlands in Horqin Sandy Land, China. Species composition, abundance and coverage of aboveground vegetation as well as soil seed bank composition and density were surveyed and their correlations with environmental factors (pH, organic matter content, total nitrogen and total phosphorus) were determined. The results showed that changes in the relationship between aboveground vegetation, soil seed bank and soil quality followed the changes in aboveground vegetation and soil seed banks. Aboveground vegetation species richness increased with sand dune stabilization, but soil seed bank species richness declined. The inter-dune lowland of active sand dunes could provide specific habitats for some endemic species and pioneer psammophyte species as indicated by data on aboveground vegetation and soil seed bank. Our results suggested that both active and stabilized sand dunes should be maintained since active sand dunes are essential for the survival of endemic or pioneer species and stabilized sand dunes are important for sustaining species richness.

Recent pharmacogenomic studies that generate sequencing data coupled with pharmacological characteristics for patient-derived cancer cell lines led to large amounts of multi-omics data for precision cancer medicine. Among various obstacles hindering clinical translation, lacking effective methods for multimodal and multisource data integration is becoming a bottleneck.Here we proposed DeepDRK, a machine learning framework for deciphering drug response through kernel-based data integration. To transfer information among different drugs and cancer types, we trained deep neural networks on more than 20 000 pan-cancer cell line-anticancer drug pairs. These pairs were characterized by kernel-based similarity matrices integrating multisource and multi-omics data including genomics, transcriptomics, epigenomics, chemical properties of compounds and known drug-target interactions. Applied to benchmark cancer cell line datasets, our model surpassed previous approaches with higher accuracy and better robustness. Then we applied our model on newly established patient-derived cancer cell lines and achieved satisfactory performance with AUC of 0.84 and AUPRC of 0.77. Moreover, DeepDRK was used to predict clinical response of cancer patients. Notably, the prediction of DeepDRK correlated well with clinical outcome of patients and revealed multiple drug repurposing candidates. In sum, DeepDRK provided a computational method to predict drug response of cancer cells from integrating pharmacogenomic datasets, offering an alternative way to prioritize repurposing drugs in precision cancer treatment.The DeepDRK is freely available via https://github.com/wangyc82/DeepDRK.

Dispersal ability is important for the introduction, establishment, and spread of alien plant species. Therefore, determination of the geographical distribution of the dispersal ability of such species, and the relationship between dispersal ability and socio-climatic factors are essential to elucidate the invasion strategies of the alien plant species. Analytic hierarchy process and inventory, risk rank, and dispersal mode data available on Chinese alien plant species were used to determine their dispersal ability, the geographical distribution thereof, and the relationship between socio-climatic factors and dispersal ability. High-risk alien plant species had a higher natural dispersal ability (or several natural dispersal modes) but a lower anthropogenic dispersal ability (or few anthropogenic dispersal modes) than low-risk alien plant species. The geographical distribution of the dispersal ability of the alien plant species showed an inverse relationship with species density. Alien plant species with low dispersal ability (i.e., with fewer dispersal modes and distribution in the southeast) showed a tendency to adapt to environments with mild climates, while those with high dispersal ability (i.e., with more disposal nodes and distribution in the northwest) showed a tendency to adapt to harsh environments. It is essential for land managers and policy makers to understand the geographical distribution of the dispersal ability of alien plant species and their socio-climatic control factors to formulate strategies to control the natural and anthropogenic dispersal of such plants.

Recent RNA knockdown experiments revealed that a dozen divergent long noncoding RNAs (lncRNAs) positively regulate the transcription of genes in cis. Here, to understand the regulatory mechanism of divergent lncRNAs, we proposed a computational model IRDL (Identify the Regulatory Divergent LncRNAs) to associate divergent lncRNAs with target genes. IRDL took advantage of the cross-tissue paired expression and chromatin accessibility data in ENCODE and a dozen experimentally validated divergent lncRNA target genes. IRDL integrated sequence similarity, co-expression and co-accessibility features, battled the scarcity of gold standard datasets with an increasingly learning framework and identified 446 and 977 divergent lncRNA-gene regulatory associations for mouse and human, respectively. We found that the identified divergent lncRNAs and target genes correlated well in expression and chromatin accessibility. The functional and pathway enrichment analysis suggests that divergent lncRNAs are strongly associated with developmental regulatory transcription factors. The predicted loop structure validation and canonical database search indicate a scaffold regulatory model for divergent lncRNAs. Furthermore, we computationally revealed the tissue/cell-specific regulatory associations considering the specificity of lncRNA. In conclusion, IRDL provides a way to understand the regulatory mechanism of divergent lncRNAs and hints at hundreds of tissue/cell-specific regulatory associations worthy for further biological validation.

