FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor.

Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.

Screening membraneless organelle participants with machine-learning models that integrate multimodal features.

Protein self-assembly is one of the formation mechanisms of biomolecular condensates. However, most phase-separating systems (PS) demand multiple partners in biological conditions. In this study, we divided PS proteins into two groups according to the mechanism by which they undergo PS: PS-Self proteins can self-assemble spontaneously to form droplets, while PS-Part proteins interact with partners to undergo PS. Analysis of the amino acid composition revealed differences in the sequence pattern between the two protein groups. Existing PS predictors, when evaluated on two test protein sets, preferentially predicted self-assembling proteins. Thus, a comprehensive predictor is required. Herein, we propose that properties other than sequence composition can provide crucial information in screening PS proteins. By incorporating phosphorylation frequencies and immunofluorescence image-based droplet-forming propensity with other PS-related features, we built two independent machine-learning models to separately predict the two protein categories. Results of independent testing suggested the superiority of integrating multimodal features. We performed experimental verification on the top-scored proteins DHX9, Ki-67, and NIFK. Their PS behavior in vitro revealed the effectiveness of our models in PS prediction. Further validation on the proteome of membraneless organelles confirmed the ability of our models to identify PS-Part proteins. We implemented a web server named PhaSePred (http://predict.phasep.pro/) that incorporates our two models together with representative PS predictors. PhaSePred displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins.

Zebrafish as model organisms for toxicological evaluations in the field of food science.

Food safety has long been an area of concern. The selection of stable and efficient model organisms is particularly important for food toxicology studies. Zebrafish (Danio rerio) are small model vertebrates, and 70% of human genes have at least one zebrafish ortholog. Zebrafish have advantages as model organisms due to their short life cycle, strong reproductive ability, easy rearing, and low cost. Zebrafish embryos have the advantage of being sensitive to the breeding environment and thus have been used as biosensors. Zebrafish and their embryos have been widely used for food toxicology assessments. This review provides a systematic and comprehensive summary of food toxicology studies using zebrafish as model organisms. First, we briefly introduce the multidimensional mechanisms and structure-activity relationship studies of food toxicological assessment. Second, we categorize these studies according to eight types of hazards in foods, including mycotoxins, pesticides, antibiotics, heavy metals, endocrine disruptors, food additives, nanoparticles, and other food-related ingredients. Finally, we list the applications of zebrafish in food toxicology studies in line with future research prospects, aiming to provide a valuable reference for researchers in the field of food science.

Tracing fossil fuel CO2 by 14C in maize leaves in Guanzhong Basin of China.

Quantifying fossil fuel CO2 (CO2ff) in the atmosphere provides a benchmark method to monitor anthropogenic carbon emissions. Radiocarbon (14C) in atmospheric CO2ff has been widely studied using the 14C in plants to document regional CO2ff patterns. However, annual CO2ff variations, reflecting spatial distributions based on plant samples, are still scarce. In this paper, the spatial distribution and temporal CO2ff changes in the Guanzhong Basin is established using Δ14C measurements from maize leaves collected in 2011 and 2012. With regard to spatial distribution, samples collected around Xi'an City showed lower Δ14C values (more CO2ff), while sites located near the perimeter of the basin showed higher Δ14C values (less CO2ff). This is likely due to the concentration of anthropogenic activities in the center of the Guanzhong Basin. The observed CO2ff mole fractions generally matched with PKU CO2 inventory and the ODIAC CO2 inventory data in the spatial distribution trend. However, it seems that thermal power plants were not well captured by the PKU CO2 inventory. Our results provide useful information for the improvement of the inventory and verification of regional carbon cycle models.

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays.

