Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.

The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.

Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data.

Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.

Immune to temperature interference sensor of carbon dioxide gas concentration based on a single modified fiber Bragg grating.

In this study, a novel method that can detect carbon dioxide (CO2) concentration and realize temperature immunity based on only one fiber Bragg grating (FBG) is proposed. The outstanding contribution lies in solving the temperature crosstalk issue of FBG and ensuring the accuracy of detection results under the condition of anti-temperature interference. To achieve immunity to temperature interference without changing the initial structure of FBG, the optical fiber cladding of FBG and adjacent optical fiber cladding at both ends of FBG are modified by a polymer coating. Moreover, a universal immune temperature demodulation algorithm is derived. The experimental results demonstrate that the temperature response sensitivity of the improved FBG is controlled within the range of 0.00407 nm/°C. Compared with the initial FBG (the temperature sensitivity of the initial FBG is 0.04 nm/°C), it decreases by nearly 10 times. Besides, the gas response sensitivity of FBG reaches 1.6 pm/ppm and has overwhelmingly ideal linearity. The detection error results manifest that the gas concentration error in 20 groups of data does not exceed 3.16 ppm. The final reproducibility research shows that the difference in detection sensitivity between the two sensors is 0.08 pm/ppm, and the relative error of linearity is 1.07%. In a word, the proposed method can accurately detect the concentration of CO2 gas and is efficiently immune to temperature interference. The sensor we proposed has the advantages of a simple production process, low cost, and satisfactory reproducibility. It also has the prospect of mass production.

The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3.

The Notch pathway transmits signals between neighboring cells to elicit downstream transcriptional programs. Notch is a major regulator of cell fate specification, proliferation, and apoptosis, such that aberrant signaling leads to a pleiotropy of human diseases, including developmental disorders and cancers. The pathway signals through the transcription factor CSL (RBPJ in mammals), which forms an activation complex with the intracellular domain of the Notch receptor and the coactivator Mastermind. CSL can also function as a transcriptional repressor by forming complexes with one of several different corepressor proteins, such as FHL1 or SHARP in mammals and Hairless in Drosophila. Recently, we identified L3MBTL3 as a bona fide RBPJ-binding corepressor that recruits the repressive lysine demethylase LSD1/KDM1A to Notch target genes. Here, we define the RBPJ-interacting domain of L3MBTL3 and report the 2.06 Å crystal structure of the RBPJ-L3MBTL3-DNA complex. The structure reveals that L3MBTL3 interacts with RBPJ via an unusual binding motif compared to other RBPJ binding partners, which we comprehensively analyze with a series of structure-based mutants. We also show that these disruptive mutations affect RBPJ and L3MBTL3 function in cells, providing further insights into Notch mediated transcriptional regulation.

Notch dimerization and gene dosage are important for normal heart development, intestinal stem cell maintenance, and splenic marginal zone B-cell homeostasis during mite infestation.

Cooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence-paired sites (SPS) located near many Notch-regulated genes. Although most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromised viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% dextran sulfate sodium (DSS). The most striking phenotypes-gender imbalance and splenic marginal zone B-cell lymphoma-emerged in combination with gene dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis and is consistent with Notch-dependent anti-parasite immune responses being compromised in Notch dimer-deficient animals.

Preoperative Biologics Exposure Predisposes Ulcerative Colitis Patients to a Distinct Delayed Postoperative Ileus Syndrome After Colectomy.

