164 research outputs found
Constitutive and Inducible Expression of the rRNA Methylase Gene erm(B) in Campylobacter
No full textMacrolides are the antimicrobials of choice for treating human campylobacteriosis. The recent emergence of erm(B) in Campylobacter bacteria threatens the utility of this class of antibiotics. Here we report the constitutive and inducible expression of erm(B) in Campylobacter isolates derived from diarrheal patients and food-producing animals. Constitutive expression of erm(B) was associated with insertion and deletion in the regulatory region of the gene, providing the first documentation of the differential expression of erm(B) in Campylobacter bacteria.This article is published as Deng, Fengru, Jianzhong Shen, Maojun Zhang, Congming Wu, Qijing Zhang, and Yang Wang. "Constitutive and inducible expression of the rRNA methylase gene erm (B) in Campylobacter." Antimicrobial agents and chemotherapy 59, no. 10 (2015): 6661-6664. doi: 10.1128/AAC.01103-15. Posted with permission.</p
Identification of a Novel Genomic Island Conferring Resistance to Multiple Aminoglycoside Antibiotics in Campylobacter coli
No full textHistorically, the incidence of gentamicin resistance in Campylobacter has been very low, but recent studies reported a high prevalence of gentamicin-resistant Campylobacter isolated from food-producing animals in China. The reason for the high prevalence was unknown and was addressed in this study. PCR screening identified aminoglycoside resistance genes aphA-3 and aphA-7 and the aadE–sat4–aphA-3 cluster among 41 Campylobacter isolates from broiler chickens. Importantly, a novel genomic island carrying multiple aminoglycoside resistance genes was identified in 26 aminoglycoside resistant Campylobacter coli strains. Sequence analysis revealed that the genomic island was inserted between cadF and COO1582 on the C. coli chromosome and consists of 14 open reading frames (ORFs), including 6 genes (the aadE–sat4–aphA-3 cluster, aacA-aphD, aac, and aadE) encoding aminoglycoside-modifying enzymes. Analysis by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing indicated that the C. coli isolates carrying this unique genomic island were clonal, and the clone of PFGE subtype III and sequence type (ST) 1625 was particularly predominant among the C. coli isolates examined, suggesting that clonal expansion may be involved in dissemination of this resistance island. Additionally, we were able to transfer this genomic island from C. coli to a Campylobacter jejuni strain using natural transformation under laboratory conditions, and the transfer resulted in a drastic increase in aminoglycoside resistance in the recipient strain. These findings identify a previously undescribed genomic island that confers resistance to multiple aminoglycoside antibiotics. Since aminoglycoside antibiotics are used for treating occasional systemic infections caused by Campylobacter, the emergence and spread of this antibiotic resistance genomic island represent a potential concern for public health.This article is published as Qin, Shangshang, Yang Wang, Qijing Zhang, Xia Chen, Zhangqi Shen, Fengru Deng, Congming Wu, and Jianzhong Shen. "Identification of a novel genomic island conferring resistance to multiple aminoglycoside antibiotics in Campylobacter coli." Antimicrobial agents and chemotherapy 56, no. 10 (2012): 5332-5339. doi: 10.1128/AAC.00809-12. Posted with permission.</p
Emergence of Multidrug-Resistant Campylobacter Species Isolates with a Horizontally Acquired rRNA Methylase
No full textAntibiotic-resistant Campylobacter constitutes a serious threat to public health, and resistance to macrolides is of particular concern, as this class of antibiotics is the drug of choice for clinical therapy of campylobacteriosis. Very recently, a horizontally transferrable macrolide resistance mediated by the rRNA methylase gene erm(B) was reported in a Campylobacter coli isolate, but little is known about the dissemination of erm(B) among Campylobacter isolates and the association of erm(B)-carrying isolates with clinical disease. To address this question and facilitate the control of antibiotic-resistant Campylobacter, we determined the distribution of erm(B) in 1,554 C. coli and Campylobacter jejuni isolates derived from food-producing