Dopamine is an essential neurotransmitter and its detection is important for bioanalytical chemistry. Two very different DNA aptamers have been reported for dopamine, one derived from an RNA aptamer (named Apt1) and other obtained via direct aptamer selection (named Apt2). In this study, we used four homogeneous binding assays to compare these two DNA dopamine aptamers. Thiazole orange (TO) fluorescence assay indicated that the Apt2 specifically bound with dopamine with a Kd of 2.37 µM, which was consistent with that from the isothermal titration calorimetry (ITC) assay. However, Apt1 had much less TO fluorescence change and also no signal from ITC. By labeling the two ends of the two aptamers by a fluorophore and a quencher, the aptamer beacons showed binding of dopamine only for Apt2. Finally, the label-free AuNP-based colorimetric assay showed no difference between these two aptamer sequences, and even non-binding random DNA showed the same response, indicating that AuNPs were not a good probe for detecting dopamine. According to the data, Apt1 does not appear to be able to bind dopamine specifically, while Apt2 showed specific binding and could be used for developing related biosensors.

A novel ESIPT fluorescent probe derived from 3-hydroxyphthalimide for hydrazine detection in aqueous solution and living cells.

Hydrazine is a highly toxic and flammable liquid that can damage human liver, kidney, and central nervous system. Therefore, it is valuable to seek a quick and sensitive method for hydrazine detection in environmental and biological science. Herein, a new fluorescent probe derived from 3-hydroxyphthalimide was synthesized. This probe can rapidly and selectively detect hydrazine with a low detection limit of 4.3 × 10-7 M. The recognition principle is based on hydrazine-induced acetyl deprotection and excited-state intramolecular proton transfer (ESIPT) process. Moreover, test paper and fluorescence image experiments showed that this probe had potential to monitor hydrazine in the environment and living cells.

The impact of COVID-19 lockdown on atmospheric CO2 in Xi'an, China.

Lockdown measures to control the spread of the novel coronavirus disease (COVID-19) sharply limited energy consumption and carbon emissions. The lockdown effect on carbon emissions has been studied by many researchers using statistical approaches. However, the lockdown effect on atmospheric carbon dioxide (CO2) on an urban scale remains unclear. Here we present CO2 concentration and carbon isotopic (δ13C) measurements to assess the impact of COVID-19 control measures on atmospheric CO2 in Xi'an, China. We find that CO2 concentrations during the lockdown period were 7.5% lower than during the normal period (prior to the Spring Festival, Jan 25 to Feb 4, 2020). The observed CO2excess (total CO2 minus background CO2) during the lockdown period was 52.3% lower than that during the normal period, and 35.7% lower than the estimated CO2excess with the effect of weather removed. A Keeling plot shows that in contrast CO2 concentrations and δ13C were weakly correlated (R2 = 0.18) during the lockdown period, reflecting a change in CO2 sources imposed by the curtailment of traffic and industrial emissions. Our study also show that the sharp reduction in atmospheric CO2 during lockdown were short-lived, and returned to normal levels within months after lockdown measures were lifted.

USP31 acetylation at Lys1264 is essential for its activity and cervical cancer cell growth.

Ubiquitin-specific protease 31 (USP31) is a member of deubiquitinase family that is involved in nuclear factor-κB activation and sarcomagenesis. However, little is known about posttranslational modification in the regulation of its activity and cervical cancer cell growth. In our study, we found that the Lys1264 residue of USP31 can be modified with an acetyl group by high-resolution mass spectrometry in HeLa cell line, and site-specific mutagenesis can significantly increase USP31 ubiquitin hydrolase activity and decrease the expression of p65. When being transfected with a plasmid expressing mutated USP31, the number of cancer cells was significantly decreased. We also observed that mutated USP31 could promote apoptosis but not cell cycle by flow cytometer analysis. Overexpression of mutated USP31 could reverse the effect in USP31 knockdown cell line. To further investigate its activity in tumorigenesis, deacetylase sirtuin 1 (Sirt1) was shown to interact with USP31 by co-immunoprecipitation and blocking the function of Sirt1 by knockdown or the inhibitor nicotinamide could increase the acetylation of USP31. When Lys1264 of USP31 mutated, Sirt1 could not remove its acetylation and alter the expression level of p65. Finally, inhibition or knockdown of Sirt1 suppressed USP31 activity in HeLa cell line, leading to cisplatin-induced apoptosis resistance. Therefore, acetylation at Lys1264 suppresses USP31 activity and plays a protective role in cancer cell growth. Our study contributes to understanding the mechanism of USP31 activity regulation and its role in tumorigenesis.