BACKGROUND Postoperative ileus (POI) remains the most common complication after colectomy for inflammatory bowel disease (IBD). Delayed POI (DPOI) can develop late (>14 days) after colectomy in clinical settings, with unknown etiology. The aim of this study was to address a novel entity of POI after colectomy for ulcerative colitis (UC). MATERIAL AND METHODS The data of 263 UC patients who underwent colectomy from Jan 1, 2013 to May 31, 2021 were collected. DPOI was defined as POI occurring on or after postoperative day (POD) 14 with apparent resolution from obligatory POI. Univariate and multivariate analysis were conducted to identify the risk factors for DPOI. RESULTS The rate of canonical prolonged POI and DPOI were 11.7% (31/263) and 9.9% (26/263), respectively. The pathophysiological process of DPOI demonstrated an ileus-dysbiosis-recovery triad. Two DPOI cases were diagnosed with UC-related severe enteritis and underwent re-laparotomy. Multivariate analysis showed preoperative biologics exposure was an independent risk factor for DPOI (OR 3.100 95% CI 1.261-7.619, P=0.018) and the number of biologics session/course moderately predicted the occurrence of DPOI (AUC=0.639, 95% CI=0.578-0.697, P=0.0129). CONCLUSIONS A distinct pattern of ileus was identified in a tertiary IBD center. Clarification of this syndrome complemented the spectrum of post-IPAA complications and offered experience to treat this condition.

Spinel-Type Materials Used for Gas Sensing: A Review.

Demands for the detection of harmful gas in daily life have arisen for a period and a gas nano-sensor acting as a kind of instrument that can directly detect gas has been of wide concern. The spinel-type nanomaterial is suitable for the research of gas sensors because of its unique structure. However, the existing instability, higher detection limit, and operating temperature of the spinel materials limit the extension of the spinel material sensor. This paper reviews the research progress of spinel materials in gas sensor technology in recent years and lists the common morphological structures and material sensitization methods in combination with previous works.

Ethanol Sensors Based on Porous In2O3 Nanosheet-Assembled Micro-Flowers.

By controlling the hydrothermal time, porous In2O3 nanosheet-assembled micro-flowers were successfully synthesized by a one-step method. The crystal structure, microstructure, and internal structure of the prepared samples were represented by an x-ray structure diffractometry, scanning electron microscopy, and transmission electron microscopy, respectively. The characterization results showed that when the hydrothermal time was 8 h, the In2O3 nano materials presented a flower-like structure assembled by In2O3 porous nanosheets. After successfully preparing the In2O3 gas sensor, the gas sensing was fully studied. The results show that the In2O3 gas sensor had an excellent gas sensing response to ethanol, and the material prepared under 8 h hydrothermal conditions had the best gas sensing property. At the optimum working temperature of 270 °C, the highest response value could reach 66, with a response time of 12.4 s and recovery time of 10.4 s, respectively. In addition, the prepared In2O3 gas sensor had a wide detection range for ethanol concentration, and still had obvious response for 500 ppb ethanol. Furthermore, the gas sensing mechanism of In2O3 micro-flowers was also studied in detail.

Dual-Functionalized Crescent Microgels for Selectively Capturing and Killing Cancer Cells.

In cancer therapy, the selective targeting of cancer cells while avoiding side effects to normal cells is still full of challenges. Here, we developed dual-functionalized crescent microgels, which selectively captured and killed lung cancer cells in situ without killing other cells. Crescent microgels with the inner surface of the cavity functionalized with antibody and containing glucose oxidase (GOX) in the gel matrix have been produced in a microfluidic device. These microgels presented high affinity and good selectivity to lung cancer cells and retained them inside the cavities for extended periods of time. Exposing the crescent hydrogels to physiological concentrations of glucose leads to the production of a locally high concentration of H2 O2 inside the microgels' cavities, due to the catalytic action by GOX inside the gel matrix, which selectively killed 90 % cancer cells entrapped in the microgel cavities without killing the cells outside. Our strategy to create synergy between different functions by incorporating them in a single microgel presents a novel approach to therapeutic systems, with potentially broad applications in smart materials, bioengineering and biomedical fields.

Interfacial Microcompartmentalization by Kinetic Control of Selective Interfacial Accumulation.

