Gene silencing dynamics are modulated by transiently active regulatory elements.

Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via the FOG1/NuRD deacetylase complex, as revealed by the study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.

Cyclin-G-associated kinase GAK/dAux regulates autophagy initiation via ULK1/Atg1 in glia.

Autophagy is a major means for the elimination of protein inclusions in neurons in neurodegenerative diseases such as Parkinson's disease (PD). Yet, the mechanism of autophagy in the other brain cell type, glia, is less well characterized and remains largely unknown. Here, we present evidence that the PD risk factor, Cyclin-G-associated kinase (GAK)/Drosophila homolog Auxilin (dAux), is a component in glial autophagy. The lack of GAK/dAux increases the autophagosome number and size in adult fly glia and mouse microglia, and generally up-regulates levels of components in the initiation and PI3K class III complexes. GAK/dAux interacts with the master initiation regulator UNC-51like autophagy activating kinase 1/Atg1 via its uncoating domain and regulates the trafficking of Atg1 and Atg9 to autophagosomes, hence controlling the onset of glial autophagy. On the other hand, lack of GAK/dAux impairs the autophagic flux and blocks substrate degradation, suggesting that GAK/dAux might play additional roles. Importantly, dAux contributes to PD-like symptoms including dopaminergic neurodegeneration and locomotor function in flies. Our findings identify an autophagy factor in glia; considering the pivotal role of glia under pathological conditions, targeting glial autophagy is potentially a therapeutic strategy for PD.

Accurate long-read sequencing allows assembly of the duplicated RHD and RHCE genes harboring variants relevant to blood transfusion.

Next-generation sequencing (NGS) technologies have transformed medical genetics. However, short-read lengths pose a limitation on identification of structural variants, sequencing repetitive regions, phasing of distant nucleotide changes, and distinguishing highly homologous genomic regions. Long-read sequencing technologies may offer improvements in the characterization of genes that are currently difficult to assess. We used a combination of targeted DNA capture, long-read sequencing, and a customized bioinformatics pipeline to fully assemble the RH region, which harbors variation relevant to red cell donor-recipient mismatch, particularly among patients with sickle cell disease. RHD and RHCE are a pair of duplicated genes located within an ∼175 kb region on human chromosome 1 that have high sequence similarity and frequent structural variations. To achieve the assembly, we utilized palindrome repeats in PacBio SMRT reads to obtain consensus sequences of 2.1 to 2.9 kb average length with over 99% accuracy. We used these long consensus sequences to identify 771 assembly markers and to phase the RHD-RHCE region with high confidence. The dataset enabled direct linkage between coding and intronic variants, phasing of distant SNPs to determine RHD-RHCE haplotypes, and identification of known and novel structural variations along with the breakpoints. A limiting factor in phasing is the frequency of heterozygous assembly markers and therefore was most successful in samples from African Black individuals with increased heterogeneity at the RH locus. Overall, this approach allows RH genotyping and de novo assembly in an unbiased and comprehensive manner that is necessary to expand application of NGS technology to high-resolution RH typing.

A LRRK2/dLRRK-mediated lysosomal pathway that contributes to glial cell death and DA neuron survival.

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial and sporadic Parkinson's disease. A plethora of evidence has indicated a role for LRRK2 in endolysosomal trafficking in neurons, while LRRK2 function in glia, although highly expressed, remains largely unknown. Here, we present evidence that LRRK2/dLRRK mediates a lysosomal pathway that contributes to glial cell death and the survival of dopaminergic (DA) neurons. LRRK2/dLRRK knockdown in the immortalized microglia or flies results in enlarged and swelling lysosomes fewer in number. These lysosomes are less mobile, wrongly acidified, exhibit defective membrane permeability and reduced activity of the lysosome hydrolase cathepsin B. In addition, LRRK2/dLRRK depletion causes glial apoptosis, DA neurodegeneration, and locomotor deficits in an age-dependent manner. Taken together, these findings demonstrate a functional role of LRRK2/dLRRK in regulating the glial lysosomal pathway; deficits in lysosomal biogenesis and function linking to glial apoptosis potentially underlie the mechanism of DA neurodegeneration, providing insights on LRRK2/dLRRK function in normal and pathological brains.

Glia-derived temporal signals orchestrate neurogenesis in the Drosophila mushroom body.

