Sequencing by avidity enables high accuracy with low reagent consumption.

We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer.

Ethyl Lithospermate Reduces Lipopolysaccharide-Induced Inflammation through Inhibiting NF-κB and STAT3 Pathways in RAW 264.7 Cells and Zebrafish.

OBJECTIVE: To explore the anti-inflammatory effects of ethyl lithospermate in lipopolysaccharide (LPS)-stimulated RAW 264.7 murine-derived macrophages and zebrafish, and its underlying mechanisms. METHODS: 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazoliumbromide (MTT) assays were performed to investigate the toxicity of ethyl lithospermate at different concentrations (12.5-100 µ mol/L) in RAW 264.7 cells. The cells were stimulated with LPS (100 ng/mL) for 12 h to establish an inflammation model in vitro, the production of pro-inflammatory cytokines interleukin (IL)-6 and tumor necrosis factor α (TNF-α) were assessed by enzyme linked immunosorbent assay (ELISA). Western blot was used to ascertain the protein expressions of signal transducer and activator of transcription 3 (STAT3), nuclear factor kappa B (NF-κB) p65, phospho-STAT3 (p-STAT3, Tyr705), inhibitor of NF-κB (IκB) α, and phospho-I κB α (p-IκB α, Ser32), and confocal imaging was used to identify the nuclear translocation of NF-κB p65 and p-STAT3 (Tyr705). Additionally, the yolk sacs of zebrafish (3 days post fertilization) were injected with 2 nL LPS (0.5 mg/mL) to induce an inflammation model in vivo. Survival analysis, hematoxylin-eosin (HE) staining, observation of neutrophil migration, and quantitative real-time polymerase chain reaction (qRT-PCR) were used to further study the anti-inflammatory effects of ethyl lithospermate and its probable mechanisms in vivo. RESULTS: The non-toxic concentrations of ethyl lithospermate have been found to range from 12.5 to 100 µ mol/L. Ethyl lithospermate inhibited the release of IL-6 and TNF-α(P<0.05 or P<0.01), decreased IκBα degradation and phosphorylation (P<0.05) as well as the nuclear translocation of NF-κB p65 and p-STAT3 (Tyr705) in LPS-induced RAW 264.7 cells (P<0.01). Ethyl lithospermate also decreased inflammatory cells infiltration and neutrophil migration while increasing the survival rate of LPS-stimulated zebrafish (P<0.05 or P<0.01). In addition, ethyl lithospermate also inhibited the mRNA expression levels of of IL-6, TNF-α, IκBα, STAT3, and NF-κB in LPS-stimulated zebrafish (P<0.01). CONCLUSION: Ethyl lithospermate exerts anti-Inflammatory effected by inhibiting the NF-κB and STAT3 signal pathways in RAW 264.7 macrophages and zebrafish.

Salvianolic acids from Salvia miltiorrhiza Bunge and their anti-inflammatory effects through the activation of α7nAchR signaling.

