Search

The fate of hydrophilic, hydrophobic, and insoluble fractions extracted from 13C-labelled maize straw and their use for the formation of bacterial and fungal-derived amino sugars (AS) were monitored during a 40-day incubation of upland and paddy soils. The highest sequestration of C in the AS pool was present in the hydrophilic fraction in both soils (1.1–1.4% of input C). Bacterial community in upland soil utilized the hydrophilic fraction the most for the formation of AS, whereas fungi used the hydrophobic fraction, suggesting that bacteria and fungi have different substrate preference. In contrast, fungi used similar portions of all fractions for AS formation in the paddy soil, which could be a substrate utilization strategy under anoxic conditions. Sequestration of microbial-derived C, formed from the added fractions, was lower in paddy than in upland soils (0.7–1.1% vs. 1.2–1.4%), while total AS content showed the opposite trend (493–509 mg kg−1 in paddy vs. 387–405 mg kg−1 in upland soils). This was attributed to the 1.5 times lower microbial activity in paddy than in upland soils based on the relative incorporation of 13C into total MBC. Thus, sequestration of microbial-derived C from various organic C sources is closely related to substrate quality, but soil management and its properties modulate the microbial utilization of substances with various hydrophobicity.

Woody agricultural wastes have created enormous pressure on the environment. In this study, mulberry and cinnamon woodchips were reclaimed and prepared for biochars through pyrolysis technique at four different temperatures. Physicochemical properties showed that mulberry biochar exhibited higher pH, CEC and ash content than cinnamon biochar at each temperature. All biochars were utilized as adsorbents to remove cadmium (Cd) and atrazine (AT) from water. The adsorption isotherms were found to be well fitted by Freundlich and Langmuir models. The maximum adsorption capacities were 5306.41 mg/kg for Cd adsorption and 538.89 mg/kg for AT adsorption, respectively. Moreover, the principal component analysis, XPS and FTIR analysis proved that precipitation with phosphate in biochars acted as the key property that governed the adsorption capacity of Cd, whereas the porosity demonstrated a significant impact on the adsorption capacity of AT. Partial least squares (PLS) model was considered to be more favorable for predicting AT adsorption than Cd adsorption. The results of the present paper will be helpful for selecting most effective biochars from locally available woody agricultural byproducts that are optimized for contaminants removal from environment.

The current study investigated the effect of biochars derived from cinnamomum woodchip, garden waste and mulberry woodchip on soil phytoavailable lead (Pb), cadmium (Cd) pools, and their uptake by Chinese cabbage (Brassica chinensis L.). The biochars were produced at 450 °C of pyrolysis temperature. The contaminated soils were collected from Yunfu (classified as Udept), Jiyuan (Ustalf) and Shaoguan (Udult) cities in China at the depth of 0–20 cm and amended with biochars at the rate of 3% w/w. After mixing the soil with biochar for 14 days, the Chinese cabbage was planted in the amended soils. Then, it was harvested on the 48th day after sowing period. In Udult soil, Chinese cabbage died 18 days after sowing period in control and soils amended with cinnamomum and mulberry biochars. Although only plants grown with the garden waste biochar treatment survived in Udult soil, amendment of garden waste or mulberry biochars at 3% w/w (450 °C) to Udult soil significantly increased (4.95–6.25) soil pH compared to other biochar treatments. In Udept and Ustalf soils, the application of garden waste and mulberry biochars significantly improved plant biomass compared to control, albeit it was dependent on both biochar and soil properties. Garden waste biochar significantly decreased soil Cd phytoavailable concentration by 26% in the Udult soil, while a decrease of soil Cd phytoavailable concentration by 16% and 9% was observed in Ustalf and Udept soils, respectively. The available phosphorus in biochar and soil pH were important factors controlling toxic metal phytouptake by the plant. Thus, the amendment of soil with biochar at 3% can effectively reduce the mobility of Cd and Pb in soil and plant uptake. However, biochar and soil properties should be well-known before being used for soil toxic metal immobilization.