Determination of the geographical distribution and life-form spectra of alien species with different invasive abilities are essential to understand the process of invasion and to develop measures to manage alien species. Based on six classifications of Chinese alien species, environmental and social data, we determined species density, life-form spectrum of alien species, and the relationship between species density of alien species and climatic or social factors. The species density of alien species increased from the northwest to the southeast regions of China for all the six ranks. The boundary line between low and high species density of alien species was consistent with the dividing line of population density (the "Hu Line"). Mean annual precipitation was the most important factor for species density in malignant invaders, serious invaders, local invaders, and species requiring further observation (Ranks I, II, III, and V, respectively). Gross domestic product per square kilometer and annual minimum temperature were the most important factors in mild invaders and cultivated aliens (Ranks IV and VI, respectively). Annual and biennial herbs made up 52.9% to 71.2% of total species in Ranks I to IV; shrubs and trees 3.7% to 14.7%. The annual and biennial herbs were 35.5% and 32.6%, and the shrubs and trees were 25.3% and 31.6% in Ranks IV and VI. Results implied that precipitation was the most important factor on species density for the invasive alien species. However, social factors and temperature were the most important factors for the non-invasive alien species. The invasive alien species had a high proportion of annual and biennial herbs and non-invasive alien had a high proportion of shrubs and trees. It is important to understand the geographical distribution and life-form spectra of various invasive alien species for alien species controls.

Over‐grazing by livestock in semiarid ecosystems is one of the main causes of desertification. Although over‐grazing contributes to global environmental challenge, only a few studies have investigated grazing impacts on the composition of species and functional groups of seedling bank. In this study, we determined whether the composition of seedling species and functional groups, as well as the correlations between the seedlings of sparse‐elm (Ulmus pumila var. sabulosa or U. pumila) and other species changed under three grazing intensities in the degraded sparse‐elm grassland in the Horqin Sandy Land, China. Species composition and abundance of established seedlings were surveyed and the relationships between seedlings of U. pumila and other species were analyzed. The results showed that plant communities under moderate grazing were more stable than the other two grazing intensities due to higher seedling density, higher species richness, and higher number of perennial herbs. Seedlings of U. pumila could even prevent noxious seedlings growth under moderate grazing. We concluded that moderate grazing could benefit the recovery of this sparse‐elm grassland in the Horqin Sandy Land.

// Wenshuai Yu 1 , Shengjie Zhao 1, 2 , Yongcui Wang 3 , Brian Nlong Zhao 4 , Weiling Zhao 5 and Xiaobo Zhou 6, 7, 8 1 Key Laboratory of Embedded System and Service Computing, College of Electronics and Information Engineering, The Ministry of Education, Tongji University, Shanghai, China 2 College of Software Engineering, Tongji University, Shanghai, China 3 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China 4 Shanghai High School International Division, Shanghai, China 5 Department of Radiology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC, USA 6 College of Electronics and Information Engineering, Tongji University, Shanghai, China 7 Center for Big Data Sciences and Network Security, Tongji University, Shanghai, China 8 Center for Bioinformatics and System Biology, Wake Forest University School of Medicine, Winston Salem, NC, USA Correspondence to: Shengjie Zhao, email: shengjiezhao@tongji.edu.cn Xiaobo Zhou, email: zhouxb2015@163.com Keywords: co-expression network; prognosis; HO-GSVD; gene module; cancer Abbreviations: DAVID: the Database for Annotation, Visualization, and Integrated Discovery; TCGA: The Cancer Genome Atlas; KEGG: Kyoto Encyclopedia of Genes and Genomes Received: July 12, 2017 Accepted: November 15, 2017 Published: December 04, 2017 ABSTRACT The rapid accumulation of cancer-related data owing to high-throughput technologies has provided unprecedented choices to understand the progression of cancer and discover functional networks in multiple cancers. Establishment of co-expression networks will help us to discover the systemic properties of carcinogenesis features and regulatory mechanisms of multiple cancers. Here, we proposed a computational workflow to identify differentially co-expressed gene modules across 8 cancer types by using combined gene differential expression analysis methods and a higher-order generalized singular value decomposition. Four co-expression modules were identified; and oncogenes and tumor suppressors were significantly enriched in these modules. Functional enrichment analysis demonstrated the significantly enriched pathways in these modules, including ECM-receptor interaction, focal adhesion and PI3K-Akt signaling pathway. The top-ranked miRNAs (mir-199, mir-29, mir-200) and transcription factors ( FOXO4 , E2A , NFAT , and MAZ ) were identified, which play an important role in deregulating cellular energetics; and regulating angiogenesis and cancer immune system. The clinical significance of the co-expressed gene clusters was assessed by evaluating their predictability of cancer patients’ survival. The predictive power of different clusters and subclusters was demonstrated. Our results will be valuable in cancer-related gene function annotation and for the evaluation of cancer patients’ prognosis.

