Jmjd3 inhibits reprogramming by upregulating expression of INK4a/Arf and targeting PHF20 for ubiquitination.

Although somatic cell reprogramming to generate inducible pluripotent stem cells (iPSCs) is associated with profound epigenetic changes, the roles and mechanisms of epigenetic factors in this process remain poorly understood. Here, we identify Jmjd3 as a potent negative regulator of reprogramming. Jmjd3-deficient MEFs produced significantly more iPSC colonies than did wild-type cells, whereas ectopic expression of Jmjd3 markedly inhibited reprogramming. We show that the inhibitory effects of Jmjd3 are produced through both histone demethylase-dependent and -independent pathways. The latter pathway involves Jmjd3 targeting of PHF20 for ubiquitination and degradation via recruitment of an E3 ligase, Trim26. Importantly, PHF20-deficient MEFs could not be converted to fully reprogrammed iPSCs, even with knockdown of Jmjd3, Ink4a, or p21, indicating that PHF20 is required for reprogramming. Our findings demonstrate, to the best of our knowledge, a previously unrecognized role of Jmjd3 in cellular reprogramming and provide molecular insight into the mechanisms by which the Jmjd3-PHF20 axis controls this process.

Correction: Stage-Dependent and Locus-Specific Role of Histone Demethylase Jumonji D3 (JMJD3) in the Embryonic Stages of Lung Development.

[This corrects the article DOI: 10.1371/journal.pgen.1004524.].

Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling.

Mitochondrial antiviral signaling platform protein (MAVS) acts as a central hub for RIG-I receptor proximal signal propagation. However, key components in the assembly of the MAVS mitochondrial platform that promote RIG-I mitochondrial localization and optimal activation are still largely undefined. Employing pooled RNAi and yeast two-hybrid screenings, we report that the mitochondrial adaptor protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial signaling complex required for maximal activation of RIG-I-mediated signaling, consisting of WHIP and protein phosphatase PPP6C. Following viral infection, the ubiquitin-binding domain in WHIP bridges RIG-I with MAVS by binding to polyUb chains of RIG-I at lysine 164. The ATPase domain in WHIP contributes to stabilization of the RIG-I-dsRNA interaction. Moreover, phosphatase PPP6C is responsible for RIG-I dephosphorylation. Together, our findings define the WHIP-TRIM14-PPP6C mitochondrial signalosome required for RIG-I-mediated innate antiviral immunity.

Impacts of renewable electricity standard and Renewable Energy Certificates on renewable energy investments and carbon emissions.

Accelerating the development of renewable energy is seen as an effective way for achieving the goals of carbon peak and carbon neutrality. The polices of Renewable Electricity Standard (RES) and Renewable Energy Certificates (REC) play increasing and important roles in developing renewable energy. In this paper, we develop an analytical model to analyze the impacts of the interaction of RES and REC polices on the renewable energy investment levels of an electricity generation firm and the carbon emissions. Our analysis reveals several interesting insights. First, we find that the green tags price under REC policy has a non-monotonic effect on the renewable energy investment, which highly depends on the quota (i.e., the required percentage of renewable electricity consumption on total electricity consumption) under the RES policy. Specifically, when the quota in RES policy is set too high, an increase in the green tags price will increase renewable energy investment; otherwise it will reduce the electricity generation firm's incentive to invest in renewable energy. Second, we show that the green tags price also has a non-monotonic effect on the carbon emissions. Specifically, when the quota in RES policy is set small enough, an increase in the green tags price will decrease the carbon emission. However, when the quota in RES policy is high enough, an increase in the green tags price will increase the carbon emission.

DHX29 functions as an RNA co-sensor for MDA5-mediated EMCV-specific antiviral immunity.