animals and clinically confirmed human diarrheal cases. The results revealed that 58 of the examined isolates harbored erm(B) and exhibited high-level resistance to macrolides, and most were recent isolates, derived in 2011-2012. In addition, the erm(B)-positive isolates were all resistant to fluoroquinolones, another clinically important antibiotic used for treating campylobacteriosis. The erm(B) gene is found to be associated with chromosomal multidrug resistance genomic islands (MDRGIs) of Gram-positive origin or with plasmids of various sizes. All MDRGIs were transferrable to macrolide-susceptible C. jejuni by natural transformation under laboratory conditions. Molecular typing of the erm(B)-carrying isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) identified diverse genotypes and outbreak-associated diarrheal isolates. Molecular typing also suggested zoonotic transmission of erm(B)-positive Campylobacter. These findings reveal an emerging and alarming trend of dissemination of erm(B) and MDRGIs in Campylobacter and underscore the need for heightened efforts to control their further spread.This article is published as Wang, Yang, Maojun Zhang, Fengru Deng, Zhangqi Shen, Congming Wu, Jianzhong Zhang, Qijing Zhang, and Jianzhong Shen. "Emergence of multidrug-resistant Campylobacter species isolates with a horizontally acquired rRNA methylase." Antimicrobial agents and chemotherapy 58, no. 9 (2014): 5405-5412. doi: 10.1128/AAC.03039-14. Posted with permission.</p
First Report of the Multidrug Resistance Gene cfr in Enterococcus faecalis of Animal Origin
No full textThe multiresistance gene cfr was identified for the first time in an Enterococcus faecalis isolate of animal origin. The 32,388-bp plasmid pEF-01, which carried the cfr gene, was sequenced completely. Three copies of the insertion sequence IS1216 were identified in pEF-01, and the detection of a cfr- and IS1216-containing amplicon by inverse PCR suggests that IS1216 may play a role in the dissemination of cfr by a recombination process.This is article published as Liu, Yang, Yang Wang, Congming Wu, Zhangqi Shen, Stefan Schwarz, Xiang-Dang Du, Lei Dai, Wanjiang Zhang, Qijing Zhang, and Jianzhong Shen. "First report of the multidrug resistance gene cfr in Enterococcus faecalis of animal origin." Antimicrobial agents and chemotherapy 56, no. 3 (2012): 1650-1654. doi: 10.1128/AAC.06091-11. Posted with permission.</p
Transferable Multiresistance Plasmids Carrying cfr in Enterococcus spp. from Swine and Farm Environment
No full textSeventy-seven porcine Enterococcus isolates with florfenicol MICs of ≥16 μg of were/ml screened for the presence of the multiresistance gene cfr, its location on plasmids, and its genetic environment. Three isolates—Enterococcus thailandicus 3-38 (from a porcine rectal swab collected at a pig farm), Enterococcus thailandicus W3, and Enterococcus faecalis W9-2 (the latter two from sewage at a different farm), carried the cfr gene. The SmaI pulsed-field gel electrophoresis patterns of the three isolates differed distinctly. In addition, E. faecalis W9-2 was assigned to a new multilocus sequence type ST469. Mating experiments and Southern blot analysis indicated that cfr is located on conjugative plasmids pW3 (∼75 kb) from E. thailandicus W3, p3-38 (∼72 kb) from E. thailandicus 3-38, and pW9-2 (∼55 kb) from E. faecalis W9-2; these plasmids differed in their sizes, additional resistance genes, and the analysis of the segments encompassing the cfr gene. Sequence analysis revealed that all plasmids harbored a 4,447-bp central region, in which cfr was bracketed by two copies of the novel insertion sequence ISEnfa4 located in the same orientation. The sequences flanking the central regions of these plasmids, including the partial tra gene regions and a ω-ε-ζ toxin-antitoxin module, exhibited >95% nucleotide sequence identity to the conjugative plasmid pAMβ1 from E. faecalis. Conjugative plasmids carrying cfr appear to play an important role in the dissemination and maintenance of the multiresistance gene cfr among enterococcal isolates and possibly other species of Gram-positive bacteria.This article is published as Liu, Yang, Yang Wang, Stefan Schwarz, Yun Li, Zhangqi Shen, Qijing Zhang, Congming Wu, and Jianzhong Shen. "Transferable multiresistance plasmids carrying cfr in Enterococcus spp. from swine and farm environment." Antimicrobial agents and chemotherapy 57, no. 1 (2013): 42-48. doi: 10.1128/AAC.01605-12. Posted with permission.</p
