Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements.

Cell type-specific transcriptional programs that drive differentiation of specialized cell types are key players in development and tissue regeneration. One of the most dramatic changes in the transcription program in Drosophila occurs with the transition from proliferating spermatogonia to differentiating spermatocytes, with >3000 genes either newly expressed or expressed from new alternative promoters in spermatocytes. Here we show that opening of these promoters from their closed state in precursor cells requires function of the spermatocyte-specific tMAC complex, localized at the promoters. The spermatocyte-specific promoters lack the previously identified canonical core promoter elements except for the Inr. Instead, these promoters are enriched for the binding site for the TALE-class homeodomain transcription factors Achi/Vis and for a motif originally identified under tMAC ChIP-seq peaks. The tMAC motif resembles part of the previously identified 14-bp ß2UE1 element critical for spermatocyte-specific expression. Analysis of downstream sequences relative to transcription start site usage suggested that ACA and CNAAATT motifs at specific positions can help promote efficient transcription initiation. Our results reveal how promoter-proximal sequence elements that recruit and are acted upon by cell type-specific chromatin binding complexes help establish a robust, cell type-specific transcription program for terminal differentiation.

Near-Infrared Light-Driven Photoredox Catalysis by Transition-Metal-Complex Nanodots.

Developing light-harvesting materials with broad spectral response is of fundamental importance in full-spectrum solar energy conversion. We found that, when a series of earth-abundant metal (Cu, Co, Ni and Fe) salts are dissolved in coordinating solvents uniformly dispersed nanodots (NDs) are formed rather than fully dissolving as molecular species. The previously unrecognized formation of this condensed state is ascribed to spontaneous aggregation of molecular transition-metal-complexes (TMCs) via weak intermolecular interactions, which results in redshifted and broadened absorption into the NIR region (200-1100 nm). Typical photoredox reactions, such as carbonylation and oxidative dehydrogenation, well demonstrate the feasibility of efficient utilization of NIR light (λ>780 nm) by TMCs NDs. Our finding provides a conceptually new strategy for extending the absorption towards low energy photons in solar energy harvesting and conversion via photoredox transformations.

Recruitment of Mediator Complex by Cell Type and Stage-Specific Factors Required for Tissue-Specific TAF Dependent Gene Activation in an Adult Stem Cell Lineage.

Onset of terminal differentiation in adult stem cell lineages is commonly marked by robust activation of new transcriptional programs required to make the appropriate differentiated cell type(s). In the Drosophila male germ line stem cell lineage, the switch from proliferating spermatogonia to spermatocyte is accompanied by one of the most dramatic transcriptional changes in the fly, as over 1000 new transcripts turn on in preparation for meiosis and spermatid differentiation. Here we show that function of the coactivator complex Mediator is required for activation of hundreds of new transcripts in the spermatocyte program. Mediator appears to act in a sequential hierarchy, with the testis activating Complex (tMAC), a cell type specific form of the Mip/dREAM general repressor, required to recruit Mediator subunits to the chromatin, and Mediator function required to recruit the testis TAFs (tTAFs), spermatocyte specific homologs of subunits of TFIID. Mediator, tMAC and the tTAFs co-regulate expression of a major set of spermatid differentiation genes. The Mediator subunit Med22 binds the tMAC component Topi when the two are coexpressed in S2 cells, suggesting direct recruitment. Loss of Med22 function in spermatocytes causes meiosis I maturation arrest male infertility, similar to loss of function of the tMAC subunits or the tTAFs. Our results illuminate how cell type specific versions of the Mip/dREAM complex and the general transcription machinery cooperate to drive selective gene activation during differentiation in stem cell lineages.

Theoretical Investigations on Mechanisms and Pathways of C2H5O2 with BrO Reaction in the Atmosphere.

