Change search
Refine search result
678679680681682683684 34001 - 34050 of 34646
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 34001. Zhang, Hua
    et al.
    Xu, Hui
    Song, Fei
    Xu, Weili
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI). Tianjin Medical University, China.
    Pallard-Borg, Stephanie
    Qi, Xiuying
    Relation of socioeconomic status to overweight and obesity: a large population-based study of Chinese adults2017In: Annals of Human Biology, ISSN 0301-4460, E-ISSN 1464-5033, Vol. 44, no 6, p. 495-501Article in journal (Refereed)
    Abstract [en]

    Background: China has been going through significant changes in social and economical aspects and with great socioeconomic disparity in different regions. However, data on the association between socioeconomic status (SES) and obesity are not available in Tianjin, China.

    Aim: This study aimed to investigate the association between SES and high adiposity among the adult population in Tianjin.

    Subjects and methods: A total of 7351 individuals aged 20-79 were included in this study. Socioeconomic information was collected through an interview following a structured questionnaire. Waist circumference, body weight and height were measured following standard procedures. Overweight and obesity were defined according to the criteria of the Working Group on Obesity in China. Data were analysed using multinomial logistic regression with adjustment for potential confounders.

    Results: Stratified analysis showed that higher monthly income and education were related to decreased odds of abdominal overweight/ obesity in women, while high education was associated with increased odds of general overweight/obesity in men. Retirement increased the odds of abdominal overweight and obesity and non-manual work was associated with low odds of abdominal obesity in women.

    Conclusions: SES was associated with general and abdominal overweight/obesity and sex may play a role in such an association.

  • 34002.
    Zhang, Huan
    et al.
    Chinese Acad Sci, Inst Hydrobiol, Wuhan, Hubei, Peoples R China;Lund Univ, Dept Biol, Aquat Ecol, SE-22362 Lund, Sweden.
    Urrutia Cordero, Pablo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Lund Univ, Dept Biol, Aquat Ecol, SE-22362 Lund, Sweden.
    He, Liang
    Nanchang Univ, Minist Educ, Key Lab Poyang Lake Environm & Resource Utilizat, Nanchang, Jiangxi, Peoples R China.
    Geng, Hong
    South Cent Univ Nationalities, Coll Life Sci, Wuhan, Hubei, Peoples R China.
    Chaguaceda, Fernando
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Lund Univ, Dept Biol, Aquat Ecol, SE-22362 Lund, Sweden.
    Xu, Jun
    Chinese Acad Sci, Inst Hydrobiol, Wuhan, Hubei, Peoples R China.
    Hansson, Lars-Anders
    Lund Univ, Dept Biol, Aquat Ecol, SE-22362 Lund, Sweden.
    Life-history traits buffer against heat wave effects on predator-prey dynamics in zooplankton2018In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 24, no 10, p. 4747-4757Article in journal (Refereed)
    Abstract [en]

    In addition to an increase in mean temperature, extreme climatic events, such as heat waves, are predicted to increase in frequency and intensity with climate change, which are likely to affect organism interactions, seasonal succession, and resting stage recruitment patterns in terrestrial as well as in aquatic ecosystems. For example, freshwater zooplankton with different life-history strategies, such as sexual or parthenogenetic reproduction, may respond differently to increased mean temperatures and rapid temperature fluctuations. Therefore, we conducted a long-term (18months) mesocosm experiment where we evaluated the effects of increased mean temperature (4 degrees C) and an identical energy input but delivered through temperature fluctuations, i.e., as heat waves. We show that different rotifer prey species have specific temperature requirements and use limited and species-specific temperature windows for recruiting from the sediment. On the contrary, co-occurring predatory cyclopoid copepods recruit from adult or subadult resting stages and are therefore able to respond to short-term temperature fluctuations. Hence, these different life-history strategies affect the interactions between cyclopoid copepods and rotifers by reducing the risk of a temporal mismatch in predator-prey dynamics in a climate change scenario. Thus, we conclude that predatory cyclopoid copepods with long generation time are likely to benefit from heat waves since they rapidly wake up even at short temperature elevations and thereby suppress fast reproducing prey populations, such as rotifers. In a broader perspective, our findings suggest that differences in life-history traits will affect predator-prey interactions, and thereby alter community dynamics, in a future climate change scenario.

  • 34003. Zhang, Hui
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Duo
    Zhang, Liang
    Kapilashrami, Mukes
    Sun, Tao
    Glans, Per-Anders
    Zhu, Junfa
    Zhong, Jun
    Hu, Zheng
    Guo, Jinghua
    Sun, Xuhui
    Comprehensive electronic structure characterization of pristine and nitrogen/phosphorus doped carbon nanocages2016In: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 103, p. 480-487Article in journal (Refereed)
    Abstract [en]

    The electronic structures of carbon nanocages (CNCs) and nitrogen/phosphorus doped carbon nanocages (N-CNCs/P-CNCs) have been studied by X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES) and resonant X-ray emission spectroscopy (RXES). The doping configurations for N/P dopants are identified from the experiments. The results have shown that there are three major doping configurations for nitrogen but only one doping configuration for phosphorus. The nitrogen doping reveals the complex coexistence of graphite-like, pyridine-like and pyrrole-like configurations that are proved by density functional theory (DFT) simulations, while the phosphorus doping presents only the "graphite-like" configuration. The different configuration profiles result in less atomic structure ordering of N-CNCs than that of P-CNCs. XAS spectra obtained from both surface and bulk sensitive detection suggest different chemical environments between the interior and shell for all types of nanocages. The electronic structure modifications show significant difference between nitrogen and phosphorus doping from the DOS calculations. (C) 2016 Elsevier Ltd. All rights reserved.

  • 34004.
    Zhang, Jiazhuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Isolation and Characterization of Uncultured Freshwater Bacterioplankton from Lake Ekoln and Lake Erken through Dilution-to-Extinction Approach and Molecular Analysis Tools2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Not many of the abundant freshwater bacterial groups have a representative cultured isolate. In this master thesis project, some abundant bacterioplankton from two lakes (Lake Ekoln and Lake Erken) could be isolated by a dilution-to-extinction approach. Sterilized lake water which was obtained through an ultrafiltration system was used resembling a natural medium. Specific fragments of 16s rRNA of the isolates were amplified by universal bacterial primers (27f and 1492r, 341f and 805r.) for genotyping against a freshwater sequence database and RDP training set (Version 7). A total of 33 isolates from the two lakes were taxonomically classified and revealed the isolation of typical and abundant freshwater bacteria. Original bacterial community of Lake Ekoln was also analyzed by 16S rRNA clone library construction for diversity study. Phylogenetic trees were built through neighbor-joining method by Mega (Version 5) to reveal the evolutionary relationships among database entries, obtained isolates and clones. 

  • 34005.
    Zhang, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Iakovleva, Irina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindberg, Mikael J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Andersson, Patrik L.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer-Eriksson, A. Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Interspecies variation between fish and human transthyretins in their binding of thyroid-disrupting chemicals2018In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 52, no 20, p. 11865-11874Article in journal (Refereed)
    Abstract [en]

    Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis. Transthyretin (TTR) is found in the serum and cerebrospinal fluid of vertebrates, where it transports thyroid hormones. Here, we explored the interspecies variation in TDC binding to human and fish TTR (exemplified by Gilthead seabream (Sparus aurata)). The in vitro binding experiments showed that TDCs bind with equal or weaker affinity to seabream TTR than to the human TTR, in particular, the polar TDCs (>500-fold lower affinity). Crystal structures of the seabream TTR TDC complexes revealed that all TDCs bound at the thyroid binding sites. However, amino acid substitution of Ser117 in human TTR to Thr117 in seabream prevented polar TDCs from binding deep in the hormone binding cavity, which explains their low affinity to seabream TTR Molecular dynamics and in silico alanine scanning simulation also suggested that the protein backbone of seabream TTR is more rigid than the human one and that Thr117 provides fewer electrostatic contributions than Ser117 to ligand binding. This provides an explanation for the weaker affinities of the ligands that rely on electrostatic interactions with Thr117. The lower affinities of TDCs to fish TTR, in particular the polar ones, could potentially lead to milder thyroid-related effects in fish.