Melanoma differentiation-associated gene-5 (MDA5) recognizes distinct subsets of viruses including Encephalomyocarditis virus (EMCV) of picornavirus family, but the molecular mechanisms underlying the specificity of the viral recognition of MDA5 in immune cells remain obscure. DHX29 is an RNA helicase required for the translation of 5' structured mRNA of host and many picornaviruses (such as EMCV). We identify that DXH29 as a key RNA co-sensor, plays a significant role for specific recognition and triggering anti-EMCV immunity. We have observed that DHX29 regulates MDA5-, but not RIG-I-, mediated type I interferon signaling by preferentially interacting with structured RNAs and specifically with MDA5 for enhancing MDA5-dsRNA binding affinity. Overall, our results identify a critical role for DHX29 in innate immune response and provide molecular insights into the mechanisms by which DHX29 recognizes 5' structured EMCV RNA and interacts with MDA5 for potent type I interferon signaling and antiviral immunity.

Novel Laser-Based Obstacle Detection for Autonomous Robots on Unstructured Terrain.

Obstacle detection is one of the essential capabilities for autonomous robots operated on unstructured terrain. In this paper, a novel laser-based approach is proposed for obstacle detection by autonomous robots, in which the Sobel operator is deployed in the edge-detection process of 3D laser point clouds. The point clouds of unstructured terrain are filtered by VoxelGrid, and then processed by the Gaussian kernel function to obtain the edge features of obstacles. The Euclidean clustering algorithm is optimized by super-voxel in order to cluster the point clouds of each obstacle. The characteristics of the obstacles are recognized by the Levenberg-Marquardt back-propagation (LM-BP) neural network. The algorithm proposed in this paper is a post-processing algorithm based on the reconstructed point cloud. Experiments are conducted by using both the existing datasets and real unstructured terrain point cloud reconstructed by an all-terrain robot to demonstrate the feasibility and performance of the proposed approach.

Inhibiting or Accelerating Crystallization of Pharmaceuticals by Manipulating Polymer Solubility.

Polymers play a central role in controlling the crystallization of pharmaceuticals with effects as divergent as amorphous form stabilization and the acceleration of crystallization. Here, using pyrazinamide and hydrochlorothiazide as model pharmaceuticals, it is demonstrated that the same functional group interactions are responsible for these opposing behaviors and that whether a polymer speeds or slows a crystallization can be controlled by polymer solubility. This concept is applied for the discovery of polymers to maintain drug supersaturation in solution: the strength of functional group interactions between drug and polymer is assessed through polymer-induced heteronucleation, and soluble polymers containing the strongest-interacting functional groups with drug are shown to succeed as precipitation inhibitors.

Multi-Sensor Based Online Attitude Estimation and Stability Measurement of Articulated Heavy Vehicles.

Articulated wheel loaders used in the construction industry are heavy vehicles and have poor stability and a high rate of accidents because of the unpredictable changes of their body posture, mass and centroid position in complex operation environments. This paper presents a novel distributed multi-sensor system for real-time attitude estimation and stability measurement of articulated wheel loaders to improve their safety and stability. Four attitude and heading reference systems (AHRS) are constructed using micro-electro-mechanical system (MEMS) sensors, and installed on the front body, rear body, rear axis and boom of an articulated wheel loader to detect its attitude. A complementary filtering algorithm is deployed for sensor data fusion in the system so that steady state margin angle (SSMA) can be measured in real time and used as the judge index of rollover stability. Experiments are conducted on a prototype wheel loader, and results show that the proposed multi-sensor system is able to detect potential unstable states of an articulated wheel loader in real-time and with high accuracy.

Stage-dependent and locus-specific role of histone demethylase Jumonji D3 (JMJD3) in the embryonic stages of lung development.

Histone demethylases have emerged as important players in developmental processes. Jumonji domain containing-3 (Jmjd3) has been identified as a key histone demethylase that plays a critical role in the regulation of gene expression; however, the in vivo function of Jmjd3 in embryonic development remains largely unknown. To this end, we generated Jmjd3 global and conditional knockout mice. Global deletion of Jmjd3 induces perinatal lethality associated with defective lung development. Tissue and stage-specific deletion revealed that Jmjd3 is dispensable in the later stage of embryonic lung development. Jmjd3 ablation downregulates the expression of genes critical for lung development and function, including AQP-5 and SP-B. Jmjd3-mediated alterations in gene expression are associated with locus-specific changes in the methylation status of H3K27 and H3K4. Furthermore, Jmjd3 is recruited to the SP-B promoter through interactions with the transcription factor Nkx2.1 and the epigenetic protein Brg1. Taken together, these findings demonstrate that Jmjd3 plays a stage-dependent and locus-specific role in the mouse lung development. Our study provides molecular insights into the mechanisms by which Jmjd3 regulates target gene expression in the embryonic stages of lung development.

The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair.

CtIP plays an important role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair and interacts with Nbs1 and BRCA1, which are linked to Nijmegen breakage syndrome (NBS) and familial breast cancer, respectively. We identified new CDK phosphorylation sites on CtIP and found that phosphorylation of these newly identified CDK sites induces association of CtIP with the N-terminus FHA and BRCT domains of Nbs1. We further showed that these CDK-dependent phosphorylation events are a prerequisite for ATM to phosphorylate CtIP upon DNA damage, which is important for end resection to activate HR by promoting recruitment of BLM and Exo1 to DSBs. Most notably, this CDK-dependent CtIP and Nbs1 interaction facilitates ATM to phosphorylate CtIP in a substrate-specific manner. These studies reveal one important mechanism to regulate cell-cycle-dependent activation of HR upon DNA damage by coupling CDK- and ATM-mediated phosphorylation of CtIP through modulating the interaction of CtIP with Nbs1, which significantly helps to understand how DSB repair is regulated in mammalian cells to maintain genome stability.

CtIP is required to initiate replication-dependent interstrand crosslink repair.

DNA interstrand crosslinks (ICLs) are toxic lesions that block the progression of replication and transcription. CtIP is a conserved DNA repair protein that facilitates DNA end resection in the double-strand break (DSB) repair pathway. Here we show that CtIP plays a critical role during initiation of ICL processing in replicating human cells that is distinct from its role in DSB repair. CtIP depletion sensitizes human cells to ICL inducing agents and significantly impairs the accumulation of DNA damage response proteins RPA, ATR, FANCD2, γH2AX, and phosphorylated ATM at sites of laser generated ICLs. In contrast, the appearance of γH2AX and phosphorylated ATM at sites of laser generated double strand breaks (DSBs) is CtIP-independent. We present a model in which CtIP functions early in ICL repair in a BRCA1- and FANCM-dependent manner prior to generation of DSB repair intermediates.

Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes.

To investigate the circuit-level neural mechanisms of behavior, simultaneous imaging of neuronal activity in multiple cortical and subcortical regions is highly desired. Miniature head-mounted microscopes offer the capability of calcium imaging in freely behaving animals. However, implanting multiple microscopes on a mouse brain remains challenging due to space constraints and the cumbersome weight of the equipment. Here, we present TINIscope, a Tightly Integrated Neuronal Imaging microscope optimized for electronic and opto-mechanical design. With its compact and lightweight design of 0.43 g, TINIscope enables unprecedented simultaneous imaging of behavior-relevant activity in up to four brain regions in mice. Proof-of-concept experiments with TINIscope recorded over 1000 neurons in four hippocampal subregions and revealed concurrent activity patterns spanning across these regions. Moreover, we explored potential multi-modal experimental designs by integrating additional modules for optogenetics, electrical stimulation or local field potential recordings. Overall, TINIscope represents a timely and indispensable tool for studying the brain-wide interregional coordination that underlies unrestrained behaviors.

Castleman disease of plasma cell type accompanied with bronchiolitis obliterans: a case report and review of the literature.

