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Design and synthesis of synthetic UP elements for modulation of gene expression in Escherichia coli

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Synthetic and Systems Biotechnology 2019年第2期4卷 99-106页

作者： kristin v.presnell Madeleine Flexer-Harrison Hal SAlper McKetta Department of Chemical Engineering The University of Texas at Austin200 E Dean Keeton St.Stop C0400AustinTX78712USA Institute for Cellular and Molecular Biology The University of Texas at Austin2500 Speedway AvenueAustinTX78712USA

Metabolic engineering requires fine-tuned gene expression for most pathway optimization *** develop a suitable suite of promoters,traditional bacterial promoter engineering efforts have focused on modifications to the core region,especially the−10 and−35 regions,of native ***,we demonstrate an alternate,unexplored route of promoter engineering through randomization of the UP element of the promoter—a region that contacts the alpha subunit carboxy-terminal domain instead of the sigma subunit of the RNA polymerase *** this work,we identify five novel UP element sequences through library-based searches in Escherichia *** resulting elements were used to activate the *** core promoter,rrnD promoter,to levels on par and higher than the prevalent strong bacterial promoter,*** relative levels of expression activation were transferrable when applied upstream of alternate core promoter sequences,including rrnA and *** work thus presents and validates a novel strategy for bacterial promoter engineering with transferability across varying core promoters and potential for transferability across bacterial species.

关键词： UP element Promoter engineering Expression modulation

Hepatocellular Ballooning is Due to Highly Pronounced Glycogenosis Potentially Associated with Steatosis and Metabolic Reprogramming

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Journal of Clinical and Translational Hepatology 2024年第1期12卷 52-61页

作者： Silvia Ribback kristin Peters Mohd Yasser Jessica Prey Paula Wilhelmi Qin Su Frank Dombrowski Peter Bannasch Institut für Pathologie Universitaetsmedizin GreifswaldGreifswaldGermany Cell Marque Millipore-SigmaRocklinCAUSA German Cancer Research Center(DKFZ) HeidelbergGermany

Background and Aims:Hepatocellular ballooning is a common finding in chronic liver disease,mainly characterized by rarefied cytoplasm that often contains Mallory-Denk bodies(MDB).Ballooning has mostly been attributed to degeneration but its striking resemblance to glycogenotic/steatotic changes characterizing preneoplastic hepatocellular lesions in animal models and chronic human liver diseases prompts the question whether ballooned hepatocytes(BH)are damaged cells on the path to death or rather viable cells,possibly involved in neoplastic ***:Using specimens from 96 cirrhotic human livers,BH characteristics were assessed for their glycogen/lipid stores,enzyme activities,and proto-oncogenic signaling cascades by enzyme-and immunohistochemical approaches with serial paraffin and cryostat ***:BH were present in 43.8%of cirrhotic *** pronounced excess glycogen storage of(glycogenosis)and/or lipids(steatosis)were characteristic,ground glass features and MDB were often *** glucose-6-phosphatase,increased glucose-6-phosphate dehydrogenase activity and altered immunoreactivity of enzymes involved in glycolysis,lipid metabolism,and cholesterol biosynthesis were ***,components of the insulin signaling cascade were upregulated along with insulin dependent glucose transporter glucose transporter 4 and the v-akt murine thymoma viral oncogene homolog/mammalian target of rapamycin signaling pathway associated with de novo ***:BH are hallmarked by particularly pronounced glycogenosis with facultative steatosis,many of their features being reminiscent of metabolic aberrations documented in preneoplastic hepatocellular lesions in experimental animals and chronic human liver ***,BH are not damaged entities facing death but rather viable cells featuring metabolic reprogramming,indicative of a preneoplastic nature.

