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Design and synthesis of synthetic promoters for consistency of gene expression across growth phases and scale in ***

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Synthetic and Systems Biotechnology 2024年第2期9卷 330-339页

作者： Kristin V.Presnell Omar Melhem Sarah M.Coleman Nicholas J.Morse hal S.Alper McKetta Department of Chemical Engineering The University of Texas at Austin200E Dean Keeton St.Stop C0400AustinTX78712USA Institute for Cellular and Molecular Biology The University of Texas at Austin2500 Speedway AvenueAustinTX78712USA

Metabolic engineering and synthetic biology endeavors benefit from promoters that perform consistently(or robustly)with respect to cellular growth phase(exponential and stationary)and fermentation scale(microtiter plates,tubes,flasks,and bioreactors).However,nearly all endogenous promoters(especially in Saccharomyces cerevisiae)do not perform in this *** this work,a hybrid promoter engineering strategy is leveraged to create novel synthetic promoters with robustness across these *** a multi-dimensional RNA-seq dataset,promoters with specific phase dependencies were *** enriched with functional transcription factors were identified using MEME *** motif-containing fragments could impart activity dependence in the opposing ***,we obtain two new promoters with high and consistent expression across both phases by increasing the exponential phase activity of the starting stationary-phase scaffold by 38 and 23-fold ***,we show that these promoters function consistently across various laboratory growth scales over time in a microtiter plate and in ***,this work presents and validates a new strategy for engineering promoters in *** with high levels of expression that are robust to cellular growth phase and the scale of the culture.

关键词： endogenous synthetic stationary

Prediction of HLA-A2-restricted CTL epitope specific to HCC by SYFPEITHI combined with polynomial method

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World Journal of Gastroenterology 2005年第2期11卷 208-211页

作者： hal-LongDong Yan-FangSui Departmentofpathology FourthMilitaryMedicalUniversityXi'an710032ShaanxiProvinceChina Departmentofpathology FourthMilitaryMedicalUniversityXi'an710032ShaanxiProvinceChina

AIM: To predict the HLA-A2-restricted CTL epitopes of tumor antigens associated with hepatocellular carcinoma (HCC).METHODS: MAGE-1, MAGE-3, MAGE-8, P53 and AFP were selected as objective antigens in this study for the close association with HCC. The HLA-A*0201 restricted CTL epitopes of objective tumor antigens were predicted by SYFPEITHI prediction method combined with the polynomial quantitative motifs method. The threshold of polynomial scores was set to -***: The SYFPEITHI prediction values of all possible nonamers of a given protein sequence were added together and the ten high-scoring peptides of each protein were chosen for further analysis in primary prediction. Thirtyfive candidates of CTL epitopes (nonamers) derived from the primary prediction results were selected by analyzing with the polynomial method and compared with reported CTL ***: The combination of SYFPEITHI prediction method and polynomial method can improve the prediction efficiency and accuracy. These nonamers may be useful in the design of therapeutic peptide vaccine for HCC and as immunotherapeutic strategies against HCC after identified by immunology experiment.

关键词： Hepatocellular carcinoma HLA-A*0201 Cytotoxic T Lymphocyte Epitope

A reflection on the contrast between the Cooper pairing in iron-based and conventional superconductors

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Frontiers of physics 2011年第4期6卷 350-356页

作者： Fa Wang Dung-hal Lee Department of Physics Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Physics University of California at Berkeley Berkeley CA 94720 USA Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA

In this Perspective article we review retrospectively the streamline of our work on iron-based superconductors, and reflect on the mechanism of Cooper pairing in conventional and unconventional, such as iron-based sup... 详细信息

关键词： Cooper pairing iron-based superconductors effective interaction renormalizationgroup

On the Bifurcations of a Hamiltonian Having Three Homoclinic Loops under Z_3 Invariant Quintic Perturbations

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Acta Mathematica Sinica,English Series 2007年第5期23卷 869-878页

作者： Yu hal WU Mao An HAN Department of Mathematics Jiang Su University Zhenjiang 212013 P. R. China Department of Mathematics Shanghai Normal University Shanghai 200234 P. R. China

A cubic system having three homoclinic loops perturbed by Z3 invariant quintic polynomials is considered. By applying the qualitative method of differential equations and the numeric computing method, the Hopf bifurcation, homoclinic loop bifurcation and heteroclinic loop bifurcation of the above perturbed system are studied. It is found that the above system has at least 12 limit cycles and the distributions of limit cycles are also given.

关键词： homoclinic loop bifurcation heteroclinic loop bifurcation Hopf bifurcation stability limit cycles

State Sampling Dependence of Hopfield Network Inference

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Communications in Theoretical Physics 2012年第1期57卷 169-172页

作者： HUANG hal-Ping Key Laboratory of Frontiers in Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China Department of Physics Hong Kong University of Science and TechnologyHong KongChina

The fully connected Hopfield network is inferred based on observed magnetizations and pairwise *** present the system in the glassy phase with low temperature and high memory *** find that the inference error is very sensitive to the form of state *** a single state is sampled to compute magnetizations and correlations,the inference error is almost indistinguishable irrespective of the sampled ***,the error can be greatly reduced if the data is collected with state *** result holds for different disorder samples and accounts for the previously observed large fluctuations of inference error at low temperatures.