In this work, feasible mechanisms and pathways of the C2H5O2 + BrO reaction in the atmosphere were investigated using quantum chemistry methods, i.e., QCISD(T)/6-311++G(2df,2p)//B3LYP/6-311++G(2df,2p) levels of theory. Our result indicates that the title reaction occurs on both the singlet and triplet potential energy surfaces (PESs). Kinetically, singlet C2H5O3Br and C2H5O2BrO were dominant products under the atmospheric conditions below 300 K. CH3CHO2 + HOBr, CH3CHO + HOBrO, and CH3CHO + HBrO2 are feasible to a certain extent thermodynamically. Because of high energy barriers, all products formed on the triplet PES are negligible. Moreover, time-dependent density functional theory (TDDFT) calculation implies that C2H5O3Br and C2H5O2BrO will photolyze under the sunlight.

The polyubiquitin gene Ubi-p63E is essential for male meiotic cell cycle progression and germ cell differentiation in Drosophila.

The ubiquitin proteasome system (UPS) regulates many biological pathways by post-translationally ubiquitylating proteins for degradation. Although maintaining a dynamic balance between free ubiquitin and ubiquitylated proteins is key to UPS function, the mechanisms that regulate ubiquitin homeostasis in different tissues through development are not clear. Here we show, via analysis of the magellan (magn) complementation group, that loss of function of the Drosophila polyubiquitin Ubi-p63E results specifically in meiotic arrest sterility in males. Ubi-p63E contributes predominantly to maintaining the free ubiquitin pool in testes. The function of Ubi-p63E is required cell-autonomously for proper meiotic chromatin condensation, cell cycle progression and spermatid differentiation. magn mutant germ cells develop normally to the spermatocyte stage but arrest at the G2/M transition of meiosis I, with lack of protein expression of the key meiotic cell cycle regulators Boule and Cyclin B. Loss of Ubi-p63E function did not strongly affect the spermatocyte transcription program regulated by the testis TBP-associated factor (tTAF) or meiosis arrest complex (tMAC) genes. Knocking down proteasome function specifically in spermatocytes caused a different meiotic arrest phenotype, suggesting that the magn phenotype might not result from general defects in protein degradation. Our results suggest a conserved role of polyubiquitin genes in male meiosis and a potential mechanism leading to meiosis I maturation arrest.

Sequential changes at differentiation gene promoters as they become active in a stem cell lineage.

Transcriptional silencing of terminal differentiation genes by the Polycomb group (PcG) machinery is emerging as a key feature of precursor cells in stem cell lineages. How, then, is this epigenetic silencing reversed for proper cellular differentiation? Here, we investigate how the developmental program reverses local PcG action to allow expression of terminal differentiation genes in the Drosophila male germline stem cell (GSC) lineage. We find that the silenced state, set up in precursor cells, is relieved through developmentally regulated sequential events at promoters once cells commit to spermatocyte differentiation. The programmed events include global downregulation of Polycomb repressive complex 2 (PRC2) components, recruitment of hypophosphorylated RNA polymerase II (Pol II) to promoters, as well as the expression and action of testis-specific homologs of TATA-binding protein-associated factors (tTAFs). In addition, action of the testis-specific meiotic arrest complex (tMAC), a tissue-specific version of the MIP/dREAM complex, is required both for recruitment of tTAFs to target differentiation genes and for proper cell type-specific localization of PRC1 components and tTAFs within the spermatocyte nucleolus. Together, the action of the tMAC and tTAF cell type-specific chromatin and transcription machinery leads to loss of Polycomb and release of stalled Pol II from the terminal differentiation gene promoters, allowing robust transcription.

Design principles and therapeutic applications of novel synthetic WNT signaling agonists.