Depending on the geochemical forms, heavy metal (HM) accumulation is one of the most serious environmental problems in the world and poses negative impacts on soil, plants, animals, and humans. Although the use of biochar to remediate contaminated soils is well known, the huge quantities of waste used and its recycling technique to sustain soil in addition to its use conditions are determinant factors for its characteristics and uses. A pot experiment was conducted in a completely randomized block design to evaluate metal forms and their availability under the application of garden waste biochar (GB) pyrolyzed at different temperatures, and a sequential extraction procedure was designed to fractionate Pb, Cd, Zn, and Cu of the contaminated soil. The results show that the TCLP-extractable Pb, Cd, Zn, and Cu were significantly decreased depending on the biochar addition rate, pyrolysis temperature, and tested metal. The acid extractable fraction was significantly decreased by 51.54, 26.42, 16.01, and 74.13% for Pb, Cd, Zn, and Cu, respectively, at the highest application level of GB400 compared to untreated pots. On the other hand, the organic matter bound fraction increased by 76.10, 54.69, 23.72, and 43.87% for the corresponding metals. The Fe/Mn oxide bound fraction was the predominant portion of lead (57.25–62.84%), whereas the acid fraction was major in the case of Cd (58.06–77.05%). The availability of these metals varied according to the application rate, pyrolysis temperature, and examined metals. Therefore, the GB is a nominee as a promising practice to reduce HM risks, especially pyrolyzed at 400 °C by converting the available fraction into unavailable ones.

Large-scale biochar field trials have been conducted worldwide to test for “carbon negative strategy” in the event of carbon credit and if other subsidies become enacted in the future. Once amended to the soil, biochar engages in complex organo-mineral interactions, fragmentation, transport, and other aging mechanisms exhibiting interactions with treatments including the irrigation and fertilizer application. As a result, quantitative tracing of biochar carbon relying on the routinely measured soil parameters, e.g., total/particulate organic carbon, poses a significant analytical uncertainty. This study utilized two biochar field trial sites to calibrate for the biochar carbon structure and quantity based on the infrared- and fluorescence-based chemometrics: (1) slow pyrolysis biochar pellets on kaolinitic Greenville fine sandy loam in Georgia and (2) fast pyrolysis biochar powder on Crider silt loam in Kentucky. Partial least squares-based calibration was constructed to predict the amount of solvent (toluene/methanol)-extractable fluorescence fingerprint (290/350 nm excitation and emission peak) attributed to biochar based on the comparison with the authentic standard. Near-infrared-based detection was sensitive to the C–H and C–C bands, as a function of biochar loading and the particulate organic carbon content (

Heavy metals (HMs) toxicity represents a global problem depending on the soil environment’s geochemical forms. Biochar addition safely reduces HMs mobile forms, thus, reducing their toxicity to plants. While several studies have shown that biochar could significantly stabilize HMs in contaminated soils, the study of the relationship of soil properties to potential mechanisms still needs further clarification, hence the importance of assessing a naturally contaminated soil amended, in this case with Paulownia biochar (PB) and Bamboo biochar (BB) to fractionate Pb, Cd, Zn, and Cu using short sequential fractionation plans. The relationship of soil pH and organic matter and its effect on the redistribution of these metals were estimated. The results indicated that the acid-soluble metals decreased while the fraction bound to organic matter increased compared to untreated pots. The increase in the organic matter metal-bound was mostly at the expense of the decrease in the acid extractable and Fe/Mn bound ones. The highest application of PB increased the organically bound fraction of Pb, Cd, Zn, and Cu (62, 61, 34, and 61%, respectively), while the BB increased them (61, 49, 42, and 22%, respectively) over the control. Meanwhile, Fe/Mn oxides bound represents the large portion associated with zinc and copper. Concerning soil organic matter (SOM) and soil pH, as potential tools to reduce the risk of the target metals, a significant positive correlation was observed with acid-soluble extractable metal, while a negative correlation was obtained with organic matter-bound metal. The principal component analysis (PCA) shows that the total variance represents 89.7% for the TCPL-extractable and HMs forms and their relation to pH and SOM, which confirms the positive effect of the pH and SOM under PB and BB treatments on reducing the risk of the studied metals. The mobility and bioavailability of these metals and their geochemical forms widely varied according to pH, soil organic matter, biochar types, and application rates. As an environmentally friendly and economical material, biochar emphasizes its importance as a tool that makes the soil more suitable for safe cultivation in the short term and its long-term sustainability. This study proves that it reduces the mobility of HMs, their environmental risks and contributes to food safety. It also confirms that performing more controlled experiments, such as a pot, is a disciplined and effective way to assess the suitability of different types of biochar as soil modifications to restore HMs contaminated soil via controlling the mobilization of these minerals.