  • 34006.
    Zhang, Jing
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Biochemistry.
    Biochemical Study and Technical Applications of Fungal Pectinase2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Pectinases are a group of enzymes produced by bacteria, fungi, higher plants and animals. Pectinases can modify and degrade pectins, a class of heterogeneous and multifunctional polysaccharides present in middle lamellae and primary cell walls of plants. Pectins have been showed to play diverse roles in cell physiology, growth, adhesion and separation. Pectinases are used technically in the processing of fiber production and fruit juice or wine making. We have studied the mechanisms and applications of pectinases, especially in retting, a microbiological process where bast fibers in flax and other bast fiber cultivars are released from each other and from the woody core.

    A strong correlation was found between the ability to perform retting and the degradation of sparsely esterified pectin, a substrate of polygalacturonase. This led to the conclusion that polygalacturonase plays a key role in the enzymatic retting of flax. We purified and characterized an extracellular polygalacturonase produced by Rhizopus oryzae, a very potent retting organism. The purified enzyme which appeared to be the single active component in retting, has non-methylated polygalacturonan as its preferred substrate. Peptide sequences indicate that the enzyme, like another polygalacturonase (EC. 3.2.1.15), belongs to glycosyl hydrolase family 28. It contains, however, an N-terminal sequence absent from other fungal pectinases, but present in an enzyme from the phytopathogenic bacterium, Ralstonia solanacearum.

    Our finding that removal of calcium ions from the plant material by pre-incubation in dilute acid in enzymatic retting could reduce enzyme consumption by several orders of magnitude, improves the economical feasibility of the enzymatic retting process. Comparisons with different acids showed that the action was mainly pH dependent.

    Pectinases were employed as analytical tools in a study of stored wood discoloration and, together with cellulases, in a mechanical process for making pulp from flax and hemp in paper production.

  • 34007.
    Zhang, Jinghan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The invasion of Smooth cordgrass (Spartina alterniflora) in China: risk assessment using spatial modeling2012Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Smooth cordgrass (Spartina alterniflora) is one of the harmful quarantine weeds in China. Since its first introduction in China in 1979, this alien species has spread rapidly and damaged local ecological environments. Research to predict a suitable new area is an important step for management of the species and to prevent a further spread. In this study, Spartina alterniflora’s ecological niche was modeled using the application MAXENT. Analysis was based on species’ current distribution. The investigations of this study were two-fold. First, a large-scale global investigation (outside China) was conducted to predict suitable areas in China by comparing global and Chinese records of the species. In the second set, the combined records were used to predict suitable areas in the Jiangsu Province. The model’s accuracy was evaluated by Receiver Operator Characteristic (ROC) curve. The areas under the ROC curve (AUC value) were all over 0.95, which indicated high predictive ability of this model. In the large scale prediction, Shanghai, Zhejiang, Fujian, Guangzhou, Guangxi and southern part of Wuhan, Jiangsu and Anhui were all potentially endangered by S. alterniflora invasion. On the smaller scale, the prone to invasion areas were mostly concentrated on southern part and some coastal areas of Jiangsu Province, where the precipitation and temperature were appropriate for this grass. Because of S. alterniflora has high dispersal ability and human induced history, the potential distribution areas in China are considerable and it may invade more areas, in result spreading faster in the future. To prevent further invasion and spread, an early eradication program should be adopted in the newly invaded areas. Meanwhile, the monitoring programs should also need to be applied in potential survival areas, especially in coastal harbors, airports, and tourism areas which are highly vulnerable to S. alterniflora invasion.

  • 34008.
    Zhang, Jingji
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Accuracy of mRNA Translation in Bacterial Protein Synthesis2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Reading of messenger RNA (mRNA) by aminoacyl-tRNAs (aa-tRNAs) on the ribosomes in the bacterial cell occurs with high accuracy. It follows from the physical chemistry of enzymatic reactions that there must be a trade-off between rate and accuracy of initial tRNA selection in protein synthesis: when the current accuracy, the A-value, approaches its maximal possible value, the d-value, the kinetic efficiency of the reaction approaches zero. We have used an in vitro system for mRNA translation with purified E. coli components to estimate the d- and A-values by which aa-tRNAs discriminate between their cognate and near cognate codons displayed in the ribosomal A site. In the case of tRNALys, we verified the prediction of a linear trade-off between kinetic efficiency of cognate codon reading and the accuracy of codon selection. These experiments have been extended to a larger set of tRNAs, including tRNAPhe, tRNAGlu, tRNAHis, tRNACys, tRNAAsp and tRNATyr, and linear efficiency-accuracy trade-off was observed in all cases. Similar to tRNALys, tRNAPhe discriminated with higher accuracy against a particular mismatch in the second than in the first codon position. Remarkably high d-values were observed for tRNAGlu discrimination against a C-C mismatch in the first codon position (70 000) and for tRNAPhe discrimination against an A-G mismatch in the second codon position (79 000). At the same time, we have found a remarkably small d-value (200) for tRNAGlu misreading G in the middle position of the codon (U-G mismatch).

    Aminoglycoside antibiotics induce large codon reading errors by tRNAs. We have studied the mechanism of aminoglycoside action and found that the drug stabilized aminoacyl-tRNA in a codon selective in relation to a codon non-selective state. This greatly enhanced the probability of near cognate aminoacyl-tRNAs to successfully transcend the initial selection step of the translating ribosome. We showed that Mg2+ ions, in contrast, favour codon non-selective states and thus induce errors in a principally different way than aminoglycosides. 

    We also designed experiments to estimate the overall accuracy of peptide bond formation with, including initial selection accuracy and proofreading of tRNAs after GTP hydrolysis on EF-Tu. Our experiments have now made it possible to calibrate the accuracy of tRNA selection in the test tube to that in the living cells. We will now also be able to investigate the degree to which the accuracy of tRNA selection has been optimized for maximal fitness.  

  • 34009.
    Zhang, Jingji
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Enhanced proofreading attenuates initial selection error hot spots in genetic code translation by transfer RNAsManuscript (preprint) (Other academic)
    Abstract [en]

    A system for cell free protein synthesis with E. coli components of high purity was used in conjunction with fast kinetics quench-flow measurements to characterize the accuracy of peptie bond formation by ribosomes with initiator tRNAfMet in P site and different codons in the A site. We used Glu-tRNAGlu, Lys-tRNALys and Phe-tRNAPhe in ternary complexes with EF-Tu and GTP to select ribosomes programmed with their respective cognate codons in competition with ribosomes containing near-cognate codons. Variation of the free Mg2+ concentration in the in vitro buffer system was used to calibrate its accuracy to that of codon selection by Glu-tRNAGlu in living E. coli cells, previously estimated from the residual activity of a beta-galactosidase mutant in which the codon for an essential Glu had been altered to near cognate codons. At 2.3 mM free Mg2+ concentration, the accuracy in the living cell agreed with that in the test tube, a feature making our biochemistry directly relevant to bacterial physiology. We found that the total accuracy of tRNA selection varied by five orders of magnitude depending on the type of tRNA, type of mismatch and mismatched codon position. We partitioned the total accuracy into initial selection of ternary complex before GTP hydrolysis on EF-Tu and proofreading selection of aminoacyl-tRNA after GTP hydrolysis. We found the contribution of proofreading to be strongly positively correlated with the accuracy of initial selection in its high range. As initial selection decreased further the proofreading contribution to accuracy increased, rather than decreased, a feature neutralizing potentially disastrous missense error hot spots associated with, in particular, tRNAGlu.    

  • 34010.
    Zhang, Jingji
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    On the mechanism of translation error induction by aminoglycoside antibioticsManuscript (preprint) (Other academic)
    Abstract [en]

    We used a cell-free system with pure Escherichia coli components to study how the aminoglycosides disrupt initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP by messenger RNA-programmed ribosomes. We take the advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near cognate and wobble codon readings increased toward the maximal asymptote, the effective d value. It turns out two ribosome bound states of ternary complex. First, one codon non-selective step, Mg2+ ions shift the equilibrium from free to ribosome bound ternary complex meaning that the equilibrium between the two ribosome bound complexes is unaltered. Second, codon selective step, aminoglycosides shift the equilibrium from codon non-selective to codon selective complex meaning that the equilibrium between the free and the codon non-selective state is unchanged.