Selection and Identification of Novel Aptamers Specific for Clenbuterol Based on ssDNA Library Immobilized SELEX and Gold Nanoparticles Biosensor.

We describe a multiple combined strategy to discover novel aptamers specific for clenbuterol (CBL). An immobilized ssDNA library was used for the selection of specific aptamers using the systematic evolution of ligands by exponential enrichment (SELEX). Progress was monitored using real-time quantitative PCR (Q-PCR), and the enriched library was sequenced by high-throughput sequencing. Candidate aptamers were picked and preliminarily identified using a gold nanoparticles (AuNPs) biosensor. Bioactive aptamers were characterized for affinity, circular dichroism (CD), specificity and sensitivity. The Q-PCR amplification curve increased and the retention rate was about 1% at the eighth round. Use of the AuNPs biosensor and CD analyses determined that six aptamers had binding activity. Affinity analysis showed that aptamer 47 had the highest affinity (Kd = 42.17 ± 8.98 nM) with no cross reactivity to CBL analogs. Indirect competitive enzyme linked aptamer assay (IC-ELAA) based on a 5'-biotin aptamer 47 indicated the limit of detection (LOD) was 0.18 ± 0.02 ng/L (n = 3), and it was used to detect pork samples with a mean recovery of 83.33⁻97.03%. This is the first report of a universal strategy including library fixation, Q-PCR monitoring, high-throughput sequencing, and AuNPs biosensor identification to select aptamers specific for small molecules.

Stable carbon isotopic characteristics of fossil fuels in China.

Good knowledge on the stable carbon isotopic composition (δ13C) of fossil fuels is critical for the estimation of atmospheric CO2 sources. Here, we complied a comprehensive δ13C database including 336 coal, 580 oil, and 1160 natural gas data based on the extensive literature search, and conducted field measurements in two megacities, to characterize the δ13C signatures of Chinese fossil fuels. Results show that coal exhibits a narrow range and the most enriched in δ13C signature, oil displays intermediate variations both in the distribution and value of δ13C. By contrast, natural gas is strongly depleted but became more enriched in δ13C signature due to the shift in production from isotopically light oil-type gas to isotopically heavy coal-type gas. We found an obvious overlap between the δ13C distributions of oil and natural gas, and the carbon isotopic difference between oil and natural gas is minimized in Ordos Basin. Therefore, we suggested that the geographic origin is a certain factor that must be considered when δ13C of fossil fuels is used to estimate CO2 source contributions, and the measurement of δ13CO2 signatures of local end members is a better alternative in the absence of detailed information about the geographical origins of fossil fuels. This work is helpful in improving the ability to quantify CO2 sources of fossil fuel emissions in China, and also make a contribute to the global carbon isotope database.

Time series of atmospheric Δ14CO2 recorded in tree rings from Northwest China (1957-2015).

Radiocarbon (14C) is a unique and important tool for understanding carbon cycle in the nature, and its use can be significantly enhanced where reliable historical atmospheric Δ14CO2 records can be established. In China, continuous atmospheric Δ14CO2 records since the 1950s are scarce, a period when dramatic variations of Δ14CO2 occurred caused by intensive human activities. In this research, Δ14C of Qinghai spruce tree rings collected from Huangzhong (HZ) (36.27°N, 101.67°E, 2982 m amsl) were measured by Accelerator Mass Spectrometry, and a Δ14CO2 time series from 1957 to 2015 was reconstructed. The results show that HZ Δ14C was generally higher than the contemporaneous average level in the mid-high latitudes of the Northern Hemisphere. The peak value of HZ Δ14C occurred in 1964 (as bomb peak) was higher than that of other tree ring records in East Asia at a similar latitude, likely due to the impact of the atmosphere nuclear tests at Semipalatinsk (Kazakhstan). The record shows no obvious disturbance of Lop Nor nuclear weapons tests (in Northwest China) during 1964-1980, except for 1971. A local Suess effect began to appear since 2001, and the estimated atmospheric fossil fuel-derived CO2 (CO2ff) concentration increased from 3.5 ppm to 8.8 ppm from 2006 to 2015. This is associated with the implementation of the "Western Development" strategy in China. HZ Δ14C records document background Δ14C data, useful for regional carbon cycle research and atmospheric CO2ff quantification in the region. These data also provide baseline values for assessment environmental safety connected with nuclear power plants in China.