Structural and functional characterisation of Photosystem II from two His-tagged transplastomic strains of Nicotiana tabacum
No full textPhotosystem II (PSII) is a polypeptide-cofactor complex organised as a homodimeric multisubunit protein embedded in the thylakoid membrane. PSII monomers are heterooligomers related to each other by a pseudo-twofold axis perpendicular to the membrane plane (Loll et al. 2005). PSII acts as a photochemical enzyme that through the chlorophylls and the other cofactors catalyses photon capture and electron transfer from water to the plastoquinone pool with concomitant evolution of oxygen. Photon capture and charge separation take place in the PSII core which consists of the D1 and D2 proteins, the cytochrome b559 alpha- and beta-chains (PsbE and F subunits) and the chlorophyll a-binding antenna proteins CP43 and CP47 (Loll et al. 2005). The remaining polypeptides are low molecular mass proteins with not clearly understood fuctions; they include chloroplast-encoded (PsbH, I, J, K, L, M, N, T and Z) and nucleus-encoded (PsbR, S, W and X) proteins consisting of one to four transmembrane helices (Barber et al. 1997). The oxygen-evolving part of PSII consists of a Mn-Ca transition complex called Mn cluster or oxygen evolving complex that is situated on the luminal side of PSII. In higher plants it is stabilised by the PsbO (33 kDa), PsbP (23 kDa) and PsbQ (17 kDa) extrinsic subunits (Soursa et al. 2006; Ifuku et al. 2005). The structure and mechanisms related to the oxygen evolving complex of PSII are not completely clarified. Currently two high resolution structures from the cyanobacteria S. elongatus are available (Loll et al. 2005; Ferreira et al. 2004) Nevertheless structural information is not as well defined in green algae and higher plants as in cyanobacteria. In fact the 8Å structure available from spinach has too low resolution for addressing questions such as the structural and functional differences in respect to PSII from cyanobateria (Rhee et al. 1997).. Therefore it is obvious that for PSII from higher plants the main general questions are still open: is the structure of PSII from higher plants equivalent to the structures observed in cyanobacteria? Is the typical higher plants subunit PsbS stably or transiently bound to PSII? Finding an answer to these questions was the main focus of this work. In this work a simple and rapid protocol to isolate the oxygen-evolving photosystem II (PSII) core complex from Nicotiana tabacum was developed. A PSII having a His-tag extension made of six or ten consecutive histidine residues at the N-terminus of the PsbE subunit was purified by a single-step Ni2+ NTA-affinity column chromatography after solubilisation of the thylakoid membranes using different mild detergents. Characterization of the oxygen evolution and the subunit composition by immunoblotting and mass spectroscopy revealed that the His-tagging did not affect the functional integrity of the PSII reaction center. The final PSII core complex was purified in a single step from solubilised thylakoids in less than 14 hours getting a very pure sample in high amount. The isolated core complex was in a dimeric form as demonstrated by Blue Native PAGE, analytical gel filtration and single particles analysis; with a molecular mass of about 500 kDa, consisting of D1, D2, CP43, CP47, 33 kDa and low molecular weight proteins. The preparation retains a high rate of oxygen-evolving activity but showed different stabilities of the binding of the three extrinsic proteins. The subunit of 33 kDa was always present in the preparations with a constant amount, whereas the 23 and 17 kDa subunits were always in less and unconstant amounts. Nevertheless the oxygen evolution was not depending on the amount of the 23 and 17 kDa subunits. Furthermore the preparation showed a high oxygen-evolving activity of 1390 micromol/mg Chl·h-1 in presence of betaine, while its activity was 440-680 micromol/mg Chl·h-1 in its absence. The presence of 1.0 mol/L betaine during the isolation of PSII increased the preservation of the photochemical