关键词： Chronic liver disease Carbohydrate metabolism Insulin signaling Preneoplasia Metabolic reprogramming

HDPairFinder:A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water

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Journal of Environmental Sciences 2024年第2期136卷 583-593页

作者： Tingting Zhao kristin Carroll Caley B.Craven Nicholas J.P.Wawryk Shipei Xing Jian Guo Xing-Fang Li Tao Huan Department of Chemistry Faculty of ScienceUniversity of British ColumbiaVancouver Campus2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6G 2G3Canada

The combination of hydrogen/deuterium(H/D)formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry(HPLC-HRMS)is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water *** the huge amount of chemical information generated in HPLC-HRMS analysis,identifying all possible H/Dlabeled amino chemicals presents a significant challenge in data *** address this,we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLC-HRMS data with high accuracy and ***,we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects,which enables reliable pairing of H-and D-labeled ***,we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation,salt adduction,and natural13C ***,we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound ***,we integrated these modules into a freely available R program,*** rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water *** further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants,thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water *** is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples,and will facilitate a better understanding of N-containing chemical compounds in water.

关键词： Isotope labeling Nontargeted analysis Reactive N-compounds HPLC-HRMS Source water

Metabolic syndrome and the urinary microbiome of patients undergoing percutaneous nephrolithotomy

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Asian Journal of Urology 2024年第2期11卷 316-323页

作者： Ryan A.Dornbier Chirag P.Doshi Shalin C.Desai Petar Bajic Michelle van Kuiken Mark Khemmani Ahmer v.Farooq Larissa Bresler Thomas M.T.Turk Alan J.Wolfe kristin G.Baldea Loyola University Medical Center Department of UrologyMaywoodILUSA Loyola University Chicago Department of Microbiology and ImmunologyMaywoodILUSA

Objective:To identify possible stone-promoting microbes,we compared the profiles of microbes grown from stones of patients with and without metabolic syndrome(MetS).The association between MetS and urinary stone disease is well established,but the exact pathophysiologic relationship remains *** evidence suggests urinary tract dysbiosis may lead to increased nephrolithiasis ***:At the time of percutaneous nephrolithotomy,bladder urine and stone fragments were collected from patients with and without *** sample types were subjected to expanded quantitative urine culture(EQUC)and 16 S ribosomal RNA gene ***:Fifty-seven patients included 12 controls(21.1%)and 45 MetS patients(78.9%).Both cohorts were similar with respect to demographics and non-MetS *** controls had uric acid stone *** EQUC,bacteria were detected more frequently in MetS stones(42.2%)compared to controls(8.3%)(p=0.041).Bacteria also were more abundant in stones of MetS patients compared to *** validate our EQUC results,we performed 16 S ribosomal RNA gene *** 12/16(75.0%)sequence-positive stones,EQUC reliably isolated at least one species of the sequenced *** were detected in both“infectious”and“non-infectious”stone ***:Bacteria are more common and more abundant in MetS stones than control *** findings support a role for bacteria in urinary stone disease for patients with MetS regardless of stone composition.

关键词： Nephrolithiasis Urolithiasis Metabolic syndrome Urinary microbiome Percutaneous nephrolithotomy

Evaluation of thermodynamic equations of state across chemistry and structure in the materials project

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npj Computational Materials 2018年第1期4卷 323-329页

作者： Katherine Latimer Shyam Dwaraknath Kiran Mathew Donald Winston kristin A.Persson Department of Physics University of California BerkeleyBerkeleyCA 94720USA Energy Storage and Distributed Resources Division Lawrence Berkeley National LabBerkeleyCA 94720USA Department of Materials Science University of California BerkeleyBerkeleyCA 94720USA

Thermodynamic equations of state(EOS)for crystalline solids describe material behaviors under changes in pressure,volume,entropy and temperature,making them fundamental to scientific research in a wide range of fields including geophysics,energy storage and development of novel *** over a century of theoretical development and experimental testing of energy–volume(E–v)EOS for solids,there is still a lack of consensus with regard to which equation is indeed optimal,as well as to what metric is most appropriate for making this *** this study,several metrics were used to evaluate quality of fit for 8 different EOS across 87 elements and over 100 compounds which appear in the *** findings do not indicate a clear“best”EOS,but we identify three which consistently perform well relative to the rest of the ***,we find that for the aggregate data set,the RMSrD is not strongly correlated with the nature of the compound,e.g.,whether it is a metal,insulator,or semiconductor,nor the bulk modulus for any of the EOS,indicating that a single equation can be used across a broad range of classes of materials.