Metal-contaminated soils are considered a global concern due to their adverse effects on ecosystem vitality. This study was conducted to assess the efficiency of garden waste biochar (GB), as a modern remediation tool of soils contaminated with heavy metals (HMs), compared with the other Paulownia biochar (PB) and bamboo biochar (BB), on the growth of Brassica juncea (L.). The experiments and analyses were carried out at the Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences (Guangzhou, China), during the year 2018. The studied contaminated soil sample was amended with 0, 2%, 4%, and 6% (w/w) of PB, BB, GB400, and GB600 biochar. The experiment was designed in a completely randomized block design with 3 replications for each treatment. Garden waste biochar significantly duplicated the soil organic matter and EC 1.43−2.21 and 1.33−1.51 times, respectively, enhanced soil pH, and improved plant growth. It was more efficient to improve soil properties than PB and BB. DTPA-extractable metals showed the highest reduction at 6% of GB400, which was 29.56, 46.04, and 59.98% for Pb, Cd, and Cu, respectively, while it was 48.29% for Zn at GB600 over the control. Moreover, GB treatments increased the nitrogen (N) and phosphorus (P) contents of the plant shoots. Besides, HM contents of soil and plant tissues were significantly reduced after biochar applications and the highest reduction was recorded using 6% of GB. The results obviously pointed out that the metal transfer coefficient (TC) of shoots was decreased compared with the control after biochar applications, and GB showed the optimum response in this regard. The huge amounts of garden waste, after transforming them to biochar (GB) which has been considered more effective in safe crop production, can be used to reduce the availability of toxic metals in the soil and keep them under safe limits, especially with large-scale vegetable crops in China. It will clean the environment and improve resource sustainability. Therefore, GB is recommended to be used in soil HM remediation on a large scale in polluted areas.

Background Intrahepatic cholestasis of pregnancy (ICP) is a liver disorder that specifically occurs in pregnancy. Elevated levels of liver transaminases aspartate aminotransferase, alanine aminotransferase and serum bilirubin levels are common biochemical characteristics in ICP. The disorder is associated with an increased risk of premature delivery and stillbirth. The characterization of the potential microbiota in ICP could go a long way in the prevention and treatment of this pregnancy disease. Methods A total of 58 patients were recruited for our study: 27 ICP patients and 31 healthy pregnant subjects with no ICP. The V3 and V4 regions of the 16S rDNA collected from fecal samples of both diseased and control groups were amplified. 16S rRNA gene amplicon sequencing was then performed on gut microbiota. Sequencing data were analyzed and the correlation between components of microbiota and patient ICP status was found. Related metabolic pathways, relative abundance and significantly different operational taxonomic units (OTUs) between ICP and controls were also identified. Results Elevated levels of total bile acid, ALT, AST, Dbil and Tbil were recorded or observed in ICP subjects as compared to the control. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was no significant clustering in Bray–Curtis distance matrices. Our results showed that there was a correlation between specific OTUs and measured clinical parameters of pregnant women. Comparison at the different taxonomy levels revealed high levels of abundance of Blautia and Citrobacter in ICP patients. At the family level, Enterobacteriaceae and Leuconostocaceae were higher in ICP patients. 638 KEGG Orthologs and 138 pathways significantly differed in the two groups. PLS-DA model with VIP plots indicated a total of eight genera and seven species were key taxa in ICP and control groups. Conclusions Our research indicated that although there was no significant clustering by PCoA analysis, patients with ICP have increased rare bacteria at different phylogenetic levels. Our results also illustrated that all 638 KEGG Orthologs and 136 in 138 KEGG pathways were less abundant in ICP patients compared to the controls.