Controlling dopamine binding by the new aptamer for a FRET-based biosensor.

Dopamine is one of the most important neurotransmitters. A high-quality DNA aptamer for dopamine was reported in 2018. However, fundamental understanding of its binding and folding is lacking, which is critical for related biosensor design. Herein, we performed careful assays using a label-free technique called isothermal titration calorimetry (ITC) to study its secondary structure. We divided this aptamer into four regions and individually examined each of them. We confirmed two stems, but the third stem is believed to be part of a loop. The aptamer was then truncated. The original aptamer had a Kd of 2.2 ± 0.3 µM at 25 °C. Shortening the structure by one or two base pairs increased the Kd to 6.9 and 44.4 µM, respectively. Dopamine binding was promoted by both increasing the Mg2+ concentration and decreasing the temperature. At 5 °C, a Kd of 0.4 µM was achieved. Based on this understanding, we designed two fluorescence resonance energy transfer (FRET) quenching biosensors that differ only by a base pair. The shorter sensor had 3-fold higher sensitivity and a detection limit of 0.9 µM. In 1% fetal bovine serum, the sensor retained a similar limit of detection of 1.14 µM. A two-fluorophore ratiometric FRET sensor was also demonstrated with a low detection limit of 0.12 µM. This work indicated the feasibility of designing folding-based sensors for dopamine, and this design can be extended to other sensing modalities such as electrochemistry and colorimetry.

14C-AMS measurements in modern tree rings to trace local fossil fuel-derived CO2 in the greater Xi'an area, China.

Fossil fuel-derived CO2 (CO2ff) time series are critical to understanding urban carbon emissions, and to devise strategies to mitigate emission reduction. Using tree ring 14C archives, we reconstruct an historical CO2ff time series from 1991 to 2015 in the greater Xi'an region, China. CO2ff concentrations from the urban sites reached 22.5 ppm, with an average of 14.0 ppm, while average values from rural and mountain sites averaged about 6.0 ppm. These values provide a good measure of the distribution of anthropogenic CO2 emissions in the region. We also observed CO2ff concentration increases from both urban and rural sites during the study period, with more significant increases among urban sites. The persistent rise in CO2ff was attributed to increasing energy consumption caused by regional socio-economic development, which are corroborated by strong correlations between CO2ff and socioeconomic parameters.

Spatial variation of soil properties and carbon under different land use types on the Chinese Loess Plateau.

Land-use affects soil properties and soil carbon storage. Fully understanding land-use impacts on soil is essential to predicting effects on soils from climate change, and providing a scientific basis for soil management. Here, we measured soil properties, soil organic carbon (SOC), soil inorganic carbon (SIC) and total carbon (TC) from 202 samples from cropland, forestland, and grassland, to a depth of 500 cm on the Chinese Loess Plateau (CLP). We find that grassland and cropland have the highest clay and silt content, and have a significantly higher soil moisture capacity than forestland. Soil moisture in forestland is scarce at depths of 100-300 cm, and does not benefit from rainfall infiltration. At the same time, the soil carbon content and stocks in grassland are not significantly different from forestland. We suggest that in the light of climate change and water shortages on the CLP, grassland is more suitable than forestland or cropland to optimize carbon fixation, and prevent soil erosion. Hence the cultivation of grass should be considered as a strategy for sustainable ecosystem management on the CLP.