activity hence the oxygen evolution. It was inferred from these results that His-tagging does not affect the functional and structural integrity of the PSII core complex and that the “Histag strategy” is highly useful for biochemical, physicochemical and structural studies of higher plant PSII. PSII is directly involved in two essential processes, the efficient capture and funnelling of light energy to the reaction centre and the controlled dissipation of excess excitation energy. Those functions require structural and functional flexibility in order to be performed with high efficiency. Moreover light-harvesting proteins respond to an external signal, the thylakoid pH, to induce feedback control regulating those activities in every moment. This process called non-photochemical quenching (NPQ) is mainly depending on the xanthophyll cycle and the PsbS protein (Szabo et al. 2005). In this work several new evidences related with those two processes were found. The subunit PsbS is a polypeptide whose involvement in the NPQ processes is debated. Nevertheless, its position in the PSII complex and the mechanisms by which this subunit contributes to carry out the NPQ functions are not definitely known. In addition it is not sure if it is a pigment binding protein or not. Currently several lines of evidence indicate that this subunit is able to bind two molecules of zeaxanthin, one of the pigments involved in the xanthophyll cycle. In this work immunolabelling indicated that PsbS is tightly bound to the PSII core dimer, monomer and incomplete PSII particles as Reaction Centre-CP47 (RC-CP47). Furthermore qualitative HPLC indicates a complete absence of zeaxanthin in the sample and the presence of violaxanthin, another pigment involved in the xanthophyll cycle. The absence of zeaxanthin was expected considering that the plants were harvested after the dark period and that the particles were purified in complete dark (or in green light), whereas the presence of violaxanthin was unexpected considering that so far no evidence of violaxanthin bound to PSII cores devoid of LHC proteins was reported. Furthermore the amount of chlorophyll b was not relevant for suspecting this pigment bound to PsbS. Therefore we conclude that if PsbS is able to bind chlorophyll it has to be a chlorophyll a. The results indicate that PsbS could be able to bind not only zeaxanthin but also violaxanthin. The extrinsic subunit Psb27 was also found in this preparation. The presence and the amount of this subunit, reported to be involved in the repair of damaged PSII, was not constant and therefore behaving as the other two extrinsic proteins 23kDa (PsbP) and 17kDa (PsbQ). Electron crystallography studies on spinach PSII particles purified by differential solubilisation resulted in crystalline tubes with new unit cell constants. From data analysis a density map at 15Å resolution was obtained with a P22121 symmetry. However, at this resolution it cannot be said if the internal symmetry axis is related with the two-fold axis of the dimer or the pseudo two-fold axis of the monomer. In conclusion a method to isolate functional, pure PSII core complexes was developped. These samples, together with the improved 2d crystallisation protocol could lead to crystals with higher quality hence better resolution density maps in the future.Photosystem II (PSII) ist ein Polypeptid-Kofaktor-Komplex, dessen Untereinheiten als Homodimer organisiert vorliegen und in höheren Pflanzen in den Granabereichen der Thylakoidmembran eingebettet sind. PSII Monomere wiederum bestehen aus Hetero-Oligomeren, die pseudo-symmetrisch um eine Achse positioniert sind, welche rechtwinklig zur Membranebene steht (Loll et al. 2005). PS II agiert als photochemisch aktives Enzym, das mit Hilfe der gebundenen Chlorophylle Photonen einfängt und unter Beteiligung weiterer Kofaktoren einen Elektronenfluss von Wasser zu Plastochinon betreibt. Dabei wird gleichzeitig molekularer Sauerstoff frei gesetzt. Die primäre Ladungstrennung findet nach Absorption eines Photons im PSII Kern statt, welcher sich aus den Untereinheiten D1, D2, den alpha- und beta-Untereinheiten von Cytochrom b559 (PsbE und PsbF) sowie den Chlorophyll a-bindenden Kernantennen CP47 und CP43 zusammensetzt (Loll et al. 2005). Bei den übrigen