Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

DOE PAGES

Kemege, Kyle E.; Hickey, John M.; Barta, Michael L.; ...

2014-11-10

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies in this paper expand on those observations through protein structure, mutagenesis andmore » cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. Finally, MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.« less

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Barta, Michael L.; Wickstrum, Jason; Balwalli, Namita; Lovell, Scott; Battaile, Kevin P.; Hefty, P. Scott

2015-01-01

Summary Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis, and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient E. coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia. PMID:25382739

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB

PubMed Central

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey

2014-01-01

The assembly of protein filaments drives many cellular processes, from nucleoid segregation, growth, and division in single cells to muscle contraction in animals. In eukaryotes, shape and motility are regulated through cycles of polymerization and depolymerization of actin cytoskeletal networks. In bacteria, the actin homolog MreB forms filaments that coordinate the cell-wall synthesis machinery to regulate rod-shaped growth and contribute to cellular stiffness through unknown mechanisms. Like actin, MreB is an ATPase and requires ATP to polymerize, and polymerization promotes nucleotide hydrolysis. However, it is unclear whether other similarities exist between MreB and actin because the two proteins share low sequence identity and have distinct cellular roles. Here, we use all-atom molecular dynamics simulations to reveal surprising parallels between MreB and actin structural dynamics. We observe that MreB exhibits actin-like polymerization-dependent structural changes, wherein polymerization induces flattening of MreB subunits, which restructures the nucleotide-binding pocket to favor hydrolysis. MreB filaments exhibited nucleotide-dependent intersubunit bending, with hydrolyzed polymers favoring a straighter conformation. We use steered simulations to demonstrate a coupling between intersubunit bending and the degree of flattening of each subunit, suggesting cooperative bending along a filament. Taken together, our results provide molecular-scale insight into the diversity of structural states of MreB and the relationships among polymerization, hydrolysis, and filament properties, which may be applicable to other members of the broad actin family. PMID:24550504

Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB.

PubMed

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey

2014-03-04

The assembly of protein filaments drives many cellular processes, from nucleoid segregation, growth, and division in single cells to muscle contraction in animals. In eukaryotes, shape and motility are regulated through cycles of polymerization and depolymerization of actin cytoskeletal networks. In bacteria, the actin homolog MreB forms filaments that coordinate the cell-wall synthesis machinery to regulate rod-shaped growth and contribute to cellular stiffness through unknown mechanisms. Like actin, MreB is an ATPase and requires ATP to polymerize, and polymerization promotes nucleotide hydrolysis. However, it is unclear whether other similarities exist between MreB and actin because the two proteins share low sequence identity and have distinct cellular roles. Here, we use all-atom molecular dynamics simulations to reveal surprising parallels between MreB and actin structural dynamics. We observe that MreB exhibits actin-like polymerization-dependent structural changes, wherein polymerization induces flattening of MreB subunits, which restructures the nucleotide-binding pocket to favor hydrolysis. MreB filaments exhibited nucleotide-dependent intersubunit bending, with hydrolyzed polymers favoring a straighter conformation. We use steered simulations to demonstrate a coupling between intersubunit bending and the degree of flattening of each subunit, suggesting cooperative bending along a filament. Taken together, our results provide molecular-scale insight into the diversity of structural states of MreB and the relationships among polymerization, hydrolysis, and filament properties, which may be applicable to other members of the broad actin family.

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB.

PubMed

Kemege, Kyle E; Hickey, John M; Barta, Michael L; Wickstrum, Jason; Balwalli, Namita; Lovell, Scott; Battaile, Kevin P; Hefty, P Scott

2015-02-01

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia. © 2014 John Wiley & Sons Ltd.

Feasibility of using 3D MR elastography to determine pancreatic stiffness in healthy volunteers.