Wingless-related integration site or Wingless and Int-1 or Wingless-Int (WNT) signaling is crucial for embryonic development, and adult tissue homeostasis and regeneration, through its essential roles in cell fate, patterning, and stem cell regulation. The biophysical characteristics of WNT ligands have hindered efforts to interrogate ligand activity in vivo and prevented their development as therapeutics. Recent breakthroughs have enabled the generation of synthetic WNT signaling molecules that possess characteristics of natural ligands and potently activate the pathway, while also providing distinct advantages for therapeutic development and manufacturing. This review provides a detailed discussion of the protein engineering of these molecular platforms for WNT signaling agonism. We discuss the importance of WNT signaling in several organs and share insights from the initial application of these new classes of molecules in vitro and in vivo. These molecules offer a unique opportunity to enhance our understanding of how WNT signaling agonism promotes tissue repair, enabling targeted development of tailored therapeutics.

Effects of Fc glycosylation on the activity of WNT mimetic agonistic antibodies.

Monoclonal antibodies have been explored in a broad range of applications including receptor agonism. Given the importance of receptor conformation in signaling, the agonistic activity of antibodies that engage these receptors are influenced by many parameters. Tetravalent bispecific antibodies that target the frizzled and lipoprotein receptor-related protein receptors and subsequently activate WNT ("Wingless-related integration site" or "Wingless and Int-1" or "Wingless-Int") signaling have been constructed. Because WNT activation stimulates stem cell proliferation and tissue regeneration, immune effector functions should be eliminated from therapeutic antibodies targeting this pathway. Here, we report an unexpected effect of Fc glycosylation on the agonistic activity of WNT mimetic antibodies. Our findings underscore the importance of antibody format, geometry and epitope in agonistic antibody design, and highlight the need to establish appropriate early discovery screening strategies to identify hits for further optimization.

BRAIDing receptors for cell-specific targeting.

Systemic toxicity is a major challenge in the development of therapeutics. Consequently, cell-type-specific targeting is needed to improve on-target efficacy while reducing off-target toxicity. Here, we describe a cell-targeting system we have termed BRAID (BRidged Activation by Intra/intermolecular Division) whereby an active molecule is divided into two inactive or less active parts that are subsequently brought together via a so-called 'bridging receptor' on the target cell. This concept was validated using the WNT/ß-catenin signaling system, demonstrating that a multivalent WNT agonist molecule divided into two inactive components assembled from different epitopes via the hepatocyte receptor ßKlotho induces signaling specifically on hepatocytes. These data provide proof of concept for this cell-specific targeting strategy, and in principle, this may also allow activation of multiple signaling pathways where desirable. This approach has broad application potential for other receptor systems.

Degradation of mevinphos and monocrotophos by OH radicals in the environment: A computational investigation on mechanism, kinetic, and ecotoxicity.

Known organophosphorus pesticides are used widely in agriculture to improve the production of crops. Based on the literature, the degradation of some organophosphorus pesticides was studied theoretically. However, the mechanisms and variation of toxicity during the degradation of mevinphos and monocrotophos are still unclear in the environment, especially in wastewater. In this study, the reaction mechanisms for the degradation of the two representative organophosphorus pesticides (i.e., mevinphos and monocrotophos) in presence of OH radicals in the atmosphere and water are proposed using quantum chemical methods wB97-XD/6-311 + +G(3df,2pd)//wB97-XD/6-311 + +G(d,p). Result shows that the dominant channel is OH-addition to the C atom in CC bond with energy barriers being 15.6 and 14.7 kJ/mol, in the atmosphere and water, respectively, for mevinphos. As for monocrotophos, H-abstraction from NH group via barriers of 8.2 and 10.6 kJ/mol is more feasible in both the atmosphere and water. Moreover, the subsequent reactions of the major products in the atmosphere with NO and O2 were also studied to evaluate the atmospheric chemistry of mevinphos and monocrotophos. Kinetically, the total rate constant is 2.68 × 10-9 and 3.86 × 10-8 cm3 molecule-1·s-1 for mevinphos and monocrotophos in the atmosphere and 4.91 × 1010 and 7.77 × 1011 M-1 s-1 in the water at 298 K, thus the lifetime is estimated to be 36.46-364.60 s (2.53-25.31 s) in the atmosphere, and 1.41 × 10-2 - 1.41 × 10-1 s (8.92 ×10-4 - 8.92 ×10-3 s) in the advanced oxidation processes (AOPs) system. Furthermore, ecotoxic predictions for rats and three aqueous organisms imply their toxicity are reduced during degradation by using ECOSAR and T.E.S.T program based quantitative structure and activity relationship (QSAR) method.