Polypeptiden des Photosystems II handelt es sich um niedermolekulare Proteine, deren Funktion in vielen Fällen noch nicht geklärt ist. Einige dieser Untereinheiten werden im Chloroplasten kodiert (PsbE, F, H, I, J, K, L, M, N, T und Z) während andere im Nukleus kodiert werden (PsbR, S, W und X). Im Allgemeinen bilden sie eine bis vier transmembrane Helices (Barber et al. 1997). Der Teil des Photosystems II, der für die Spaltung von Wasser zuständig ist, besteht aus einem Mn4-Ca Übergangskomplex. Dieser ist im Thylakoidlumen lokalisiert und wird Wasser spaltender oder Sauerstoff bildender Komplex genannt. In höheren Pflanzen wird er durch die extrinsischen Untereinheiten PsbO (33 kDa), PsbP (23 kDa) und PsbQ (17 kDa) stabilisiert (Soursa et al. 2006; Ifuku et al. 2005). Weder die Struktur dieses Komplexes noch der Reaktionsmechanismus der Wasserspaltung konnten bisher vollständig aufgeklärt werden. Zurzeit existieren zwei Strukturen mit hoher Auflösung von Photosystem II, welches aus dem Cyanobakterium Synechococcus elongatus isoliert wurde (Loll et al. 2005; Ferreira et al. 2004). Nichtsdestotrotz bleibt eine Reihe von Fragen unbeantwortet, vor allem in Bezug auf die Funktion und Position der kleineren Untereinheiten des PS II, die in den Strukturdaten nicht ausreichend bestimmt werden konnten, sowie in Bezug auf den definitiven Wasserspaltungsmechanismus (Loll et al. 2005; Ferreira et al. 2004). Da für Grünalgen und höhere Pflanzen bisher keine Strukturen mit hoher Auflösung verfügbar sind (Rhee et al. 1997), bleiben einige der wichtigsten Fragen weiterhin offen. Ist die Struktur des Photosystems II höherer Pflanzen tatsächlich äquivalent zur Struktur des Photosystems II der Cyanobakterien? Ist die für höhere Pflanzen typische PsbS Untereinheit stabil an Photosystem II gebunden oder interagiert sie mit den Lichtsammelkomplexen? Die Beantwortung dieser Fragen bildete den Schwerpunkt der vorliegenden Arbeit. Aufreinigungsprotokolle für Photosystem II aus höheren Pflanzen sind mit einigen Nachteilen verbunden, vor allem in Bezug auf Verunreinigungen durch Photosystem I und LHCII (Light harvesting complex II), die Verwendung starker Detergenzien und die im Vergleich zu thermophilen Organismen geringe Stabilität des Photosystems II. Die bestehenden Protokolle für die Aufreinigung von Photosystem II mittels differentieller Zentrifugation oder Saccharosedichtezentrifugation resultieren entweder in Proben geringer Reinheit oder haben zumindest den Nachteil, auf spezielle, später schwer zu entfernende Detergenzien angewiesen zu sein. Für diese Arbeit wurde deshalb ein Protokoll zur schnellen Isolierung von Sauerstoff bildenden PSII Kernkomplexen aus Nicotiana tabacum entwickelt. Mit Hilfe von sechsfachem oder zehnfachem Histidin-tag am N-Terminus der PsbE Untereinheit war es möglich Photosystem II, nach Solubilisierung der Thylakoidmembranen durch milde Detergenzien, durch Ni-NTA Chromatographie in einem Schritt zu präparieren. Die Bestimmung der Sauerstoffbildungsraten und die Zusammensetzung der Proteinuntereinheiten belegten hierbei, dass die funktionelle Integrität der PSII Reaktionszentren erhalten blieb. Im Endeffekt konnten so signifikante Mengen von hoch reinen PSII Kernkomplexen mit nur einem Aufreinigungsschritt aus solubilisierten Thylakoidmembranen innerhalb von höchstens vierzehn Stunden isoliert werden. Mit Hilfe von Blue Native PAGE, analytischer Gelfiltration, Massenspektroskopie, immonologischem Nachweis und Single Particle Analyse konnte demonstriert werden, dass die isolierten Komplexe mit einer Größe von circa 500 kDa in dimerer Form vorlagen und sich aus den Untereinheiten D1, D2, CP47, PsbO (33 kDa Protein) und einer Reihe niedermolekularer Proteine zusammensetzten. Das auf diese Art und Weise präparierte Photosystem II zeichnete sich durch eine hohe maximale Sauerstoffbildungsaktivität aus, mit Raten bis zu 1800 mikromol O2 / (mg Chl • h). Diese PSII Komplexe zeigten ein sehr konstantes Mengenverhältnis von PsbO (33 kDa Protein), während die beiden anderen Untereinheiten des Sauerstoffbildenden Komplexes (PsbP & PsbQ) in schwankenden Mengen auftraten. Nichtsdestotrotz zeigte sich, dass die maximalen Sauerstoffbildungsraten nicht von den Mengen an PsbP und PsbQ in der Probe abhängig waren, sondern dass vielmehr das Vorhandensein