  • 34011.
    Zhang, Jingji
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Ieong, Ka-Weng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Johansson, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 31, p. 9602-9607Article in journal (Refereed)
    Abstract [en]

    We used a cell-free system with pure Escherichia coli components to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, the d value. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-cognate codon readings comprising about 15% of the genetic code. Their d values varied about 400-fold in the 200-80,000 range depending on type of mismatch, mismatch position in the codon, and tRNA isoacceptor type. We identified error hot spots (d = 200) for U:G misreading in second and U:U or G:A misreading in third codon position by His-tRNA(His) and, as also seen in vivo, Glu-tRNA(Glu). We suggest that the proofreading mechanism has evolved to attenuate error hot spots in initial selection such as those found here.

  • 34012.
    Zhang, Jingji
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Ieong, Ka-Weng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Johansson, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Large accuracy variation in initial codon selection by aminoacyl-tRNAs on the bacterial ribosomeManuscript (preprint) (Other academic)
  • 34013.
    Zhang, Jingji
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Ieong, Ka-Weng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Mellenius, Harriet
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Proofreading neutralizes potential error hotspots in genetic code translation by transfer RNAs2016In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 22, no 6, p. 896-904Article in journal (Refereed)
    Abstract [en]

    The ribosome uses initial and proofreading selection of aminoacyl-tRNAs for accurate protein synthesis. Anomalously high initial misreading in vitro of near-cognate codons by tRNAHis and tRNAGlu suggested potential error hotspots in protein synthesis, but in vivo data suggested their partial neutralization. To clarify the role of proofreading in this error reduction, we varied the Mg2+ ion concentration to calibrate the total accuracy of our cell-free system to that in the living Escherichia coli cell. We found the total accuracy of tRNA selection in our system to vary by five orders of magnitude depending on tRNA identity, type of mismatch, and mismatched codon position. Proofreading and initial selection were positively correlated at high, but uncorrelated at low initial selection, suggesting hyperactivated proofreading as a means to neutralize potentially disastrous initial selection errors.

  • 34014.
    Zhang, Jingji
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Pavlov, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions2018In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 3, p. 1362-1374Article in journal (Refereed)
    Abstract [en]

    We studied the effects of aminoglycosides and changing Mg2+ ion concentration on the accuracy of initial codon selection by aminoacyl-tRNA in ternary complex with elongation factor Tu and GTP (T-3) on mRNA programmed ribosomes. Aminoglycosides decrease the accuracy by changing the equilibrium constants of 'monitoring bases' A1492, A1493 and G530 in 16S rRNA in favor of their 'activated' state by large, aminoglycoside-specific factors, which are the same for cognate and near-cognate codons. Increasing Mg2+ concentration decreases the accuracy by slowing dissociation of T-3 from its initial codon-and aminoglycoside-independent binding state on the ribosome. The distinct accuracy-corrupting mechanisms for aminoglycosides and Mg2+ ions prompted us to re-interpret previous biochemical experiments and functional implications of existing high resolution ribosome structures. We estimate the upper thermodynamic limit to the accuracy, the 'intrinsic selectivity' of the ribosome. We conclude that aminoglycosides do not alter the intrinsic selectivity but reduce the fraction of it that is expressed as the accuracy of initial selection. We suggest that induced fit increases the accuracy and speed of codon reading at unaltered intrinsic selectivity of the ribosome.

  • 34015.
    Zhang, Jingpu
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Rasmuson-Lestander, Åsa
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Expression preference of the S-adenosylmethionine synthetase (SamS) gene in Drosophila melanogaster1997In: Dev Rep Biol, Vol. 6, p. 7-17Article in journal (Other (popular science, discussion, etc.))
  • 34016. Zhang, Jun-Jun
    et al.
    Malekpour, Mahdi
    Luo, Wentian
    Ge, Linna
    Olaru, Florina
    Wang, Xu-Ping
    Bah, Maimouna
    Sado, Yoshikazu
    Heidet, Laurence
    Kleinau, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Fogo, Agnes B.
    Borza, Dorin-Bogdan
    Murine Membranous Nephropathy: Immunization with alpha 3(IV) Collagen Fragment Induces Subepithelial Immune Complexes and Fc gamma R-Independent Nephrotic Syndrome2012In: Journal of Immunology, ISSN 0022-1767, E-ISSN 1550-6606, Vol. 188, no 7, p. 3268-3277Article in journal (Refereed)
    Abstract [en]

    Membranous nephropathy (MN) is a leading cause of nephrotic syndrome in adults and a significant cause of end-stage renal disease, yet current therapies are nonspecific, toxic, and often ineffective. The development of novel targeted therapies requires a detailed understanding of the pathogenic mechanisms, but progress is hampered by the lack of a robust mouse model of disease. We report that DBA/1 mice as well as congenic Fc gamma RIII-/- and FcR gamma(-/-) mice immunized with a fragment of alpha 3(IV) collagen developed massive albuminuria and nephrotic syndrome, because of subepithelial deposits of mouse IgG and C3 with corresponding basement membrane reaction and podocyte foot process effacement. The clinical presentation and histopathologic findings were characteristic of MN. Although immunized mice produced genuine anti-alpha 3NC1 autoantibodies that bound to kidney and lung basement membranes, neither crescentic glomerulonephritis nor alveolitis ensued, likely because of the predominance of mouse IgG1 over IgG2a and IgG2b autoantibodies. The ablation of activating IgG Fc receptors did not ameliorate injury, implicating subepithelial deposition of immune complexes and consequent complement activation as a major effector pathway. We have thus established an active model of murine MN. This model, leveraged by the availability of genetically engineered mice and mouse-specific reagents, will be instrumental in studying the pathogenesis of MN and evaluating the efficacy of novel experimental therapies. 

  • 34017.
    Zhang, Lai
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Technical University of Denmark, Denmark ; International Institute for Applied Systems Analysis, Laxenburg, Austria.
    Andersen, Ken H.
    Dieckmann, Ulf
    Brannstrom, Ake
    Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 380, p. 280-290Article in journal (Refereed)
    Abstract [en]

    We investigate how four types of interference competition which alternatively affect foraging, metabolism, survival, and reproduction impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population's reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models. (C) 2015 Elsevier Ltd. All rights reserved.

  • 34018.
    Zhang, Lai
    et al.
    Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark.
    Hartvig, Martin
    Knudsen, Kim
    Andersen, Ken Haste
    Size-based predictions of food web patterns2014In: Theoretical Ecology, ISSN 1874-1738, E-ISSN 1874-1746, Vol. 7, no 1, p. 23-33Article in journal (Refereed)
    Abstract [en]

    We employ size-based theoretical arguments to derive simple analytic predictions of ecological patterns and properties of natural communities: size-spectrum expo- nent, maximum trophic level, and susceptibility to invasive species. The predictions are brought about by assuming that an infinite number of species are continuously distributed on a size–trait axis. It is, however, an open question whether such predictions are valid for a food web with a finite num- ber of species embedded in a network structure. We address this question by comparing the size-based predictions to results from dynamic food web simulations with varying species richness. To this end, we develop a new size- and trait-based food web model that can be simplified into an analytically solvable size-based model. We confirm existing solutions for the size distribution and derive novel predic- tions for maximum trophic level and invasion resistance. Our results show that the predicted size-spectrum exponent is borne out in the simulated food webs even with few species, albeit with a systematic bias. The predicted max- imum trophic level turns out to be an upper limit since simulated food webs may have a lower number of trophic levels, especially for low species richness, due to structural constraints. The size-based model possesses an evolutionary stable state and is therefore un-invadable. In contrast, the food web simulations show that all communities, irrespec- tive of number of species, are equally open to invasions. We use these results to discuss the validity of size-based pre- dictions in the light of the structural constraints imposed by food webs. 

