The rise of baobab trees in Madagascar.

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.

Neutrophil CD64 combined with PCT, CRP and WBC improves the sensitivity for the early diagnosis of neonatal sepsis.

BACKGROUND: The aim of this study was to determine whether neutrophil CD64 (nCD64) combined with procalcitonin (PCT), C-reactive protein (CRP) and white blood cell count (WBC) can increase the sensitivity and accuracy of neonatal sepsis diagnosis. METHODS: The serum levels of nCD64, CRP, PCT and WBC were detected in 60 patients with neonatal sepsis and 60 patients with non-sepsis. Sensitivity, specificity, positive and negative predictive values, receiver operating characteristic (ROC) area under the curve (AUC), and logistic regression analysis were performed to evaluate the diagnostic value of these markers on neonatal sepsis. RESULTS: Serum levels of nCD64, PCT, CRP and WBC were higher in the sepsis group than non-sepsis group (p<0.001). The sensitivities of nCD64, PCT, CRP and WBC at the recommended cut-off level for all infants were 79.5%, 68.2%, 38.6% and 52.3%, respectively. The best combination was nCD64 and PCT, which obtained sensitivity of 90.9%, largest AUC of 0.922, and a negative predictive value of 89.2%. However by using an optimal cut-off value, the sensitivities of all four biomarkers for the diagnosis of neonatal sepsis were increased to 95.5%. Except for WBC, the birth weight and gestational age had no effects on the diagnostic value of these serum biomarkers. CONCLUSIONS: nCD64 and PCT are better diagnostic biomarkers for early diagnosis of neonatal sepsis as compared to CRP. With the help of optimal cut-off value based on ROC curve and logistic regression analysis, the combination of these biomarkers could improve the sensitivity for the diagnosis of suspected late-onset neonatal sepsis based on common serum biomarkers.

Dihydro-Resveratrol Ameliorates Lung Injury in Rats with Cerulein-Induced Acute Pancreatitis.

Acute pancreatitis is an inflammatory process originated in the pancreas; however, it often leads to systemic complications that affect distant organs. Acute respiratory distress syndrome is indeed the predominant cause of death in patients with severe acute pancreatitis. In this study, we aimed to delineate the ameliorative effect of dihydro-resveratrol, a prominent analog of trans-resveratrol, against acute pancreatitis-associated lung injury and the underlying molecular actions. Acute pancreatitis was induced in rats with repetitive injections of cerulein (50 µg/kg/h) and a shot of lipopolysaccharide (7.5 mg/kg). By means of histological examination and biochemical assays, the severity of lung injury was assessed in the aspects of tissue damages, myeloperoxidase activity, and levels of pro-inflammatory cytokines. When treated with dihydro-resveratrol, pulmonary architectural distortion, hemorrhage, interstitial edema, and alveolar thickening were significantly reduced in rats with acute pancreatitis. In addition, the production of pro-inflammatory cytokines and the activity of myeloperoxidase in pulmonary tissues were notably repressed. Importantly, nuclear factor-kappaB (NF-κB) activation was attenuated. This study is the first to report the oral administration of dihydro-resveratrol ameliorated acute pancreatitis-associated lung injury via an inhibitory modulation of pro-inflammatory response, which was associated with a suppression of the NF-κB signaling pathway.

Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms.

Petroleum-based products are a primary energy source in the industry and daily life. During the exploration, processing, transport and storage of petroleum and petroleum products, water or soil pollution occurs regularly. Biodegradation of the hydrocarbon pollutants by indigenous microorganisms is one of the primary mechanisms of removal of petroleum compounds from the environment. However, the physical contact between microorganisms and hydrophobic hydrocarbons limits the biodegradation rate. This paper presents an updated review of the petroleum hydrocarbon uptake and transport across the outer membrane of microorganisms with the help of outer membrane proteins.

Factors influencing the trans-membrane transport of n-octadecane by Pseudomonas sp. DG17.

In soil bioremediation techniques, the trans-membrane transport of hydrocarbons across the cell membrane is a new and complex point of understanding the process of hydrocarbons biodegradation. In this study, the effect of different environmental factors, including substrate concentration, bacterial inoculums, pH, salinity, substrate analogues and nutrients, on the transport of [14C]n-octadecane by Pseudomonas sp. DG17 was investigated. The results showed that cellular [14C]n-octadecane levels increased along with the increase in the substrate concentration. However, the trans-membrane transport of [14C]n-octadecane was a saturable process in the case of equal amounts of inoculum (biomass). The highest concentration of accumulated [14C]n-octadecane was 0.51 µmol mg-1 ± 0.028 µmol mg-1 after incubation for 20 min. Meanwhile, the cellular n-octadecane concentration decreased along with the biomass increase, and reached a stable level. Acidic/alkaline conditions, high salinity, and supplement of substrate analogues could inhibit the transport of [14C]n-octadecane by Pseudomonas sp. DG17, whereas nitrogen or phosphorus deficiency did not influence this transport. The results suggested that trans-membrane transport of octadecane depends on both the substrate concentration and the microorganism biomass, and extreme environmental conditions could influence the biodegradation ability of microorganisms through inhibiting the transport of extracellular octadecane.

Immobilization of Pseudomonas sp. DG17 onto sodium alginate-attapulgite-calcium carbonate.

A strain of Pseudomonas sp. DG17, capable of degrading crude oil, was immobilized in sodium alginate-attapulgite-calcium carbonate for biodegradation of crude oil contaminated soil. In this work, proportion of independent variables, the laboratory immobilization parameters, the micromorphology and internal structure of the immobilized granule, as well as the crude oil biodegradation by sodium alginate-attapulgite-calcium carbonate immobilized cells and sodium alginate-attapulgite immobilized cells were studied to build the optimal immobilization carrier and granule-forming method. The results showed that the optimal concentrations of sodium alginate-attapulgite-calcium carbonate and calcium chloride were 2.5%-3.5%, 0.5%-1%, 3%-7% and 2%-4%, respectively. Meanwhile, the optimal bath temperature, embedding cell amount, reaction time and multiplication time were 50-60 °C, 2%, 18 h and 48 h, respectively. Moreover, biodegradation was enhanced by immobilized cells with a total petroleum hydrocarbon removal ranging from 33.56% ± 3.84% to 56.82% ± 3.26% after 20 days. The SEM results indicated that adding calcium carbonate was helpful to form internal honeycomb-like pores in the immobilized granules.

Study on Calculation Method of Bending Performance of Concrete Sandwich Composite Slab.

In order to explore the flexural behavior of a concrete sandwich panel under concentrated boundary conditions, based on Kirachhoff's elastic thin plate theory in this paper, the geometric deformation, physical conditions, and equilibrium relationship of a sandwich panel are deduced by constructing the layered analysis model of the sandwich panel, the basic differential equation of the flexural deformation of the concrete sandwich thin plate is obtained, and the mathematical expression of the internal force and displacement under the boundary condition of concentrated support is given. Combined with an engineering example, the proposed calculation method is verified. The results show that, in the arrangement of reliable connectors for concrete sandwich panels, the concrete wythes bear the load while the contribution of the core layer to the bending capacity of the structure can be ignored. When subjected to a laterally distributed load, the sandwich panel mainly experiences out-of-plane bending deformation, and the bending normal stress in the concrete panel layer shows a linear non-uniform distribution along the thickness direction of the panel. The bending deformation performance and bearing efficiency of a concrete sandwich slab with the change in concentrated support position have significant effects, and the load transfer efficiency can be improved by optimizing the arrangement of supports. Except for small local areas near the supports, the bending stress distribution and deformation behavior of the concrete sandwich panel can be accurately analyzed by the calculation method established in this paper.

Fluorescence protection assay: a novel homogeneous assay platform toward development of aptamer sensors for protein detection.

Development of novel aptamer sensor strategies for rapid and selective assays of protein biomarkers plays crucial roles in proteomics and clinical diagnostics. Herein, we have developed a novel aptamer sensor strategy for homogeneous detection of protein targets based on fluorescence protection assay. This strategy is based on our reasoning that interaction of aptamer with its protein target may dramatically increase steric hindrance, which protects the fluorophore, fluorescein isothiocyannate (FITC), labeled at the binding pocket from accessing and quenching by the FITC antibody. The aptamer sensor strategy is demonstrated using a model protein target of immunoglobulin E (IgE), a known biomarker associated with atopic allergic diseases. The results reveal that the aptamer sensor shows substantial (>6-fold) fluorescence enhancement in response to the protein target, thereby verifying the mechanism of fluorescence protection. Moreover, the aptamer sensor displays improved specificity to other co-existing proteins and a desirable dynamic range within the IgE concentration from 0.1 to 50 nM with a readily achieved detection limit of 0.1 nM. Because of great robustness, easy operation and scalability for parallel assays, the developed homogeneous fluorescence protection assay strategy might create a new methodology for developing aptamer sensors in sensitive, selective detection of proteins.

Chromosome-level genome assembly and resequencing of camphor tree (Cinnamomum camphora) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of Cinnamomum.

Cinnamomum species attract attentions owing to their scents, medicinal properties, and ambiguous relationship in the phylogenetic tree. Here, we report a high-quality genome assembly of Cinnamomum camphora, based on which two whole-genome duplication (WGD) events were detected in the C. camphora genome: one was shared with Magnoliales, and the other was unique to Lauraceae. Phylogenetic analyses illustrated that Lauraceae species formed a compact sister clade to the eudicots. We then performed whole-genome resequencing on 24 Cinnamomum species native to China, and the results showed that the topology of Cinnamomum species was not entirely consistent with morphological classification. The rise and molecular basis of chemodiversity in Cinnamomum were also fascinating issues. In this study, six chemotypes were classified and six main terpenoids were identified as major contributors of chemodiversity in C. camphora by the principal component analysis. Through in vitro assays and subcellular localization analyses, we identified two key terpene synthase (TPS) genes (CcTPS16 and CcTPS54), the products of which were characterized to catalyze the biosynthesis of two uppermost volatiles (i.e. 1,8-cineole and (iso)nerolidol), respectively, and meditate the generation of two chemotypes by transcriptional regulation and compartmentalization. Additionally, the pathway of medium-chain triglyceride (MCT) biosynthesis in Lauraceae was investigated for the first time. Synteny analysis suggested that the divergent synthesis of MCT and long-chain triglyceride (LCT) in Lauraceae kernels was probably controlled by specific medium-chain fatty acyl-ACP thioesterase (FatB), type-B lysophosphatidic acid acyltransferase (type-B LPAAT), and diacylglycerol acyltransferase 2b (DGAT 2b) isoforms during co-evolution with retentions or deletions in the genome.

Homogeneous label-free genotyping of single nucleotide polymorphism using ligation-mediated strand displacement amplification with DNAzyme-based chemiluminescence detection.

Genotyping of single nucleotide polymorphisms (SNPs) is a central challenge in disease diagnostics and personalized medicine. A novel label-free homogeneous SNP genotyping technique is developed on the basis of ligation-mediated strand displacement amplification (SDA) with DNAzyme-based chemiluminescence detection. Discrimination of single-base mismatches is first accomplished using DNA ligase to generate a ligation product between a discriminant probe and a common probe. The ligated product then initiates two consecutive SDA reactions to produce a great abundance of aptamer sequences against hemin, which can be probed by chemiluminscence detection. The developed strategy is demonstrated using a model SNP target of cytochrome P450 monooxygenase CYP2C19*2, a molecular marker for personalized medicines. The results reveal that the developed technique displays superb selectivity in discriminating single-base mismatches, very low detection limit as low as 0.1 fM, a wide dynamic range from 1 fM to 1 nM, and a high signal-to-background ratio of 150. Due to its label-free, homogeneous, and chemiluminescence-based detection format, this technique can be greatly robust, cost-efficient, readily automated, and scalable for parallel assays of hundreds of samples. The developed genotyping strategy might provide a robust, highly sensitive, and specific genotyping platform for genetic analysis and molecular diagnostics.

Fluorescence aptameric sensor for strand displacement amplification detection of cocaine.

A new fluorescence method based on aptamer-target interactions has been developed for cocaine detection with target-induced strand displacement. Here we describe new probes, the hairpin-probe and the single strand-probe (ss-probe), that possess two recognition sequences of cocaine aptamer. In the presence of cocaine, both probes would associate with the target to form a tripartite complex. The conformational change in the hairpin-probe causes the opening of a hairpin structure and the hybridization to primer. With polymerase and the dNTPs, the replication of the single-stranded domain of hairpin-probe triggers the process of primer extension. When the hairpin-probe is converted into a fully double-stranded form, the ss-probe and cocaine are displaced to bind another hairpin-probe and initiate new amplification cycles. Fluorescence signal generation would be observed upon SYBR Green I intercalating into the new DNA double helix. The new protocol design permits detection of as low as 2 nM cocaine in a closed tube, offering a convenient approach for a homogeneous assay. Compared with previously reported cocaine aptameric sensors, our new method is highly sensitive, selective, and economical.

Salidroside can target both P4HB-mediated inflammation and melanogenesis of the skin.