Background: Intrahepatic cholestasis of pregnancy (ICP) is a liver disorder that specifically occurs in pregnancy. Elevated levels of liver transaminases aspartate aminotransferase (AST), alanine aminotransferase (ALT) and serum bilirubin levels are common biochemical characteristics in ICP. The disorder is associated with an increased risk of premature delivery and stillbirth. We hypothesized that there was a link between gut microbiota and the progression of ICP and characterization of the potential microbiota could go a long way in the prevention and treatment of ICP.Methods: A total of 58 patients were recruited for our study; 27 ICP patients and 31 healthy pregnant subjects with no ICP. The V3 and V4 regions of the 16S rRNA region of DNA collected from fecal samples of both diseased and control groups were amplified. 16S rRNA gene amplicon sequencing was then performed on gut microbiota from fecal samples obtained. Sequencing data were analyzed and the correlation between components of microbiota and patient ICP status was found. Related metabolic pathways, relative abundance and significantly different OTUs (Operational Taxonomic Units) between ICP and controls were also identified.Results: Elevated levels of total bile acid, ALT, AST, Dbil and Tbil were recorded or observed in ICP subjects as compared to the control. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was no significant clustering in Bray-Curtis distance matrices. Our results showed that there was a correlation between specific OTUs and measured clinical parameters of pregnant women. Comparison at the different taxonomy levels revealed high levels of abundance of Blautia and Citrobacter in ICP patients. At the family level, Enterobacteriaceae and Leuconostocaceae were higher in ICP patients. 638 KEGG Orthologs and 138 pathways significantly differed in the two groups; ICP patients and control group and PLS-DA model with VIP plots indicated a total of eight genera and seven species were key taxa in ICP and control groups.Conclusions: Our research indicated that patients with ICP have altered phylogenetic gut microbiota profiles compared to controls, and illustrated that there are significant differences in KEGG pathways.

Cell migration involves front-to-rear asymmetric focal adhesion (FA) dynamics, which facilitates trailing edge detachment and directional persistence. Here, we show that kindlin-2 is crucial for FA sliding and disassembly in migrating cells. Loss of kindlin-2 markedly reduced FA number and selectively impaired rear FA sliding and disassembly, resulting in defective rear retraction and reduced directional persistence during cell migration. Kindlin-2-deficient cells failed to develop serum-induced actomyosin-dependent tension at FAs. At the molecular level, kindlin-2 directly interacted with myosin light chain kinase (MYLK, hereafter referred to as MLCK), which was enhanced in response to serum stimulation. Serum deprivation inhibited rear FA disassembly, which was released in response to serum stimulation. Overexpression of the MLCK-binding kindlin-2 F0F1 fragment (amino acid residues 1-167), which inhibits the interaction of endogenous kindlin-2 with MLCK, phenocopied kindlin-2 deficiency-induced migration defects. Inhibition of MLCK, like loss of kindlin-2, also impaired trailing-edge detachment, rear FA disassembly and directional persistence. These results suggest a role of kindlin-2 in promoting actomyosin contractility at FAs, leading to increased rear FA sliding and disassembly, and directional persistence during cell migration.