ETHNOPHARMACOLOGICAL RELEVANCE: Cardiovascular disease (CVD) is a serious disease with a high incidence rate and mortality. Inflammation is closely related to the occurrence of CVDs. As an essential medicine of promoting blood circulation and removing blood stasis in China, Salvia miltiorrhiza Bunge (Danshen) is widely used to treat CVDs due to its anti-inflammatory and cardiovascular protective effects. Salvianolic acids are the most abundant component in the water extract of S. miltiorrhiza, which has a significant effect on the treatment of CVDs. However, due to the complex composition of salvianolic acids, the active molecules and their underlying mechanisms have not been fully explored. AIM OF THIS STUDY: The present study aims to isolate and identify salvianolic acids from Danshen with anti-inflammatory activity and explore the potential mechanisms of isolates. METHODS: The structures of isolated salvianolic acids were elucidated by UV, IR, NMR, MS and electronic circular dichroism (ECD) calculations. Then anti-inflammatory activities of isolates were screened out by the zebrafish inflammation models. The most active compound was further used to explore the anti-inflammatory mechanisms on LPS-stimulated RAW 264.7 cells. The key inflammatory cytokines IL-6 and TNF-α were measured by enzyme-linked immunosorbent assay (ELISA). The protein expression levels of STAT3, p-STAT3 (Tyr705), NF-κB p65, IκBα, p-IκBα (Ser32) and α7nAchR were determined by Western blotting. The nuclear translocation of p-STAT3 (Tyr705) and NF-κB p65 was evaluated by immunofluorescence assays. Finally, the in vivo anti-inflammatory mechanisms were investigated by observation of neutrophil migration, H&E staining, survival analysis and quantitative PCR (Q-PCR) in LPS-microinjected zebrafish. RESULTS: Two new and four known compounds were isolated from Danshen. Among them, isosalvianolic acid A-1 (C1) and ethyl lithospermate (C5) inhibited neutrophil migrations in three zebrafish inflammation models and C1 with the best activities decreased the secretion of IL-6 and TNF-α and inhibited the expression level of p-IκBα (Ser32) in LPS stimulated RAW 264.7 cells. In addition, C1 also reduced the nuclear translocation of NF-κB p65 and p-STAT3 (Tyr705). Moreover, C1 significantly upregulated the protein expression of α7nAchR, and the knockdown of α7nAchR counteracted the effects of C1 on the production of IL-6 and TNF-α and the expression levels of p-STAT3 (Tyr705), NF-κB p65 and p-IκBα (Ser32). In vivo experiments, C1 decreased the migration and infiltration of inflammatory cells, increased the survival ratio and inhibited the mRNA level of IL-6, TNF-α, STAT3, NF-κB and IκBα in LPS-microinjected zebrafish. CONCLUSION: Two new and four known compounds were isolated from Danshen. Among them, C1 exerted anti-inflammatory activities by activating α7nAchR signaling and subsequently inhibiting STAT3 and NF-κB pathways. This study provided evidence for the clinical application of Danshen and contributed to the development of C1 as a novel in the treatment of cardiovascular disease.

Response of Soil Detachment Rate to Sediment Load and Model Examination: A Key Process Simulation of Rill Erosion on Steep Loessial Hillslopes.

The rate of soil detachment by water flow indicates soil erosion intensity directly. The exact relation between soil detachment rate and actual sediment load in water flow, however, is still unclear, and the existing relationships have not been adequately tested. The aims of the present study were to investigate the response of soil detachment rate to sediment load using rill flume data with loessial soil and to quantitatively examine the soil detachment equations in the WEPP and EUROSEM soil erosion models. Six slopes were combined with seven flow discharges to measure detachment rates under seven sediment loads using a rill flume with a soil-feeding hopper. Significant differences were found among the soil detachment rate by different sediment loads in low sediment load levels, but an insensitive response of soil detachment rate to sediment load was found under high levels of sediment load. The soil detachment rate was proved to be negatively linearly correlated with sediment load. The rill detachment equation in the WEPP model predicted the soil detachment rate by rill flow very well under our experiment condition. The soil detachment equation in the EUROSEM model underestimated the detachment rates under controlled conditions, but removing the setting velocity from the equation greatly improved prediction. Further experiments that could reflect the dynamic convective detachment and deposition process need to be conducted to compare with the present examination results and to further understand rill erosion processes.

Modeling study on the roles of the deposition and transport of PM2.5 in air quality changes over central-eastern China.

The role of PM2.5 (particles with aerodynamic diameters ≤ 2.5 µm) deposition in air quality changes over China remains unclear. By using the three-year (2013, 2015, and 2017) simulation results of the WRF/CUACE v1.0 model from a previous work (Zhang et al., 2021), a non-linear relationship between the deposition of PM2.5 and anthropogenic emissions over central-eastern China in cold seasons as well as in different life stages of haze events was unraveled. PM2.5 deposition is spatially distributed differently from PM2.5 concentrations and anthropogenic emissions over China. The North China Plain (NCP) is typically characterized by higher anthropogenic emissions compared to southern China, such as the middle-low reaches of Yangtze River (MLYR), which includes parts of the Yangtze River Delta and the Midwest. However, PM2.5 deposition in the NCP is significantly lower than that in the MLYR region, suggesting that in addition to meteorology and emissions, lower deposition is another important factor in the increase in haze levels. Regional transport of pollution in central-eastern China acts as a moderator of pollution levels in different regions, for example by bringing pollution from the NCP to the MLYR region in cold seasons. It was found that in typical haze events the deposition flux of PM2.5 during the removal stages is substantially higher than that in accumulation stages, with most of the PM2.5 being transported southward and deposited to the MLYR and Sichuan Basin region, corresponding to a latitude range of about 24°N-31°N.