Rationale: Many external factors can induce the melanogenesis and inflammation of the skin. Salidroside (SAL) is the main active ingredient of Rhodiola, which is a perennial grass plant of the Family Crassulaceae. This study evaluated the effect and molecular mechanism of SAL on skin inflammation and melanin production. It then explored the molecular mechanism of melanin production under ultraviolet (UV) and inflammatory stimulation. Methods: VISIA skin analysis imaging system and DermaLab instruments were used to detect the melanin reduction and skin brightness improvement rate of the volunteers. UV-treated Kunming mice were used to detect the effect of SAL on skin inflammation and melanin production. Molecular docking and Biacore were used to verify the target of SAL. Immunofluorescence, luciferase reporter assay, CO-IP, pull-down, Western blot, proximity ligation assay (PLA), and qPCR were used to investigate the molecular mechanism by which SAL regulates skin inflammation and melanin production. Results: SAL can inhibit the inflammation and melanin production of the volunteers. SAL also exerted a protective effect on the UV-treated Kunming mice. SAL can inhibit the tyrosinase (TYR) activity and TYR mRNA expression in A375 cells. SAL can also regulate the ubiquitination degradation of interferon regulatory factor 1 (IRF1) by targeting prolyl 4-hydroxylase beta polypeptide (P4HB) to mediate inflammation and melanin production. This study also revealed that IRF1 and upstream stimulatory factor 1 (USF1) can form a transcription complex to regulate TYR mRNA expression. IRF1 also mediated inflammatory reaction and TYR expression under UV- and lipopolysaccharide-induced conditions. Moreover, SAL derivative SAL-plus (1-(3,5-dihydroxyphenyl) ethyl-ß-d-glucoside) showed better effect on inflammation and melanin production than SAL. Conclusion: SAL can inhibit the inflammation and melanogenesis of the skin by targeting P4HB and regulating the formation of the IRF1/USF1 transcription complex. In addition, SAL-plus may be a new melanin production and inflammatory inhibitor.

EDTA-enhanced phytoremediation of lead contaminated soil by Bidens maximowicziana.

Phytoremediation is a potential cleanup technology for the removal of heavy metals from contaminated soils. Bidens maximowicziana is a new Pb hyperaccumulator, which not only has remarkable tolerance to Pb but also extraordinary accumulation capacity for Pb. The maximum Pb concentration was 1509.3 mg/kg in roots and 2164.7 mg/kg in overground tissues. The Pb distribution order in the B. maximowicziana was: leaf > stem > root. The effect of amendments on phytoremediation was also studied. The mobility of soil Pb and the Pb concentrations in plants were both increased by EDTA application. Compared with CK (control check), EDTA application promoted translocation of Pb to overground parts of the plant. The Pb concentrations in overground parts of plants was increased from 24.23-680.56 mg/kg to 29.07-1905.57 mg/kg. This research demonstrated that B. maximowicziana appeared to be suitable for phytoremediation of Pb contaminated soil, especially, combination with EDTA.

Isolation and characterization of gasoline-degrading bacteria from gas station leaking-contaminated soils.

The effects of culture conditions in vitro and biosurfactant detection were studied on bacterial strains capable of degrading gasoline from contaminated soils near gas station. The main results were summarized as follows. Three bacteria (strains Q 10, Q14 and Q18) that were considered as efficiently degrading strains were isolated and identified as Pseudomonas sp., Flavobacterium sp. and Rhodococcus sp., respectively. The optimal growth conditions of three bacteria including pH, temperature and the concentration of gasoline were similar. The reduction in surface tension was observed with all the three bacteria, indicating the production of biosurfactant compounds. The value of surface tension reduced by the three strains Q10, Q14 and Q18 was 32.6 mN x m, 12.4 mNx m and 21.9 mN x m, respectively. Strain Q10 could be considered as a potential biosurfactant producer. Gasoline, diesel oil, benzene, toluene, ethylbenzene and xylene (BTEX) could easily be degraded by the three isolates. The consortium was more effective than the individual cultures in degrading added gasoline, diesel oil, and BTEX. These results indicate that these strains have great potential for in situ remediation of soils contaminated by gas station leaking.

Integrated numerical model of nitrogen transportation, absorption and transformation by two-dimension in soil-crop system.

A series of simulation experiments of nitrogen transportation, absorption and transformation were conducted, and the different cropping patterns of winter wheat and wastewater irrigation plans were taken into consideration. Based on the experiments, an integrated model of crop growth, roots distribution, water and nitrogen absorption by roots, water and nitrogen movement and transformation in soil-crop system by two-dimension was developed. Parameters and boundary conditions were identified and an effective computing method for optimizing watering and wastewater irrigating plans was provided.

Pseudosolubilized n-alkanes analysis and optimization of biosurfactants production by Pseudomonas sp. DG17.