Regional perception and multi-scale feature fusion network for cardiac segmentation.

Objective.Cardiovascular disease (CVD) is a group of diseases affecting cardiac and blood vessels, and short-axis cardiac magnetic resonance (CMR) images are considered the gold standard for the diagnosis and assessment of CVD. In CMR images, accurate segmentation of cardiac structures (e.g. left ventricle) assists in the parametric quantification of cardiac function. However, the dynamic beating of the heart renders the location of the heart with respect to other tissues difficult to resolve, and the myocardium and its surrounding tissues are similar in grayscale. This makes it challenging to accurately segment the cardiac images. Our goal is to develop a more accurate CMR image segmentation approach.Approach.In this study, we propose a regional perception and multi-scale feature fusion network (RMFNet) for CMR image segmentation. We design two regional perception modules, a window selection transformer (WST) module and a grid extraction transformer (GET) module. The WST module introduces a window selection block to adaptively select the window of interest to perceive information, and a windowed transformer block to enhance global information extraction within each feature window. The WST module enhances the network performance by improving the window of interest. The GET module grids the feature maps to decrease the redundant information in the feature maps and enhances the extraction of latent feature information of the network. The RMFNet further introduces a novel multi-scale feature extraction module to improve the ability to retain detailed information.Main results.The RMFNet is validated with experiments on three cardiac data sets. The results show that the RMFNet outperforms other advanced methods in overall performance. The RMFNet is further validated for generalizability on a multi-organ data set. The results also show that the RMFNet surpasses other comparison methods.Significance.Accurate medical image segmentation can reduce the stress of radiologists and play an important role in image-guided clinical procedures.

Research progress of novel magnetic two-dimensional carbon composites in photocatalytic degradation of pollutants: a review.

With the improvement of economic level and the development of science and technology, the problem of water pollution needs to be solved now. Various water pollutants have a negative impact on nature and restrict its development. In recent years, photocatalysis is considered to be a promising wastewater treatment method. Two-dimensional carbon materials have become the hotspot of photocatalytic degradation of pollutants because of their excellent conductivity, large specific surface area, and good hydrophilicity. Nevertheless, it is very hard for these photocatalysts based on carbon materials to separate and recover from the system. For solving such a problem, the composition with magnetic components is an effective way which can facilitate separation and keep the catalytic activity of the samples. In this review, the main roles of magnetic carbon-based composites in the field of pollutant degradation are introduced, and their synthesis technology, classification, and application are summarized. In the end, the current challenges and prospects in this field are involved, aiming to provide useful insights and enlightments into the fields of pollutant treatment and photocatalytic degradation.

Novel Frizzled-specific antibody-based Wnt mimetics and Wnt superagonists selectively activate WNT/ß-catenin signaling in target tissues.

WNTs are essential factors for stem cell biology, embryonic development, and for maintaining homeostasis and tissue repair in adults. Difficulties in purifying WNTs and their lack of receptor selectivity have hampered research and regenerative medicine development. While breakthroughs in WNT mimetic development have overcome some of these difficulties, the tools developed so far are incomplete and mimetics alone are often not sufficient. Here, we developed a complete set of WNT mimetic molecules that cover all WNT/ß-catenin-activating Frizzleds (FZDs). We show that FZD1,2,7 stimulate salivary gland expansion in vivo and salivary gland organoid expansion. We further describe the discovery of a novel WNT-modulating platform that combines WNT and RSPO mimetics' effects into one molecule. This set of molecules supports better organoid expansion in various tissues. These WNT-activating platforms can be broadly applied to organoids, pluripotent stem cells, and in vivo research, and serve as bases for future therapeutic development.