Confined catalysis of MOF-818 nanozyme and colorimetric aptasensing for cardiac troponin I.

Understanding the catalytic performance of nanozymes assembled in confined environment is an interesting topic. Herein, a three-dimensional nanozyme-catalytic nanoreactor was constructed by confining MOF-818 nanozyme in the pore of macroporous tungsten trioxide (p-WO3). The catalytic activity of MOF-818 assembled in-situ for the oxidation of 3,5-Di-tert-butylcatechol (3,5-DTBC) could be regulated by changing the pore size of p-WO3. Only when being confined in the pores of p-WO3 with an appropriate pore size, MOF-818 could exhibit high affinity towards 3,5-DTBC, and excellent catalytic activity for 3,5-DTBC oxidation, the catalytic rate constant kcat and Michaelis constant Km were determined to be 31.47 s-1 and 1.42 mM, respectively, and the maximum yield of 3,5-DTBC oxidation reached 95.2%. Furthermore, the as-constructed nanozyme-catalytic nanoreactor could be designed to construct a colorimetric aptasensor for selective determining cardiac troponin I based on the enzymatic inhibition effect and the exonuclease I-assisted target recycling signal amplification, which exhibited a good linear range of 50 fg mL-1 - 100 ng mL-1, low detection limit of 18 fg mL-1, and was applied for human serum analysis with RSD less than 5.2% and the recoveries ranged from 95% to 107%.

Ethyl Acetate Fraction of Hedyotis diffusa Willd Induces Apoptosis via JNK/Nur77 Pathway in Hepatocellular Carcinoma Cells.

Background: Hepatocellular carcinoma (HCC) is characterized by poor diagnosis and high mortality. Novel and efficient therapeutic agents are urgently needed for the treatment. Hedyotis diffusa Willd (HDW) is used to treat cancers, especially HCC in China. Purpose: The study aimed to identify the main anti-HCC extract in HDW and to explore the mechanism of the active extract. Materials and Methods: The high-performance liquid chromatography-quadrupole-time of flight mass spectrometry (HPLC-QTOF-MS) method was used for the simultaneous determination of main compounds in the ethyl acetate fraction of HDW (EHDW). The toxicity test of different HDW fractions was carried out on larvae at 2 day-post-fertilization (dpf) for 72 h. The in vivo anti-HCC effect of different HDW fractions was evaluated on a zebrafish tumor model by immersion administration. The antiproliferative effect of HDW fractions was determined with MTT assay, as well as hematoxylin and eosin (HE) staining assay. Hoechst 33258 staining was used to observe changes in nucleus morphology. Flow cytometry analysis was used to investigate apoptosis induction. Western blot analysis was used to examine apoptosis-related proteins, and key proteins in JNK/Nur77 signaling pathway. SP600125 was served to validate the apoptotic mechanism. Results: EHDW showed the strongest tumor cell growth inhibitory effect on zebrafish tumor model. Further study revealed that EHDW induced apoptosis in zebrafish tumor model and in cultured Hep3B cells. Meanwhile, it has been shown that the levels of BCL2-associated X (Bax), cytochrome c (cyto c), cleaved-caspase 3, and poly-ADP-ribose polymerase (PARP) cells were upregulated. In contrast, the level of antiapoptotic B cell lymphoma-2 (Bcl-2) was downregulated in Hep3B cells. Additionally, EHDW activated JNK/Nur77 pathway by increasing the levels of p-JNK(Thr183/Tyr185) and p-Nur77(Ser351). Further study showed that blockage of JNK by SP600125 reversed EHDW-induced JNK/Nur77 pathway and the downstream apoptotic proteins. Conclusion: In conclusion, EHDW exerted the anti-HCC effect, which may be attributed to the activation of JNK/Nur77 pathway. This study supported the rationale of HDW as an HCC therapeutic agent.