The pseudosolubilized medium-chain-length n-alkanes during biodegradation process, and optimization of medium composition and culture conditions for rhamnolipid production by Pseudomonas sp. DG17 using Plackett-Burman design and Box-Behnken design, were examined in this study. The results showed that pseudosolubilized concentration of C14 to C20 n-alkanes was higher than that of C24 to C26. After incubation for 120 h, pseudosolubilized C16H34 increased to 2.63 ± 0.21 mg. Meanwhile, biodegradation rates of n-alkanes decreased along with the increase of carbon chain length. Carbon-14 assay suggested that nonlabeled C14H30, C16H34, and C20H42 inhibited the biodegradation of (14)C n-octadecane, and Pseudomonas sp. DG17 utilized different alkanes simultaneously. Three significant variables (substrate concentration, salinity, and C/N) that could influence rhamnolipid production were screened by Plackett-Burman design. Results of Box-Behnken design suggested that rhamnolipid concentration could be achieved at 91.24 mg L(-1) (observed value) or 87.92 mg L(-1) (predicted value) with the optimal levels of concentration, salinity, and C/N of 400 mg L(-1), 1.5 %, and 45, respectively.

An aptamer-based signal-on bio-assay for sensitive and selective detection of Kanamycin A by using gold nanoparticles.

In this study, a simple and sensitive aptamer-based fluorescence method for the detection of Kanamycin A by using gold nanoparticles (AuNPs) has been developed. In this assay, AuNPs were utilized as DNA nanocarrier as well as efficient fluorescence quencher. In the absence of Kanamycin A, dye-labeled aptamer could be adsorbed onto the surface of AuNPs and the fluorescence signal was quenched. In the presence of Kanamycin A, the specific binding between dye-labeled aptamer and its target induced the formation of rigid structure, which led to dye-labeled aptamer releasing from the surface of AuNPs and the fluorescence intensity was recovered consequently. Under optimum conditions, calibration modeling showed that the analytical linear range covered from 0.8nM to 350nM and the detection limit of 0.3nM was realized successfully. This proposed bio-assay also showed high selectivity over other antibiotics. Meanwhile, this strategy was further used to determine the concentrations of Kanamycin A in milk sample with satisfying results.

Numerical model of compressible gas flow in soil pollution control.

Based on the theory of fluid dynamics in porous media, a numerical model of gas flow in unsaturated zone is developed with the consideration of gas density change due to variation of air pressure. This model is characterized of its wider range of availability. The accuracy of this numerical model is analyzed through comparison with modeling results by previous model with presumption of little pressure variation and the validity of this numerical model is shown. Thus it provides basis for the designing and management of landfill gas control system or soil vapor extraction system in soil pollution control.

Experimental analysis of a nitrogen removal process simulation of wastewater land treatment under three different wheat planting densities.

Nitrogen contaminant transport, transformation and uptake simulation experiments were conducted in green house under three different planting density of winter wheat. They were Group A, planting density of 0.0208 plants/cm2, Group B, 0.1042 plants/cm2, and Group C, 0.1415 plants/cm2. The capacity and ratio of nitrogen removal were different on three kinds of conditions of wastewater land treatment. From analysis of wastewater treatment capacity, wastewater concentration and irrigation intensity for Group C were suitable and nitrogen quantity added was 2 times of that for Group B, 2.6 times for Group A while nitrogen residue was only 7.06%. Hence, wastewater irrigation and treatment design with purpose of waste water treatment should select the design with maximum capacity, optimal removal ratio and least residue in soil, which was closely related to crop planting density, crop growth status and also background nitrogen quantity in soil.

A simulation analysis of the migration and transformation of pollutants contained in landfill leachate.

A dynamic composite model for a soil-water system that can be used to simulate the movement of leachate from a landfill. The composite model includes nine sub-models that trace water movement and the migration and transformation of five pollutants (organic N, NH4-, NO3-, NO2-, and Cl-) in saturated and unsaturated soil. The model to simulate the movement of leachate from a landfill in Laogang Town, Shanghai City was used. In this application, the values for the model parameters were obtained by performing a laboratory simulation experiment of water movement and pollutant migration and transformation in soil columns. Soil and leachate obtained from the landfill site and its vicinity were used in the laboratory experiments. The model was then used to simulate leachate movement and pollutant activity during the ten-year period when the landfill was in operation and in the twenty-year period following its closure. The simulation results revealed that the leachate migrated into the groundwater at the rate of 90-100 meters per year. This model can be applied in the design of future landfills in China for the purpose of assessing and forecasting leachate plumes.