Fine-grained calibrated double-attention convolutional network for left ventricular segmentation.

Objective.Left ventricular (LV) segmentation of cardiac magnetic resonance imaging (MRI) is essential for diagnosing and treating the early stage of heart diseases. In convolutional neural networks, the target information of the LV in feature maps may be lost with convolution and max-pooling, particularly at the end of systolic. Fine segmentation of ventricular contour is still a challenge, and it may cause problems with inaccurate calculation of clinical parameters (e.g. ventricular volume). In order to improve the similarity of the neural network output and the target segmentation region, in this paper, a fine-grained calibrated double-attention convolutional network (FCDA-Net) is proposed to finely segment the endocardium and epicardium from ventricular MRI.Approach.FCDA-Nettakes the U-net as the backbone network, and the encoder-decoder structure incorporates a double grouped-attention module that is constructed by a fine calibration spatial attention module (fcSAM) and a fine calibration channel attention module (fcCAM). The double grouped-attention mechanism enhances the expression of information in both spatial and channelwise feature maps to achieve fine calibration.Main Results.The proposed approach is evaluated on the public MICCAI 2009 challenge dataset, and ablation experiments are conducted to demonstrate the effect of each grouped-attention module. Compared with other advanced segmentation methods,FCDA-Netcan obtain better LV segmentation performance.Significance.The LV segmentation results of MRI can be used to perform more accurate quantitative analysis of many essential clinical parameters and it can play an important role in image-guided clinical surgery.

A theoretical investigation on the degradation reactions of CH3CH2CH2NH and (CH3CH2CH2)2N radicals in the presence of NO, NO2 and O2.

The degradation reactions of propylamino and dipropylamino radicals in the presence of NO, NO2 and O2 were investigated at the CCSD(T)/6-311++G (2d, 2p)//B3LYP/6-311++G (d,p) levels of theory. Result indicates that nitrosamines, nitramines, nitroso-oxy compounds and imines can be formed at atmosphere. Time dependent density functional theory (TDDFT) calculation shows that nitrosamines and nitroso-oxy compounds can photolyze under sunlight, while nitramines cannot undergo photolysis in the daytime. Moreover, the ecotoxicity assessment result implies that the degradation of propyl-substituted amines by OH radicals, NO and NO2 will reduce their toxicity to fish, daphnia and green algae in the aquatic environment.

A new theoretical investigation on ·OH initiated oxidation of acephate in the environment: mechanism, kinetics, and toxicity.

Acephate (O,S-dimethyl acetylphosphoramidothioate) is a typical organophosphorus pesticide used widely in agriculture. It can be released into the atmosphere and water during production and application. In this work, mechanisms in the ·OH initiated degradation of acephate were investigated using quantum chemical methods. Results show that addition, substitution and H-abstraction mechanisms can take place, with the latter being dominant. Moreover, the subsequent reactions of dominant products with O2 and NO in the atmosphere were considered, as well. The rate constant in the atmosphere and aqueous phase was calculated by transition state theory (TST) with the Wigner tunneling contribution. The total rate constant in the atmosphere and aqueous phase is 7.86 × 10-10 and 1.83 × 10-12 cm3 per molecule per s, respectively, the latter being in accordance with the available experimental value of 1.50 × 10-12 cm3 per molecule per s. Moreover, the ecotoxicity of acephate and degradation products was assessed in fish, daphnia, green algae and rats.

Investigations on mechanisms, kinetics, and ecotoxicity in OH-initiated degradation of 1,2,4,5-tetramethylbenzene in the environment.