Alteration of podocyte behavior is critically involved in the development and progression of many forms of human glomerular diseases. The molecular mechanisms that control podocyte behavior, however, are not well understood. Here, we investigated the role of Kindlin-2, a component of cell-matrix adhesions, in podocyte behavior in vivo. Ablation of Kindlin-2 in podocytes resulted in alteration of actin cytoskeletal organization, reduction of the levels of slit diaphragm proteins, effacement of podocyte foot processes, and ultimately massive proteinuria and death due to kidney failure. Through proteomic analyses and in vitro coimmunoprecipitation experiments, we identified Rho GDP-dissociation inhibitor α (RhoGDIα) as a Kindlin-2–associated protein. Loss of Kindlin-2 in podocytes significantly reduced the expression of RhoGDIα and resulted in the dissociation of Rac1 from RhoGDIα, leading to Rac1 hyperactivation and increased motility of podocytes. Inhibition of Rac1 activation effectively suppressed podocyte motility and alleviated the podocyte defects and proteinuria induced by the loss of Kindlin-2 in vivo. Our results identify a novel Kindlin-2–RhoGDIα–Rac1 signaling axis that is critical for regulation of podocyte structure and function in vivo and provide evidence that it may serve as a useful target for therapeutic control of podocyte injury and associated glomerular diseases.

Cell-free DNA (cfDNA) has been widely used in prenatal test and cancer diagnosis nowadays. The cost- and time-effective isolation kits are needed especially in large-scale clinical application. Here, we compared three domestic kits: VAHTS Serum/Plasma Circulating DNA kit (VZ), MagPure Gel Pure DNA mini kit (MG) and Serum/Plasma Circulating DNA Kit (TG), together with QIAamp Circulating Nucleic Acid Kit (QC) and QIAamp DNA Blood Mini Kit (QD) in cfDNA isolation. cfDNA was isolated from the pooled samples with spike-in fragments, qPCR was conducted to quantify the spike-in fragments recovery. The results indicated that all of the five kits could isolate cfDNA with different efficiency. The VZ kit had an efficiency as high as 90 percent, which is comparable to QC kit. The libraries were constructed using the isolated cfDNAs, quantified by Qubit and analyzed by 2100 bioanalyzer. Both showed the libraries were qualified. Finally, cffDNAs were detected by qPCR targeting SRY gene using libraries from pregnant women bearing male fetuses. All five kits could isolate cffDNAs that could be detected by qPCR. Our results provided more choices in wide-scale clinical application of cfDNA-based non-invasive genetic tests.

Cell-free RNA, including both long RNA and small RNA, has been considered important for its biological functions and potential clinical usage, but the major challenge is to effectively sequence them at the same time. Here we present PolyAdenylation Ligation Mediated-Seq (PALM-Seq), an integrated sequencing method for cell-free long and small RNA. Through terminal modification and addition of 3’ polyadenylation and 5’ adaptor, we could get mRNA, long non-coding RNA, microRNA, tRNA, piRNA and other RNAs in a single library. With target RNA depletion, all these RNAs could be sequenced with relatively low depth. Using PALM-Seq, we identified pregnant-related mRNAs, long non-coding RNAs and microRNAs in female plasma. We also applied PALM-Seq to sequence RNA from amniotic fluids, leukocytes and placentas, and could find RNA signatures associated with specific sample type. PALM-Seq provides an integrated, cost-effective and simple method to characterize the landscape of cell-free RNA, and can stimulate further progress in cell-free RNA study and usage.