Reported here is a 2D, interfacial microcompartmentalization strategy governed by 3D phase separation. In aqueous polyethylene glycol (PEG) solutions doped with biotinylated polymers, the polymers spontaneously accumulate in the interfacial layer between the oil-surfactant-water interface and the adjacent polymer phase. In aqueous two-phase systems, these polymers first accumulated in the interfacial layer separating two polymer solutions and then selectively migrated to the oil-PEG interfacial layer. By using polymers with varying photopolymerizable groups and crosslinking rates, kinetic control and capture of spatial organisation in a variety of compartmentalized macroscopic structures, without the need of creating barrier layers, was achieved. This selective interfacial accumulation provides an extension of 3D phase separation towards synthetic compartmentalization, and is also relevant for understanding intracellular organisation.

Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster.

Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila, the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo.

Mineralized Supramolecular Hydrogels Bearing Tunable Thermo-Responsiveness.

Although a variety of biomimetic mineralized materials have been created in the lab, the vast majority of these manmade examples lack response to external stimuli. Here, mineralized supramolecular hydrogels with on-demand thermo-responsiveness that are formed by a simple, physical crosslinking between amorphous CaCO3 (ACC) nanoparticles and poly(acrylic acid) (PAA) are reported. Upon the addition of Na2 CO3 solution into a mixture composed of PAA and CaCl2 , amorphous ACC nanoparticles are formed in situ and simultaneously crosslinked by PAA chains, giving rise to the mineralized hydrogels. Interestingly, upon tuning the content of the formed ACC, hydrogels with different types of thermo-responsiveness can be easily obtained, and the transparencies of the resulting hydrogels are dramatically changed during the temperature-driven phase transitions. As an application, these thermo-responsive mineralized hydrogels are used to control the exposure of UV light, which is successfully applied to switch fluorescent signals in response to temperature.

Approaches to Enhancing Gas Sensing Properties: A Review.

A gas nanosensor is an instrument that converts the information of an unknown gas (species, concentration, etc.) into other signals (for example, an electrical signal) according to certain principles, combining detection principles, material science, and processing technology. As an effective application for detecting a large number of dangerous gases, gas nanosensors have attracted extensive interest. However, their development and application are restricted because of issues such as a low response, poor selectivity, and high operation temperature, etc. To tackle these issues, various measures have been studied and will be introduced in this review, mainly including controlling the nanostructure, doping with 2D nanomaterials, decorating with noble metal nanoparticles, and forming the heterojunction. In every section, recent advances and typical research, as well mechanisms, will also be demonstrated.

Structure-function analysis of RBP-J-interacting and tubulin-associated (RITA) reveals regions critical for repression of Notch target genes.

The Notch pathway is a cell-to-cell signaling mechanism that is essential for tissue development and maintenance, and aberrant Notch signaling has been implicated in various cancers, congenital defects, and cardiovascular diseases. Notch signaling activates the expression of target genes, which are regulated by the transcription factor CSL (CBF1/RBP-J, Su(H), Lag-1). CSL interacts with both transcriptional corepressor and coactivator proteins, functioning as both a repressor and activator, respectively. Although Notch activation complexes are relatively well understood at the structural level, less is known about how CSL interacts with corepressors. Recently, a new RBP-J (mammalian CSL ortholog)-interacting protein termed RITA has been identified and shown to export RBP-J out of the nucleus, thereby leading to the down-regulation of Notch target gene expression. However, the molecular details of RBP-J/RITA interactions are unclear. Here, using a combination of biochemical/cellular, structural, and biophysical techniques, we demonstrate that endogenous RBP-J and RITA proteins interact in cells, map the binding regions necessary for RBP-J·RITA complex formation, and determine the X-ray structure of the RBP-J·RITA complex bound to DNA. To validate the structure and glean more insights into function, we tested structure-based RBP-J and RITA mutants with biochemical/cellular assays and isothermal titration calorimetry. Whereas our structural and biophysical studies demonstrate that RITA binds RBP-J similarly to the RAM (RBP-J-associated molecule) domain of Notch, our biochemical and cellular assays suggest that RITA interacts with additional regions in RBP-J. Taken together, these results provide molecular insights into the mechanism of RITA-mediated regulation of Notch signaling, contributing to our understanding of how CSL functions as a transcriptional repressor of Notch target genes.