In this study, broilers were fed with heavy-metal-containing diets (Zn, Cu, Pb, Cr, As, Hg) at three rates (T1: 5 kg premix/ton feed, T2: 10 kg premix/ton feed and T3: 15 kg premix/ton feed) and Doxycycline (DOX) and Gatifloxacin (GAT) at low or high doses (T4: 31.2 mg DOX/bird/day and 78 mg GAT/bird/day, T5: 15.6 mg DOX/bird/day and 48 mg GAT/bird/day) to assess the accumulation of various heavy metals and the fate of two antibiotics in broiler manure after 35 days of aerobic composting. The results indicated that the two antibiotics changed quite differently during aerobic composting. About 14.96–15.84% of Doxycycline still remained at the end of composting, while Gatifloxacin was almost completely removed within 10 days of composting. The half-lives of Doxycycline were 13.75 and 15.86 days, while the half-lives of Gatifloxacin were only 1.32 and 1.38 days. Based on the Redundancy analysis (RDA), the concentration of antibiotics was significantly influenced by physico-chemical properties (mainly temperature and pH) throughout the composting process. Throughout the composting process, all heavy metal elements remained concentrated in organic fertilizer. In this study the Cr content reached 160.16 mg/kg, 223.98 mg/kg and 248.02 mg/kg with increasing premix feed rates, similar to Zn, which reached 258.2 mg/kg, 312.21 mg/kg and 333.68 mg/kg. Zn and Cr concentrations well exceeded the United States and the European soil requirements. This experiment showed that antibiotic residues and the accumulation of heavy metals may lead to soil contamination and pose a risk to the soil ecosystem.

Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. With the advantages of epigenetic features, DeepCode significantly improves the performance in predicting the splicing patterns and their changes during hESC differentiation. Meanwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding AS patterns, highlighting the necessity of including the epigenetic properties when assembling a more comprehensive splicing code. Moreover, DeepCode allows the robust predictions across cell lineages and datasets. Especially, we identified a putative H3K36me3-regulated AS event leading to a nonsense-mediated mRNA decay of BARD1. Reduced BARD1 expression results in the attenuation of ATM/ATR signalling activities and further the hESC differentiation. These results suggest a novel candidate mechanism linking histone modifications to hESC fate decision. In addition, when trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields.

Soil water is one of the most important environmental factors that influences seed germination, seedling establishment, and plant distribution. There is a close relationship between the distribution of pioneer plants and soil water content in sandy regions. By observing the distribution patterns of pioneer plants and soil water, we determined the relationship between soil water and the distribution patterns of pioneer plants during the process of sand dune invasion in the Horqin Sandy Land, northeast China. The results showed Artemisia wudanica, Agriophyllum squarrosum, Corispermum candelabrum, and Setaria viridis serve as pioneer plants on sand dunes, and the first three of these species accounted for 99.9% of all plant individuals. The majority of these pioneer plants germinated after the first and second effective precipitation events (quantity of rainfall >5 mm) under suitable temperature conditions. Pioneer plants showed non-continuous, patchy, and mosaic distribution patterns on sand dunes. Significant relationships were found between the pioneer plant distribution pattern and soil water content. The distribution pattern of C. candelabrum was significantly influenced by soil water content at depths of 0–5 cm, and A. squarrosum was significantly influenced by soil water content at depths of 0–40 cm. This study contributes to understanding of the distribution patterns of pioneer plants and their adaptation to soil moisture in sand dune environments.

