Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

<p>Abstract</p> <p>Background</p> <p><it>Pichia pastoris </it>has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive <it>in silico </it>model of <it>P. pastoris </it>can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.</p> <p>Results</p> <p>A fully compartmentalized metabolic model of <it>P. pastoris </it>(<it>iPP</it>668), composed of 1,361 reactions and 1,177 metabolites, was reconstructed based on its genome annotation and biochemical information. The constraints-based flux analysis was then used to predict achievable growth rate which is consistent with the cellular phenotype of <it>P. pastoris </it>observed during chemostat experiments. Subsequent <it>in silico </it>analysis further explored the effect of various carbon sources on cell growth, revealing sorbitol as a promising candidate for culturing recombinant <it>P. pastoris </it>strains producing heterologous proteins. Interestingly, methanol consumption yields a high regeneration rate of reducing equivalents which is substantial for the synthesis of valuable pharmaceutical precursors. Hence, as a case study, we examined the applicability of <it>P. pastoris </it>system to whole-cell biotransformation and also identified relevant metabolic engineering targets that have been experimentally verified.</p> <p>Conclusion</p> <p>The genome-scale metabolic model characterizes the cellular physiology of <it>P. pastoris</it>, thus allowing us to gain valuable insights into the metabolism of methylotrophic yeast and devise possible strategies for strain improvement through <it>in silico </it>simulations. This computational approach, combined with synthetic biology techniques, potentially forms a basis for rational analysis and design of <it>P. pastoris </it>metabolic network to enhance humanized glycoprotein production.</p

Consistency of Lambda-Lambda hypernuclear events

Highlights of Lambda-Lambda emulsion events are briefly reviewed. Given three accepted events, shell-model predictions based on p-shell Lambda hypernuclear spectroscopic studies are shown to reproduce the Lambda-Lambda (LL) binding energies of LL10Be and LL13B in terms of the LL binding energy of LL6He. Predictions for other species offer judgement on several alternative assignments of the LL13B KEK-E176 event, and on the assignments LL11Be and LL12Be suggested recently for the KEK-E373 HIDA event. The predictions of the shell model, spanning a wide range of A values, are compared with those of cluster models, where the latter are available.Comment: Based on talk given by Avraham Gal at EXA 2011, Vienna, September 2011; Proceedings version prepared for the journal Hyperfine Interactions; v2--slight changes, matches published versio

AROS Is a Significant Biomarker for Tumor Aggressiveness in Non-cirrhotic Hepatocellular Carcinoma

Despite a low risk of liver failure and preserved liver function, non-cirrhotic hepatocellular carcinoma (HCC) has a poor prognosis. In the current study, we evaluated an active regulator of SIRT1 (AROS) as a prognostic biomarker in non-cirrhotic HCC. mRNA levels of AROS were measured in tumor and non-tumor tissues obtained from 283 non-cirrhotic HCC patients. AROS expression was exclusively up-regulated in recurrent tissues from the non-cirrhotic HCC patients (P = 0.015) and also in tumor tissues irrespective of tumor stage (P < 0.001) or BCLC stage (P < 0.001). High mRNA levels of AROS were statistically significantly associated with tumor stage (P < 0.001), BCLC stage (P = 0.007), alpha fetoprotein (AFP) level (P = 0.013), microvascular invasion (P = 0.001), tumor size (P = 0.036), and portal vein invasion (P = 0.005). Kaplan-Meir curve analysis demonstrated that HCC patients with higher AROS levels had shorter disease-free survival (DFS) in both the short-term (P < 0.001) and long-term (P = 0.005) compared to those with low AROS. Cox regression analysis demonstrated that AROS is a significant predictor for DFS along with large tumor size, tumor multiplicity, vascular invasion, and poor tumor differentiation, which are the known prognostic factors. In conclusion, AROS is a significant biomarker for tumor aggressiveness in non-cirrhotic hepatocellular carcinoma.1122Ysciescopu

A Large-Scale, Open-Domain, Mixed-Interface Dialogue-Based ITS for STEM

We present Korbit, a large-scale, open-domain, mixed-interface, dialogue-based intelligent tutoring system (ITS). Korbit uses machine learning, natural language processing and reinforcement learning to provide interactive, personalized learning online. Korbit has been designed to easily scale to thousands of subjects, by automating, standardizing and simplifying the content creation process. Unlike other ITS, a teacher can develop new learning modules for Korbit in a matter of hours. To facilitate learning across a widerange of STEM subjects, Korbit uses a mixed-interface, which includes videos, interactive dialogue-based exercises, question-answering, conceptual diagrams, mathematical exercises and gamification elements. Korbit has been built to scale to millions of students, by utilizing a state-of-the-art cloud-based micro-service architecture. Korbit launched its first course in 2019 on machine learning, and since then over 7,000 students have enrolled. Although Korbit was designed to be open-domain and highly scalable, A/B testing experiments with real-world students demonstrate that both student learning outcomes and student motivation are substantially improved compared to typical online courses