As one of the volatile organic compounds (VOCs) in the environment, 1,2,4,5-tetramethylbenzene (1,2,4,5-TeMB) present in oily wastewater, and it can occur substitution, abstraction, and addition reactions with OH radicals in the atmosphere and wastewater. Electrostatic potential (ESP) and average local ionization energy (ALIE) prediction indicate that H atoms from CH3 group and the benzene ring are the most active sites in 1,2,4,5-TeMB. The result shows that potential energy surfaces (PESs) in the gas and aqueous phase are similar, and the relevant barriers in the latter one are higher. The dominant channel is H abstraction from the benzene ring, and the subdominant one is OH radical addition to the benzene ring. Furthermore, subsequent reactions of dominant products with O2, NO2, NO, and OH radicals in the atmosphere are studied, as well. The total reaction rate constant is calculated to be 2.36×10-10 cm3 molecule-1 s-1 at 1 atm and 298 K in the atmosphere, which agrees well with the experimental data. While the total rate constant in the aqueous phase is much lower than that in the gas phase. Ecologic toxicity analysis shows that 1,2,4,5-TeMB is very toxic to fish, daphnia, and green algae; and OH-initiated degradation in the environment will reduce its toxicity.

Constructing 3D magnetic flower-like Fe3O4@SiO2@Co3O4@BiOCl heterojunction photocatalyst for degrading rhodamine B.

In this work, the 3D magnetic flower-like Fe3O4@SiO2@Co3O4@BiOCl heterojunction photocatalyst was successfully prepared. The combination of BiOCl with Co3O4 favored to increase specific surface area and separate photo-generated carriers of the resulting composite, resulting in the improvement of catalytic efficiency. The photocatalytic activities of Fe3O4@SiO2@Co3O4@BiOCl were researched in details. In 50 min of visible light, the degradation efficiency for rhodamine B (RhB) of Fe3O4@SiO2@Co3O4@BiOCl was 98.41%. It still maintained 94.22% even after three tests. Furthermore, the photodegradation mechanisms were also investigated, indicating that the improved efficiency was ascribed to the superior separation of photo-induced electron-hole pairs. This study supplies a new perception to fabricate photocatalysts for actual uses.

Robust Colonic Epithelial Regeneration and Amelioration of Colitis via FZD-Specific Activation of Wnt Signaling.

BACKGROUND AND AIMS: Current management of inflammatory bowel disease leaves a clear unmet need to treat the severe epithelial damage. Modulation of Wnt signaling might present an opportunity to achieve histological remission and mucosal healing when treating IBD. Exogenous R-spondin, which amplifies Wnt signals by maintaining cell surface expression of Frizzled (Fzd) and low-density lipoprotein receptor-related protein receptors, not only helps repair intestine epithelial damage, but also induces hyperplasia of normal epithelium. Wnt signaling may also be modulated with the recently developed Wnt mimetics, recombinant antibody-based molecules mimicking endogenous Wnts. METHODS: We first compared the epithelial healing effects of RSPO2 and a Wnt mimetic with broad Fzd specificity in an acute dextran sulfate sodium mouse colitis model. Guided by Fzd expression patterns in the colon epithelium, we also examined the effects of Wnt mimetics with subfamily Fzd specificities. RESULTS: In the DSS model, Wnt mimetics repaired damaged colon epithelium and reduced disease activity and inflammation and had no apparent effect on uninjured tissue. We further identified that the FZD5/8 and LRP6 receptor-specific Wnt mimetic, SZN-1326-p, was associated with the robust repair effect. Through a range of approaches including single-cell transcriptome analyses, we demonstrated that SZN-1326-p directly impacted epithelial cells, driving transient expansion of stem and progenitor cells, promoting differentiation of epithelial cells, histologically restoring the damaged epithelium, and secondarily to epithelial repair, reducing inflammation. CONCLUSIONS: It is feasible to design Wnt mimetics such as SZN-1326-p that impact damaged intestine epithelium specifically and restore its physiological functions, an approach that holds promise for treating epithelial damage in inflammatory bowel disease.