  • 34019.
    Zhang, Lai
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. School of Mathematical Science, Yangzhou University, Si Wang Ting Road, Yangzhou 225002, People’s Republic of China.
    Takahashi, Daisuke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Hartvig, Martin
    Andersen, Ken H.
    Food-web dynamics under climate change2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1867, article id 20171772Article in journal (Refereed)
    Abstract [en]

    Climate change affects ecological communities through its impact on the physiological performance of individuals. However, the population dynamic of species well inside their thermal niche is also determined by competitors, prey and predators, in addition to being influenced by temperature changes. We use a trait-based food-web model to examine how the interplay between the direct physiological effects from temperature and the indirect effects due to changing interactions between populations shapes the ecological consequences of climate change for populations and for entire communities. Our simulations illustrate how isolated communities deteriorate as populations go extinct when the environment moves outside the species' thermal niches. High-trophic-level species are most vulnerable, while the ecosystem function of lower trophic levels is less impacted. Open communities can compensate for the loss of ecosystem function by invasions of new species. Individual populations show complex responses largely uncorrelated with the direct impact of temperature change on physiology. Such complex responses are particularly evident during extinction and invasion events of other species, where climaticallywell-adapted species may be brought to extinction by the changed food-web topology. Our results highlight that the impact of climate change on specific populations is largely unpredictable, and apparently well-adapted species may be severely impacted.

  • 34020.
    Zhang, Li
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Jiang, Wangshu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Nan, Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Almqvist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Huang, Yafei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite2014In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1838, no 7, p. 1809-1816Article in journal (Refereed)
    Abstract [en]

    The Escherichia coli inner membrane protein CysZ mediates the sulfate uptake subsequently utilized for the synthesis of sulfur-containing compounds in cells. Here we report the purification and functional characterization of CysZ. Using Isothermal Titration Calorimetry, we have observed interactions between CysZ and its putative substrate sulfate. Additional sulfur-containing compounds from the cysteine synthesis pathway have also been analyzed for their abilities to interact with CysZ. Our results suggest that CysZ is dedicated to a specific pathway that assimilates sulfate for the synthesis of cysteine. Sulfate uptake via CysZ into E. coil whole cells and proteoliposome offers direct evidence of CysZ being able to mediate sulfate uptake. In addition, the cysteine synthesis pathway intermediate sulfite can interact directly with CysZ with higher affinity than sulfate. The sulfate transport activity is inhibited in the presence of sulfite, suggesting the existence of a feedback inhibition mechanism in which sulfite regulates sulfate uptake by CysZ. Sulfate uptake assays performed at different extracellular pH and in the presence of a proton uncoupler indicate that this uptake is driven by the proton gradient. (C) 2014 Elsevier B.V. All rights reserved.

  • 34021. Zhang, Liang
    et al.
    Fontana, Jacopo
    Bernhem, Kristoffer
    Nilsson, Linnéa
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Scott, Lena
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Aperia, Anita
    Ouabain intervenes early in the apoptotic process by preventing BAD activationManuscript (preprint) (Other academic)
  • 34022. Zhang, Lifang
    et al.
    Carlberg, Inger
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Norling, Birgitta
    Deletion of Synechocystis sp PCC 6803 Leader Peptidase LepB1 Affects Photosynthetic Complexes and Respiration2013In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 12, no 5, p. 1192-1203Article in journal (Refereed)
    Abstract [en]

    The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (SII0716) and LepB2 (SIr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b(6)f complexes. The impaired assembly of PSI and Cyt b(6)f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b(6)f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes.

  • 34023. Zhang, Lifang
    et al.
    Selao, Tiago Toscano
    Selstam, Eva
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Norling, Birgitta
    Subcellular Localization of Carotenoid Biosynthesis in Synechocystis sp PCC 68032015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 6, article id e0130904Article in journal (Refereed)
    Abstract [en]

    The biosynthesis pathway of carotenoids in cyanobacteria is partly described. However, the subcellular localization of individual steps is so far unknown. Carotenoid analysis of different membrane subfractions in Synechocystis sp. PCC6803 shows that "light" plasma membranes have a high carotenoid/protein ratio, when compared to "heavier" plasma membranes or thylakoids. The localization of CrtQ and CrtO, two well-defined carotenoid synthesis pathway enzymes in Synechocystis, was studied by epitope tagging and western blots. Both enzymes are locally more abundant in plasma membranes than in thylakoids, implying that the plasma membrane has higher synthesis rates of beta-carotene precursor molecules and echinenone.

  • 34024.
    Zhang, Liquan
    Uppsala University, Disciplinary Domain of Science and Technology, Faculty of Mathematics and Science.
    Vegetation ecology and population biology of Fritillaria meleagris L. at the Kungsängen nature reserve, eastern Sweden1983Doctoral thesis, monograph (Other academic)
  • 34025.
    Zhang, Lu
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ding, Zhoujie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Xu, Hui
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Heyman, Birgitta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Marginal-zone B cells transport IgG3-antigen immune complexes into splenic B cell follicles2014In: Molecular Immunology, ISSN 0161-5890, E-ISSN 1872-9142, Vol. 61, no 2, p. 278-278Article in journal (Other academic)
  • 34026. Zhang, Lu
    et al.
    Hu, Jin
    Zirakzadeh, Ali
    Rosvall, Jesper
    Hedlund, Mats
    Hu, Pingsheng
    Wallin, Robert
    Sherif, Amir
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Urology and Andrology.
    Winqvist, Ola
    Immune responses against Human Papilloma virus in draining lymph nodes from patients with penile cancer2017In: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 86, no 4, p. 339-339Article in journal (Other academic)
  • 34027. Zhang, M.
    et al.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Y.
    Comprehensive theoretical studies on the reaction of 1-bromo-3,3,3- trifluoropropene with OH free radicals2013In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 18, no 7, p. 7873-7885Article in journal (Refereed)
    Abstract [en]

    The potential energy surfaces (PES) for the reaction of 1-bromo-3,3,3- trifluoropropene (CF3CHCBrH) with hydroxyl (OH) free radicals is probed theoretically at the CCSD/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of theory. All the possible stationary and first-order saddle points along the reaction paths were verified by the vibrational analysis. The calculations account for all the product channels. Based on the calculated CCSD/aug-cc-pVDZ potential energy surface, the possible reaction mechanism is discussed. Six distinct reaction pathways of 1-bromo-3,3,3-trifluoropropene (BTP) with OH are investigated. The geometries, reaction enthalpies and energy barriers are determined. Canonical transition-state theory with Wigner tunneling correction was used to predict the rate constants for the temperature range of 290-3,000 K without any artificial adjustment, and the computed rate constants for elementary channels can be accurately fitted with three-parameter Arrhenius expressions. OH addition reaction channel and the H atom abstraction channels related to the carbon-carbon double bond are found to be the main reaction channels for the reaction of 1-bromo-3,3,3-trifluoropropene (CF3CHCBrH) with hydroxyl (OH) free radicals while the products leading to CF3CHCH + BrOH and COHF 2CHCBrH + F play a negligible role.

  • 34028. Zhang, Ming-Dong
    et al.
    Barde, Swapnali
    Szodorai, Edit
    Josephson, Anna
    Mitsios, Nicholas
    Watanabe, Masahiko
    Attems, Johannes
    Lubec, Gert
    Kovacs, Gabor G.
    Uhlen, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mulder, Jan
    Harkany, Tibor
    Hokfelt, Tomas
    Erratum to: Comparative anatomical distribution of neuronal calcium-binding protein (NECAB) 1 and -2 in rodent and human spinal cord2016In: Brain Structure and Function, ISSN 1863-2653, E-ISSN 1863-2661, Vol. 221, no 7, p. 3843-3843Article in journal (Refereed)
  • 34029.
    Zhang, Min-Ying
    Stockholm University, Faculty of Science.
    Molecular studies of virulence factors of the insect pathogen Bacillus thuringiensis1994Doctoral thesis, comprehensive summary (Other academic)
  • 34030. Zhang, Peng
    et al.
    Chen, Lin
    Zhang, Qingsong
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hong, Feng F.
    Using in situ nanocellulose-coating technology based on dynamic bacterial cultures for upgrading conventional biomedical materials and reinforcing nanocellulose hydrogels2016In: Biotechnology progress (Print), ISSN 8756-7938, E-ISSN 1520-6033, Vol. 32, no 4, p. 1077-1084Article in journal (Refereed)
    Abstract [en]

    Bacterial nanocellulose (BNC) is a microbial nanofibrillar hydrogel with many potential applications. Its use is largely restricted by insufficient strength when in a highly swollen state and by inefficient production using static cultivation. In this study, an in situ nanocellulose-coating technology created a fabric-frame reinforced nanocomposite of BNC hydrogel with superior strength but retained BNC native attributes. By using the proposed technology, production time could be reduced from 10 to 3 days to obtain a desirable hydrogel sheet with approximately the same thickness. This novel technology is easier to scale up and is more suitable for industrial-scale manufacture. The mechanical properties (tensile strength, suture retention strength) and gel characteristics (water holding, absorption and wicking ability) of the fabric-reinforced BNC hydrogel were investigated and compared with those of ordinary BNC hydrogel sheets. The results reveal that the fabric-reinforced BNC hydrogel was equivalent with regard to gel characteristics, and exhibited a qualitative improvement with regard to its mechanical properties. For more advanced applications, coating technology via dynamic bacterial cultures could be used to upgrade conventional biomedical fabrics, i.e. medical cotton gauze or other mesh materials, with nanocellulose.