bestimmter Reagenzien während der Isolation einen maßgeblichen Einfluss hatten. Tatsächlich zeigten die PSII Komplexe eine hohe Sauerstoffbildungsrate von 1390 mikromol O2 / (mg Chl • h) in der Anwesenheit von Betain, während die Aktivität ohne Betain nur 440 bis 680 mikromol O2 / (mg Chl • h) betrug, auch wenn in beiden Fällen die künstlichen Elektronenakzeptoren Kaliumhexacyanoferrat und 2,6-Dichloro-p-benzochinon in der Reaktionslösung vorhanden waren. Die deutlichste Erhöhung der Sauerstoffbildungsraten wurde durch die Verwendung von 1,0 mol/l Glycinbetain während der Aufreinigung von Photosystem II erreicht. Zusammengenommen konnte also festgestellt werden, dass trotz der Einführung des His-tags Photosystem II strukturell intakt bleibt und dass sich daher diese His-PSII Komplexe sehr gut für biochemische, physikochemische und strukturelle Untersuchungen am Photosystem II höherer Pflanzen eignen. Photosystem II ist direkt an zwei essentiellen Vorgängen der Lichtreaktionen beteiligt. Zum einen sammelt Photosystem II Lichtenergie und leitet diese gezielt zum Reaktionszentrum weiter und zum anderen sorgt es dafür, dass überschüssige Anregungsenergie sicher abgeleitet werden kann. Die Vorraussetzungen für eine hohe Effizienz dieser Funktionen sind funktionelle und strukturelle Flexibilität. Des Weiteren bestehen Kontrollmechanismen darin, dass die Lichtsammelkomplexe (LHCII) auf äußere Signale, wie zum Beispiel den pH-Wert des Thylakoidlumens reagieren können. Das heißt, es existiert eine effiziente Feedbackkontrolle zur Steuerung der Menge an Anregungsenergie, die tatsächlich dem Reaktionszentrum zugeführt wird. Wichtige Funktionen im Abbau überschüssiger Lichtenergie (nicht-photochemisches Quenching, NPQ) werden hierbei durch den so genannten Xanthophyllzyklus und das PsbS Protein übernommen (Szabo et al. 2005). In dieser Arbeit wurden einige neue Informationen in Bezug auf diese beiden Prozesse erarbeitet. Es ist zwar bekannt, dass die viel diskutierte PsbS Untereinheit eine Rolle im NPQ Mechanismus spielt, allerdings sind weder die genaue Position noch die tatsächlichen Funktionen dieses Proteins bisher geklärt worden. Darüber hinaus ist es weiterhin unklar, ob es sich bei PsbS um ein pigmentbindendes Protein handelt. Zurzeit existieren mehrere Belege, dass die PsbS Untereinheit in der Lage ist zwei Moleküle Zeaxanthin, welches ein Pigment des Xanthophyllcyclus darstellt, zu binden (Szabo et al. 2005). Die vorliegende Arbeit konnte zeigen, dass PsbS stabil an PSII Kerndimere, PSII Kernmonomere und unvollständige PSII Partikel, wie die RC47 Komplexe (CP47 + Reaktionszentrum), gebunden ist. Darüber hinaus konnte in qualitativen Pigmentbestimmungen mittels HPLC kein Zeaxanthin, aber stattdessen Violaxanthin, ein weiteres Pigment des Xanthophyllzyklus, in den genannten PSII Komplexen nachgewiesen werden. Die Abwesenheit von Zeaxanthin entspricht insofern den Erwartungen, dass die Pflanzen am Ende der Dunkelperiode geerntet und die PSII Komplexe in völliger Dunkelheit oder unter grünem Licht präpariert wurden. Die Anwesenheit von Violaxanthin war allerdings unerwartet, da es bis zum jetzigen Zeitpunkt noch keinen Hinweis darauf gab, dass Violaxanthin an PS II bindet. Somit ist dies der erste Hinweis für ein Vorkommen von Violaxanthin in PSII Kernkomplexen. Des Weiteren war die Menge an Chlorophyll b in den Proben so gering, dass man davon ausgehen kann, dass PsbS - wenn es denn überhaupt Chlorophylle bindet - ausschließlich Chlorophyll a bindet. Zusammengenommen lässt dies den Schluss zu, dass PsbS sowohl Violaxanthin als auch Zeaxanthin binden kann, das heißt der gesamte Xanthophyllcyclus kann mit Hilfe der PsbS Untereinheit abgewickelt werden. Es gilt außerdem zu beachten, dass in den durchgeführten PSII Präparationen auch die extrinsische Psb27 Untereinheit gefunden und mittels Massenspektrometrie eine erste Charakterisierung vorgenommen wurde. Allerdings waren das Vorhandensein und die Mengen an Psb27, welches vermutlich eine Rolle im Reparaturzyklus von beschädigten PSII Komplexen in vivo spielt, in den PSII Proben nicht konstant wie das auch für die ebenfalls extrinsischen Untereinheiten PsbP (27 kDa Protein) und PsbQ (17 kDa Protein) der Fall war. PSII Partikel, die mittels differentieller Solubilisierung und