Intrinsic mechanisms such as temporal series of transcription factors orchestrate neurogenesis from a limited number of neural progenitors in the brain. Extrinsic regulations, however, remain largely unexplored. Here we describe a two-step glia-derived signal that regulates neurogenesis in the Drosophila mushroom body (MB). In a temporal manner, glial-specific ubiquitin ligase dSmurf activates non-cell-autonomous Hedgehog signaling propagation by targeting the receptor Patched to suppress and promote the exit of MB neuroblast (NB) proliferation, thereby specifying the correct α/ß cell number without affecting differentiation. Independent of NB proliferation, dSmurf also stabilizes the expression of the cell-adhesion molecule Fasciclin II (FasII) via its WW domains and regulates FasII homophilic interaction between glia and MB axons to refine α/ß-lobe integrity. Our findings provide insights into how extrinsic glia-to-neuron communication coordinates with NB proliferation capacity to regulate MB neurogenesis; glial proteostasis is likely a generalized mechanism in orchestrating neurogenesis.

Bioinformatics analysis of differentially expressed genes related to ischemia and hypoxia in spinal cord injury and construction of miRNA-mRNA or mRNA-transcription factor interaction network.

BACKGROUND: Previous studies show that spinal cord ischemia and hypoxia is an important cause of spinal cord necrosis and neurological loss. Therefore, the study aimed to identify genes related to ischemia and hypoxia after spinal cord injury (SCI) and analyze their functions, regulatory mechanism, and potential in regulating immune infiltration. METHODS: The expression profiles of GSE5296, GSE47681, and GSE217797 were downloaded from the Gene Expression Omnibus database. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to determine the function and pathway enrichment of ischemia- and hypoxia-related differentially expressed genes (IAHRDEGs) in SCI. LASSO model was constructed, and support vector machine analysis was used to identify key genes. The diagnostic values of key genes were evaluated using decision curve analysis and receiver operating characteristic curve analysis. The interaction networks of miRNAs-IAHRDEGs and IAHRDEGs-transcription factors were predicted and constructed with the ENCORI database and Cytoscape software. CIBERSORT algorithm was utilized to analyze the correlation between key gene expression and immune cell infiltration. RESULTS: There were 27 IAHRDEGs identified to be significantly expressed in SCI at first. These genes were mostly significantly enriched in wound healing function and the pathway associated with lipid and atherosclerosis. Next, five key IAHRDEGs (Abca1, Casp1, Lpl, Procr, Tnfrsf1a) were identified and predicted to have diagnostic value. Moreover, the five key genes are closely related to immune cell infiltration. CONCLUSION: Abca1, Casp1, Lpl, Procr, and Tnfrsf1a may promote the pathogenesis of ischemic or hypoxic SCI by regulating vascular damage, inflammation, and immune infiltration.

Short-Term Prediction of Multi-Energy Loads Based on Copula Correlation Analysis and Model Fusions.

To improve the accuracy of short-term multi-energy load prediction models for integrated energy systems, the historical development law of the multi-energy loads must be considered. Moreover, understanding the complex coupling correlation of the different loads in the multi-energy systems, and accounting for other load-influencing factors such as weather, may further improve the forecasting performance of such models. In this study, a two-stage fuzzy optimization method is proposed for the feature selection and identification of the multi-energy loads. To enrich the information content of the prediction input feature, we introduced a copula correlation feature analysis in the proposed framework, which extracts the complex dynamic coupling correlation of multi-energy loads and applies Akaike information criterion (AIC) to evaluate the adaptability of the different copula models presented. Furthermore, we combined a NARX neural network with Bayesian optimization and an extreme learning machine model optimized using a genetic algorithm (GA) to effectively improve the feature fusion performances of the proposed multi-energy load prediction model. The effectiveness of the proposed short-term prediction model was confirmed by the experimental results obtained using the multi-energy load time-series data of an actual integrated energy system.

Construction of Folate-Conjugated and pH-Responsive Cell Membrane Mimetic Mixed Micelles for Desirable DOX Release and Enhanced Tumor-Cellular Target.

Smart multifunctional polymeric micelles are in urgent demand for future cancer diagnosis and therapy. In this paper, doxorubicin (DOX)-loaded folic acid (FA)-targeting and pH-responsive cell membrane mimetic mixed micelles of P(DMAEMA-co-MaPCL) (PCD) and FA-P(MPC-co-MaPCL) (PMCF) (mass ratio 5/5) were prepared by a dialysis method. The micelle size, morphology, X-ray powder diffraction (XRD), pH responsiveness, in vitro DOX release, cytotoxicity, and cellular uptake were studied in detail. The results indicated that DOX could be efficiently loaded into mixed micelles (PDMCF micelles), and the DOX-loaded mixed micelles (DOX@PDMCF micelles) exhibited a size of 150 nm and pH-responsive DOX release in an extended period. Furthermore, the DOX@PDMCF micelles could efficiently suppress the proliferation of tumor cells, HeLa and MCF-7 cells. Our data suggest that the DOX@PDMCF micelles have the potential to be applied in tumor therapy, especially for treating various folate receptor overexpressed tumors.

Enhanced Water Adsorption Performance of UiO-66 Modulated with p-Nitrobenzoic or p-Hydroxybenzoic Acid: Introduced Defects and Functional Groups.

Adding appropriate modulators can effectively improve the porosity and adsorption performance of UiO-66. Herein, UiO-66 samples were synthesized with p-nitrobenzoic acid (PNBA) and p-hydroxybenzoic acid (PHBA) as modulators. All samples exhibited good crystallinity and thermal stability. The polar functional groups (-NO2 and -OH) and defects were introduced into UiO-66, which significantly improved its water adsorption performance and applications in adsorption heat transformation. With the addition of six equiv PNBA, the saturated water uptake of UiO-66 increased from 0.40 to 0.58 g/g. Also, 4eqPNBA-UiO-66 exhibited the highest water uptake under low relative pressure, which was almost twice that of "low-defect" LD-UiO-66. The addition of PHBA had little effect on the saturated water absorption. However, its highest water uptake at P/P0 = 0.3 is 0.23 g/g, which is equivalent to that of 4eqPNBA-UiO-66. Ten consecutive adsorption/desorption cycles indicated that these samples had good cycle stability.

Size segregation of disk particle in two-dimensional chute.

Size segregation will lead to stratification of a particle system. At present, people have not fully understood the segregation mechanism. In this work, we have studied the size segregation behavior of two-component disk particles in chute flows. The effects of particle size ratio η, particle density ρ, static friction coefficient µ and chute angle α on size segregation are discussed. We use the discrete element method to simulate and calculate the force of disk large particles during segregation. Results show that the 'squeeze expulsion' mechanism plays a key role in the size segregation of a disk particle flow. We establish a physical model of 'squeeze expulsion' of disk particles and obtain the conditions for the formation of 'squeeze expulsion' mechanism.

Pathogenesis of α-Synuclein in Parkinson's Disease: From a Neuron-Glia Crosstalk Perspective.

Parkinson's disease (PD) is a progressive neurodegenerative disorder. The classical behavioral defects of PD patients involve motor symptoms such as bradykinesia, tremor, and rigidity, as well as non-motor symptoms such as anosmia, depression, and cognitive impairment. Pathologically, the progressive loss of dopaminergic (DA) neurons in the substantia nigra (SN) and the accumulation of α-synuclein (α-syn)-composed Lewy bodies (LBs) and Lewy neurites (LNs) are key hallmarks. Glia are more than mere bystanders that simply support neurons, they actively contribute to almost every aspect of neuronal development and function; glial dysregulation has been implicated in a series of neurodegenerative diseases including PD. Importantly, amounting evidence has added glial activation and neuroinflammation as new features of PD onset and progression. Thus, gaining a better understanding of glia, especially neuron-glia crosstalk, will not only provide insight into brain physiology events but also advance our knowledge of PD pathologies. This review addresses the current understanding of α-syn pathogenesis in PD, with a focus on neuron-glia crosstalk. Particularly, the transmission of α-syn between neurons and glia, α-syn-induced glial activation, and feedbacks of glial activation on DA neuron degeneration are thoroughly discussed. In addition, α-syn aggregation, iron deposition, and glial activation in regulating DA neuron ferroptosis in PD are covered. Lastly, we summarize the preclinical and clinical therapies, especially targeting glia, in PD treatments.

Supramolecular assembly of the beta-catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo.

Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in cancers. The tumor suppressors APC and Axin form the core of the multiprotein destruction complex, which targets the Wnt-effector beta-catenin for phosphorylation, ubiquitination and destruction. Based on earlier work, we hypothesize that the destruction complex is a supramolecular entity that self-assembles by Axin and APC polymerization, and that regulating assembly and stability of the destruction complex underlie its function. We tested this hypothesis in Drosophila embryos, a premier model of Wnt signaling. Combining biochemistry, genetic tools to manipulate Axin and APC2 levels, advanced imaging and molecule counting, we defined destruction complex assembly, stoichiometry, and localization in vivo, and its downregulation in response to Wnt signaling. Our findings challenge and revise current models of destruction complex function. Endogenous Axin and APC2 proteins and their antagonist Dishevelled accumulate at roughly similar levels, suggesting competition for binding may be critical. By expressing Axin:GFP at near endogenous levels we found that in the absence of Wnt signals, Axin and APC2 co-assemble into large cytoplasmic complexes containing tens to hundreds of Axin proteins. Wnt signals trigger recruitment of these to the membrane, while cytoplasmic Axin levels increase, suggesting altered assembly/disassembly. Glycogen synthase kinase3 regulates destruction complex recruitment to the membrane and release of Armadillo/beta-catenin from the destruction complex. Manipulating Axin or APC2 levels had no effect on destruction complex activity when Wnt signals were absent, but, surprisingly, had opposite effects on the destruction complex when Wnt signals were present. Elevating Axin made the complex more resistant to inactivation, while elevating APC2 levels enhanced inactivation. Our data suggest both absolute levels and the ratio of these two core components affect destruction complex function, supporting models in which competition among Axin partners determines destruction complex activity.

Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation.

Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.

Motion behaviour of ellipsoidal granular system under vertical vibration and airflow.

We studied the motion behaviour of ellipsoid particles under vertical vibration and airflow. Three typical convection patterns were observed when submitted to vertical vibration with frequency (f) from 20 Hz to 80 Hz and dimensionless vibration acceleration (Γ) from one to six. We studied the effects of f and Γ on the change of convection patterns. We quantitatively studied the effects of f, Γ, airflow direction, airflow velocity, and particle shape on the convection area and intensity using the area fraction λ and average velocity vz characterizing the convection area and intensity, respectively. Results showed that the convection first occured occurred in the upper part of the granular system. Increasing f and A can both increase the convection area and strengthen the convection intensity. A had a greater influence than f at the same Γ. The wheat particles were more likely to enter the global convection state under the action of the airflow in the opposite direction of gravity. The maximum convection intensity of wheat particles under the airflow in the opposite direction of gravity was approximately 30-35% of the value measured under the airflow along the direction of gravity. The convection area and maximum convection intensity of the spherical particles were approximately 85% and 93% of the measured values for the ellipsoidal particles, respectively. We also analysed the effects of f, Γ, airflow direction, airflow velocity, and particle shape on the convection area on the basis of energy dissipation.

Folate-Conjugated Cell Membrane Mimetic Polymer Micelles for Tumor-Cell-Targeted Delivery of Doxorubicin.

Tumor-targeting nano-drug-delivery systems hold great potential to improve the therapeutic efficacy and alleviate the side effects of cancer treatments. Herein, folic acid (FA)-decorated amphiphilic copolymer of FA-P(MPC- co-MaPCL) (MPC: 2-methacryloxoethyl phosphorylcholine, MaPCL: poly(ε-caprolactone) macromonomer) is synthesized and its micelles are fabricated for doxorubicin (DOX) delivery. And non-FA-decorated P(MPC- co-MaPCL) micelles are used as the control. Dynamic light scattering and scanning electron microscopy measurements reveal that FA-P(MPC- co-MaPCL) and P(MPC- co-MaPCL) micelles are spherical with average diameters of 140 and 90 nm, respectively. The evaluation in vitro demonstrates that the blank micelles are nontoxic, while DOX-loaded FA-P(MPC- co-MaPCL) micelles show significant cytotoxicity to HeLa cells and slight cytotoxicity to L929 cells. Moreover, the cellular uptake of DOX-loaded FA-P(MPC- co-MaPCL) micelles in HeLa cells are 4.3-fold and 1.7-fold higher than that of DOX-loaded P(MPC- co-MaPCL) micelles and free DOX after 6 h of incubation, respectively. These results indicate the great potential of this system in anticancer target drug-delivery applications.

Pretreatment nutritional risk as a prognostic factor in head and neck cancer patients receiving radiotherapy or chemoradiotherapy.

BACKGROUND AND OBJECTIVES: Head and neck cancer patients often experience nutritional deterioration, which decreases their treatment tolerance and is associated with poor outcomes. We analyzed nutritional status in head and neck cancer patients before and during treatment, and its impact on clinical outcomes. METHODS AND STUDY DESIGN: Between January 2009 and April 2012, 336 head and neck cancer patients receiving radiotherapy or chemoradiotherapy were prospectively entered into the study. The Nutritional Risk Screening 2002 (NRS 2002) assessment was used to evaluate their nutritional status. RESULTS: A total of 227 patients with nasopharyngeal carcinoma and 109 patients with head and neck cancers were analyzed. The proportion of patients receiving radiotherapy or chemoradiotherapy at nutritional risk was 61.3%, with 11.9% at risk before treatment and 49.4% developing risk during treatment. In multivariate analysis, nutritional risk before treatment was associated with T stage for the two groups. Risk was significantly higher in patients receiving concurrent chemoradiotherapy during treatment for nasopharygeal carcinoma patients. The prognosis of pretreatment nutritional risk patients was worse than those becoming at risk during treatment and those without nutritional risk (3-year overall survival 62.9% vs 81.7% vs 80.6%, p=0.026; 3-year disease-free survival 64.8% vs 84.5% vs 84.4%, p=0.019). CONCLUSIONS: The incidence of nutritional risk is high in head and neck cancer patients receiving radiotherapy or chemoradiotherapy, especially during treatment. Pretreatment nutritional risk evaluated using the NRS 2002 can predict patient prognosis.

Synthesis and Self-Assembly of the pH-Responsive Anionic Copolymers for Enhanced Doxorubicin-Loading Capacity.

Polyelectrolyte complex micelles self-assembled from an ionic polymer and oppositely charged small molecules are a promising drug delivery system. In this study, the anionic block copolymers composed of poly(ethylene glycol), poly(ε-caprolactone), and carboxyl modified poly(ε-caprolactone), COOH-PCEC, were designed to encapsulate doxorubicin (DOX) via electrostatic and hydrophobic interactions to form spherical micelles with a particle size of 90-140 nm. The higher payload capacity of these micelles than noncharged micelles of PCL-poly(ethylene glycol)-PCL (PCEC) was achieved, and it was strongly dependent on the composition of the micelles. In vitro drug release studies showed that the release of DOX from the micelles was faster at pH 5.5 than at pH 7.4, which was mainly due to the protonation of carboxyl groups and the solubility of DOX. Studies of intracellular uptake demonstrated that the DOX-loaded micelles could be internalized effectively by HeLa cells. In vitro cytotoxicity revealed that the blank COOH-PCEC micelles had a low cytotoxicity against both L929 and HeLa cells. However, the DOX-loaded micelles inhibited the growth of HeLa cells remarkably, demonstrating their potential for use as an efficient carrier for the delivery of DOX.

Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP.

Novel or rare variants in mitochondrial tRNA sequences may be observed after mitochondrial DNA analysis. Determining whether these variants are pathogenic is critical, but confirmation of the effect of a variant on mitochondrial function can be challenging. We have used available databases of benign and pathogenic variants, alignment between diverse tRNAs, structural information and comparative genomics to predict the impact of all possible single-base variants and deletions. The Mitochondrial tRNA Informatics Predictor (MitoTIP) is available through MITOMAP at www.mitomap.org. The source code for MitoTIP is available at www.github.com/sonneysa/MitoTIP.

Pelle Modulates dFoxO-Mediated Cell Death in Drosophila.

Interleukin-1 receptor-associated kinases (IRAKs) are crucial mediators of the IL-1R/TLR signaling pathways that regulate the immune and inflammation response in mammals. Recent studies also suggest a critical role of IRAKs in tumor development, though the underlying mechanism remains elusive. Pelle is the sole Drosophila IRAK homolog implicated in the conserved Toll pathway that regulates Dorsal/Ventral patterning, innate immune response, muscle development and axon guidance. Here we report a novel function of pll in modulating apoptotic cell death, which is independent of the Toll pathway. We found that loss of pll results in reduced size in wing tissue, which is caused by a reduction in cell number but not cell size. Depletion of pll up-regulates the transcription of pro-apoptotic genes, and triggers caspase activation and cell death. The transcription factor dFoxO is required for loss-of-pll induced cell death. Furthermore, loss of pll activates dFoxO, promotes its translocation from cytoplasm to nucleus, and up-regulates the transcription of its target gene Thor/4E-BP. Finally, Pll physically interacts with dFoxO and phosphorylates dFoxO directly. This study not only identifies a previously unknown physiological function of pll in cell death, but also shed light on the mechanism of IRAKs in cell survival/death during tumorigenesis.

Enhanced roles of biochar and organic fertilizer in microalgae for soil carbon sink.

Improved soil carbon sink capability is important for the mitigation of carbon dioxide emissions and the enhancement of soil productivity. Biochar and organic fertilizer (OF) showed a significant improving effect on microalgae in soil carbon sink capacity, and the ultimate soil total organic carbons with microalgae-OF, microalgae-biochar, microalgae-OF-biochar were about 16, 67 and 58% higher than that with microalgae alone, respectively, indicating that carbon fixation efficiency of microalgae applied in soil was improved with biochar and OF whilst the soil carbon capacity was promoted, the mechanism of which is illustrated through simulative experiments. Organic fertilizer could spur algal conversion of carbon into cell molecules by increasing intracellular polysaccharide production of microalgae. Biochar could change carbon metabolism pathway of microalgae through altering the yield of intracellular saccharides, and yield and type of extracellular saccharides. There was a superimposition effect on the soil carbon sink when biochar and OF were both present with microalgae.