Determination of dispersal strategies of alien species and its relationship with social and climatic factors are essential to understand the mechanisms of species invasion and adaption. Based on morphological trait, dispersal mode, and dispersal agent of diaspore of 562 alien species across China, we determined: (i) the proportions of five dispersal strategies (i.e., autochory, anemochory, hydrochory, zoochory, and anthropochory), (ii) the relationships between the dispersal strategies and socio-climatic factors in 34 administrative regions across China, and (iii) the correlations between different dispersal strategies. Anthropochory, zoochory, and anemochory account for nearly 90.0% of all the dispersal strategies of alien species. Mean frost days (MFD), mean annual humidity (MAH), and gross domestic product (GDP) were the main climatic and social factors that were correlated to different dispersal strategies. Zoochory was positively related to MFD, but negatively related to the autochory and anthropochory. MAH negatively influenced the anemochory, while GDP positively influenced the hydrochory. We classified the six dispersal strategies into two groups based on the correlations among dispersal strategies, group I included autochory and anthropochory, and group II included anemochory, hydrochory, and zoochory. Within a group, dispersal strategies were positively correlated, while between groups, dispersal strategies were negatively correlated. Positive correlation between different strategies might be co-owned while negative correlation between different strategies might not be co-owned by one alien species. Understanding the characteristics of the dispersal strategies of alien species is important for policy makers when controlling the dispersal of malignant invasive alien species, predicting the distribution, and decreasing or cutting off the dispersal pathways of invasive alien species.

Livestock grazing is a crucial cause of vegetation degradation and desertification in sandy lands. The sparse-elm grassland of Horqin Sandy Land, China has suffered severe degradation of biodiversity and ecosystem services. Management to exclude grazing is often necessary for ecological restoration, especially in arid and semi-arid regions. We report effects on vegetation and soils in a 10-year experiment to exclude livestock, completely or seasonally, in comparison with a continuously grazed area in Horqin. Complete exclusion of grazing and restriction of grazing to summer both led to significantly increased plant cover and density relative to the grazed control. Species richness increased, reflected in higher Shannon-Wiener indices; only complete exclusion increased the Simpson diversity index, whereas Pielou evenness was significantly lowest under seasonal grazing. Exclosure treatments were also associated with improved soil texture, and increased water retention, available nitrogen, total nitrogen, total carbon and total phosphorus. Soil pH and C/N ratio were highest under the seasonal grazing regime. The results indicated that exclosure management indeed improved biodiversity and ecosystem services in an erosion-prone region. Although total exclosure was most effective in restoration of degraded sparse-elm grassland, seasonal grazing management was highly beneficial and represented a good compromise with resource utilization and economic development.

As a native tree species, Ulmus pumila var. sabulosa (sandy elm) is widely distributed in the Horqin Sandy Land, China. However, seedlings of this species have to withstand various depths of sand burial after emergence because of increasing soil degradation, which is mainly caused by overgrazing, climate change, and wind erosion. An experiment was conducted to evaluate the changes in its survivorship, morphological traits, and biomass allocation when seedlings were buried at different burial depths: unburied controls and seedlings buried vertically up to 33, 67, 100, or 133 % of their initial mean seedling height. The results showed that partial sand burial treatments (i.e., less than 67 % burial) did not reduce seedling survivorship, which still reached 100 %. However, seedling mortality increased when sand burial was equal to or greater than 100 %. In comparison with the control treatment, seedling height and stem diameter increased at least by 6 and 14 % with partial burial, respectively. In the meantime, seedling taproot length, total biomass, and relative mass growth rates were at least enhanced by 10, 15.6, and 27.6 %, respectively, with the partial sand burial treatment. Furthermore, sand burial decreased total leaf area and changed biomass allocation in seedlings, partitioning more biomass to aboveground organs (e.g., leaves) and less to belowground parts (roots). Complete sand burial after seedling emergence inhibited its re-emergence and growth, even leading to death. Our findings indicated that seedlings of sandy elm showed some resistance to partial sand burial and were adapted to sandy environments from an evolutionary perspective. The negative effect of excessive sand burial after seedling emergence might help in understanding failures in recruitments of sparse elm in the study region.