  • 34031. Zhang, Pu
    et al.
    Dixon, Morag
    Zucchelli, Marco
    Hambiliki, Fredwell
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Levkov, Lev
    Hovatta, Outi
    Kere, Juha
    Expression analysis of the NLRP gene family suggests a role in human preimplantation development2008In: PLoS ONE, ISSN 1932-6203, Vol. 3, no 7, p. e2755-Article in journal (Refereed)
    Abstract [en]

    Background: The NLRP (Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing) family, also referred to as NALP family, is well known for its roles in apoptosis and inflammation. Several NLRPs have been indicated as being involved in reproduction as well.

    Methodology: We studied, using the unique human gametes and embryo materials, the expression of the NLRP family in human gametes and preimplantation embryos at different developmental stages, and compared the expression levels between normal and abnormal embryos using real-time PCR.

    Principal Findings: Among 14 members of the NLRP family, twelve were detected in human oocytes and preimplantation embryos, whereas seven were detected in spermatozoa. Eight NLRPs (NLRP4, 5, 8, 9, 11, 12, 13, and 14) showed a similar expression pattern: their expression levels were high in oocytes and then decreased progressively in embryos, resulting in a very low level in day 5 embryos. However, NLRP2 and NLRP7 showed a different expression pattern: their expression decreased from oocytes to the lowest level by day 3, but increased again by day 5. The expression levels of NLRP5, 9, and 12 were lower in day 1 abnormal embryos but higher in day3 and day5 arrested embryos, when compared with normal embryos at the same stages. NLRP7 was down-regulated in day 1 and day 5 abnormal embryos but over-expressed in day3 arrested embryos.

    Conclusions: According to our results, different NLRPs possibly work in a stage-dependent manner during human preimplantation development.

  • 34032. Zhang, Qi
    et al.
    Wang, Guangji
    Du, Yu
    Zhu, Lingling
    Jiye, A
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    GC/MS analysis of the rat urine for metabonomic research2007In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 854, no 1-2, p. 20-25Article in journal (Refereed)
    Abstract [en]

    In this paper, an optimized protocol was established and validated for the metabonomic profiling in rat urine using GC/MS. The urine samples were extracted by methanol after treatment with urease to remove excessive urea, then the resulted supernatant was dried, methoximated, trimethylsilylated, and analyzed by GC/MS. Forty-nine endogenous metabolites were separated and identified in GC/MS chromatogram, of which 26 identified compounds were selected for quantitative analysis to evaluate the linearity, precision, and sensitivity of the method. It showed good linearity between mass spectrometry responses and relative concentrations of the 26 endogenous compounds over the range from 0.063 to 1.000(v/v, urine/urine+ water) and satisfactory reproducibility with intra-day and inter-days precision values all below 15%. The metabonomic profiling method based on GC/MS was successfully applied to urine samples from hyperlipidemia model rats. Obviously, separated clustering of model rats and the control rats were shown by principal components analysis (PCA); time-dependent metabonomic modification was detected as well. It was suggested that metabonomic profiling based on GC/MS be a robust method for urine samples.

  • 34033. Zhang, Qian
    et al.
    Keller, Rainer
    Dircksen, Heinrich
    Institute of Zoophysiology, University of Bonn, Germany.
    Crustacean hyperglycaemic hormone in the nervous system of the primitive crustacean species Daphnia magna and Artemia salina (Crustacea: Branchiopoda)1997In: Cell and Tissue Research, ISSN 0302-766X, E-ISSN 1432-0878, Vol. 287, no 3, p. 565-576Article in journal (Refereed)
    Abstract [en]

    Crustacean hyperglycaemic hormone-immunoreactive neuronal systems are detected in the central and peripheral nervous systems of two entomostracan crustaceans, Daphnia magna and Artemia salina, by immunocytochemistry using specific antisera against crustacean hyperglycaemic hormones of the decapod crustaceans Orconectes limosus and Carcinus maenas. In D. magna, four small putative interneurones are detected in the brain. In the thorax, ten bipolar peripheral neurones are stained by both antisera. They are obviously segmental homologues with centrally projecting axons that form interdigitating varicose fibres and terminals in putative neurohaemal areas next to the surface of the anterior part of the thoracic ganglia. Similar immunopositive neurones occur both in the central and peripheral nervous systems of A. salina. A total of five groups of neurones occur in the protocerebrum, the deutocerebrum and the mandibular ganglion. Some of the protocerebral neurones are bipolar and project to the dorsal frontal organ. A single pair of peripheral multipolar neurones in the maxillary segment projects centrally into the ventral nerve cord and innervates unidentified somatic muscles and tissues in the maxillary and the first appendage segments. None of the brain neurones in both species show similarities to decapod X-organ sinus gland neurosecretory neurones. Chromatography of brain extracts of D. magna combined with immunodot blotting revealed two strongly immunoreactive fractions at retention times close to that of the crustacean hyperglycaemic hormone of crayfish. Moreover, preabsorption controls suggest that the cross-reacting peptides of D. magna and A. salina are structurally closely related to those of decapods.

  • 34034.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present thesis honors contemporary molecular dynamics simulation methodologies which provide powerful means to predict data, interpret observations and widen our understanding of the dynamics, structures and interactions of carbohydrate systems. With this as starting point my thesis work embarked on several cutting edge problems summarized as follows.

    In my first work the thermal response in crystal cellulose Iβ was studied with special emphasis on the temperature dependence of the crystal unit cell parameters and the organization of the hydrogen bonding network. The favorable comparison with available experimental data, like the phase transition temperature, the X-ray diffraction crystal structures of cellulose Iβ at room and high temperatures, and temperature dependent IR spectra supported our conclusions on the good performance of the GLYCAM06 force field for the description of cellulose crystals, and that a cautious parameterization of the non-bonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

    The adsorption properties of xyloglucans on the cellulose Iβ surface were investigated in my second paper. In our simulations, the interaction energies between xyloglucan and cellulose in water were found to be considerably lower than those in vacuo. The van der Waals interactions played a prevailing role over the electrostatic interactions in the adsorption. Though the variation in one side chain did not have much influence on the interaction energy and the binding affinity, it did affect the structural properties of the adsorbed xyloglucans.

    The interaction of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 was studied in the third paper. The effect of the charge state of the “nucleophile helper” residue Asp87 on the PttXET16-34 active site structure was emphasized. The results indicate that the catalysis is optimal when the catalytic nucleophile is deprotonated, while the “helper” residue and general acid/base residue are both protonated.

    In my forth paper, the working mechanism for a redox-responsive bistable [2]rotaxane based on an α-cyclodextrin ring was investigated. The umbrella sampling technique was employed to calculate the free energy profiles for the shuttling motion of the α-cyclodextrin ring between two recognition sites on the dumbbell of the rotaxane. The calculated free energy profiles verified the binding preferences observed experimentally. The driving force for the shuttling movement of the α-cyclodextrin ring was revealed by the analysis of the free energy components.