PubMed

Shi, Yu; Glaser, Kevin J; Venkatesh, Sudhakar K; Ben-Abraham, Ephraim I; Ehman, Richard L

2015-02-01

To evaluate the feasibility of using three-dimensional (3D) MR elastography (MRE) to determine the stiffness of the pancreas in healthy volunteers. Twenty healthy volunteers underwent 1.5 Tesla MRE exams using an accelerated echo planar imaging (EPI) pulse sequence with low-frequency vibrations (40 and 60 Hz). Stiffness was calculated with a 3D direct inversion algorithm. The mean shear stiffness in five pancreatic subregions (uncinate, head, neck, body, and tail) and the corresponding liver stiffness were calculated. The intrasubject coefficient of variation (CV) was calculated as a measure of the reproducibility for each volunteer. The mean shear stiffness (average of values obtained in different pancreatic subregions) was (1.15 ± 0.17) kPa at 40 Hz, and (2.09 ± 0.33) kPa at 60 Hz. The corresponding liver stiffness was higher than the pancreas stiffness at 40 Hz ([1.60 ± 0.21] kPa, mean pancreas-to-liver stiffness ratio: 0.72), but similar at 60Hz ([2.12 ± 0.23) kPa, mean ratio: 0.95). The mean intrasubject CV for each pancreatic subregion was lower at 40 Hz than 60 Hz (P < 0.05 for all subregions, range: 11.9-15.7% at 40 Hz and 16.5-19.6% at 60 Hz). The 3D pancreatic MRE can provide promising and reproducible stiffness measurements throughout the pancreas, with more consistent data acquired at 40 Hz. © 2014 Wiley Periodicals, Inc.

Magnetic resonance elastography is as accurate as liver biopsy for liver fibrosis staging.

PubMed

Morisaka, Hiroyuki; Motosugi, Utaroh; Ichikawa, Shintaro; Nakazawa, Tadao; Kondo, Tetsuo; Funayama, Satoshi; Matsuda, Masanori; Ichikawa, Tomoaki; Onishi, Hiroshi

2018-05-01

Liver MR elastography (MRE) is available for the noninvasive assessment of liver fibrosis; however, no previous studies have compared the diagnostic ability of MRE with that of liver biopsy. To compare the diagnostic accuracy of liver fibrosis staging between MRE-based methods and liver biopsy using the resected liver specimens as the reference standard. A retrospective study at a single institution. In all, 200 patients who underwent preoperative MRE and subsequent surgical liver resection were included in this study. Data from 80 patients were used to estimate cutoff and distributions of liver stiffness values measured by MRE for each liver fibrosis stage (F0-F4, METAVIR system). In the remaining 120 patients, liver biopsy specimens were obtained from the resected liver tissues using a standard biopsy needle. 2D liver MRE with gradient-echo based sequence on a 1.5 or 3T scanner was used. Two radiologists independently measured the liver stiffness value on MRE and two types of MRE-based methods (threshold and Bayesian prediction method) were applied. Two pathologists evaluated all biopsy samples independently to stage liver fibrosis. Surgically resected whole tissue specimens were used as the reference standard. The accuracy for liver fibrosis staging was compared between liver biopsy and MRE-based methods with a modified McNemar's test. Accurate fibrosis staging was achieved in 53.3% (64/120) and 59.1% (71/120) of patients using MRE with threshold and Bayesian methods, respectively, and in 51.6% (62/120) with liver biopsy. Accuracies of MRE-based methods for diagnoses of ≥F2 (90-91% [108-9/120]), ≥F3 (79-81% [95-97/120]), and F4 (82-85% [98-102/120]) were statistically equivalent to those of liver biopsy (≥F2, 79% [95/120], P ≤ 0.01; ≥F3, 88% [105/120], P ≤ 0.006; and F4, 82% [99/120], P ≤ 0.017). MRE can be an alternative to liver biopsy for fibrosis staging. 3. Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:1268-1275. © 2017 International Society for Magnetic Resonance in Medicine.

Comparison of magnetic resonance elastography and diffusion-weighted imaging for differentiating benign and malignant liver lesions.

PubMed

Hennedige, Tiffany P; Hallinan, James Thomas Patrick Decourcy; Leung, Fiona P; Teo, Lynette Li San; Iyer, Sridhar; Wang, Gang; Chang, Stephen; Madhavan, Krishna Kumar; Wee, Aileen; Venkatesh, Sudhakar K

2016-02-01

Comparison of magnetic resonance elastography (MRE) and diffusion-weighted imaging (DWI) for differentiating malignant and benign focal liver lesions (FLLs). Seventy-nine subjects with 124 FLLs (44 benign and 80 malignant) underwent both MRE and DWI. MRE was performed with a modified gradient-echo sequence and DWI with a free breathing technique (b = 0.500). Apparent diffusion coefficient (ADC) maps and stiffness maps were generated. FLL mean stiffness and ADC values were obtained by placing regions of interest over the FLLs on stiffness and ADC maps. The accuracy of MRE and DWI for differentiation of benign and malignant FLL was compared using receiver operating curve (ROC) analysis. There was a significant negative correlation between stiffness and ADC (r = -0.54, p < 0.0001) of FLLs. Malignant FLLs had significantly higher mean stiffness (7.9kPa vs. 3.1kPa, p < 0.001) and lower mean ADC (129 vs. 200 × 10(-3)mm(2)/s, p < 0.001) than benign FLLs. The sensitivity/specificity/positive predictive value/negative predictive value for differentiating malignant from benign FLLs with MRE (cut-off, >4.54kPa) and DWI (cut-off, <151 × 10(-3)mm(2)/s) were 96.3/95.5/97.5/93.3% (p < 0.001) and 85/81.8/88.3/75% (p < 0.001), respectively. ROC analysis showed significantly higher accuracy for MRE than DWI (0.986 vs. 0.82, p = 0.0016). MRE is significantly more accurate than DWI for differentiating benign and malignant FLLs. • MRE is superior to DWI for differentiating benign and malignant focal liver lesions. • Benign lesions with large fibrous components may have higher stiffness with MRE. • Cholangiocarcinomas tend to have higher stiffness than hepatocellular carcinomas. • Hepatocellular adenomas tend to have lower stiffness than focal nodular hyperplasia. • MRE is superior to conventional MRI in differentiating benign and malignant liver lesions.

Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria.

PubMed

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2014-04-18

The mreB gene family encodes actin-like proteins that determine cell shape by directing cell wall synthesis and often exists in one to three copies in the genomes of non-spherical bacteria. Intriguingly, while most wall-less bacteria do not have this gene, five to seven mreB homologs are found in Spiroplasma and Haloplasma, which are both characterized by cell contractility. To investigate the molecular evolution of this gene family in wall-less bacteria, we sampled the available genome sequences from these two genera and other related lineages for comparative analysis. The gene phylogenies indicated that the mreB homologs in Haloplasma are more closely related to those in Firmicutes, whereas those in Spiroplasma form a separate clade. This finding suggests that the gene family expansions in these two lineages are the results of independent ancient duplications. Moreover, the Spiroplasma mreB homologs can be classified into five clades, of which the genomic positions are largely conserved. The inference of gene gains and losses suggests that there has been an overall trend to retain only one homolog from each of the five mreB clades in the evolutionary history of Spiroplasma. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Magnetic Resonance Elastography of the Brain using Multi-Shot Spiral Readouts with Self-Navigated Motion Correction

PubMed Central

Johnson, Curtis L.; McGarry, Matthew D. J.; Van Houten, Elijah E. W.; Weaver, John B.; Paulsen, Keith D.; Sutton, Bradley P.; Georgiadis, John G.

2012-01-01

MRE has been introduced in clinical practice as a possible surrogate for mechanical palpation, but its application to study the human brain in vivo has been limited by low spatial resolution and the complexity of the inverse problem associated with biomechanical property estimation. Here, we report significant improvements in brain MRE data acquisition by reporting images with high spatial resolution and signal-to-noise ratio as quantified by octahedral shear strain metrics. Specifically, we have developed a sequence for brain MRE based on multi-shot, variable-density spiral imaging and three-dimensional displacement acquisition, and implemented a correction scheme for any resulting phase errors. A Rayleigh damped model of brain tissue mechanics was adopted to represent the parenchyma, and was integrated via a finite element-based iterative inversion algorithm. A multi-resolution phantom study demonstrates the need for obtaining high-resolution MRE data when estimating focal mechanical properties. Measurements on three healthy volunteers demonstrate satisfactory resolution of grey and white matter, and mechanical heterogeneities correspond well with white matter histoarchitecture. Together, these advances enable MRE scans that result in high-fidelity, spatially-resolved estimates of in vivo brain tissue mechanical properties, improving upon lower resolution MRE brain studies which only report volume averaged stiffness values. PMID:23001771

Evolution of the cytoskeleton

PubMed Central

Erickson, Harold P.

2009-01-01

Summary The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40−50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP. PMID:17563102

Brain mechanical property measurement using MRE with intrinsic activation

NASA Astrophysics Data System (ADS)

Weaver, John B.; Pattison, Adam J.; McGarry, Matthew D.; Perreard, Irina M.; Swienckowski, Jessica G.; Eskey, Clifford J.; Lollis, S. Scott; Paulsen, Keith D.

2012-11-01

Many pathologies alter the mechanical properties of tissue. Magnetic resonance elastography (MRE) has been developed to noninvasively characterize these quantities in vivo. Typically, small vibrations are induced in the tissue of interest with an external mechanical actuator. The resulting displacements are measured with phase contrast sequences and are then used to estimate the underlying mechanical property distribution. Several MRE studies have quantified brain tissue properties. However, the cranium and meninges, especially the dura, are very effective at damping externally applied vibrations from penetrating deeply into the brain. Here, we report a method, termed ‘intrinsic activation’, that eliminates the requirement for external vibrations by measuring the motion generated by natural blood vessel pulsation. A retrospectively gated phase contrast MR angiography sequence was used to record the tissue velocity at eight phases of the cardiac cycle. The velocities were numerically integrated via the Fourier transform to produce the harmonic displacements at each position within the brain. The displacements were then reconstructed into images of the shear modulus based on both linear elastic and poroelastic models. The mechanical properties produced fall within the range of brain tissue estimates reported in the literature and, equally important, the technique yielded highly reproducible results. The mean shear modulus was 8.1 kPa for linear elastic reconstructions and 2.4 kPa for poroelastic reconstructions where fluid pressure carries a portion of the stress. Gross structures of the brain were visualized, particularly in the poroelastic reconstructions. Intra-subject variability was significantly less than the inter-subject variability in a study of six asymptomatic individuals. Further, larger changes in mechanical properties were observed in individuals when examined over time than when the MRE procedures were repeated on the same day. Cardiac pulsation, termed intrinsic activation, produces sufficient motion to allow mechanical properties to be recovered. The poroelastic model is more consistent with the measured data from brain at low frequencies than the linear elastic model. Intrinsic activation allows MRE to be performed without a device shaking the head so the patient notices no differences between it and the other sequences in an MR examination.

Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification.

PubMed

Deng, Sarah K; Yin, Yi; Petes, Thomas D; Symington, Lorraine S

2015-11-05

Foldback priming at DNA double-stranded breaks is one mechanism proposed to initiate palindromic gene amplification, a common feature of cancer cells. Here, we show that small (5-9 bp) inverted repeats drive the formation of large palindromic duplications, the major class of chromosomal rearrangements recovered from yeast cells lacking Sae2 or the Mre11 nuclease. RPA dysfunction increased the frequency of palindromic duplications in Sae2 or Mre11 nuclease-deficient cells by ∼ 1,000-fold, consistent with intra-strand annealing to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. The palindromic duplications were frequently associated with duplication of a second chromosome region bounded by a repeated sequence and a telomere, suggesting the dicentric chromosome breaks and repairs by recombination between dispersed repeats to acquire a telomere. We propose secondary structures within single-stranded DNA are potent instigators of genome instability, and RPA and Mre11-Sae2 play important roles in preventing their formation and propagation, respectively. Copyright © 2015 Elsevier Inc. All rights reserved.

Magnetic resonance enteroclysis in patients with Crohn's disease: fat saturated T2-weighted sequences for evaluation of inflammatory activity.

PubMed

Grieser, Christian; Denecke, Timm; Steffen, Ingo G; Werner, Scarlett; Kröncke, Thomas; Guckelberger, Olaf; Pape, Ulrich-Frank; Meier, Johannes; Thiel, Regina; Kivelitz, Dietmar; Sturm, Andreas; Hamm, Bernd; Röttgen, Rainer

2012-04-01

To evaluate fat saturated (fs) T2-weighted (w) fast relaxation fast spin echo (FRFSE)-sequences compared to the standard protocol with contrast agent for the evaluation of inflammatory activity in patients with Crohn's Disease (CD). Fourty-eight patients (male, 17; female, 33; mean age, 37 years) with suspicion of inflammatory activity in proven CD who underwent MR enteroclysis (MRE) at 1.5T (GE Healthcare) were retrospectively included. Two blinded radiologists analyzed MRE images for presence and extent of CD lesions and degree of local inflammation for fsT2-w FRFSE and contrast enhanced T1-w images (T2-activity; T1-activity; score, 1-4) in consensus. Furthermore, mural signal intensity (SI) ratios (T2-ratio; T1-ratio) were recorded. Patient based MRE findings were correlated with endoscopic (45 patients), surgical (6 patients), histopathological, and clinical data (CDAI) as a surrogate reference standard. In total, 24 of 48 eligible patients presented with acute inflammatory activity with 123 affected bowel segments. ROC analysis of the total inflammatory score presented an AUC of 0.93 (p<0.001) for T2-activity (T1-activity, AUC 0.63; p=0.019). ROC analysis revealed an AUC of 0.76 (p<0.001) for the T2-ratio (T1-ratio, AUC 0.51; p=0.93). General linear regression model revealed T2-activity (p=0.001) and age (p=0.024) as predictive factors of acute bowel inflammation. T2-w FRFSE-sequences can depict CD lesions and help to assess the inflammation activity, even with improved accuracy as compared to contrast-enhanced T1-w sequences. Copyright © 2011 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

Studies on nanosecond 532nm and 355nm and ultrafast 515nm and 532nm laser cutting super-hard materials

NASA Astrophysics Data System (ADS)

Zhang, Jie; Tao, Sha; Wang, Brian; Zhao, Jay

2017-02-01

In this paper, micro-processing of three kinds of super-hard materials of poly-crystal diamond (PCD)/tungsten-carbide (WC), CVD-diamond and cubic boron nitride (CNB) has been systematically studied using nanosecond laser (532nm and 355nm), and ultrafast laser (532nm and 515nm). Our purpose is to investigate a full laser micro-cutting solution to achieve a ready-to-use cutting tool insert (CTI). The results show a clean cut with little burns and recasting at edge. The cutting speed of 2-10mm/min depending on thickness was obtained. The laser ablation process was also studied by varying laser parameters (wavelength, pulse width, pulse energy, repetition rate) and tool path to improve cutting speed. Also, studies on material removal efficiency (MRE) of PCD/WC with 355nm-ns and 515nm-fs laser as a function of laser fluence show that 355nm-ns laser is able to achieve higher MRE for PCD and WC. Thus, ultrafast laser is not necessarily used for superhard material cutting. Instead, post-polishing with ultrafast laser can be used to clean cutting surface and improve smoothness.

The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex.

PubMed

Kruse, Thomas; Bork-Jensen, Jette; Gerdes, Kenn

2005-01-01

MreB proteins of Escherichia coli, Bacillus subtilis and Caulobacter crescentus form actin-like cables lying beneath the cell surface. The cables are required to guide longitudinal cell wall synthesis and their absence leads to merodiploid spherical and inflated cells prone to cell lysis. In B. subtilis and C. crescentus, the mreB gene is essential. However, in E. coli, mreB was inferred not to be essential. Using a tight, conditional gene depletion system, we systematically investigated whether the E. coli mreBCD-encoded components were essential. We found that cells depleted of mreBCD became spherical, enlarged and finally lysed. Depletion of each mre gene separately conferred similar gross changes in cell morphology and viability. Thus, the three proteins encoded by mreBCD are all essential and function in the same morphogenetic pathway. Interestingly, the presence of a multicopy plasmid carrying the ftsQAZ genes suppressed the lethality of deletions in the mre operon. Using GFP and cell fractionation methods, we showed that the MreC and MreD proteins were associated with the cell membrane. Using a bacterial two-hybrid system, we found that MreC interacted with both MreB and MreD. In contrast, MreB and MreD did not interact in this assay. Thus, we conclude that the E. coli MreBCD form an essential membrane-bound complex. Curiously, MreB did not form cables in cell depleted for MreC, MreD or RodA, indicating a mutual interdependency between MreB filament morphology and cell shape. Based on these and other observations we propose a model in which the membrane-associated MreBCD complex directs longitudinal cell wall synthesis in a process essential to maintain cell morphology.

Transcription factor MBF-I interacts with metal regulatory elements of higher eucaryotic metallothionein genes.

PubMed Central

Imbert, J; Zafarullah, M; Culotta, V C; Gedamu, L; Hamer, D

1989-01-01

Metallothionein (MT) gene promoters in higher eucaryotes contain multiple metal regulatory elements (MREs) that are responsible for the metal induction of MT gene transcription. We identified and purified to near homogeneity a 74-kilodalton mouse nuclear protein that specifically binds to certain MRE sequences. This protein, MBF-I, was purified employing as an affinity reagent a trout MRE that is shown to be functional in mouse cells but which lacks the G+C-rich and SP1-like sequences found in many mammalian MT gene promoters. Using point-mutated MREs, we showed that there is a strong correlation between DNA binding in vitro and MT gene regulation in vivo, suggesting a direct role of MBF-I in MT gene transcription. We also showed that MBF-I can induce MT gene transcription in vitro in a mouse extract and that this stimulation requires zinc. Images PMID:2586522

Measurement of in vivo local shear modulus using MR elastography multiple-phase patchwork offsets.

PubMed

Suga, Mikio; Matsuda, Tetsuya; Minato, Kotaro; Oshiro, Osamu; Chihara, Kunihiro; Okamoto, Jun; Takizawa, Osamu; Komori, Masaru; Takahashi, Takashi

2003-07-01

Magnetic resonance elastography (MRE) is a method that can visualize the propagating and standing shear waves in an object being measured. The quantitative value of a shear modulus can be calculated by estimating the local shear wavelength. Low-frequency mechanical motion must be used for soft, tissue-like objects because a propagating shear wave rapidly attenuates at a higher frequency. Moreover, a propagating shear wave is distorted by reflections from the boundaries of objects. However, the distortions are minimal around the wave front of the propagating shear wave. Therefore, we can avoid the effect of reflection on a region of interest (ROI) by adjusting the duration of mechanical vibrations. Thus, the ROI is often shorter than the propagating shear wavelength. In the MRE sequence, a motion-sensitizing gradient (MSG) is synchronized with mechanical cyclic motion. MRE images with multiple initial phase offsets can be generated with increasing delays between the MSG and mechanical vibrations. This paper proposes a method for measuring the local shear wavelength using MRE multiple initial phase patchwork offsets that can be used when the size of the object being measured is shorter than the local wavelength. To confirm the reliability of the proposed method, computer simulations, a simulated tissue study and in vitro and in vivo studies were performed.

Magnetic resonance elastography using an air ball-actuator.

PubMed

Numano, Tomokazu; Kawabata, Yoshihiko; Mizuhara, Kazuyuki; Washio, Toshikatsu; Nitta, Naotaka; Homma, Kazuhiro

2013-07-01

The purpose of this study was to develop a new technique for a powerful compact MR elastography (MRE) actuator based on a pneumatic ball-vibrator. This is a compact actuator that generates powerful centrifugal force vibrations via high speed revolutions of an internal ball using compressed air. This equipment is easy to handle due to its simple principles and structure. Vibration frequency and centrifugal force are freely adjustable via air pressure changes (air flow volume), and replacement of the internal ball. In order to achieve MRI compatibility, all parts were constructed from non-ferromagnetic materials. Vibration amplitudes (displacements) were measured optically by a laser displacement sensor. From a bench test of displacement, even though the vibration frequency increased, the amount of displacement did not decrease. An essential step in MRE is the generation of mechanical waves within tissue via an actuator, and MRE sequences are synchronized to several phase offsets of vibration. In this system, the phase offset was detected by a four-channel optical-fiber sensor, and it was used as an MRI trigger signal. In an agarose gel phantom experiment, this actuator was used to make an MR elastogram. This study shows that the use of a ball actuator for MRE is feasible. Copyright © 2013 Elsevier Inc. All rights reserved.

Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus.

PubMed

Kim, So Yeon; Gitai, Zemer; Kinkhabwala, Anika; Shapiro, Lucy; Moerner, W E

2006-07-18

The actin cytoskeleton represents a key regulator of multiple essential cellular functions in both eukaryotes and prokaryotes. In eukaryotes, these functions depend on the orchestrated dynamics of actin filament assembly and disassembly. However, the dynamics of the bacterial actin homolog MreB have yet to be examined in vivo. In this study, we observed the motion of single fluorescent MreB-yellow fluorescent protein fusions in living Caulobacter cells in a background of unlabeled MreB. With time-lapse imaging, polymerized MreB [filamentous MreB (fMreB)] and unpolymerized MreB [globular MreB (gMreB)] monomers could be distinguished: gMreB showed fast motion that was characteristic of Brownian diffusion, whereas the labeled molecules in fMreB displayed slow, directed motion. This directional movement of labeled MreB in the growing polymer provides an indication that, like actin, MreB monomers treadmill through MreB filaments by preferential polymerization at one filament end and depolymerization at the other filament end. From these data, we extract several characteristics of single MreB filaments, including that they are, on average, much shorter than the cell length and that the direction of their polarized assembly seems to be independent of the overall cellular polarity. Thus, MreB, like actin, exhibits treadmilling behavior in vivo, and the long MreB structures that have been visualized in multiple bacterial species seem to represent bundles of short filaments that lack a uniform global polarity.

Brain Mechanical Property Measurement Using MRE with Intrinsic Activation

PubMed Central

Pattison, Adam J.; McGarry, Matthew D.; Perreard, Irina M.; Swienckowski, Jessica G.; Eskey, Clifford J.; Lollis, S. Scott; Paulsen, Keith D.

2013-01-01

Problem Addressed Many pathologies alter the mechanical properties of tissue. Magnetic resonance elastography (MRE) has been developed to noninvasively characterize these quantities in vivo. Typically, small vibrations are induced in the tissue of interest with an external mechanical actuator. The resulting displacements are measured with phase contrast sequences and are then used to estimate the underlying mechanical property distribution. Several MRE studies have quantified brain tissue properties. However, the cranium and meninges, especially the dura, are very effective at damping externally applied vibrations from penetrating deeply into the brain. Here, we report a method, termed ‘intrinsic activation’, that eliminates the requirement for external vibrations by measuring the motion generated by natural blood vessel pulsation. Methodology A retrospectively gated phase contrast MR angiography sequence was used to record the tissue velocity at eight phases of the cardiac cycle. The velocities were numerically integrated via the Fourier transform to produce the harmonic displacements at each position within the brain. The displacements were then reconstructed into images of the shear modulus based on both linear elastic and poroelastic models. Results, Significance and Potential Impact The mechanical properties produced fall within the range of brain tissue estimates reported in the literature and, equally important, the technique yielded highly reproducible results. The mean shear modulus was 8.1 kPa for linear elastic reconstructions and 2.4 kPa for poroelastic reconstructions where fluid pressure carries a portion of the stress. Gross structures of the brain were visualized, particularly in the poroelastic reconstructions. Intra-subject variability was significantly less than the inter-subject variability in a study of 6 asymptomatic individuals. Further, larger changes in mechanical properties were observed in individuals when examined over time than when the MRE procedures were repeated on the same day. Cardiac pulsation, termed intrinsic activation, produces sufficient motion to allow mechanical properties to be recovered. The poroelastic model is more consistent with the measured data from brain at low frequencies than the linear elastic model. Intrinsic activation allows MR elastography to be performed without a device shaking the head so the patient notices no differences between it and the other sequences in an MR examination. PMID:23079508

Influence of heterologous MreB proteins on cell morphology of Bacillus subtilis.