Fossil fuel CO2 traced by radiocarbon in fifteen Chinese cities.

China is an important fossil fuel CO2 (CO2ff) emitter and the international community is thus concerned with quantifying reductions in Chinese carbon emissions in the recent past. Compared to traditional statistical method, radiocarbon (14C) offers a different approach to quantify atmospheric CO2 derived from fossil fuel emissions. Here, we carry out a multi-year (2011-2016) CO2ff tracing by 14C in Xi'an, and a three-year (2014-2016) CO2ff tracing in 15 Chinese cities. The Xi'an results show that average CO2ff concentrations fell 35.9 ± 6.6% from 2014- 2016, compared to 2011-2013, and the timing of this decrease coincides with the implementation of nationwide carbon reduction measures in China, known as the Action Plan on Prevention and Control of Air Pollution. A WRF-Chem forward modeling simulation reveals that the CO2ff in Xi'an is mainly derived from local sources, and a source apportionment combined stable-carbon isotope showed that the CO2ff in this city is dominated by coal combustion (72.6 ± 10.4%). Strong CO2ff differences are found between January and July in most Chinese cities. High CO2ff concentrations often correspond to severe haze episodes and there are generally positive correlations between CO2ff and fine particulate (PM2.5) concentrations. Our study provides scientific data to understand the effects of CO2ff reduction strategies in China that can be applied to other countries as well.

Determining diurnal fossil fuel CO2 and biological CO2 by Δ14CO2 observation on certain summer and winter days at Chinese background sites.

Diurnal atmospheric Δ14CO2 was measured on two consecutive days in summer and winter, 2016 at Shangdianzi, Lin'an and Luhuitou regional background sites, and at Waliguan global background site in China. The objectives of this study were to determine diurnal fossil fuel CO2 (CO2ff) and biological CO2 (CO2bio) concentrations and to ascertain the factors influencing them. Evident CO2ff inputs (0-33.0 ± 1.4 ppm) were found, with some small morning and afternoon rush hour signals. Particularly, the long-range transport of air masses influenced the seasonal differences and rapid diurnal variations in CO2ff. Diurnal CO2bio showed violent variations (-20.9-113.3 ppm), with high values at night and low or negative values during the daytime. Diurnal CO2bio variations resulted from the tradeoffs between photosynthetic CO2 uptake and biological respiration CO2 emission as well as atmospheric boundary layer heights variations. These results might help to understand the roles of fossil fuel sources and biological sources on atmospheric CO2 diurnal variations at Chinese background sites.

Construction, expression and functional analysis of anti-clenbuterol codon-optimized scFv recombinant antibody.

The construction, expression and functional analysis of codon-optimized single-chain variable fragment (coscFv) against clenbuterol (CBL) prepared from the Escherichia coli system is described. First, the ionic concentration for coscFv expression was optimized through single-factor experiments. Then, the extraction conditions of inclusion bodies were optimized, and coscFv was affinity-purified. Finally, the functional analysis of coscFv was elucidated by indirect competitive enzyme-linked immunosorbent assay (icELISA) and molecular docking. After optimizing the ionic concentration, the yield of coscFv increased from 21.69% to 23.26%. The molecular weight of coscFv was determined to be approximately 27 kDa according to the SDS-PAGE and Western blot assay. The percentage of coscFv was as high as 43.9% after the inclusion bodies were extracted, washed, and dissolved. Functional analysis indicated that the coscFv recognized CBL, and the 50% inhibition average concentration of CBL (IC50) was 4.22 ± 0.01 (n = 3) ng/mL. The binding site between coscFv and CBL consisted of Asp33H, Met34H, Ser50H, Arg52H, Tyr57H, Leu59H, Asp99H, and Tyr93L. Our study confirms that coscFv can bind with CBL through the key amino acid residues and can be used to sensitively detect CBL.