High-birefringence photonic crystal fiber polarization filter based on surface plasmon resonance.

In this paper, we designed a C2v-symmetry-structured photonic crystal fiber with triangular lattice and Au-filled air holes. The finite element method is used to analyze the dispersion and confinement loss characteristics of the core mode and the surface plasmon mode of the metal wire. In this work, we found that the positions of resonance peaks and the resonance strength of core mode and surface plasmon mode can be well adjusted by changing the pitch between the cladding air holes and the diameters of the air holes or metal wires around the core. By optimizing the parameters of the fiber structure, a polarization filter at the communication band is designed. At the wavelength of 1.31 µm, which is located in the communication band, the fundamental mode in X pol can be filtered with the diameter of the metal wire d(m)=1.2 µm. When d(m)=1.4 µm, the fundamental mode in Y pol can be filtered at the wavelength of 1.55 µm, which is also located in the communication band. Compared with the ordinary single-polarization and single-mode photonic crystal fiber, the fiber we proposed in this paper can selectively filter out the polarized light in one direction by adjusting the wire diameter. It is meaningful for the development of the polarization filter in the communication band.

Seismic resolution improving by a sequential convolutional neural network.

Thin-bed soft rock is one of the main factors causing large deformations of tunnels. In addition to relying on some innovative construction techniques, detecting thin beds early during surface geological exploration and advanced geological prediction can provide a basis for planning and implementing effective coping measures. The commonly used seismic methods cannot meet the requirement for thin beds detection accuracy. A high-resolution (HR) seismic signal processing method is proposed by introducing a sequential convolutional neural network (SCNN). The deep learning dataset including low-resolution (LR) and HR seismic is firstly prepared through forward modeling. Then, a one-dimension (1D) SCNN architecture is proposed to establish the mapping relationship between LR and HR sequences. Training on the prepared dataset, the HR seismic processing model with high accuracy is achieved and applied to some practical seismic data. The applications on both poststack and prestack seismic data demonstrate that the trained HR processing model can effectively improve the seismic resolution and restore the high-frequency seismic energy so that to recognize the thin-bed rocks.

Polysaccharide- and protein-based edible films combined with microwave technology for meat preservation.

To reduce food-borne bacterial infection caused by food spoilage, developing highly efficient food packing film is still an urgent need for food preservation. Herein, microwave-assisted antibacterial nanocomposite films CaO2@PVP/EA/CMC-Na (CP/EC) were synthesized using waste eggshell as precursor, egg albumen (EA) and sodium carboxymethylcellulose (CMCNa) as matrix by casting method. The size of CaO2@PVP (CP) nanoparticles with monodisperse spherical structures was 100-240 nm. When microwave and CP nanoparticles (0.05 mg/mL) were treated for 5 min, the mortality of E. coli and S. aureus could reach >97 %. Under microwave irradiation (6 min), the bactericidal rate of 2.5 % CP/EC film against E. coli and S. aureus reached 98.6 % and 97.2 %, respectively. After adding CP nanoparticles, the highest tensile strength (TS) and elongation at break (EB) of CP/EC film reached 19.59 MPa and 583.43 %, respectively. At 18 °C, the proliferation of bacterial colonies on meat can be significantly inhibited by 2.5 % CP/EC film. Detailed characterization showed that the excellent meat preservation activity was due to the synergistic effect of dynamic effect generated by ROS and thermal effect of microwave. This study provides a promising approach for the packaging application of polysaccharide- and protein-based biomass nanocomposite antibacterial edible films.

Characterization of CSL (CBF-1, Su(H), Lag-1) mutants reveals differences in signaling mediated by Notch1 and Notch2.

Notch is a conserved signaling pathway that plays essential roles during embryonic development and postnatally in adult tissues; misregulated signaling results in human disease. Notch receptor-ligand interactions trigger cleavage of the Notch receptor and release of its intracellular domain (NICD) from the membrane. NICD localizes to the nucleus where it forms a transcriptionally active complex with the DNA-binding protein CSL and the coactivator Mastermind (MAM) to up-regulate transcription from Notch target genes. Previous studies have determined the structure of the CSL-NICD-MAM ternary complex and characterized mutations that affect complex assembly in functional assays. However, as CSL is expressed in all cell types, these studies have been limited to analyzing mutations in NICD and MAM. Here, we describe a novel set of cellular reagents to characterize how mutations in CSL affect its function as a transcriptional activator. Using retrovirally transduced embryonic fibroblasts from a CSL-null mouse, we generated cell lines that express either wild-type or mutant CSL molecules. We then analyzed these mutants for defects in Notch1- (NICD1) or Notch2 (NICD2)-mediated activation from two different transcriptional reporters (HES-1 or 4×CBS). Our results show that mutations targeted to the different domains of CSL display significant differences in their ability to adversely affect transcription from the two reporters. Additionally, a subset of CSL mutants is sensitive to whether NICD1 or NICD2 was used to activate the reporter. Taken together, these studies provide important molecular insights into how Notch transcription complexes assemble at different target genes and promoter arrangements in vivo.

Highly Selective and ppb-Level Butanone Sensors Based on SnO2/NiO Heterojunction-Modified ZnO Nanosheets with Electron Polarity Transport Properties.

Gas sensors require the construction of composites with high reactivity to reduce the detection limit, but this can lead to a broad-spectrum response between the adsorbed oxygen and the target gas, making it difficult to improve selectivity. In this study, the phenomenon of electron polar transport properties of the two-dimensional heterojunction material is first discovered in gas sensing and utilized to greatly improve the selectivity of butanone sensors. Ultra-thin porous ZnO nanosheets modified with SnO2/NiO heterogeneous particles are synthesized to achieve 20 ppb detection limits for butanone with a response of 328 to 100 ppm butanone, which is the lowest known detection limit. The combination of reaction kinetics and liquid chromatography-mass spectrometry reveals a good synergistic catalytic effect of SnO2/NiO heterogeneous particles, which may contribute to the high response and low detection limit of butanone. Finally, the possible mechanism for the generation of electron polar transport phenomenon is analyzed in the two-dimensional heterojunction material. This work provides a novel perspective for achieving both selectivity and detection limits in gas sensors, with universal applicability and application potential.

Being on the same page matters: A meta-analytic investigation of leader-member exchange (LMX) agreement.

Although leader-member exchange (LMX) theory offers a detailed account of leader-follower relationship building, the importance of LMX agreement as a theoretically meaningful relational phenomenon has received less attention. This has, in turn, limited scholarly understanding of its pivotal role in leader-follower relationships. We conducted a meta-analysis to synthesize the substantive implications of LMX agreement for leader-follower relationships and to further understand which factors may influence its variation across samples. Results from the random-effects metaregression analyses provided strong support for the moderating role of LMX agreement at the between-study level. Specifically, with higher levels of sample-level LMX agreement, the relationships between LMX and followers' task performance and organizational citizenship behaviors were stronger. Moreover, different national culture configurations (i.e., horizontal individualism vs. vertical collectivism) and changes in relationship tenure were significantly associated with LMX agreement. We also examined a host of methodological factors, which generally had a very limited impact on the study findings. Overall, these meta-analytic findings suggest LMX agreement should be considered as a key relational contingency in LMX theory, as it can help unlock the full potential of high-quality leader-follower relationships. Moreover, as a substantively meaningful phenomenon, its variation across situations is intricately related to contextual influences. Based on our theoretical integration and empirical synthesis, we discuss the implications for LMX theory and identify important directions for the next stages of LMX research. (PsycInfo Database Record (c) 2023 APA, all rights reserved).