Biochar continues to receive worldwide enthusiasm as means of augmenting recalcitrant organic carbon in agricultural soils. Realistic biochar amendment rate (typically less than 1 wt%) in the field scale, and subsequent loss by sizing, rain, and other transport events demand reliable methods to quantify the remaining portions of amended biochar. This study employed fluorescence excitation-emission (EEM) spectrophotometry and parallel factor analysis (PARAFAC) to specifically target pyrogenic dissolved organic carbon (DOC) released by amended biochar during the course of a field trial at Bowling Green, KY experimental site. Toluene/methanol (1:6 v/v) extracts of surface (0-15 cm) soils amended with 21.28 t ha(-1) fast pyrolysis biochar afforded PARAFAC fingerprints representing different degrees of aromaticity. Compared to the control without treatments, biochar treatment (with and without poultry manure or chemical fertilizer) increased the relative contribution of PARAFAC fingerprint attributable to labile polyaromatic DOC structures. Poultry manure or chemical fertilizer alone (without biochar) did not influence the amounts of polyaromatic DOC structures. Existence of biochar could be further validated by the changes in %DOC (relative to the total carbon), fixed C content, and UV absorbance (360 nm), whereas FTIR, %O, and sorption of model agrochemical (deisopropylatrazine) did not reflect the presence of biochar in the soil samples. Developed toluene/methanol-based EEM-PARAFAC technique will provide a sensitive, rapid, and cost-competitive method to validate the long-term carbon sequestration by the biochar soil amendment.

Xenopus tropicalis is an emerging vertebrate genetic model. A gene knock-in method has not yet been reported in this species. Here, we report that heritable targeted integration can be achieved in this diploid frog using a concurrent cleavage strategy mediated by the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (CRISPR/Cas9) system. The key point of the strategy is the addition of a Cas9/guide RNA cleavage site in the donor vector, allowing simultaneous cutting of the chromosomal target site and circular donor DNA in vivo. For the 3 distinct loci tested, all showed efficient targeted integration that was verified by both germ-line transmission and Southern blot analyses. By designing the target sites in introns, we were able to get precise editing of the tyrosinase coding sequence and green fluorescent protein expression from endogenous n-tubulin promoter and enhancers. We were unable to detect off-target effects with the T7 endonuclease I assay. Precise editing of protein coding sequences in X. tropicalis expands the utility of this diploid frog, such as for establishing models to study human inherited diseases.

The effect of interactions between soil minerals and organic matter as a function of aggregate size on butachlor sorption was quantified in natural soils with various degrees of organo-mineral aggregation. The smallest size clay microaggregates sorbed most butachlor (58% to 71%) and the fine sand fraction sorbed the least (less than 4.3%). When normalized to organic carbon, butachlor sorption to the clay microaggregates was even smaller than to the silt and sand fractions under specific soil conditions. The sum of sorption to the different fractions was, on average, above 78% greater than sorption to the bulk soils, with the greatest differences in the soils with relatively higher ratios of clay to soil organic carbon (RCO). This suggests that minerals can physically protect favorable sorption sites within soil organic matter (SOM), and inhibit butachlor sorption by influencing SOM physical conformation. Comparisons of changes in butachlor sorption coefficients (both Kd and Koc) in two different series of soils, with the same mineral components but gradients of total organic carbon (TOC) and RCO values also showed that minerals can directly contribute to soil butachlor sorption processes, which may be even more pronounced in soils with relative higher RCOs. A new adsorption model was proposed and verified to quantify the net contribution of minerals to butachlor sorption, based upon 38 different soils. This study has increased our ability to quantify the positive direct contribution of soil minerals and their negative indirect contribution through associated effects on SOM physical conformation during butachlor sorption in natural soils.

Precise control of mesenchymal stem cell (MSC) differentiation is critical for tissue development and regeneration. We show here that kindlin-2 is a key determinant of MSC fate decision. Depletion of kindlin-2 in MSCs is sufficient to induce adipogenesis and inhibit osteogenesis in vitro and in vivo. Mechanistically, kindlin-2 regulates MSC differentiation through controlling YAP1/TAZ at both the transcript and protein levels. Kindlin-2 physically associates with myosin light-chain kinase in response to mechanical cues of cell microenvironment and intracellular signaling events and promotes myosin light-chain phosphorylation. Loss of kindlin-2 inhibits RhoA activation and reduces myosin light-chain phosphorylation, stress fiber formation, and focal adhesion assembly, resulting in increased Ser127 phosphorylation, nuclear exclusion, and ubiquitin ligase atrophin-1 interacting protein 4–mediated degradation of YAP1/TAZ. Our findings reveal a novel kindlin-2 signaling axis that senses the mechanical cues of cell microenvironment and controls MSC fate decision, and they suggest a new strategy to regulate MSC differentiation, tissue repair, and regeneration.