  • 34035.
    Zhang, Qiong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation2011In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, no 16, p. 2595-2602Article in journal (Refereed)
    Abstract [en]

    The interaction between para-crystalline cellulose and the cross-linking glycan xyloglucan (XG) plays a central role for the strength and extensibility of plant cell walls. The coating of XGs on cellulose surfaces is believed to be one of the most probable interaction patterns. In this work, the effects of explicit water and side chain variation on the adsorption of XGs on cellulose are investigated by means of atomistic molecular dynamics simulations. The adsorption properties are studied in detail for three XGs on cellulose I beta 1-10 surface in aqueous environment, namely GXXXGXXXG, GXXLGXXXG, and GXXFGXXXG, which differ in the length and composition of one side chain. Our work shows that when water molecules are included in the theoretical model, the total interaction energies between the adsorbed XGs and cellulose are considerably smaller than in vacuo. Furthermore, in water environment the van der Waals interactions prevail over the electrostatic interactions in the adsorption. Variation in one side chain does not have significant influence on the interaction energy and the binding affinity, but does affect the equilibrium structural properties of the adsorbed XGs to facilitate the interaction between both the backbone and the side chain residues with the cellulose surface. Together, this analysis provides new insights into the nature of the XG-cellulose interaction, which helps to further refine current molecular models of the composite plant cell wall.

  • 34036. Zhang, Qu
    et al.
    Hill, Geoffrey E
    Edwards, Scott V
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines.2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, article id 305Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen.

    RESULTS: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response.

    CONCLUSIONS: The two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.

  • 34037. Zhang, Ranran
    et al.
    Liu, Xujie
    Xiong, Zhiyuan
    Huang, Qianli
    Yang, Xing
    Yan, Hao
    Ma, Jing
    Feng, Qingling
    Shen, Zhijian
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Tsinghua University, Beijing, China.
    The immunomodulatory effects of Zn-incorporated micro/nanostructured coating in inducing osteogenesis2018In: Artificial cells nanomedicine and biotechnology, ISSN 2169-1401, Vol. 46, p. S1123-S1130Article in journal (Refereed)
    Abstract [en]

    Micro/nanostructured TiO2/ZnO coating has been shown to possess multiple functions, including antibacterial activity and bioactivity. Osteoblast-like SaOS-2 cells were employed for evaluating the in vitro osteogenic capacity of this coating and positive results were obtained. However, traditional principles of osseointegration focus only on the osteogenic differentiation alone. The effects of immunomodulation on the osteogenic activity have been largely ignored. In this study, the inflammatory responses of macrophages on the micro/nanostructured TiO2/ZnO coating were investigated. The extract media of macrophage cell line RAW264.7 cultured on the TiO2/ZnO coating were collected as indirect co-culture conditioned media. The osteogenic activity of SaOS-2 cells in the conditioned media was investigated. Adhesion, ALP activity and extracellular mineralization of cells grown in the conditioned media extracted from the micro/nanostructured TiO2/ZnO coating were found to be enhanced, compared to those grown in the conditioned media extracted from the macroporous TiO2 coating. The immune microenvironment produced by the micro/nanostructured TiO2/ZnO coating showed excellent capacity to promote osteogenesis, indicating that this coating could be a promising candidate for implant surface modification in orthopaedic and dental applications. Furthermore, this work could help us understand the interplay between the host immune system and the osteoimmunomodulatory properties of the biomaterials, and optimize the design for coating biomaterials.

  • 34038.
    Zhang, Rong
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Biochemistry.
    New approaches to concentration, desalting and separation of biopolymers in capillary electrophoresis1997Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the first part of the thesis five new on-tube methods for concentration and desalting ofampholytes, such as peptides and proteins, are described in Papers I and II. The methods arebased on the fact that electrophoretic migration velocities decrease upon a decrease in theabsolute value of the zeta potential of a solute and the pore size of the electrophoresis mediumand upon an increase in the cross section of the electrophoresis chamber, the viscosity and theelectrical conductivity of the electrophoresis medium. A combination of displacementelectrophoresis and a hydrodynamic counter flow is also utilized to create a stationary zone inwhich the sample solute can be concentrated continuously. Paper III describes an on-tubedesalting technique for IEF, which is based on an automatic substitution of the salts in thesample with an ampholyte solution in a short focusing pre-step. A simple off-tubeconcentration and desalting method using a hollow fiber is described in Paper IV, which isbased on the transport of water by evaporation or the Donnan effect out of the fiber throughthe pores in its wall and has the advantage that solute adsorption is negligible. The method canbe used not only for macromolecules but also for low-molecular-weight compounds.

    The second part of thesis consists of two publications about HPCE in the presence ofadditives. In Paper V liposomes were used as a pseudostationary phase in CZE. The decreasein the mobility of an analyte owing to the presence of liposomes reflected interaction betweenanalytes and liposomes. Paper VI deals with the shifts in mobilities of peptides and proteinswhen buffers are supplemented with β-cyclodextrin sulfate and 6-amino β-cyclodextrin. A newdefinition of resolution of two very adjacent peaks, without knowing peak widths, is suggested.

    Studies of crystals of lysozyme and MBP by HPCE were presented in the last part of thethesis (Paper VII), which show that HPCE can be used to shed some light on the question whysome protein crystals afford low resolution upon X-ray diffraction.

  • 34039.
    Zhang, Rui
    et al.
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, North Third Ring Rd 15, Beijing 100029, Peoples R China.
    Zhang, Tianji
    Natl Inst Metrol, Div Chem & Analyt Sci, Beijing, Peoples R China.
    Lv, Yongqin
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, North Third Ring Rd 15, Beijing 100029, Peoples R China.
    Qin, Peiyong
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, North Third Ring Rd 15, Beijing 100029, Peoples R China.
    Li, Hongmei
    Natl Inst Metrol, Div Chem & Analyt Sci, Beijing, Peoples R China.
    Li, Jin-Ping
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Beijing Univ Chem Technol, Int Res Ctr Soft Matter, Beijing, Peoples R China.
    Tan, Tianwei
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, North Third Ring Rd 15, Beijing 100029, Peoples R China.
    Selective binding of heparin oligosaccharides in a magnetic thermoresponsive molecularly imprinted polymer2019In: Talanta: The International Journal of Pure and Applied Analytical Chemistry, ISSN 0039-9140, E-ISSN 1873-3573, Vol. 201, p. 441-449Article, review/survey (Refereed)
    Abstract [en]

    Heparin is a highly sulfated polysaccharide, applied in clinic for treatment of thrombotic diseases. The biological activity is closely related to its molecular structure e.g. compositions of disaccharides and oligosaccharides units. The classical method to isolate the oligosaccharides after depolymerization by heparinases or nitrous acid I s by size exclusion chromatography which is a time-consuming process. In this study, we explored the possibility for rapid separation of oligosaccharides using a novel polymer material. The magnetic thermoresponsive molecularly imprinted polymers (MIPs) were synthesized using heparin disaccharide as a template, AEM, NIPAAm, and AAm as functional monomer, and MBAA as crosslinker by surface radical polymerization in an aqueous media. Incubation of the MIP with hepairn oligosaccharides demonstrated specific binding to the template molecule. This binding to the targeted molecule was affected by reaction temperature with regard to binding capacity and specificity. The recognition specificity and selectivity can be modulated by varying the compositions of multifunctional monomers. The pseudo-second-order kinetic model and Langmuir isotherm model provide the best fit to the equilibrium adsorption of heparin disaccharides by MIPs. The results suggest that the new material can be used for rapid separation of di- and tetra-saccharides of heparin, which can also be adapted to the applications for isolation of oligosaccharides from other polysaccharides, e.g. heparan sulfate and chondoriting sulfate.

  • 34040. Zhang, Ruiying
    et al.
    Song, Gang
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Alström, Per
    Ramos, Raül
    Xing, Xiaoying
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fjeldså, Jon
    Wang, Haitao
    Yang, Xiaojun
    Kristin, Anton
    Shestopalov, Alexander M
    Choe, Jae Chun
    Lei, Fumin
    Comparative phylogeography of two widespread magpies: importance of habitat preference and breeding behavior on genetic structure in China.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 2, p. 562-72Article in journal (Refereed)
    Abstract [en]

    Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.

  • 34041.
    Zhang, Shi-Jin
    Stockholm University.
    Regulation of Intracellular Calcium in Brown Adipocytes1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Intracellular Ca2+ is considered a primary regulator of cell function. In the present study, the control and the effects of intracellular Ca2+ in brown adipocytes have been investigated. Cytosolic Ca2+ levels ([Ca2+]i) are the resultant of the activity of Ca2+ transport systems. Results concerning Ca2+transport systems in the plasma membrane, endoplasmic reticulum and mitochondria are presented.