[Zebrafish's Circular RNAs].

Circular RNAs (circRNAs),a group of highly conserved small RNAs,are characterized by a closed circular structure from precursor linear RNA through reverse splicing.They are powerful regulators of the physiological and pathological processes in organisms at different development stages.Zebrafish can be used for the high-throughput drug screening with low cost.Thus,the circRNAs associated with development and inflammation can be mined from zebrafish.Recently,a variety of circRNAs in zebrafish have been identified and characterized.Studies have proved that circRNAs play a vital role in the development and inflammation of zebrafish.The paper summarizes the classification,characteristics,and biological functions of circRNAs,and reviews the research progress in zebrafish's circRNAs.

Research on Key Competency Elements of an Excellent Front-Line Health Inspector.

In order to find out the competency elements of excellent front-line health inspector, and to improve the comprehensive quality and law enforcement level, we conducted this study. Firstly, key Behavior Event Interview (BEI) was used to find out the competency elements of front-line inspector. From May to September in 2020, 7 health inspectors engaged in front-line inspection and law enforcement work in the Pudong New Area Health Inspection agency were interviewed by using the method of key Behavior Event Interview (BEI). Meanwhile, the competency differences of front-line personnel with different performance levels were compared by analyzing the difference of the average grade score, the highest grade score and so on of inspectors in different performance groups. Then the method of expert consultation was used to verify the rationality of the extracted competency elements. Combined with the results of expert consultation and the results of key Behavior Event Interview (BEI), the prominent competency elements of excellent front-line health inspector were found out. The total 6 prominent competency elements were investigation and evidence collection ability, on-site control ability, legal awareness, career love, communication and coordination ability, teamwork ability. Cohen's Kappa coefficient of the 2 coders was more than 0.6, which had high consistency. The key Behavior Event Interview (BEI) is scientific and reasonable method to find out prominent competency elements of excellent front-line health inspector, and the prominent competency elements found out will be helpful in the human resources planning and management of health inspection in the future.

Effect of vegetation seasonal cycle alterations to aerosol dry deposition on PM2.5 concentrations in China.

The effect of vegetation seasonal cycle alterations to aerosol dry deposition on PM2.5 concentrations (hereafter referred as the VSC effect) in China was investigated using a numerical modelling system (WRF/CUACE). Two simulation experiments using the vegetation parameters in particle dry deposition schemes typical for January and July revealed an absolute increase in surface PM2.5 concentrations of about 2.4 µg/m3 and a 5.5% relative increase in China (within model domain 2). The effect in non-urban areas was more significant than that in urban areas. The increases in PM2.5 concentrations in Beijing-Tianjin-Hebei (BTH), Yangtze River Delta (YRD), Pearl River Delta (PRD), Sichuan Basin (SCB), and Central China (CC) were calculated as 1.9 µg/m3, 3.4 µg/m3, 3.1 µg/m3, 4.3 µg/m3, and 4.9 µg/m3, respectively, corresponding to relative increases of 2.9%, 4.5%, 5.4%, 5.8%, and 5.9%. These results demonstrate that the effect of decreased particle dry deposition due to reduced vegetation in southern areas was stronger, which was partially attributed to the increased vegetation cover and more significant seasonal changes in those regions. Furthermore, the increased PM2.5 concentrations caused by the VSC effect were transported from north to south via the winter northerly winds, which weakened the effect in North China Plain and enhanced the effect in parts of central and southern China, such as the south of CC. Although the surface PM2.5 concentration was relatively high in North China Plain, the effects of the northerly wind and relatively small dry deposition velocity meant that the removal of PM2.5 in that region was relatively less than in southern areas of China. These results will contribute to understanding of the underlying mechanisms of PM2.5 enhancement during winter in China.