Sorption and desorption of butachlor were simultaneously investigated on synthesized pure amorphous hydrated Fe oxides (AHOs Fe), and soils both with and without surface coating of AHOs Fe, with special interest towards how amorphous sesquioxides affect and contribute to butachlor retention in soils. The AHOs Fe was artificially synthesized pure materials. Two soils with contrasting physicochemical properties selected for study were black soil and latosol, belonging to permanent charged soil and variable charged soil, respectively. Both soils were further treated using AHOs Fe for detecting the differentiation from native soils regarding butachlor retention produced after the soils were surface-coated by AHOs Fe. A sorption experiment was conducted using a batch equilibrium technique, and desorption was carried out immediately following sorption by three sequential dilution. Hysteresis index (HI) values were calculated to investigate desorption hysteresis by developing desorption isotherms concentration dependent and time dependent, respectively. The sorption capacity for butachlor increased in the order of AHOs Fe, uncoated soils, and soils with surface coating of AHOs Fe. The sorption capacity of both soils significantly increased after surface coating by AHOs Fe (p

Construction of next-generation sequencing (NGS) libraries involves RNA manipulation, which often creates noisy, biased, and artifactual data that contribute to errors in transcriptome analysis. In this study, a total of 19 whole transcriptome termini site sequencing (WTTS-seq) and seven RNA sequencing (RNA-seq) libraries were prepared from Xenopus tropicalis adult and embryo samples to determine the most effective library preparation method to maximize transcriptomics investigation. We strongly suggest that appropriate primers/adaptors are designed to inhibit amplification detours and that PCR overamplification is minimized to maximize transcriptome coverage. Furthermore, genome annotation must be improved so that missing data can be recovered. In addition, a complete understanding of sequencing platforms is critical to limit the formation of false-positive results. Technically, the WTTS-seq method enriches both poly(A)+ RNA and complementary DNA, adds 5′- and 3′-adaptors in one step, pursues strand sequencing and mapping, and profiles both gene expression and alternative polyadenylation (APA). Although RNA-seq is cost prohibitive, tends to produce false-positive results, and fails to detect APA diversity and dynamics, its combination with WTTS-seq is necessary to validate transcriptome-wide APA.

Background The RNA guided CRISPR/Cas9 nucleases have been proven to be effective for gene disruption in various animal models including Xenopus tropicalis. The neural crest (NC) is a transient cell population during embryonic development and contributes to a large variety of tissues. Currently, loss-of-function studies on NC development in X. tropicalis are largely based on morpholino antisense oligonucleotide. It is worthwhile establishing targeted gene knockout X. tropicails line using CRISPR/Cas9 system to study NC development. Methods We utilized CRISPR/Cas9 to disrupt genes that are involved in NC formation in X. tropicalis embryos. A single sgRNA and Cas9 mRNA synthesized in vitro, were co-injected into X. tropicalis embryos at one-cell stage to induce single gene disruption. We also induced duplex mutations, large segmental deletions and inversions in X. tropicalis by injecting Cas9 and a pair of sgRNAs. The specificity of CRISPR/Cas9 was assessed in X. tropicalis embryos and the Cas9 nickase was used to reduce the off-target cleavages. Finally, we crossed the G0 mosaic frogs with targeted mutations to wild type frogs and obtained the germline transmission. Results Total 16 target sites in 15 genes were targeted by CRISPR/Cas9 and resulted in successful indel mutations at 14 loci with disruption efficiencies in a range from 9.3 to 57.8 %. Furthermore, we demonstrated the feasibility of generation of duplex mutations, large segmental deletions and inversions by using Cas9 and a pair of sgRNAs. We observed that CRISPR/Cas9 displays obvious off-target effects at some loci in X. tropicalis embryos. Such off-target cleavages was reduced by using the D10A Cas9 nickase. Finally, the Cas9 induced indel mutations were efficiently passed to G1 offspring. Conclusion Our study proved that CRISPR/Cas9 could mediate targeted gene mutation in X. tropicalis with high efficiency. This study expands the application of CRISPR/Cas9 platform in X. tropicalis and set a basis for studying NC development using genetic approach. Electronic supplementary material The online version of this article (doi:10.1186/s13578-016-0088-4) contains supplementary material, which is available to authorized users.