30 inch Roll-Based Production of High-Quality Graphene Films for Flexible Transparent Electrodes

We report that 30-inch scale multiple roll-to-roll transfer and wet chemical doping considerably enhance the electrical properties of the graphene films grown on roll-type Cu substrates by chemical vapor deposition. The resulting graphene films shows a sheet resistance as low as ~30 Ohm/sq at ~90 % transparency which is superior to commercial transparent electrodes such as indium tin oxides (ITO). The monolayer of graphene shows sheet resistances as low as ~125 Ohm/sq with 97.4% optical transmittance and half-integer quantum Hall effect, indicating the high-quality of these graphene films. As a practical application, we also fabricated a touch screen panel device based on the graphene transparent electrodes, showing extraordinary mechanical and electrical performances

SUMO-Specific Protease 2 (SENP2) Is an Important Regulator of Fatty Acid Metabolism in Skeletal Muscle

Small ubiquitin-like modifier (SUMO)-specific proteases (SENPs) that reverse protein modification by SUMO are involved in the control of numerous cellular processes, including transcription, cell division, and cancer development. However, the physiological function of SENPs in energy metabolism remains unclear. Here, we investigated the role of SENP2 in fatty acid metabolism in C2C12 myotubes and in vivo. In C2C12 myotubes, treatment with saturated fatty acids, like palmitate, led to nuclear factor-B-mediated increase in the expression of SENP2. This increase promoted the recruitment of peroxisome proliferator-activated receptor (PPAR) and PPAR, through desumoylation of PPARs, to the promoters of the genes involved in fatty acid oxidation (FAO), such as carnitine-palmitoyl transferase-1 (CPT1b) and long-chain acyl-CoA synthetase 1 (ACSL1). In addition, SENP2 overexpression substantially increased FAO in C2C12 myotubes. Consistent with the cell culture system, muscle-specific SENP2 overexpression led to a marked increase in the mRNA levels of CPT1b and ACSL1 and thereby in FAO in the skeletal muscle, which ultimately alleviated high-fat diet-induced obesity and insulin resistance. Collectively, these data identify SENP2 as an important regulator of fatty acid metabolism in skeletal muscle and further implicate that muscle SENP2 could be a novel therapeutic target for the treatment of obesity-linked metabolic disorders.11116Ysciescopu

A Novel Role of Three Dimensional Graphene Foam to Prevent Heater Failure during Boiling

We report a novel boiling heat transfer (NBHT) in reduced graphene oxide (RGO) suspended in water (RGO colloid) near critical heat flux (CHF), which is traditionally the dangerous limitation of nucleate boiling heat transfer because of heater failure. When the heat flux reaches the maximum value (CHF) in RGO colloid pool boiling, the wall temperature increases gradually and slowly with an almost constant heat flux, contrary to the rapid wall temperature increase found during water pool boiling. The gained time by NBHT would provide the safer margin of the heat transfer and the amazing impact on the thermal system as the first report of graphene application. In addition, the CHF and boiling heat transfer performance also increase. This novel boiling phenomenon can effectively prevent heater failure because of the role played by the self-assembled three-dimensional foam-like graphene network (SFG).open2

Carrier-mediated magnetoelectricity in complex oxide heterostructures

While tremendous success has been achieved to date in creating both single phase and composite magnetoelectric materials, the quintessential electric-field control of magnetism remains elusive. In this work, we demonstrate a linear magnetoelectric effect which arises from a novel carrier-mediated mechanism, and is a universal feature of the interface between a dielectric and a spin-polarized metal. Using first-principles density functional calculations, we illustrate this effect at the SrRuO$_3$/SrTiO$_3$ interface and describe its origin. To formally quantify the magnetic response of such an interface to an applied electric field, we introduce and define the concept of spin capacitance. In addition to its magnetoelectric and spin capacitive behavior, the interface displays a spatial coexistence of magnetism and dielectric polarization suggesting a route to a new type of interfacial multiferroic