关键词： inference Hopfield network spin glass

Highly Oxygenated Monoterpenes from Eupatorium fortunei

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Chinese Chemical Letters 2005年第9期16卷 1217-1219页

作者： hal Xia JIANG Kun GAO State Key Laboratory of Applied Organic Chemistry College of Chemistry and Chemical Engineering Lanzhou University Lanzhou 730000

A pair of epimers of highly-oxygenated monoterpenes were isolated from the traditional Chinese medicine Eupatorium fortunei. Their structures were elucidated on the basis of the spectral analysis as （1R＊, 2S＊, 3R＊, 4R＊, 6S＊）-1, 2, 3, 6-tetrehydroxy-p-menthane （1） and （1S＊, 2S＊, 3S＊, 4R＊, 6R＊）-1, 2, 3, 6-tetrehydroxy-p-menthane （2）.

关键词： Eupatorium fortunei traditional Chinese medicine epimer highly-oxygenated monoterpenes

Molecular Interaction Study to Explore the Nigella sativa Bioactive Components as an Inhibitor of Peptide Deformylase to Inhibit the Xanthomonas oryzae *** via Applying Computational Approach

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Phyton-International Journal of Experimental Botany 2022年第9期91卷 1923-1931页

作者： Pravej Alam Thamer hal balawi Department of Biology College of Sciences and HumanitiesPrince Sattam bin Abdulaziz UniversityAl-Kharj11942Saudi Arabia

Bacterial leaf blight(BLB)caused by Xanthomonas oryzae ***(Xoo)is one of the most damaging diseases to rice across the *** chemicals have been employed so far for the management of bacterial leaf *** the other hand,these compounds are damaging to the ecosystem and have an impact on non-target species such as humans and *** a result,there is a need to create a new natural inhibitor for BLB ***(PDF)enzyme is present in all eubacteria and its necessity in bacterial protein synthesis reveals it as an attractive target for drug *** this study,the active components of Nigella sativa have been selected based on their previously reported antimicrobial activity and screened on the active site of bacterial PDF by the in silico art of *** these compounds,dithymoquinone and p-cymene strongly bind with the PDF enzyme with binding energy values of 7.77 kcal/mol and 7.26 kcal/mol,respectively,which is comparatively higher than the control compound(−6.73 kcal/mol).Hence,the“dithymoquinone-PDF”and“p-cymene-PDF”complexes were selected for further study,and their stability was assessed by molecular dynamic(MD)*** MD simulation,both selected compounds exhibited steady-state interaction with PDF for 20 *** has been hypothesized that p-cymene and dithymoquinone inhibit peptide deformylase and could be used as antibacterials or pesticides against Xoo against the BLB disease.

关键词： Nigella sativa peptide deformylase molecular dynamic dithymoquinone

A thermodynamic model on predicting density of medium-Mn steels with experimental verification

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Journal of Iron and Steel Research International 2017年第11期24卷 1078-1084页

作者： Guo-hui Shen Peng-yu Wen hal-wen Luo School of Metallurgical and Ecological Engineering University of Science and Technology BeijingBeijing 100083China

A new model on predicting the density of hot-rolled multi-phased medium-Mn steel has been presen ted on the basis of thermodynamic calculations. This is an integrated model, which includes one for calculating the retained austenite （RA） fraction and the other for volume expansion during the aus tenite-to martensite transformation, because both of them are key parameters for calculating the den- sity of steel at ambient temperature. The existing empirical equations for calculating Mx temperature and lattice constants of both martensite and austenite have been all rcassessed by the XRD measure ments on the microstructures of seven hot-rolled medium-Mn steels. Finally, the densities ot seven steels were calculated merely from compositions and compared with the measured ones. The differ ence between them is no more than 1 %, suggesting that the presented model should be of good value in designing the low density steels.

关键词： Density Medium Mn steel Retained austenite fraction Volume expansion Transformation

On Some Diophantine Fourier Series

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Acta Mathematica Sinica,English Series 2010年第6期26卷 1125-1132页

作者： hal Long LI Jing MA Wen Peng ZHANG Department of Mathematics Weinan Teachers University Weinan 714000 P. R. China Department of Mathematics Jilin University Changchun 130012 P. R. China Department of Mathematics Northwest University Xi'an 710069 P. R. China

We continue our study on arithmetical Fourier series by considering two Fourier series which are related to Diophantine analysis. The first one was studied by Hardy and Littlewood in connection with the classification... 详细信息

关键词： Diophantine Fourier series Diophantine Dirichlet series Riesz sum