Additional file 1. Supplementary figures and legends.

Purpose Adsorption and desorption are important processes that influence the transport, transformation, and bioavailability of atrazine in soils. Equilibrium batch experiments were carried out to investigate the adsorption–desorption characteristics of atrazine. The objectives of this study were to (1) determine and quantify the main soil parameters governing atrazine adsorption and desorption phenomena; (2) find the correlativity between the identified soil parameters; and (3) investigate the universal desorption hysteresis traits.

Sorption of butachlor to various types of common soil components was investigated. Six pure minerals (montmorillonite [Mont], kaolinite [Kaol], Ca homoionic montmorillonite [Ca-Mont] and kaolinite [Ca-Kaol], amorphous hydrated Al and Fe oxides [AHOs-Al, AHOs-Fe]), four soil alkali-extractable pure humic acids (HAs), and the four corresponding HAs originated real unmodified and HO-treated soils were selected as the representative sorbents. Results showed that the HAs played a crucial role, and clay minerals (especially Mont) also showed an important effect in butachlor sorption. The AHOs may likely influence only in a mediator way by enhancing the availability of sorption domains of HAs. By removing 78% (on average) of the total organic carbon (TOC) from the soils with HO, the content ratio of clay to TOC (RCO) increased by an average of 367% and became >60. This change simultaneously decreased the sorption capacity of soils (40%, on average). Considering that the surface sorption domain on clay minerals may be highly exposed and more competitive after the partial removal of soil organic matter (SOM), this reaffirmed the potential contribution from clay minerals. It can thus be inferred that in the real soil where SOM and clay minerals are associated, the coating of clay minerals may have weakened the partition function of SOM or blocked some sorption domain within SOM, resulting in a decreased sorption of butachlor. Therefore, clay minerals, especially 2:1 type expanding minerals, may play a dual function vs. SOM content for the sorption of butachlor in soil.

The Hedgehog (Hh) signaling pathway regulates many developmental processes both in vertebrates and in invertebrates. However, little is known about this pathway in the cephalochordate amphioxus. In this paper, we focus on the Ptc, Smo, and Sufu homologs in amphioxus, which are the key members of the Hh signaling pathway. Their genomic structures show their comparability with homologs in vertebrates. In situ hybridization reveals that amphioxus Ptc, Smo, and Sufu have similar expression patterns in embryogenesis. They are expressed in the neural plate at early neurula stage, and then down-regulated in dorsal neural ectoderm. During development, their transcripts appear and persist in the notochord, the wall of the head cavity, the epithelium of the pharynx, and the gut. The data show that the expression patterns of these three genes are overlapping with Hh and Gli during the embryonic development in amphioxus. Moreover, injection of amphioxus Hh RNA into zebrafish-fertilized eggs can expand the expression domains of Ptc1 and Nk2.2a, the target genes of the Hh signaling pathway, which is similar to the injection of zebrafish Sonic hh a (zShha) and Sonic hh b (zShhb). Our results suggest that amphioxus may possess a conserved and functional Hh signaling pathway similar to that of vertebrates.