BACKGROUND: Castleman disease, also known as giant lymph node hyperplasia or angiofollicular lymph node hyperplasia, is a highly heterogeneous clinicopathological entity that belongs to the family lymphoproliferative disorders. Castleman disease accompanied by bronchiolitis obliterans is uncommon and often poses a great diagnostic challenge, which is easily confused with respiratory diseases and impeding the correct diagnosis and treatment. The main aim in presenting such rare case studies is to raise awareness and expand the diagnostic horizon of clinicians for appropriate management. CASE PRESENTATION: Here, we present a 69-year-old Chinese male who was admitted to our hospital due to right chest pain for 6 months, accompanied by cough, expectoration, and fever. Laboratory examinations revealed elevated immunoglobulin G and C-reactive protein, and normal serum levels of tumor markers and interleukin-6. Computed tomography scan detected diffuse bronchial wall thickening and patchy area of air trapping consistent with small airway disease. Pulmonary function test showed mild small airway obstructive ventilation dysfunction and moderate decrease in diffusion capacity. The pathological result of the right axillary lymph node was consistent with the plasma cell type Castleman disease. According to the above examinations, the patient was finally diagnosed with the plasma cell type Castleman disease accompanied with bronchiolitis obliterans. He received immunosuppressive medication after surgery and has been followed up for 11 months. Now the patient is currently in stable condition without recurrence. CONCLUSION: Castleman disease is a rare lymphoproliferative disorder with a variety of symptoms. At present, the treatment of Castleman disease accompanied with bronchiolitis obliterans is mostly based on experiences or previous case reports, and there is no standard treatment. Here, we report an uncommon case of Castleman disease accompanied with bronchiolitis obliterans in which the patient received immunosuppressive medication after surgery and has been followed up for 11 months without experiencing a recurrence, which may deepen and extend our understanding of this disease.

Deep learning-based dose map prediction for high-dose-rate brachytherapy.

Background. Creating a clinically acceptable plan in the time-sensitive clinic workflow of brachytherapy is challenging. Deep learning-based dose prediction techniques have been reported as promising solutions with high efficiency and accuracy. However, current dose prediction studies mainly target EBRT which are inappropriate for brachytherapy, the model designed specifically for brachytherapy has not yet well-established.Purpose. To predict dose distribution in brachytherapy using a novel Squeeze and Excitation Attention Net (SE_AN) model.Method. We hypothesized the tracks of192Ir inside applicators are essential for brachytherapy dose prediction. To emphasize the applicator contribution, a novel SE module was integrated into a Cascaded UNet to recalibrate informative features and suppress less useful ones. The Cascaded UNet consists of two stacked UNets, with the first designed to predict coarse dose distribution and the second added for fine-tuning 250 cases including all typical clinical applicators were studied, including vaginal, tandem and ovoid, multi-channel, and free needle applicators. The developed SE_AN was subsequently compared to the classic UNet and classic Cascaded UNet (without SE module) models. The model performance was evaluated by comparing the predicted dose against the clinically approved plans using mean absolute error (MAE) of DVH metrics, includingD2ccandD90%.Results. The MAEs of DVH metrics demonstrated that SE_AN accurately predicted the dose with 0.37 ± 0.25 difference for HRCTVD90%, 0.23 ± 0.14 difference for bladderD2cc, and 0.28 ± 0.20 difference for rectumD2cc. In comparison studies, UNet achieved 0.34 ± 0.24 for HRCTV, 0.25 ± 0.20 for bladder, 0.25 ± 0.21 for rectum, and Cascaded UNet achieved 0.42 ± 0.31 for HRCTV, 0.24 ± 0.19 for bladder, 0.23 ± 0.19 for rectum.Conclusion. We successfully developed a method specifically for 3D brachytherapy dose prediction. Our model demonstrated comparable performance to clinical plans generated by experienced dosimetrists. The developed technique is expected to improve the standardization and quality control of brachytherapy treatment planning.

Decoding anterior-posterior axis emergence among mouse, monkey, and human embryos.

Anterior-posterior axis formation regulated by the distal visceral endoderm (DVE) and anterior visceral endoderm (AVE) is essential for peri-implantation embryogenesis. However, the principles of the origin and specialization of DVE and AVE remain elusive. Here, with single-cell transcriptome analysis and pseudotime prediction, we show that DVE and AVE independently originate from the specialized primary endoderm in mouse blastocysts. Along distinct developmental paths, these two lineages, respectively, undergo four representative states with stage-specific transcriptional patterns around implantation. Further comparative analysis shows that AVE, but not DVE, is detected in human and non-human primate embryos, defining differences in polarity formation across species. Moreover, stem cell-assembled human blastoids lack DVE or AVE precursors, implying that additional induction of stem cells with DVE/AVE potential could promote the current embryo-like models and their post-implantation growth. Our work provides insight into understanding of embryonic polarity formation and early mammalian development.

High precision vibration sectioning for 3D imaging of the whole central nervous system.

BACKGROUND: Imaging and reconstruction of the morphology of neurons within the entire central nervous system (CNS) is important for deciphering the neural circuitry and related brain functions. With combination of tissue clearing and light sheet microscopy, previous studies have imaged the mouse CNS at cellular resolution, while remaining single axons unresolvable due to the tradeoff between sample size and imaging resolution. This could be improved by sectioning the sample into thick slices and imaged with high resolution light sheet microscopy as described in our previous study. However, the achievable quality for 3D imaging of serial thick slices is often hindered by surface undulation and other artifacts introduced by sectioning and handling limitations. NEW METHODS: In order to improve the imaging quality for mouse CNS, we develop a high-performance vibratome system for sample sectioning and handling automation. The sectioning mechanism of the system was modeled theoretically and verified experimentally. The effects of process parameters and sample properties on sectioning accuracy were studied to optimize the sectioning outcome. The resultant imaging outcome was demonstrated on mouse samples. RESULTS: Our theoretical model of vibratome effectively depicts the relationship between the sample surface undulation errors and the sectioning parameters. With the guidance of the theoretical model, the vibratome is able to achieve a local surface undulation error of ±0.5 µm and a surface arithmetic mean deviation (Sa) of 220 nm for 300-µm-thick tissue slices. Imaging results of mouse CNS show the continuous sectioning capability of the vibratome. COMPARISON WITH EXISTING METHOD: Our automatic sectioning and handling system is able to process serial thick slices for 3D imaging of the whole CNS at a single-axon resolution, superior to the commercially available vibratome devices. CONCLUSION: Our automatic sectioning and handling system can be optimized to prepare thick sample slices with minimal surface undulation and manual manipulation in support of 3D brain mapping with high-throughput and high-accuracy.

Cynomolgus monkey embryo model captures gastrulation and early pregnancy.

Human stem cell-derived blastoids display similar morphology and cell lineages to normal blastocysts. However, the ability to investigate their developmental potential is limited. Here, we construct cynomolgus monkey blastoids resembling blastocysts in morphology and transcriptomics using naive ESCs. These blastoids develop to embryonic disk with the structures of yolk sac, chorionic cavity, amnion cavity, primitive streak, and connecting stalk along the rostral-caudal axis through prolonged in vitro culture (IVC). Primordial germ cells, gastrulating cells, visceral endoderm/yolk sac endoderm, three germ layers, and hemato-endothelial progenitors in IVC cynomolgus monkey blastoids were observed by single-cell transcriptomics or immunostaining. Moreover, transferring cynomolgus monkey blastoids to surrogates achieves pregnancies, as indicated by progesterone levels and presence of early gestation sacs. Our results reveal the capacity of in vitro gastrulation and in vivo early pregnancy of cynomolgus monkey blastoids, providing a useful system to dissect primate embryonic development without the same ethical concerns and access challenges in human embryo study.