    [Ca2+]i, monitored with Fura-2/AM, is increased when brown adipocytes are stimulated with norepinephrine (NE). The NE effect is mediated via a1-adrenoceptors and involves both release from intracellular Ca2+ stores and influx of extracellular Ca2+. The NE-induced [Ca2+]i response could be desensitized by pretreatment with NE. The desensitization is also mediated by a1-receptors and intracellularly by increased [Ca2+]i and calmodulin but not by protein kinase C. The kinetics of the desensitization are similar to those of inhibition of protein synthesis or transcription and the desensitization is associated with a comparable decrease in the number of a1-receptors.

    Mitochondrial Ca2+ levels ([Ca2+]m) were monitored within brown adipocytes with mitochondrially targeted aequorin. [Ca2+]m was not a simple reflection of [Ca2+]i; rather, evidence is presented for the existence of a b-adrenergic, cAMP-mediated signal that augments the [Ca2+]m/[Ca2+]i ratio. This signal causes the mitochondria to sequester Ca2+ even in the absence of increased cytosolic levels. Inhibition of mitochondrial Ca2+ uptake augments the cytosolic responses. Mitochondria may thus play an important role even in cytosolic Ca2+homeostasis in brown adipocytes.

    Chronic treatment of brown adipocytes with NE resulted in marked alterations of cytosolic Ca2+ handling, but the mitochondria retained their ability to sequester Ca2+during adrenergic stimulation, i.e. under conditions when UCP1 should be active.

    The effects of an increase in [Ca2+]i involve activation of a cAMP phosphodiesterase, and the presence of this component explains the unusual kinetic characteristics of norepinephrine-induced cAMP accumulation. [Ca2+]i is also involved in the regulation of gene expression: increased [Ca2+]i interacts synergistically with cAMP in the control of c-fos expression which may be of significance for regulation of cell proliferation and differentiation.

    It was concluded that Ca2+ is a primary regulator of physiological functions in brown adipocytes. The Ca2+ transport systems in brown adipocytes are involved in the regulation of intracellular and intraorganellar Ca2+. Changes of the free cytosolic Ca2+ concentration by hormone stimulation induces the activation of many physiological processes.

  • 34042.
    Zhang, Shouting
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Studies on the Molecular Biology of the Mouse Pneumotropic Polyomavirus2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The Murine Pneumotropic Virus (MPtV), in contrast to the other MurinePolyomavirus (MPyV), appears to be non-tumourigenic in its natural host. Instead, MPtV causes acute pneumonia and can serve as a model in studies of polyomavirus-induced disease. In initial experiments, MPtV large T-antigen (LT) was expressed in a heterologous system. LT was characterized with regard to its metabolic stability and cell immortalizing activity and, after purification, to its specific DNA binding.

    The absence of permissive cell culture system for MPtV has hampered its study. We made attempts to widen the host range of the virus by modifying the regulatory and late regions of the genome. The enhancer substitution mutant (KVm1), having a transcriptional enhancer substituted with a corresponding DNA segment from MPyV, was able to replicate in mouse 3T3 cells and form virus particles that were infectious in mice. However, efficient infection of cells in vitro was not achieved with this mutant virus, possibly due to the absence of virus-specific receptors on the cells. The capsid protein substitution mutants, having capsid protein genes of MPyV, for which receptors are present on a variety of cell types, showed also no cytopathic effect, despite an enhanced viral DNA replication and assembly of virus particles.

    MPtV-DNA extracted from virus in lung tissue of infected mice had a heterogeneous enhancer segment. A majority of the DNA molecules had a structure differing from the standard-type. A 220 base-pair insertion at nucleotide position 142 with a concomitant deletion of nucleotides 143 to 148 was a prominent variation. Other genome variants showed complete or partial deletions of the insertion and surrounding sequences in the viral enhancer. In relation to the standard-type, all variant genomes showed differences in the activities of transcriptional promoters and the origin DNA replication. Analysis by DNA reassociation showed that a large number of nucleotide sequences related to the 220 base-pair insert in the MPtV genome were present in mouse and human DNA, but not in Escherichia coli DNA. Together, the data suggest that the 220 base-pair insertion is related to a transposable element of a novel type.

  • 34043. Zhang, Shuo
    et al.
    Winestrand, Sandra
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Guo, Xiang
    Chen, Lin
    Hong, Feng
    Jönsson, Leif
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Effects of aromatic compounds on the production of bacterial nanocellulose by Gluconacetobacter xylinus2014In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 13, p. 62-Article in journal (Refereed)
    Abstract [en]

    Background:

    Bacterial cellulose (BC) is a polymeric nanostructured fibrillar network produced by certain microorganisms, principally Gluconacetobacter xylinus. BC has a great potential of application in many fields. Lignocellulosic biomass has been investigated as a cost-effective feedstock for BC production through pretreatment and hydrolysis. It is well known that detoxification of lignocellulosic hydrolysates may be required to achieve efficient production of BC. Recent results suggest that phenolic compounds contribute to the inhibition of G. xylinus. However, very little is known about the effect on G. xylinus of specific lignocellulose-derived inhibitors. In this study, the inhibitory effects of four phenolic model compounds (coniferyl aldehyde, ferulic acid, vanillin and 4-hydroxybenzoic acid) on the growth of G. xylinus, the pH of the culture medium, and the production of BC were investigated in detail. The stability of the phenolics in the bacterial cultures was investigated and the main bioconversion products were identified and quantified.

    Results:

    Coniferyl aldehyde was the most potent inhibitor, followed by vanillin, ferulic acid, and 4-hydroxybenzoic acid. There was no BC produced even with coniferyl aldehyde concentrations as low as 2 mM. Vanillin displayed a negative effect on the bacteria and when the vanillin concentration was raised to 2.5 mM the volumetric yield of BC decreased to similar to 40% of that obtained in control medium without inhibitors. The phenolic acids, ferulic acid and 4-hydroxybenzoic acid, showed almost no toxic effects when less than 2.5 mM. The bacterial cultures oxidized coniferyl aldehyde to ferulic acid with a yield of up to 81%. Vanillin was reduced to vanillyl alcohol with a yield of up to 80%.

    Conclusions:

    This is the first investigation of the effect of specific phenolics on the production of BC by G. xylinus, and is also the first demonstration of the ability of G. xylinus to convert phenolic compounds. This study gives a better understanding of how phenolic compounds and G. xylinus cultures are affected by each other. Investigations in this area are useful for elucidating the mechanism behind inhibition of G. xylinus in lignocellulosic hydrolysates and for understanding how production of BC using lignocellulosic feedstocks can be performed in an efficient way.

  • 34044.
    Zhang, Shuping
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Shandong Univ, Sch Life Sci, Inst Ecol & Biodivers, Jinan 250100, Shandong, Peoples R China.
    Isermann, Maike
    Bremen Univ, Dept Ecol, Vegetat Ecol & Conservat Biol, FB 2, D-28359 Bremen, Germany..
    Gan, Wenhao
    Shandong Univ, Sch Life Sci, Inst Ecol & Biodivers, Jinan 250100, Shandong, Peoples R China..
    Breed, Martin
    Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005, Australia..
    Invasive Rosa rugosa populations outperform native populations, but some populations have greater invasive potential than others2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 5735Article in journal (Refereed)
    Abstract [en]

    Increased performance of invasive plant species in their introduced range vs. their native range has been previously documented. However, performance differences among invasive populations have rarely been explored, despite this information being central to understanding the evolution of invasiveness as well as being a useful basis to inform management of invasive species. To examine variation in performance among populations of Rosa rugosa in its introduced range, and whether introduced populations perform better than native populations, we quantified growth and reproductive traits in five invasive populations in northwest Europe and two native and declining populations in China. Overall, we found that the introduced R. rugosa populations we sampled performed significantly better than the sampled native populations for growth and reproductive traits (2 to 4 fold increase). However, there was significant variation for most traits among the five invasive populations, demonstrating that some introduced populations we sampled were more successful invaders than others. Our findings provide a useful foundation for management of invasive R. rugosa in Europe, and support the recent call for more intra-species research in invasive species biology.