Dichtegradientenzentrifugation aus Spinat isoliert wurden, konnten für 2D Kristallisationsexperimente verwendet und elektronenmikroskopisch untersucht werden. Es zeigten sich röhrenartige Kristalle, die sich durch vollkommen neuartige Einheitszellenkonstanten auszeichneten. Die Analyse der Kristalle wurde für das Erstellen einer Dichtekarte mit einer Auflösung von 15 Å und einer Raumgruppe von P22121 herangezogen. Die ermittelte Dichtekarte zeigt eine interne Symmetrieachse, allerdings ist es bei dieser Auflösung nicht möglich eine Aussage darüber zu treffen, ob es sich hierbei um die Symmetrieachse des PSII Dimers oder die pseudo-symmetrische Achse des Monomers handelt. Abschließend lässt sich feststellen, dass die bestehenden Protokolle für die Kristallisation von PSII aus Spinat durchaus verbessert werden können und sich damit Dichtekarten mit höherer Auflösung erreichen lassen. Diese verbesserten Protokolle können nun für Kristallisationsversuche mit His-tag PSII aus Tabak herangezogen werden, um mit diesen hochreinen Präparationen die Auflösung nochmals zu verbessern
Parallel Domain Decomposition Methods For Simulating Blood Flows In Three-Dimensional Compliant Arteries
No full textNumerical simulation of blood flows in compliant arteries is becoming an useful tool in studying the sophisticated hemodynamics in the human circulation system. Accurate modeling is important in prediction and treatment of artery diseases. In this thesis, we propose and study a parallel domain decomposition method for solving the corresponding fluid-structure interaction problem in three-dimensional space, with emphasis on the strong coupling between fluid and structure and on the parallel scalability of the solution algorithm.
We model the fluid-structure interaction by using a monolithically coupled system of linear elasticity equations for the arterial walls and incompressible Navier-Stokes equations for the blood. The fluid equations are derived in an arbitrary Lagrangian-Eulerian framework to address the complicated moving boundaries and keep track of the coupling on the interface. A finite element method based on the unstructured mesh is introduced and validated for discretizing the problem in space, and a fully implicit scheme is used for the temporal discretization.
For solving the nonlinear systems arising from the fully coupled discretization, we develop a class of Newton-Krylov-Schwarz algorithms. The investigation focuses on the parallel efficiency of the fully implicit solution algorithm, as well as the performance of one-level and two-level additive Schwarz preconditioners used in accelerating the convergence of the Newton-Krylov algorithm. Simulations based on some patient-specific pulmonary artery geometries are performed on a large scale supercomputer. Our algorithm is shown to have excellent parallel scalability with over three thousand processors and for problems with millions of unknowns, and is also robust with respect to several important physical parameters including the fluid density, the structure density, the Reynolds number, and the Poisson ratio
Parallel Domain Decomposition Methods For Simulating Blood Flows In Three-Dimensional Compliant Arteries
No full textNumerical simulation of blood flows in compliant arteries is becoming an useful tool in studying the sophisticated hemodynamics in the human circulation system. Accurate modeling is important in prediction and treatment of artery diseases. In this thesis, we propose and study a parallel domain decomposition method for solving the corresponding fluid-structure interaction problem in three-dimensional space, with emphasis on the strong coupling between fluid and structure and on the parallel scalability of the solution algorithm.
We model the fluid-structure interaction by using a monolithically coupled system of linear elasticity equations for the arterial walls and incompressible Navier-Stokes equations for the blood. The fluid equations are derived in an arbitrary Lagrangian-Eulerian framework to address the complicated moving boundaries and keep track of the coupling on the interface. A finite element method based on the unstructured mesh is introduced and validated for discretizing the problem in space, and a fully implicit scheme is used for the temporal discretization.
For solving the nonlinear systems arising from the fully coupled discretization, we develop a class of Newton-Krylov-Schwarz algorithms. The investigation focuses on the parallel efficiency of the fully implicit solution algorithm, as well as the performance of one-level and two-level additive Schwarz preconditioners used in accelerating the convergence of the Newton-Krylov algorithm. Simulations based on some patient-specific pulmonary artery geometries are performed on a large scale supercomputer. Our algorithm is shown to have excellent parallel scalability with over three thousand processors and for problems with millions of unknowns, and is also robust with respect to several important physical parameters including the fluid density, the structure density, the Reynolds number, and the Poisson ratio
Taiwanese Scientists and its “Retrocession” in 1945: Du Congming's Administration of the National Taiwan University College of Medicine
No full textThis article examines the activities and ideals of Taiwanese scientists during “retrocession” (guangfub 光復), focusing on the administration of the National Taiwan University College of Medicine by Du Congming 杜聡明 (1893-1986). Du Congming was one of the most well-known medical scientists in modem Taiwan and had been the only Taiwanese professor in the Taihoku Imperial University (TIU) Faculty of Medicine (employed in its Pharmacological Institute) during the colonial era. He would be appointed dean of NTU’s College of Medicine after the war. In 1954 he founded Kaohsiung Medical College and became its first president (1954-1966). Du was a key person not only in Taiwan’s history of medicine, but also in the history of colonial science there. The author asks three major questions here, which have not been sufficiently covered in the research to date. First, what were the circumstances under which the Faculty of Medicine at TIU had been taken over by the Ministry of Education of the Republic of China, an action in which Du had played an important role? Secondly, what was Du’s role in personnel and administrative affairs of the NTU College of Medicine? Thirdly, what were Du’s own ideas about how a college of medicine should be run? The author uses a variety of sources to answer these questions, including a report on the takeover of TIU written by Luo Zongluo 羅宗洛, who was a chief of requisition policy, and submitted in 1946 1o his superiors at the Republic of China’s Ministry of Education. Another important source is Luo’s diary, which he kept between 17 0ctober 1945 and 3 June 1946. Du Congming appears often in the diary, which reveals Du’s rule in the takeover of the TIU Faculty of Medicine and his relationship with Luo and other key figures. Then there are compilations edited by Du himself; which comprise medical articles published in newspapers and magazines, speeches given on ceremonial occasions, etc, revealing his own plans and ideas concerning the takeover of the Faculty of Medicine. Through this exploration of Du’s actions and ideas, the author examines the meaning of “retrocession” for the Taiwanese scientists community, focusing on the theme of continuity from the colonial era.journal articl
Distribution of the Multidrug Resistance Gene cfr in Staphylococcus Species Isolates from Swine Farms in China
No full textA total of 149 porcine Staphylococcus isolates with florfenicol MICs of ≥16 μg/ml were screened for the presence of the multiresistance gene cfr, its location on plasmids, and its genetic environment. In total, 125 isolates carried either cfr (16 isolates), fexA (92 isolates), or both genes (17 isolates). The 33 cfr-carrying staphylococci, which included isolates of the species Staphylococcus cohnii, S. arlettae, and S. saprophyticus in which the cfr gene has not been described before, exhibited a wide variety of SmaI pulsed-field gel electrophoresis patterns. In 18 cases, the cfr gene was located on plasmids. Four different types of cfr-carrying plasmids—pSS-01 (n = 2; 40 kb), pSS-02 (n = 3; 35.4 kb), pSS-03 (n = 10; 7.1 kb), and pBS-01 (n = 3; 16.4 kb)—were differentiated on the basis of their sizes, restriction patterns, and additional resistance genes. Sequence analysis revealed that in plasmid pSS-01, the cfr gene was flanked in the upstream part by a complete aacA-aphD-carrying Tn4001-like transposon and in the downstream part by a complete fexA-carrying transposon Tn558. In plasmid pSS-02, an insertion sequence IS21-558 and the cfr gene were integrated into transposon Tn558 and thereby truncated the tnpA and tnpB genes. The smallest cfr-carrying plasmid pSS-03 carried the macrolide-lincosamide-streptogramin B resistance gene erm(C). Plasmid pBS-01, previously described in Bacillus spp., harbored a Tn917-like transposon, including the macrolide-lincosamide-streptogramin B resistance gene erm(B) in the cfr downstream region. Plasmids, which in part carry additional resistance genes, seem to play an important role in the dissemination of the gene cfr among porcine staphylococci.This article is published as Wang, Yang, Wanjiang Zhang, Juan Wang, Congming Wu, Zhangqi Shen, Xiao Fu, Yang Yan, Qijing Zhang, Stefan Schwarz, and Jianzhong Shen. "Distribution of the multidrug resistance gene cfr in Staphylococcus species isolates from swine farms in China." Antimicrobial agents and chemotherapy 56, no. 3 (2012): 1485-1490. doi: 10.1128/AAC.05827-11. Posted with permission.</p
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