关键词： materials. solids state

Update on the Development of Anti-viral Agents Against Hepatitis C

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Journal of Clinical and Translational Hepatology 2013年第1期1卷 9-21页

作者： kristin L. MacArthur Robert Smolic Martina v. Smolic Catherine H. Wu George Y. Wu Department of Medicine Beth Israel Deaconess Medical Center Boston MA02215 Faculty of Medicine Osijek Croatia University of Connecticut Health Center Farmington CT USA Department of Medicine Division of Gastroenterology-Hepatology University of Connecticut Health Center Farmington CT USA

Hepatitis C virus (HCv) infects nearly 170 million people worldwide and causes chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The search for a drug regimen that maximizes efficacy and minimizes side effects is quickly evolving. This review will discuss a wide range of drug targets currently in all phases of development for the treatment of HCv. Direct data from agents in phase Ⅲ/Ⅳ clinical trials will be presented, along with reported side-effect profiles. The mechanism of action of all treatments and resistance issues are highlighted. Special attention is given to available trial data supporting interferon-free treatment regimens. HCv has become an increasingly important public health concern, and it is important for physicians to stay up to date on the rapidly growing novel therapeutic options.

关键词： HCv Protease Polymerase Triple therapy Drug.

小型田鼠:研究单配制进化与调控的模型(英文)

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兽类学报 2005年第2期25卷 182-199页

作者： Bruce S Cushing kristin M Kramer The Brain Body Center Department of PsychiatryCollege of MedicineUniversity of Illinoisat ChicagoChicagoIL60612USAThe Brain Body CenterDepartment of PsychiatryCollege of MedicineUniversity of Illinoisat ChicagoChicagoIL60612USA

哺乳动物的单配制通常被认为是社会性单配制,它不是单纯地由性行为来决定,而是由诸多因素,包括长期的pairbond、夫妻双方共同抚育后代、免近亲交配以及雌雄两性相似等来决定的。在这篇综述中,我们论述了如何以啮齿类田鼠属(Microtus)为... 详细信息

哺乳动物的单配制通常被认为是社会性单配制,它不是单纯地由性行为来决定,而是由诸多因素,包括长期的pairbond、夫妻双方共同抚育后代、免近亲交配以及雌雄两性相似等来决定的。在这篇综述中,我们论述了如何以啮齿类田鼠属(Microtus)为模型,通过比较研究来帮助我们理解社会性单配制的进化以及其神经调控机制。对田鼠属的研究不仅证实了单配制起源于艰苦的生存条件的假说,而且还证实了雌性性选择可能有利于维持单配制。不仅如此,哺乳动物单配制的进化还需要雄性的prosocial行为的不断强化。例如,亲近行为可以促进pairbond的形成并强化雄性对后代的哺育行为,而这种强化则来源于神经多肽催产素(OT)和加压素(AvP)与类固醇类激素的相互作用。催产素和加压素调控pairbond和双亲哺育行为的表达,而单配制和多配制田鼠的催产素和加压素受体在脑内的分布有显著的不同。比较研究揭示了小型田鼠单配制的调控机制,而种内差异和行为上的可塑性则有助于我们进一步理解这种机制。比如,在某些条件下,多配制的草原田鼠(Microtuspennsylvanicu)的雄性个体具有哺育后代的行为。尽管草原田鼠的加压素v1a受体在脑内的分布与其他多配制的田鼠相似,但是如果脑室注射加压素,仍可以诱发其哺育后代的行为。

关键词：单配制进化模型哺乳动物调控机制比较研究草原田鼠攻击行为加压素雌激素受体催产素 pair bond 近亲交配生存条件相互作用神经多肽种内差异脑室注射橙腹田鼠受体表达终纹床核敏感程度社会性性行为

Effective mass and Fermi surface complexity factor from ab initio band structure calculations

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npj Computational Materials 2017年第1期3卷 417-423页