  • 34045. Zhang, Sicai
    et al.
    Berntsson, Ronnie P. A.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Stockholm Univ, Dept Biochem & Biophys, SE-10691 Stockholm, Sweden.
    Tepp, William H.
    Tao, Liang
    Johnson, Eric A.
    Stenmark, Pal
    Dong, Min
    Structural basis for the unique ganglioside and cell membrane recognition mechanism of botulinum neurotoxin DC2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1637Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins (BoNTs), the most potent toxins known, are potential bioterrorism agents. It is well established that all seven serotypes of BoNTs (BoNT/A-G) require complex gangliosides as co-receptors. Here, we report that BoNT/DC, a presumed mosaic toxin between BoNT/D and BoNT/C1, binds and enters efficiently into neurons lacking complex gangliosides and shows no reduction in toxicity in mice deficient in complex gangliosides. The co-crystal structure of BoNT/DC with sialyl-Thomsen-Friedenreich antigen (Sialyl-T) suggests that BoNT/DC recognizes only the sialic acid, but not other moieties in gangliosides. Using liposome flotation assays, we demonstrate that an extended loop in BoNT/DC directly interacts with lipid membranes, and the co-occurring sialic acid binding and loop-membrane interactions mediate the recognition of gangliosides in membranes by BoNT/DC. These findings reveal a unique mechanism for cell membrane recognition and demonstrate that BoNT/DC can use a broad range of sialic acid-containing moieties as co-receptors.

  • 34046. Zhang, Sicai
    et al.
    Berntsson, Ronnie P. -A.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Umeå University, Sweden.
    Tepp, William H.
    Tao, Liang
    Johnson, Eric A.
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dong, Min
    Structural basis for the unique ganglioside and cell membrane recognition mechanism of botulinum neurotoxin DC2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1637Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins (BoNTs), the most potent toxins known, are potential bioterrorism agents. It is well established that all seven serotypes of BoNTs (BoNT/A-G) require complex gangliosides as co-receptors. Here, we report that BoNT/DC, a presumed mosaic toxin between BoNT/D and BoNT/C1, binds and enters efficiently into neurons lacking complex gangliosides and shows no reduction in toxicity in mice deficient in complex gangliosides. The co-crystal structure of BoNT/DC with sialyl-Thomsen-Friedenreich antigen (Sialyl-T) suggests that BoNT/DC recognizes only the sialic acid, but not other moieties in gangliosides. Using liposome flotation assays, we demonstrate that an extended loop in BoNT/DC directly interacts with lipid membranes, and the co-occurring sialic acid binding and loop-membrane interactions mediate the recognition of gangliosides in membranes by BoNT/DC. These findings reveal a unique mechanism for cell membrane recognition and demonstrate that BoNT/DC can use a broad range of sialic acid-containing moieties as co-receptors.

  • 34047. Zhang, Sicai
    et al.
    Lebreton, Francois
    Mansfield, Michael J.
    Miyashita, Shin-Ichiro
    Zhang, Jie
    Schwartzman, Julia A.
    Tao, Liang
    Masuyer, Geoffrey
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Martínez-Carranza, Markel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gilmore, Michael S.
    Doxey, Andrew C.
    Dong, Min
    Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium2018In: Cell Host and Microbe, ISSN 1931-3128, E-ISSN 1934-6069, Vol. 23, no 2, p. 169-+Article in journal (Refereed)
    Abstract [en]

    Botulinumneurotoxins (BoNTs), produced by various Clostridium strains, are a family of potent bacterial toxins and potential bioterrorism agents. Here we report that an Enterococcus faecium strain isolated from cow feces carries a BoNT-like toxin, designated BoNT/En. It cleaves both VAMP2 and SNAP-25, proteins that mediate synaptic vesicle exocytosis in neurons, at sites distinct from known BoNT cleavage sites on these two proteins. Comparative genomic analysis determines that the E. faecium strain carrying BoNT/En is a commensal type and that the BoNT/En gene is located within a typical BoNT gene cluster on a 206 kb putatively conjugative plasmid. Although the host species targeted by BoNT/En remains to be determined, these findings establish an extended member of BoNTs and demonstrate the capability of E. faecium, a commensal organism ubiquitous in humans and animals and a leading cause of hospital-acquired multi-drug-resistant (MDR) infections, to horizontally acquire, and possibly disseminate, a unique BoNT gene cluster.

  • 34048.
    Zhang, Sicai
    et al.
    Harvard Med Sch, USA.
    Masuyer, Geoffrey
    Stockholm University.
    Zhang, Jie
    Harvard Med Sch, USA.
    Shen, Yi
    Harvard Med Sch, USA.
    Lundin, Daniel
    Stockholm University.
    Henriksson, Linda
    Stockholm University.
    Miyashita, Shin-Ichiro
    Harvard Med Sch, USA.
    Martinez-Carranza, Markel
    Stockholm University.
    Dong, Min
    Harvard Med Sch, USA.
    Stenmark, Pål
    Stockholm University.
    Identification and characterization of a novel botulinum neurotoxin2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14130Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Remarkably, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5 and Ykt6. To validate its activity, a small amount of full-length BoNT/X was assembled by linking two non-toxic fragments using a transpeptidase (sortase). Assembled BoNT/X cleaves VAMP2 and VAMP4 in cultured neurons and causes flaccid paralysis in mice. Thus, BoNT/X is a novel BoNT with a unique substrate profile. Its discovery posts a challenge to develop effective countermeasures, provides a novel tool for studying intracellular membrane trafficking, and presents a new potential therapeutic toxin for modulating secretions in cells.

  • 34049. Zhang, Sicai
    et al.
    Masuyer, Geoffrey
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zhang, Jie
    Shen, Yi
    Lundin, Daniel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Henriksson, Linda
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Miyashita, Shin-Ichiro
    Martinez-Carranza, Markel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dong, Min
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Identification and characterization of a novel botulinum neurotoxin2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14130Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Remarkably, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5 and Ykt6. To validate its activity, a small amount of full-length BoNT/X was assembled by linking two non-toxic fragments using a transpeptidase (sortase). Assembled BoNT/X cleaves VAMP2 and VAMP4 in cultured neurons and causes flaccid paralysis in mice. Thus, BoNT/X is a novel BoNT with a unique substrate profile. Its discovery posts a challenge to develop effective countermeasures, provides a novel tool for studying intracellular membrane trafficking, and presents a new potential therapeutic toxin for modulating secretions in cells.

  • 34050.
    Zhang, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Biochemistry.
    Directed Evolution of Glutathione Transferases with Altered Substrate Selectivity Profiles: A Laboratory Evolution Study Shedding Light on the Multidimensional Nature of Epistasis2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Directed evolution is generally regarded as a useful approach in protein engineering. By subjecting members of a mutant library to the power of Darwinian evolution, desired protein properties are obtained. Numerous reports have appeared in the literature showing the success of tailoring proteins for various applications by this method. Is it a one-way track that protein practitioners can only learn from nature to enable more efficient protein engineering?

    A structure-and-mechanism-based approach, supplemented with the use of reduced amino acid alphabets, was proposed as a general means for semi-rational enzyme engineering. Using human GST A2-2*E, the most active human enzyme in the bioactivation of azathioprine, as a parental enzyme to test this approach, a L107G/L108D/F222H triple-point mutant of GST A2-2*E (thereafter designated as GDH) was discovered with 70-fold increased activity, approaching the upper limit of specific activity of the GST scaffold. The approach was further experimentally verified to be more successful than intuitively choosing active-site residues in proximity to the bound substrate for the improvement of enzyme performance.

    By constructing all intermediates along all putative mutational paths leading from GST A2-2*E to mutant GDH and assaying them with nine alternative substrates, the fitness landscapes were found to be “rugged” in differential fashions in substrate-activity space. The multidimensional fitness landscapes stemming from functional promiscuity can lead to alternative outcomes with enzymes optimized for other features than the selectable markers that were relevant at the origin of the evolutionary process. The results in this thesis suggest that in this manner an evolutionary response to changing environmental conditions can readily be mounted.

    In summary, the thesis demonstrates the attractive features of the structure-and-mechanism-based semi-rational directed evolution approach for optimizing enzyme performance. Moreover, the results gained from the studies show that laboratory evolution may refine our understanding of evolutionary process in nature.

678679680681682683684 34001 - 34050 of 34646
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf