Structure-aware parametric representations for time-resolved light transport.

Time-resolved illumination provides rich spatiotemporal information for applications such as accurate depth sensing or hidden geometry reconstruction, becoming a useful asset for prototyping and as input for data-driven approaches. However, time-resolved illumination measurements are high-dimensional and have a low signal-to-noise ratio, hampering their applicability in real scenarios. We propose a novel method to compactly represent time-resolved illumination using mixtures of exponentially modified Gaussians that are robust to noise and preserve structural information. Our method yields representations two orders of magnitude smaller than discretized data, providing consistent results in such applications as hidden-scene reconstruction and depth estimation, and quantitative improvements over previous approaches.

Benchmark Examination of Blood Amino Acids Patterns in Phenylketonuria Neonates and Young Children on Phenylalanine-Restricted Dietary Treatment.

Background: Phenylalanine-restricted diets have been the basis of therapy for phenylketonuria; however, little is known how this treatment effects homeostasis of other amino acids. This study aimed to assess blood amino acid alterations in phenylketonuric neonates before and after treatment to identify any residual amino acid alterations with phenylalanine restriction in these treated children. Methods: Concentrations of 11 amino acids were measured using liquid chromatography-tandem mass spectrometry performed on dried blood spots. Results: Elevated blood phenylalanine, arginine, citrulline, valine, methionine concentrations and decreased tyrosine, proline concentrations were observed in phenylketonuria neonates relative to controls, of which phenylalanine, arginine, methionine, tyrosine, and proline levels could be either partially or completely restored with dietary intervention, whereas citrulline and valine were not restored and remained higher. Conclusions: Blood amino acid homeostasis is disrupted in phenylketonuria. Although dietary intervention adjusts amino acid homeostasis in the direction of a healthy equilibrium, complete restoration is not achieved.

Clinical, biochemical and molecular spectrum of mild 6-pyruvoyl-tetrahydropterin synthase deficiency and a case report.

Background 6-Pyruvoyl-tetrahydropterin synthase (PTS) is the key enzyme in BH4 synthesis. PTS deficiency is classified as severe type and mild type, and the prognosis and treatment differ for these types. Distinguishing between two types in the early stage is difficult. Reference to reported cases is needed for interpretation of the correlation between genotype and prognosis. Case report: We report a full-term female newborn with mild PTS deficiency. On the day 21 after birth, the phenylalanine level was 859.6 mmol/L (reference range: 30-117 mmol/L). After 1 year of observation, the patient was found to be in a healthy condition without treatment. Conclusions: Although the phenylalanine level is high in mild PTS deficiency patients after birth, some of them may have few symptoms with no treatment. We review 19 cases and find 8 mutations of PTS that may be associated with mild PTS deficiency.

UNG2 deacetylation confers cancer cell resistance to hydrogen peroxide-induced cytotoxicity.

Cancer therapeutics produce reactive oxygen species (ROS) that damage the cancer genome and lead to cell death. However, cancer cells can resist ROS-induced cytotoxicity and survive. We show that nuclear-localized uracil-DNA N-glycosylase isoform 2 (UNG2) has a critical role in preventing ROS-induced DNA damage and enabling cancer-cell resistance. Under physiological conditions, UNG2 is targeted for rapid degradation via an interaction with the E3 ligase UHRF1. In response to ROS, however, UNG2 protein in cancer cells exhibits a remarkably extended half-life. Upon ROS exposure, UNG2 is deacetylated at lysine 78 by histone deacetylases, which prevents the UNG2-UHRF1 interaction. Accumulated UNG2 protein can thus excise the base damaged by ROS and enable the cell to survive these otherwise toxic conditions. Consequently, combining HDAC inhibitors (to permit UNG2 degradation) with genotoxic agents (to produce cytotoxic cellular levels of ROS) leads to a robust synergistic killing effect in cancer cells in vitro. Altogether, these data support the application of a novel approach to cancer treatment based on promoting UNG2 degradation by altering its acetylation status using an HDAC inhibitor.

Analyzing the suitability of a baffled orbitally shaken bioreactor for cells cultivation using the computational fluid dynamics approach.

Orbitally shaken bioreactors (OSRs) is one of important bioreactors for mammalian cells cultivation in suspension, especially for the screening of valuable microorganisms and in basic bioprocess development experiments. However, the suitability of OSRs for cells culture in large scale is still under development. In this article, a new kind of OSRs with baffle structure was proposed and a three-dimensional CFD model was established to analyze the influence of baffle structure on the flow field. Lower installation height of baffles was found suitable for improving the mixing efficiency. Compared to the unbaffled OSR, the baffled OSR could enhance the level of oxygen transfer largely but the oxygen transfer rate was independent on the baffle installation height. Moreover, as the baffle installation height increased, the energy transferred for liquid motion was decreased. Finally, the shear stress of the baffled OSRs proposed was gentle for mammalian cells growth. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2746, 2019.

Characterizing the fluid dynamics of the inverted frustoconical shaking bioreactor.

The authors conducted a three-dimensional computational fluid dynamics (CFD) simulation to calculate the flow field in the inverted frustoconical shaking bioreactor with 5 L working volume (IFSB-5L). The CFD models were established for the IFSB-5L at different operating conditions (different shaking speeds and filling volumes) and validated by comparison of the liquid height distribution in the agitated IFSB-5L. The "out of phase" operating conditions were characterized by analyzing the flow field in the IFSB-5L at different filling volumes and shaking speeds. The values of volumetric power consumption (P/VL ) and volumetric mass transfer coefficient (kL a) were determined from simulated and experimental results, respectively. Finally, the operating condition effect on P/VL and kL a was investigated. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:478-485, 2018.

Characterizing the fluid dynamics in the flow fields of cylindrical orbitally shaken bioreactors with different geometry sizes.

Orbitally shaken bioreactors (OSRs) are commonly used for the cultivation of mammalian cells in suspension. To aid the geometry designing and optimizing of OSRs, we conducted a three-dimensional computational fluid dynamics (CFD) simulation to characterize the flow fields in a 10 L cylindrical OSR with different vessel diameters. The liquid wave shape captured by a camera experimentally validated the CFD models established for the cylindrical OSR. The geometry size effect on volumetric mass transfer coefficient (kLa) and hydromechanical stress was analyzed by varying the ratio of vessel diameter (d) to liquid height at static (h L), d/h L. The highest value of kLa about 30 h-1 was observed in the cylindrical vessel with the d/h L of 6.35. Moreover, the magnitudes of shear stress and energy dissipation rate in all the vessels tested were below their minimum values causing cells damage separately, which indicated that the hydromechanical-stress environment in OSRs is suitable for cells cultivation in suspension. Finally, the CFD results suggested that the d/h L higher than 8.80 should not be adopted for the 10 L cylindrical OSR at the shaking speed of 180 rpm because the "out of phase" state probably will happen there.

Studies on fluid dynamics of the flow field and gas transfer in orbitally shaken tubes.

Orbitally shaken cylindrical bioreactors [OrbShake bioreactors (OSRs)] without an impeller or sparger are increasingly being used for the suspension cultivation of mammalian cells. Among small volume OSRs, 50-mL tubes with a ventilated cap (OSR50), originally derived from standard laboratory centrifuge tubes with a conical bottom, have found many applications including high-throughput screening for the optimization of cell cultivation conditions. To better understand the fluid dynamics and gas transfer rates at the liquid surface in OSR50, we established a three-dimensional simulation model of the unsteady liquid forms (waves) in this vessel. The studies verified that the operating conditions have a large effect on the interfacial surface. The volumetric mass transfer coefficient (kL a) was determined experimentally and from simulations under various working conditions. We also determined the liquid-phase mass transfer coefficient (kL ) and the specific interfacial area (a) under different conditions to demonstrate that the value of a affected the gas transfer rate more than did the value of kL . High oxygen transfer rates, sufficient for supporting the high-density culture of mammalian cells, were found. Finally, the average axial velocity of the liquid was identified to be an important parameter for maintaining cells in suspension. Overall these studies provide valuable insights into the preferable operating conditions for the OSR50, such as those needed for cell cultures requiring high oxygen levels. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:192-200, 2017.

SET7/9 regulates cancer cell proliferation by influencing ß-catenin stability.

ß-Catenin, which is a key mediator of the wingless-integration site (Wnt)/ß-catenin signaling pathway, plays an important role in cell proliferation, cell fate determination, and tumorigenesis, by regulating the expression of a wide range of target genes. Although a variety of posttranslational modifications are involved in ß-catenin activity, the role of lysine methylation in ß-catenin activity is largely unknown. In this study, su(var)3-9, enhancer-of-zeste, trithorax (SET) domain-containing protein 7 (SET7/9), a lysine methyltransferase, interacted with and methylated ß-catenin, as demonstrated both in vitro and in vivo. The interaction and methylation were significantly enhanced in response to H2O2 stimulation. A mutagenesis assay and mass spectrometric analyses revealed that ß-catenin was monomethylated by SET7/9 at lysine residue 180. Methylated ß-catenin was easily recognized by phosphokinase glycogen synthase kinase (GSK)-3ß for degradation. Consistent with this finding, the mutated ß-catenin (K180R) that cannot be methylated exhibited a longer half-life than did the methylated ß-catenin. The consequent depletion of SET7/9 by shRNA or the mutation of the ß-catenin (K180R) significantly enhanced the expression of Wnt/ß-catenin target genes such as c-myc and cyclin D1 and promoted the growth of cancer cells. Together, these results provide a novel mechanism by which Wnt/ß-catenin signaling is regulated in response to oxidative stress.

Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTOR-dependent pathway.

Macroautophagy is an evolutionarily conserved cellular process involved in the clearance of proteins and organelles. Although the autophagy regulation machinery has been widely studied, the key epigenetic control of autophagy process still remains unknown. Here we report that the methyltransferase EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) epigenetically represses several negative regulators of the MTOR (mechanistic target of rapamycin [serine/threonine kinase]) pathway, such as TSC2, RHOA, DEPTOR, FKBP11, RGS16 and GPI. EZH2 was recruited to these genes promoters via MTA2 (metastasis associated 1 family, member 2), a component of the nucleosome remodeling and histone deacetylase (NuRD) complex. MTA2 was identified as a new chromatin binding protein whose association with chromatin facilitated the subsequent recruitment of EZH2 to silenced targeted genes, especially TSC2. Downregulation of TSC2 (tuberous sclerosis 2) by EZH2 elicited MTOR activation, which in turn modulated subsequent MTOR pathway-related events, including inhibition of autophagy. In human colorectal carcinoma (CRC) tissues, the expression of MTA2 and EZH2 correlated negatively with expression of TSC2, which reveals a novel link among epigenetic regulation, the MTOR pathway, autophagy induction, and tumorigenesis.

Systematic identification of Class I HDAC substrates.

Lysine acetylation is a common post-translational modification of histone and non-histone proteins. This process has an important function in regulating transcriptional activities and other biological processes. Although several computer programs have been developed to predict protein acetylation sites, deacetylases responsible for known or predicted acetylation sites remain unknown. In this research, Class I histone deacetylases (HDACs) substrates were manually obtained, and sequence features of deacetylation sites were analyzed. We found that three members of Class I HDACs (HDAC1, HDAC2 and HDAC3) shared similar sequence features. Therefore, a method was proposed to identify the substrates of Class I HDACs. We evaluated the efficiency of the prediction based on P-value distribution analysis and leave-one-out test. To validate the result of the prediction, we overexpressed Class I HDACs in cells and detected the acetylation levels of potential substrates. In the experiment, five of the seven predicted proteins were deacetylated by Class I HDACs. These results suggested that our method could effectively predict protein deacetylation sites. The work has been integrated to the website ASEB, which was freely available at http://cmbi.bjmu.edu.cn/huac.

Methylation of SUV39H1 by SET7/9 results in heterochromatin relaxation and genome instability.

Suppressor of variegation 3-9 homolog 1 (SUV39H1), a histone methyltransferase, catalyzes histone 3 lysine 9 trimethylation and is involved in heterochromatin organization and genome stability. However, the mechanism for regulation of the enzymatic activity of SUV39H1 in cancer cells is not yet well known. In this study, we identified SET domain-containing protein 7 (SET7/9), a protein methyltransferase, as a unique regulator of SUV39H1 activity. In response to treatment with adriamycin, a DNA damage inducer, SET7/9 interacted with SUV39H1 in vivo, and a GST pull-down assay confirmed that the chromodomain-containing region of SUV39H1 bound to SET7/9. Western blot using antibodies specific for antimethylated SUV39H1 and mass spectrometry demonstrated that SUV39H1 was specifically methylated at lysines 105 and 123 by SET7/9. Although the half-life and localization of methylated SUV39H1 were not noticeably changed, the methyltransferase activity of SUV39H1 was dramatically down-regulated when SUV39H1 was methylated by SET7/9. Consequently, H3K9 trimethylation in the heterochromatin decreased significantly, which, in turn, led to a significant increase in the expression of satellite 2 (Sat2) and α-satellite (α-Sat), indicators of heterochromatin relaxation. Furthermore, a micrococcal nuclease sensitivity assay and an immunofluorescence assay demonstrated that methylation of SUV39H1 facilitated genome instability and ultimately inhibited cell proliferation. Together, our data reveal a unique interplay between SET7/9 and SUV39H1--two histone methyltransferases--that results in heterochromatin relaxation and genome instability in response to DNA damage in cancer cells.

[Advances in effector protein of histone methylation].

As a significant epigenetic regulation mechanism, histone methylation plays an important role in many biological processes. In cells, there are various histone methyltransferases and histone demethylases working cooperatively to regulate the histone methylation state. Upon histone modification, effector proteins recognize modification sites specifically, and affect gene transcriptional process. This review mainly focuses on recent advances in histone methylation effector protein's function mechanism.