Tracking chromatin state changes using nanoscale photo-proximity labelling.

Interactions between biomolecules underlie all cellular processes and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects1,2. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health1. However, in the complex environment of the nucleus, it is challenging to determine protein-protein interactions owing to low abundance, transient or multivalent binding and a lack of technologies that are able to interrogate these interactions without disrupting the protein-binding surface under study3. Here, we describe a method for the traceless incorporation of iridium-photosensitizers into the nuclear micro-environment using engineered split inteins. These Ir-catalysts can activate diazirine warheads through Dexter energy transfer to form reactive carbenes within an approximately 10 nm radius, cross-linking with proteins in the immediate micro-environment (a process termed µMap) for analysis using quantitative chemoproteomics4. We show that this nanoscale proximity-labelling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. µMap improves our fundamental understanding of nuclear protein-protein interactions and, in doing so, is expected to have a significant effect on the field of epigenetic drug discovery in both academia and industry.

P-N Heterojunction Embedded CuS/TiO2 Bifunctional Photocatalyst for Synchronous Hydrogen Production and Benzylamine Conversion.

The coupling of photocatalytic hydrogen production and selective oxidation of benzylamine is a topic of significant research interest. However, enhancing the bifunctional photocatalytic activity in this context is still a major challenge. The construction of Z-scheme heterojunctions is an effective strategy to enhance the activity of bifunctional photocatalysts. Herein, a p-n type direct Z-scheme heterojunction CuS/TiO2 is constructed using metal-organic framework (MOF)-derived TiO2 as a substrate. The carrier density is measured by Mott-Schottky under photoexcitation, which confirms that the Z-scheme electron transfer mode of CuS/TiO2 is driven by the diffusion effect caused by the carrier concentration difference. Benefiting from efficient charge separation and transfer, photogenerated electrons, and holes are directedly transferred to active oxidation and reduction sites. CuS/TiO2 also exhibits excellent bifunctional photocatalytic activity without noble metal cocatalysts. Among them, the H2 evolution activity of the CuS/TiO2 is found to be 17.1 and 29.5 times higher than that of TiO2 and CuS, respectively. Additionally, the yields of N-Benzylidenebenzylamine (NBB) are 14.3 and 47.4 times higher than those of TiO2 and CuS, respectively.

TSPAN31 suppresses cell proliferation in human cervical cancer through down-regulation of its antisense pairing with CDK4.

Natural antisense transcripts (NAT) are prevalent phenomena in the mammalian genome and play significant regulatory roles in gene expression. While new insights into NAT continue to be revealed, their exact function and their underlying mechanisms in human cancer remain largely unclear. We identified a NAT of CDK4, referred to TSPAN31, which inhibits CDK4 mRNA and protein expression in human cervical cancer by targeting the 3'-untranslated region (3'-UTR) of the CDK4 mRNA. Furthermore, silencing the expression of the TSPAN31 mRNA rescued the TSPAN31 3'-UTR- or the TSPAN31 full-length-induced decrease in CDK4 expression. Noteworthy, we discovered that TSPAN31, as a member of the tetraspanin family, suppressed cell proliferation by down-regulating its antisense pairing with CDK4 and decreasing retinoblastoma protein phosphorylation in human cervical cancer. Therefore, the results of the present study suggest that TSPAN31 may serve as a potential molecular target for the development of novel anti-cancer agents. SIGNIFICANCE OF THE STUDY: Natural antisense transcripts are widely found in the genome and play an important role in the growth and development of cells. TSPAN31 is natural antisense transcript, and CDK4 is an important gene in the regulation of the cell cycle. Therefore, TSPAN31 and CDK4 have great significance in the study of tumour therapeutic targets.

[Effects of biomechanics on colorectal organoid culture].

In recent years, organoids have become a crucial model for studying the physiopathological processes in tissues and organs. The emergence of organoids has promoted the research on the mechanisms of the occurrence and clinical translation of diseases. Among these organoid models, colorectal organoid models are increasingly mature. Colorectal cancer is a common gastrointestinal malignant tumor worldwide, posing a serious threat to human health. Colorectal organoids provide a new model for studying the pathophysiology, drug sensitivity, and precision medicine of colorectal cancer. The conventional culture systems of colorectal organoids focus more on the role of biochemical factors, neglecting the fact that the gut is also influenced by biophysical signals in vivo. Therefore, in this review, we discuss the theories related to colorectal organoids and biomechanics and expound the effects of biomechanics on colorectal organoid culture.

Interplay between TRIM7 and antiviral immunity.

TRIM7 has been demonstrated to have significant roles in promoting host defense against viral infections and regulating immune signaling pathways. As an E3 ubiquitin ligase, it catalyzes the ubiquitination of various substrates, including adaptor proteins (MAVS and STING) and transcription factors (NF-κB and IRF3), thereby exerting positive or negative regulation on immune signal pathways. However, viruses have developed immune evasion mechanisms to counteract TRIM7. Some viruses can inhibit TRIM7 function by targeting it for degradation or sequestering it away from its targets. Moreover, TRIM7 may even facilitate viral infection by ubiquitinating viral proteins, including envelope proteins that are critical for tissue and species tropism. A comprehensive understanding of the interaction between TRIM7 and antiviral immunity is crucial for the development of innovative treatments for viral diseases.

Chemical Method to Sequence 5-Formylcytosine on RNA.

Epitranscriptomic RNA modifications can regulate biological processes, but there remains a major gap in our ability to identify and measure individual modifications at nucleotide resolution. Here we present Mal-Seq, a chemical method for sequencing 5-formylcytosine (f5C) modifications on RNA based on the selective and efficient malononitrile-mediated labeling of f5C residues to generate adducts that are read as C-to-T mutations upon reverse transcription and polymerase chain reaction amplification. We apply Mal-Seq to characterize the prevalence of f5C at the wobble position of mt-tRNA(Met) in different organisms and tissue types and find that high-level f5C modification is present in mammals but lacking in lower eukaryotes. Our work sheds light on mitochondrial tRNA modifications throughout eukaryotic evolution and provides a general platform for characterizing the f5C epitranscriptome.

Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases.

Epitranscriptomic RNA modifications can regulate fundamental biological processes, but we lack approaches to map modification sites and probe writer enzymes. Here we present a chemoproteomic strategy to characterize RNA 5-methylcytidine (m5C) dioxygenase enzymes in their native context based upon metabolic labeling and activity-based crosslinking with 5-ethynylcytidine (5-EC). We profile m5C dioxygenases in human cells including ALKBH1 and TET2 and show that ALKBH1 is the major hm5C- and f5C-forming enzyme in RNA. Further, we map ALKBH1 modification sites transcriptome-wide using 5-EC-iCLIP and ARP-based sequencing to identify ALKBH1-dependent m5C oxidation in a variety of tRNAs and mRNAs and analyze ALKBH1 substrate specificity in vitro. We also apply targeted pyridine borane-mediated sequencing to measure f5C sites on select tRNA. Finally, we show that f5C at the wobble position of tRNA-Leu-CAA plays a role in decoding Leu codons under stress. Our work provides powerful chemical approaches for studying RNA m5C dioxygenases and mapping oxidative m5C modifications and reveals the existence of novel epitranscriptomic pathways for regulating RNA function.

Different phosphorylation and farnesylation patterns tune Rnd3-14-3-3 interaction in distinct mechanisms.

Protein posttranslational modifications (PTMs) are often involved in the mediation or inhibition of protein-protein interactions (PPIs) within many cellular signaling pathways. Uncovering the molecular mechanism of PTM-induced multivalent PPIs is vital to understand the regulatory factors to promote inhibitor development. Herein, Rnd3 peptides with different PTM patterns as the binding epitopes and 14-3-3ζ protein were used as models to elucidate the influences of phosphorylation and farnesylation on binding thermodynamics and kinetics and their molecular mechanism. The quantitative thermodynamic results indicate that phosphorylated residues S210 and S218 (pS210 and pS218) and farnesylated C241 (fC241) enhance Rnd3-14-3-3ζ interactions in the presence of the essential pS240. However, distinct PTM patterns greatly affect the binding process. Initial association of pS240 with the phosphate-binding pocket of one monomer of the 14-3-3ζ dimer triggers the binding of pS210 or pS218 to another monomer, whereas the binding of fC241 to the hydrophobic groove on one 14-3-3ζ monomer induces the subsequent binding of pS240 to the adjacent pocket on the same monomer. Based on the experimental and molecular simulation results, we estimate that pS210/pS218 and pS240 mediate the multivalent interaction through an additive mechanism, whereas fC241 and pS240 follow an induced fit mechanism, in which the cooperativity of these two adjacent PTMs is reflected by the index ε described in our established thermodynamic binding model. Besides, these proposed binding models have been further used for describing the interaction between 14-3-3ζ and other substrates containing adjacent phosphorylation and lipidation groups, indicating their potential in general applications. These mechanistic insights are significant for understanding the regulatory factors and the design of PPI modulators.

Comprehensive screen the lead and other toxic metals in total environment from a coal-gas industrial city (NW, China): Based on integrated source-specific risks and site-specific blood lead levels of 0-6 aged children.

A new integrated source-specific risk model and site-specific blood lead levels (BLLs) of 0-6 children were introduced to comprehensive understand the status of the toxic metals in soil-dust-plant total environment from a Coal-Gas industrial city, NW China. 144 samples were collected and ten toxic metals (As, Ba, Co, Cr, Cu, Mn, Ni, Sr, Pb, and Zn) were screened by XRF and ICP-MS. It was found that the occurrences of toxic metals deferred in the different medium, such as Co, Cu, Pb, and Zn observed the trend of accumulating in soil and plant compared to clustered distributions of Cr, Mn and Ni preferred to accumulate in dust. However, few bioaccumulations observed in Ulmus pumila L. Toxic metals distributions in majority of sites influenced by coal combustion mixed sources and industrial activities posed the high integrated ecological risks and caused significant non-carcinogenic and carcinogenic integrated risks for local 0-6 children identified by new integrated source-specific risk model, especially observed in the priority contaminants Co and Pb. The site-specific BLLs confirmed that younger children fewer than 4 lived in the north region were more vulnerable to priority Pb pollution as their BLLs above 50 µg/L, almost up to 80 µg/L. Although proportions of source-specific risks to toxic metals changed in soil and dust, the critical sources from coal combustions and industrial activities posed the most important contribution to the local risks. Therefore, effective strategies targeting at critical sources on coal industries should be conducted to reduce risks, and mostly emphasize on the north hotspot areas.

Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.

The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.

Major ions in drinking and surface waters from five cities in arid and semi-arid areas, NW China: spatial occurrence, water chemistry, and potential anthropogenic inputs.

A total of 161 water samples were collected from five large and medium-sized city rivers and residential tap waters, Xi'an and Yan'an in Shaanxi province, Xining in Qinghai province, Lanzhou in Gansu, and Urumqi in Xinjiang province, within arid and semi-arid area (NW China). The pH, EC parameters, and concentrations of 10 major ions (F-, Cl-, HCO3-, NO3-, SO42-, NH4+, K+, Na+, Mg2+, Ca2+) in the drinking waters (DWs) and surface waters (SWs) were analyzed to determine the ion chemistry, geochemical process, and potential anthropogenic input sources and to assess the water quality for drinking, domestic, and irrigation purposes. Durove diagrams and Gibbs diagram indicated that the ions Ca2+ and HCO3- dominant in DWs from Xi'an and Xining were of Ca2+-(HCO3- + SO42-) type, while sulfate and Na+ dominant in SWs, and Na+/K+-SO42- type was for Yan River in Yan'an and Peaceful Canal in Urumqi, their water chemistry influenced by evaporation and rock dominance, and evaporation and fractional crystallization, respectively. Meanwhile, Na+/K+/Ca2+-HCO3-/SO42- type dominated in Huang River in Xining and Yellow River in Lanzhou, which dominated by rock weathering. The quality assessments showed that in general the drinking waters were suitable for domestic purposes. However, the high values of NO3- at some sites influenced by agricultural and industrial inputs made it unsafe for drinking and demand detailed regional drinking water investigations. The assessment of SWs showed that the waters from Yan River in Yan'an and Yellow River in Lanzhou and Huang River in Xining would be used for irrigation. However, high values of SAR, Na%, RSC, and EC at sites in Peaceful Canal restricted suitability for irrigation, and not recommended for drinking water sources. It was noted that for the sustainable development of surface water, a reduction of discharge water from human activities and/or an increase in the fresh water inflow to the surface were needed.

Comprehensive Urumqi screening for potentially toxic metals in soil-dust-plant total environment and evaluation of children's (0-6 years) risk-based blood lead levels prediction.

Environmental contaminations by potentially toxic metals (PTMs) are associated with energy exploitation and present a significant problem in urban areas due to their impacts on human health. The PTMs status in Urumqi total environment inevitably impacted by extensive development of coal and oil industries has been lack of understanding comprehensively. A series of PTMs (As, Ba, Ce, Co, Cr, Cu, Ga, La, Mn, Ni, Pb, Rb, Sr, Th, U, V, Y, Zn, Zr) in the soil-dust-plant (foliage of Ulmus pumila L.) system of Urumqi (NW China) were screened by XRF and ICPMS. Multivariate statistics, risk models, GIS-based geostatistics, Positive Matrix Factorization (PMF) receptor modelling and blood lead levels of 0-6 aged children evaluated by IEUBK model are used to determine the priority pollutants, sources and health effects of the investigated elements. The spatial distribution of PTMs in soil-dust-plant system significantly coincides with coal combustion, traffic emission, and industrial activity. Although all PTM toxicants in soil, dust and tree foliage show some effects, the priority contaminants are observed for Cu, Pb and Zn as single element. The total carcinogenic and non-carcinogenic risks from PTMs are beyond the tolerance range of 0-6 year's old children, and the dust (TCR = 1.07E-04) PTMs pose approximatively equivalent carcinogenic risk to soil PTMs (TCT = 1.09E-04). The predicted BLLs (75-83 µ g·L-1) of 1-2 years children are most strongly influenced by Pb in soil and dust, and therefore more attention should be focused on sources of Pb to support the primary health care of the toddlers in Urumqi.

Use of a Survey to Assess the Environmental Exposure and Family Perception to Lead in Children (<6 Years) in Four Valley Cities, Northwestern China.

With the growth of industry, the extensive use of lead, and urban expansion in Northwestern Valley Cities (NVC) China, there is probable reason for presuming an increasing risk of lead exposure. However, little is known about the lead exposure of children less than 6 years old in NVC. As a first investigation, this study uses a survey to systematically determine the influences of various risk factors within the family environment, parents' background, children's behavior, mother's behavior during pregnancy, and parental perception about children's blood lead (CBL). A total of 596 families were recruited from the general population in Urumqi, Lanzhou, Xining and Yan'an. Parents, and their children (<6 years old), were asked about the environment and behaviors which could possibly relate with lead exposure. The results indicated that in the typical NVC of China, children's environment and behavior, parents' education level, and mother's pregnancy behavior, were associated with potential CBL. It was noted that not all parents in NVC China recognized the importance of children's lead exposure. Therefore, children's health care and medical screening campaigns need to be designed to improve family's fundamental knowledge of lead hazards, associated health effects, and prevention in the NVC of China.

A Novel Pb-Resistant Bacillus subtilis Bacterium Isolate for Co-Biosorption of Hazardous Sb(III) and Pb(II): Thermodynamics and Application Strategy.

The present work is the first to study co-biosorption of Pb(II) and Sb(III) by a novel bacterium and its application strategy. The biosorption characteristics of Pb(II) and Sb(III) ions from aqueous solution using B. subtilis were investigated. Optimum pH, biomass dosage, contact time and temperature were determined to be 5.00, 6.00 mg/L, 45 min and 35 °C, respectively. Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (D-R) models were applied to describe the biosorption isotherm of the metal ions by B. subtilis. Results showed that Langmuir model fitted the equilibrium data of Pb(II) better than others, while biosorption of Sb(III) obeyed the Freundlich model well. The biosorption capacity of B. subtilis biomass for Pb(II) and Sb(III) ions was found to be 17.34 ± 0.14 and 2.32 ± 0.30 mg/g, respectively. Kinetic data showed the biosorption process of Pb(II) and Sb(III) ions both followed the pseudo-second-order kinetic model, with R² ranging from 0.974 to 0.999 for Pb(II) and from 0.967 to 0.979 for Sb(III). The calculated thermodynamic parameters, negative ∆G and positive ∆H and ∆S values, indicated the biosorption of Pb(II) and Sb(III) ions onto B. subtilis biomass in water was feasible, endothermic, and spontaneous. Bacterial bioleaching experiment revealed B. subtilis can increase the mobility of Pb(II) and Sb(III) in polluted soil when pH was close to 6 at low temperature. Consequently, B. subtilis, as a cheap and original bacterial material, could be a promising biomass to remove Pb or isolate Sb from industrial wastewater and to assist phytoremediation of Pb and Sb from weak acid or near neutral pH polluted soils at low temperature.

TSPAN31 is a critical regulator on transduction of survival and apoptotic signals in hepatocellular carcinoma cells.