Photoelectrochemical aptasensing for thrombin based on exonuclease III-assisted recycling signal amplification and nanoceria enzymatic strategy.

In the present work, a capture DNA (c-DNA) was immobilized on the TNA/g-C3N4 to develop a sensitive and selective TNA/g-C3N4/c-DNA photoelectrochemical aptasensor for determining thrombin. With the aid of the specific recognition of anti-thrombin aptamer towards thrombin, ingenious design of hairpin DNA, and exonuclease III-assisted recycling signal amplification, more nanoceria could be assembled on the TNA/g-C3N4/c-DNA to form TNA/g-C3N4/nanoceria in the presence of thrombin. Due to the oxidase-mimic catalytic efficiency of nanoceria and the oxygen consumption for glucose oxidation, the photoexcited electrons at the conduction band of g-C3N4 could be well transferred to that of TNA under visible light irradiation, resulting in the increase of the photocurrent of TNA/g-C3N4/nanoceria, and the increase value of photocurrent had a linear relationship with the concentration of thrombin under the optimal conditions. So, the constructed TNA/g-C3N4/c-DNA photoelectrochemical aptasensor exhibited a satisfactory quantitative range from 0.01 pM to 0.5 nM, low detection limit with 3.4 fM for thrombin determination, and was applied for the human serum analysis successfully with RSD of less than 4.8% and the recovery between 95% and 113%.

Measurement of Human Resource Demand of Medical Institution Inspection Based on Task Analysis.

PURPOSE: To estimate the human resource demand of health inspection agencies to carry out the medical institution inspection function, and to provide the basis for the rational allocation of health inspection human resources. METHODS: Through policy documents review, inquiry of data from national health inspection report, Shanghai Health Inspection core business system, the basic data were collected. Based on the task analysis, the inspection functions of health inspection agency were investigated. The functional work links were analyzed, and the working time consumption was measured. The manpower needed to complete the inspection tasks of medical institutions was calculated combining with the annual functional workload and the effective working time of inspectors. RESULTS: There were three main routine functions of medical institution inspection, namely, on-site inspection, administrative punishment, and handling of emergencies and complaints. There were 1871 medical institutions at all levels and types in Pudong New Area, with an average annual inspection frequency of 2.8 times, annual administrative penalty of 245 cases, and handling of emergencies and complaints of 330 cases. The total time required for functional work was 1656029.30 minutes, and the annual effective working time of single inspector was 66705.21 minutes. About 25 people were taken to complete the inspection tasks of medical institutions throughout the year. The number of personnel engaged in the inspection of medical institutions was 18, and the personnel gap was 7. CONCLUSION: The task analysis was an effective method to estimate the human resource demand of health inspection. In Pudong New Area, there were insufficient inspectors in medical institutions. In the case of insufficient human resource supplement, it was suggested to use technical means to improve work efficiency and save manpower investment.

A new parameterization of uptake coefficients for heterogeneous reactions on multi-component atmospheric aerosols.

Based on laboratory studies and field observations, a new parameterization of uptake coefficients for heterogeneous reactions on multi-component aerosols is developed in this work. The equivalent ratio (ER) of inorganic aerosol is used to establish the quantitative relationship between the heterogeneous uptake coefficients and the composition of aerosols. Incorporating the new ER-dependent scheme, the WRF-CUACE model has been applied to simulate sulfate mass concentrations during December 2017 in the Beijing-Tianjin-Hebei region and evaluate the role of aerosol chemical components played in the sulfate formation. Simulated temporal variations and magnitudes of sulfate show good agreement with the observations by using this new scheme. From clean to polluted cases, although both dominant cations and anions increase significantly, the equivalent ratio decreases gradually and is closer to unity, representing the variation of aerosol compositions, which inhibits the heterogeneous uptake of SO2, with the uptake coefficient decreasing from 1 × 10-4 to 5.3 × 10-5. Based on this phenomenon, a self-limitation process for heterogeneous reactions with the increasing secondary inorganic aerosol from clean to polluted cases is proposed.

Self-powered aptasensing for prostate specific antigen based on a membraneless photoelectrochemical fuel cell.