The processes whereby vegetation characteristics, soil properties, and disturbance events interact to determine the characteristics of plant bud bank are of considerable significance with respect to population recruitment and vegetation restoration in sand dune ecosystems. However, gaining an understanding of these processes represents a major challenge. In this study, we examined variations in the bud bank demographics of dune vegetation and the role of vegetation, soil properties, and disturbance in determining the size and composition of bud bank during the stabilization processes from active to fixed sand dunes. We investigated bud bank size and composition, vegetation characteristics, and soil properties in the interdune lowlands of active and fixed sand dunes in Inner Mongolia, China. We found that sand dune fixation increased bud bank density. Soil properties were determined to be the primary factors affecting bud bank in the interdune lowlands of an active dune, whereas vegetation density was the most important factor affecting bud bank in the interdune lowlands of a fixed sand dune. Among the different bud types, we found that rhizome and root-sprouting buds were dependent to a greater extent on soil moisture content in the interdune lowlands of active dunes, while in the interdune lowlands of fixed dunes, rhizome and root-sprouting buds had a greater dependence on soil total carbon. In contrast, tiller buds tended to be more related to vegetation density, whereas no evidence showed there was a prominent influence of any factor on collar buds. The mechanisms (vegetation, stress, and disturbance) affecting bud bank demographics are modified by sand dune fixation. The responses of different bud types to environmental factors differ in the interdune lowlands of both active and fixed sand dunes.

Soil salinity is a major abiotic stress affecting crop growth and productivity. Ricinus communis has good salt tolerance and is also an important oilseed crop throughout the world. Early seedling stage (such as cotyledon expansion stage) is the most vulnerable period for plant under stresses. However, little information exist concerning the physiological and molecular mechanisms of Ricinus communis seedlings and the role play by cotyledons and true leaf under salt stress. In the present study, biomass, photosynthesis, chlorophyll fluorescence, inorganic ions and organic solutes contents were measured, and two dimensional gel electrophoresis-based proteomic technology was employed to identify the differentially abundant proteins in the salt-treated Ricinus communis cotyledons and true leaves. The results showed that salt stress reduced growth and photosynthesis in the seedlings. With increasing salinity, the Na+ content increased and K+ content decreased in both cotyledons and leaves, but the true leaves had lower Na+ and higher K+ contents. Soluble sugars and proline are the primary organic solutes to cope with osmotic stress. In addition, proteomic analysis revealed 30 and 42 differentially accumulated protein spots in castor cotyledon and true leaf under salt stress, respectively. Most of the identified proteins were involved in carbohydrate and energy metabolism, photosynthesis, genetic information process, reactive oxygen species metabolism, amino acid metabolism and cell structure. The physiological and proteomic results highlighted that cotyledons accumulated a large number of Na+ and provided more energy to help true leaves cope with salt stress. The true leaves saved carbon structures to synthesize osmotic substances, and the enhancement of chlorophyll synthesis and electron transfer in true leaves could also maintain photosynthesis under salt stress. These findings provide new insights into different physiological mechanisms in cotyledon and true leaf of Ricinus communis response to salt stress during early seedling stage.

Artemisia wudanica is an endemic, perennial, pioneering psammophyte species in the sand dune ecosystems of western Horqin Sand Land in northern China. However, no studies have addressed how sexual and asexual reproduction modes of A. wudanica perform at the transitional zones between active dune inter-dune lowlands and active dunes. In early spring, quadrats were randomly set up in the study area to monitor surviving seedling and/or ramet density and frequency coming from sexual/asexual reproduction of A. wudanica. Iron sticks were inserted near each quadrat to determine wind erosion intensity (WE). Additionally, soil samples were collected nearby each quadrat to test for soil moisture (SM), organic matter (OM) and pH. Surviving seedlings of A. wudanica showed an inverse response in comparison with ramets to SM, OM and WE. Soil moisture showed the most positive effect, and WE the negative effect, on surviving, sexual reproduction seedlings. Contrarily, WE had the most positive effect, and SM the negative effect, on asexual reproduction ramets. This suggests that increases in SM and decreases in WE should benefit recruitment of A. wudanica seedlings. On the contrary, ramets coming from asexual reproduction showed a different response to environmental factors in transition zone habitats. While SM was not a key constraint for the survival of seedlings, they showed a better, positive response to wind erosion environments. Overall, various study environmental parameters could be improved to foster A. wudanica invasion and settlement in the plant community through different reproductive modes, thereby promoting vegetation restoration and rehabilitation.

Long noncoding RNA (lncRNA) transcripts have emerging impacts in cancer studies, which suggests their potential as novel therapeutic agents. However, the molecular mechanism behind their treatment effects is still unclear. Here, we designed a computational model to Associate LncRNAs with Anti-Cancer Drugs (ALACD) based on a bilevel optimization model, which optimized the gene signature overlap in the upper level and imputed the missing lncRNA-gene association in the lower level. ALACD predicts genes coexpressed with lncRNAs mean while matching drug’s gene signatures. This model allows us to borrow the target gene information of small molecules to understand the mechanisms of action of lncRNAs and their roles in cancer. The ALACD model was systematically applied to the 10 cancer types in The Cancer Genome Atlas (TCGA) that had matched lncRNA and mRNA expression data. Cancer type-specific lncRNAs and associated drugs were identified. These lncRNAs show significantly different expression levels in cancer patients. Follow-up functional and molecular pathway analysis suggest the gene signatures bridging drugs and lncRNAs are closely related to cancer development. Importantly, patient survival information and evidence from the literature suggest that the lncRNAs and drug-lncRNA associations identified by the ALACD model can provide an alternative choice for cancer targeting treatment and potential cancer pognostic biomarkers. The ALACD model is freely available at https://github.com/wangyc82/ALACD-v1., Author summary LncRNAs are RNA transcripts that are longer than 200 bp and do not encode proteins. Recent experimental studies have indicated the crucial role of lncRNAs in cancer. We proposed a computational model, ALACD, to understand a lncRNA’s molecular mechanism by associating it with a drug through the drug’s target genes. ALACD reveals lncRNAs, the associated anti-cancer drug, and the induced gene signatures that are involved in the regulation of cancer. Furthermore, these cancer-related lncRNAs are differentially expressed in cancer patients and closely associated with patient survival.

Degradation of semi-arid ecosystems leading to desertification presents a global environmental challenge. However, few studies have investigated seed bank and above-ground species composition in degraded semi-arid dune systems, particularly in relation to their potential to contribute to stabilisation and revegetation. We determined whether soil seed bank and above-ground species composition differed along a chronosequence in the inter-dune lowlands of an active dune field in Inner Mongolia, China. Soil cores were collected in early April 2011 and soil seed bank composition determined using a combination of the seedling emergence and seed extraction methods. Established vegetation, including species composition and abundance, was also surveyed. Relative importance values for all above-ground species and similarities in species composition of vegetation and soil seed bank along the chronosequence were analysed. A clear successional trend was shown for established vegetation along the first three stages identified, followed by a final stage reverting to more mobile substrate due to disturbance by dune movement. This trend was not reflected in the seed bank. Plant and seed bank density increased over time, however, species composition of the seed bank reflected earlier stages rather than the corresponding established vegetation. There was a relationship between established vegetation and the soil seed bank at the earliest stage, driven mainly by the persistence of seeds of the pioneer species Agriophyllum squarrosum and Corispermum candelabrum . A relatively close relationship was also found at the final stage, where frequent disturbance occurred as a result of increasing sand burial, caused by constant directional sand dune movement. While a clear relationship between the seed bank and associated vegetation was not found along the whole chronosequence, the seed bank displayed potential for restoration of pioneer psammophytes and annual herb species, suggesting that it would contribute to regeneration, as well as support latter-stage annuals and several rare and endemic species.

Effective methods of restoring lands stressed by desertification and sand movement are needed. The stabilization of sand dunes with shrub planting with the help of straw checkerboard (PCS) and grazing exclusion was evaluated in degraded sandy grasslands in Horqin sandy land, China. The characteristics of vegetation and soil chemical properties were studied in PSC sites and grazing exclusion sites 0, 6, and 12 years after implementation. Natural community sites were also examined in 2012. Results showed that the implementation of PSC and grazing exclusion not only significantly ( P

The structure and dynamics of plant populations and communities are largely influenced by seed dispersal. How the wind dispersal trajectory of seeds shifts with differences in seed morphology remains unknown. We used a wind tunnel and video camera to track the dispersal trajectory of seven species of Calligonum whose seeds have different kinds of appendages and other morphological traits, using variable wind speeds and release heights to determine the relationship between seed morphological traits and wind dispersal trajectory. Concave-, straight-line-, horizontal-projectile- and projectile-shaped trajectories were found. Dispersal trajectories such as the horizontal projectile (HP) and projectile (P) tended to have a long dispersal distance. Straight line (SL) and concave curve (CC) trajectories tended to have a short dispersal distance. Seeds with bristles and large mass tended to have SL and CC trajectories, those with wings or balloon and small mass tended to have HP and P trajectories. Wind speed tended to have a stronger influence on the dispersal trajectory of light and low-wing-loading seeds, and release height tended to have a stronger influence on the dispersal trajectory of heavy and high-wing-loading seeds. Thus, seed wind dispersal trajectory is not only determined by seed morphological characteristics but also by environmental factors such as wind speed and release height.