MicroRNA-101 targets MAPK phosphatase-1 to regulate the activation of MAPKs in macrophages.

MAPK phosphatase-1 (MKP-1) is an archetypical member of the dual-specificity phosphatase family that deactivates MAPKs. Induction of MKP-1 has been implicated in attenuating the LPS- or peptidoglycan-induced biosynthesis of proinflammatory cytokines, but the role of noncoding RNA in the expression of the MKP-1 is still poorly understood. In this study, we show that MKP-1 is a direct target of microRNA-101 (miR-101). Transfection of miR-101 attenuates induction of MKP-1 by LPS as well as prolonged activation of p38 and JNK/stress-activated protein kinase, whereas inhibition of miR-101 enhances the expression of MKP-1 and shortens p38 and JNK activation. We also found that expression of miR-101 is induced by multiple TLR ligands, including LPS, peptidoglycan, or polyinosinic-polycytidylic acid, and that inhibition of PI3K/Akt by LY294002 or Akt RNA interference blocks the induction of miR-101 by LPS in RAW264.7 macrophage cells. Moreover, treatment of cells with dexamethasone, a widely used anti-inflammatory agent, markedly inhibits miR-101 expression and enhances the expression of MKP-1 in LPS-stimulated macrophages. Together, these results indicate that miR-101 regulates the innate immune responses of macrophages to LPS through targeting MKP-1.

Evaluating China's regional energy and environmental efficiency by considering three internal parallel industries.

With the rapid development of China's economy, high energy consumption and high pollution emission have become serious problems. To solve these problems, many studies have been done to evaluate energy and environmental efficiency, as the results can provide valuable information to improve performance. However, the previous research mainly evaluates China's regional energy and environmental efficiency by considering each region's industry as a whole system, ignoring the internal structure. In reality, each region mainly includes three parallel types of industry: primary, secondary, and tertiary. Therefore, this paper provides a parallel data envelopment analysis (DEA) approach to evaluate China's regional energy and environment efficiency by considering these parallel industrial systems. The following findings can be obtained based on the empirical results: (1) the overall energy efficiency of China is low, and the inefficiency of the economic system is mainly sourced from the lower energy and environmental performance of the primary industry and the tertiary industry. (2) the introduction of the environmental variable (CO2) leads to the increase of some backward areas' efficiencies. (3) the energy efficiency of each provincial region is different, and most of them have their own inefficient industries. (4) the total factor productivity of China is declining, mainly because of the decline of technical efficiency.

Effects of different oxygen conditions on pollutants removal and the abundances of tetracycline resistance genes in activated sludge systems.

The individual and combined effects of tetracycline (TC) and divalent copper (Cu2+) on the performance of activated sludge systems and the abundances of tetracycline resistance genes (TRGs) in activated sludge, under both aerobic and anaerobic conditions, were studied. Activated sludge systems received TC (0.2 mg L-1) and Cu2+ (5 mg L-1) separately or jointly under either aerobic or anaerobic conditions. The addition of TC did not affect the performance of activated sludge systems and the addition of Cu2+ and mixed TC/Cu2+ inhibited biological phosphorus removal. The TC removal efficiencies in systems under aerobic and anaerobic conditions were 98.4%-99.7% and 96.8%-99.9%, respectively, and Cu2+ promoted TC removal in activated sludge systems. The TC degradation product was 4-epitetracycline (ETC) in activated sludge systems under both aerobic and anaerobic conditions. The total relative abundances of TRGs (tetA, tetC, tetE, tetM, tetO, tetW, tetX and tetB(P)) in activated sludge showed opposite development trends under the two oxygen conditions and aerobic condition was beneficial to the attenuation of high-risk TRGs. The results of this study might improve evaluation of the combined effects of antibiotics and heavy metals on wastewater biological treatment systems.