A self-powered aptasensor for prostate specific antigen (PSA) based on a membraneless photoelectrochemical fuel cell (PEFC) with double photoelectrodes was constructed, in which, PSA-binding aptamer was electrostatically immobilized on the KOH-doped g-C3N4 modified TiO2 nanotube arrays (TNA/A-g-C3N4/aptamer), which was used as a photoanode, and Fe3+-doped CuBi2O4 modified indium doped tin oxide (ITO) substrate (ITO/CBFeO) was used as a photocathode. Under visible light irradiation, glucose was photocatalytically oxidized by A-g-C3N4 and generated H2O2 in situ, which was used as the electron acceptor for ITO/CBFeO photocathode, thus producing a high cell output response with a maximum output power of 133.5 µW cm-2 and an open circuit potential of 0.98 V. Due to the specific recognition of PSA by the aptamer and the output power decrease of the PEFC caused by the steric hindrance of the captured PSA on the TNA/A-g-C3N4, the PEFC could be used as a self-powered aptasensor for PSA with a quantitative range of 0.005-50 ng mL-1, a low detection limit of 1.3 pg mL-1 and good selectivity, and has been successfully applied for the analysis of real human serum samples with good precision of the relative standard deviation (RSD) less than 5.6% and good accuracy of the recoveries ranged from 91% to 108%.

Photoelectrochemical determination of alkaline phosphatase activity based on a photo-excited electron transfer strategy.

A sensitive photoelectrochemical (PEC) biosensor for determination of alkaline phosphatase (ALP) activity was constructed based on a photo-excited electron transfer strategy. Immobilization of CdTe quantum dots (QDs) on TiO2 nanotube arrays (TNAs), addition of iron (III) and adenosine triphosphate (ATP) in turn can effectively adjust the photocurrent response of TNAs under visible light irradiation due to a photo-excited electron transfer process, and alkaline phosphatase (ALP) activity can be determined for its catalysis toward dephosphorylation of ATP. The preparation of CdTe QDs, construction of TNA/QD PEC biosensor and the mechanism of photo-excited electron transfer are investigated in the present work. Under the optimal experimental conditions, the TNA/QD PEC biosensor shows a low limits of detection (LODs) (0.05 U L-1) and limits of quantification detection (LOQs) (0.15 U L-1), wide linear range from 0.2 to 15 U L-1, and good selectivity towards ALP determination, which has been successfully applied for human serum analysis with good precision (RSD ≤ 5.4%) and high accuracy (recovery rate, 91-112%).

Temporal and spatial variations in sand and dust storm events in East Asia from 2007 to 2016: Relationships with surface conditions and climate change.

We analyzed the frequency and intensity of sand and dust storms (SDSs) in East Asia from 2007 to 2016 using observational data from ground stations, numerical modeling, and vegetation indices obtained from both satellite and reanalysis data. The relationships of SDSs with surface conditions and the synoptic circulation pattern were also analyzed. The statistical analyses demonstrated that the number and intensity of SDS events recorded in spring during 2007 to 2016 showed a decreasing trend. The total number of spring SDSs decreased from at least ten events per year before 2011 to less than ten events per year after 2011. The overall average annual variation of the surface dust concentration in the main dust source regions decreased 33.24µg/m3 (-1.75%) annually. The variation in the temperatures near and below the ground surface and the amount of precipitation and soil moisture all favored an improvement in vegetation coverage, which reduced the intensity and frequency of SDSs. The strong winds accompanying the influx of cold air from high latitudes showed a decreasing trend, leading to a decrease in the number of SDSs and playing a key role in the decadal decrease of SDSs. The decrease in the intensity of the polar vortex during study period was closely related to the decrease in the intensity and frequency of SDSs.

Development of a New Marker System for Identification of Spirodela polyrhiza and Landoltia punctata.