Tetraspanins are commonly believed to act as 'molecular facilitators', not directly involved in signal transduction. Tetraspanin 31 (TSPAN31), recently discovered to be linked to cancer, has not yet been studied in hepatocellular carcinoma (HCC). Here, we show that TSPAN31 is the natural antisense transcript of cyclin dependent kinase 4 (CDK4), and regulates the expression of CDK4 mRNA and protein. Target analysis indicates that miR-135b can directly regulate TSPAN31 expression. miR-135b-induced TSPAN31 silencing increases CDK4 protein levels. Interestingly, p53 negatively regulates TSPAN31 expression. siRNA-induced TSPAN31 knockdown reduces the expression of Akt signaling pathway components phosphorylated Akt, p-GSK3ß and ß-catenin, and restrains ß-catenin migration to cell nucleus. TSPAN31 knockdown also significantly inhibits HCC cell invasion and migration. These findings thus point to TSPAN31 as a novel regulator in transduction of intracellular survival and apoptotic signals.

Multi-Elements in Source Water (Drinking and Surface Water) within Five Cities from the Semi-Arid and Arid Region, NW China: Occurrence, Spatial Distribution and Risk Assessment.

The purpose of this study was to identify the concentration of multi-elements (MEs) in source water (surface and drinking water) and assess their quality for sustainability. A total of 161 water samples including 88 tap drinking waters (DW) and 73 surface waters (SW) were collected from five cities in Xi'an, Yan'an, Xining, Lanzhou, and Urumqi in northwestern China. Eighteen parameters including pH, electrical conductivity (EC), total organic carbon (TOC) total nitrogen (TN), chemical compositions of anions (F-, Cl-, NO3-,HCO3-, SO42-), cations (NH4⁺, K⁺, Na⁺, Ca2+,Mg2+), and metals (lead (Pb), chromium (Cr), cadmium (Cd), copper (Cu)) were analyzed in the first time at the five cities . The results showed that pH values and concentrations of Cl-, SO42-, Na⁺, K⁺, Ca2+, Mg2+ and Cd, Cr, Cu in DW were within the permissible limits of the Chinese Drinking Water Quality Criteria, whereas the concentrations of other ions (F-, NO3-, NH4⁺ and Pb) exceeded their permissible values. In terms of the SW, the concentrations of F-, Cl-, NO3-, SO42- were over the third range threshold i.e., water suitable for fishing and swimming of the Surface Water Quality Standards in China. The spatial distributions of most MEs in source water are similar, and there was no clear variation for all ions and metals. The metals in DW may be caused by water pipes, faucets and their fittings. The noncarcinogenic risk of metals in DW for local children are in decreasing order Cr > Cd > Pb > Cu. The carcinogenic risk from Cr exposure was at the acceptable level according to threshold of USEPA. Although the comprehensive index of potential ecological assessment of Cr, Cd, Pb and Cu in SW ranked at low risk level and was in the order of Huang River in Xining > Peaceful Canal in Urumqi > Yan River in Yan'an > Yellow River in Lanzhou, their adverse effects to ecology and human health at a low concentration in local semi-arid and arid areas should not be ignored in the long run.

Surface plasmon resonance effect cooperated with Z-scheme heterostructure for enhancing photocatalytic nitrogen reduction to ammonia.

The photocatalytic efficiency can be improved by constructing a Z-scheme heterojunction, but hindered by the only half utilization efficiency of photogenerated carriers. Thus, a novel material, UiO-66-NH2@TAPB-BTCA-COP-Ag (U6N@COP-Ag), with surface plasmon resonance (SPR) effect synergistic Z-scheme heterostructure has been prepared by depositing Ag nanoparticles (Ag NPs) on TAPB-BTCA-COP (COP)-coated UiO-66-NH2. The deposited Ag NPs expand the range of light absorption and introduce more photogenerated electrons in the composite. The SPR effect of noble metal compensates for the limited utilization of the Z-scheme heterojunction photogenerated carriers and the increased density of semiconductor carriers at the reducing end, which is more conducive to the redox reaction of the catalyst. Without sacrificial agents, U6N@COP-Ag shows great photocatalytic nitrogen reduction conversion efficiency with the rate of NH4+ in ammonia water at 167.63µmol g-1h-1, which is 6.6 and 2.8 times that of the original UiO-66-NH2 and COP, respectively. In-situ XPS and Kelvin probe technology verify that UiO-66-NH2 and Ag nanoparticles provide more photogenerated electrons to COP. The cleavage and conversion of N2 to NH4+ on U6N@COP-Ag was confirmed by the enhancement of NH bonds and NH4+ characteristic absorption peaks in the in-situ diffuse reflectance infrared Fourier transform spectroscopy (in-situ DRIFTS). This work presents a great method to improve the Z-scheme heterojunction photogenerated carrier utilization and the density of semiconductor carriers at the reducing end by the noble metal SPR effect, which is more conducive to enhance the redox reaction of the catalyst.