作者： Zachary M.Gibbs Francesco Ricci Guodong Li Hong Zhu kristin Persson Gerbrand Ceder Geoffroy Hautier Anubhav Jain G.Jeffrey Snyder California Institute of Technology Division of Chemistry and Chemical EngineeringPasadenaCAUSA Institute of Condensed Matter and Nanosciences(IMCN) Universitécatholique de LouvainChemin desétoiles 8bte L7.03.01Louvain-la-NeuveBelgium Department of Materials Science and Engineering Northwestern University2220 Campus DriveEvanstonILUSA Department of Materials Science and Engineering Massachusetts Institute of Technology77 Massachusetts AvenueMassachusettsMAUSA Lawrence Berkeley National Lab 1 Cyclotron RoadBerkeleyCAUSA

The effective mass is a convenient descriptor of the electronic band structure used to characterize the density of states and electron transport based on a free electron *** effective mass is an excellent first-order descriptor in real systems,the exact value can have several definitions,each of which describe a different aspect of electron *** we use Boltzmann transport calculations applied to ab initio band structures to extract a density-of-states effective mass from the Seebeck Coefficient and an inertial mass from the electrical conductivity to characterize the band structure irrespective of the exact scattering *** identify a Fermi Surface Complexity Factor:N_(v)^(*)K^(*) from the ratio of these two masses,which in simple cases depends on the number of Fermi surface pockets eN_(v)^(*) T and their anisotropy K^(*),both of which are beneficial to high thermoelectric performance as exemplified by the high values found in *** Fermi Surface Complexity factor can be used in high-throughput search of promising thermoelectric materials.

关键词： mechanism materials Fermi

Inhibition of Cdk5 increases osteoblast differentiation and bone mass and improves fracture healing

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Bone Research 2022年第3期10卷 469-481页

作者： Mubashir Ahmad Benjamin Thilo Krüger Torsten Kroll Sabine vettorazzi Ann-kristin Dorn Florian Mengele Sooyeon Lee Sayantan Nandi Dilay Yilmaz Miriam Stolz Naveen Kumar Tangudu David Carro vázquez Johanna Pachmayr Ion Cristian Cirstea Maja vujic Spasic Aspasia Ploubidou Anita Ignatius Jan Tuckermann Institute of Comparative Molecular Endocrinology(CME) Ulm UniversityHelmholtzstrasse 8/189081 UlmGermany Institute of Orthopedic Research and Biomechanics Ulm UniversityHelmholtzstrasse 1489081 UlmGermany Leibniz Institute on Aging–Fritz Lipmann Institute(FLI) Beutenbergstrasse 11D-07745 JenaGermany Praxisklinik für Orthopädie Unfall-und Neurochirurgie Prof.Bischoff/Dr.Spies/Dr.Mengele89231 Neu-UlmGermany Paracelsus Medizinische Privatuniverstät Institute of PharmacyStrubergasse 215020 SalzburgAustria Department of Endocrinology Ludwig Maximilians University MunichMunich 80336Germany Present address:Institute of Orthopedic Research and Biomechanics Ulm UniversityHelmholtzstrasse 1489081 UlmGermany Present address:UPMC Hillman Cancer Center Department of Pharmacology and Chemical BiologyUniversity of Pittsburgh5115 Center Avenue15232 PittsburghPAUSA Present address:TAmiRNA GmbH Leberstrasse 201110 ViennaAustria

Identification of regulators of osteoblastogenesis that can be pharmacologically targeted is a major goal in combating osteoporosis,a common disease of the elderly population. Here, unbiased kinome RNAi screening in primary murine osteoblasts identified cyclin-dependent kinase 5(Cdk5) as a suppressor of osteoblast differentiation in both murine and human preosteoblastic cells. Cdk5 knockdown by si RNA, genetic deletion using the Cre-lox P system, or inhibition with the small molecule roscovitine enhanced osteoblastogenesis in vitro. Roscovitine treatment significantly enhanced bone mass by increasing osteoblastogenesis and improved fracture healing in mice. Mechanistically, downregulation of Cdk5 expression increased Erk phosphorylation, resulting in enhanced osteoblast-specific gene expression. Notably, simultaneous Cdk5 and Erk depletion abrogated the osteoblastogenesis conferred by Cdk5 depletion alone, suggesting that Cdk5 regulates osteoblast differentiation through MAPK pathway modulation. We conclude that Cdk5 is a potential therapeutic target to treat osteoporosis and improve fracture healing.

关键词： Cdk5 healing expression