Lemnaceae (commonly called duckweed) is an aquatic plant ideal for quantitative analysis in plant sciences. Several species of this family represent the smallest and fastest growing flowering plants. Different ecotypes of the same species vary in their biochemical and physiological properties. Thus, selecting of desirable ecotypes of a species is very important. Here, we developed a simple and rapid molecular identification system for Spirodela polyrhiza and Landoltia punctata based on the sequence polymorphism. First, several pairs of primers were designed and three markers were selected as good for identification. After PCR amplification, DNA fragments (the combination of three PCR products) in different duckweeds were detected using capillary electrophoresis. The high-resolution capillary electrophoresis displayed high identity to the sequencing results. The combination of the PCR products containing several DNA fragments highly improved the identification frequency. These results indicate that this method is not only good for interspecies identification but also ideal for intraspecies distinguishing. Meanwhile, 11 haplotypes were found in both the S. polyrhiza and L. punctata ecotypes. The results suggest that this marker system is useful for large-scale identification of duckweed and for the screening of desirable ecotypes to improve the diverse usage in duckweed utilization.

Modeling the interplay between the HIF-1 and p53 pathways in hypoxia.

Both the hypoxia-inducible factor-1 (HIF-1) and tumor suppressor p53 are involved in the cellular response to hypoxia. How the two transcription factors interact to determine cell fates is less well understood. Here, we developed a network model to characterize crosstalk between the HIF-1 and p53 pathways, taking into account that HIF-1α and p53 are targeted for proteasomal degradation by Mdm2 and compete for binding to limiting co-activator p300. We reported the network dynamics under various hypoxic conditions and revealed how the stabilization and transcriptional activities of p53 and HIF-1α are modulated to determine the cell fate. We showed that both the transrepression and transactivation activities of p53 promote apoptosis induction. This work provides new insight into the mechanism for the cellular response to hypoxia.

DNA sequencing using polymerase substrate-binding kinetics.

Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing. However, whole-genome sequencing is still costly and complex for diagnostics purposes. In the clinical space, targeted sequencing has the advantage of allowing researchers to focus on specific genes of interest. Routine clinical use of targeted NGS mandates inexpensive instruments, fast turnaround time and an integrated and robust workflow. Here we demonstrate a version of the Sequencing by Synthesis (SBS) chemistry that potentially can become a preferred targeted sequencing method in the clinical space. This sequencing chemistry uses natural nucleotides and is based on real-time recording of the differential polymerase/DNA-binding kinetics in the presence of correct or mismatch nucleotides. This ensemble SBS chemistry has been implemented on an existing Illumina sequencing platform with integrated cluster amplification. We discuss the advantages of this sequencing chemistry for targeted sequencing as well as its limitations for other applications.

Involvement of miR-605 and miR-34a in the DNA damage response promotes apoptosis induction.

MicroRNAs are key regulators of gene expression at the posttranscriptional level. In this study, we focus on miR-605 and miR-34a, which are direct transcriptional targets of p53 and in turn enhance its tumor suppressor function by acting upstream and downstream of it, respectively. miR-605 promotes p53 activation by repressing the expression of mdm2, whereas miR-34a promotes p53-dependent apoptosis by suppressing the expression of antiapoptotic genes such as bcl-2. What roles they play in the p53-mediated DNA damage response is less well understood. Here, we develop a four-module model of the p53 network to investigate the effect of miR-605 and miR-34a on the cell-fate decision after ionizing radiation. Results of numerical simulation indicate that the cell fate is closely associated with network dynamics. The concentration of p53 undergoes few pulses in response to repairable DNA damage, or it first oscillates and then switches to high plateau levels after irreparable damage. The amplitude of p53 pulses rises to various extents depending on miR-605 expression, and miR-605 accelerates the switching behavior of p53 levels to induce apoptosis. In parallel, miR-34a promotes apoptosis by enhancing the accumulation of free p53AIP1, a key proapoptotic protein. Thus, both miR-605 and miR-34a can mediate cellular outcomes and the timing of apoptosis. Moreover, miR-605 and PTEN complement each other in elevating p53 levels to trigger apoptosis. Taken together, miR-605 and miR-34a cooperate to endow the network with a fail-safe mechanism for apoptosis induction. This computational study also enriches our understanding of the action modes of p53-targeted microRNAs.