PubMed

Schirner, Kathrin; Errington, Jeff

2009-11-01

The prokaryotic cytoskeletal protein MreB is thought to govern cell shape by positioning the cell wall synthetic apparatus at growth sites in the cell. In rod-shaped bacteria it forms helical filaments that run around the periphery of the rod during elongation. Gram-positive bacteria often contain more than one mreB gene. Bacillus subtilis has three mreB-like genes, mreB, mbl and mreBH, the first two of which have been shown to be essential under normal growth conditions. Expression of an mreB homologue from the closely related organism Bacillus licheniformis did not have any effect on cell growth or morphology. In contrast, expression of mreB from the phylogenetically more distant bacterium Clostridium perfringens produced shape defects and ultimately cell death, due to disruption of the endogenous MreB cytoskeleton. However, expression of either mreB(B. licheniformis) (mreB(Bl)) or mreB(C. perfringens) (mreB(Cp)) was sufficient to confer a rod shape to B. subtilis deleted for the three mreB isologues, supporting the idea that the three proteins have largely redundant functions in cell morphogenesis. Expression of mreBCD(Bl) could fully compensate for the loss of mreBCD in B. subtilis and led to the formation of rod-shaped cells. In contrast, expression of mreBCD(Cp) was not sufficient to confer a rod shape to B. subtilis Delta mreBCD, indicating that a complex of these three cell shape determinants is not enough for cell morphogenesis of B. subtilis.

The small protein MbiA interacts with MreB and modulates cell shape in Caulobacter crescentus

PubMed Central

Yakhnina, Anastasiya A.; Gitai, Zemer

2014-01-01

Summary In Caulobacter crescentus, the actin homologue MreB is critical for cell shape maintenance. Despite the central importance of MreB for cell morphology and viability, very little is known about MreB-interacting factors. Here, we use an overexpression approach to identify a novel MreB interactor, MbiA. MbiA interacts with MreB in both biochemical and genetic assays, colocalizes with MreB throughout the cell cycle, and relies on MreB for its localization. MbiA over-expression mimics the loss of MreB function, severely perturbing cell morphology, inhibiting growth and inducing cell lysis. Additionally, mbiA deletion shows a synthetic growth phenotype with a hypomorphic allele of the MreB interactor RodZ, suggesting that these two MreB-interacting proteins either have partially redundant functions or participate in the same functional complex. Our work thus establishes MbiA as a novel cell shape regulator that appears to function through regulating MreB, and opens avenues for discovery of more MreB-regulating factors by showing that overexpression screens are a valuable tool for uncovering potentially redundant cell shape effectors. PMID:22804814

The small protein MbiA interacts with MreB and modulates cell shape in Caulobacter crescentus.

PubMed

Yakhnina, Anastasiya A; Gitai, Zemer

2012-09-01

In Caulobacter crescentus, the actin homologue MreB is critical for cell shape maintenance. Despite the central importance of MreB for cell morphology and viability, very little is known about MreB-interacting factors. Here, we use an overexpression approach to identify a novel MreB interactor, MbiA. MbiA interacts with MreB in both biochemical and genetic assays, colocalizes with MreB throughout the cell cycle, and relies on MreB for its localization. MbiA overexpression mimics the loss of MreB function, severely perturbing cell morphology, inhibiting growth and inducing cell lysis. Additionally, mbiA deletion shows a synthetic growth phenotype with a hypomorphic allele of the MreB interactor RodZ, suggesting that these two MreB-interacting proteins either have partially redundant functions or participate in the same functional complex. Our work thus establishes MbiA as a novel cell shape regulator that appears to function through regulating MreB, and opens avenues for discovery of more MreB-regulating factors by showing that overexpression screens are a valuable tool for uncovering potentially redundant cell shape effectors. © 2012 Blackwell Publishing Ltd.

Analysis of shear wave propagation derived from MR elastography in 3D thigh skeletal muscle using subject specific finite element model.

PubMed

Dao, Tien Tuan; Pouletaut, Philippe; Charleux, Fabrice; Tho, Marie-Christine Ho Ba; Bensamoun, Sabine

2014-01-01

The purpose of this study was to develop a subject specific finite element model derived from MRI images to numerically analyze the MRE (magnetic resonance elastography) shear wave propagation within skeletal thigh muscles. A sagittal T2 CUBE MRI sequence was performed on the 20-cm thigh segment of a healthy male subject. Skin, adipose tissue, femoral bone and 11 muscles were manually segmented in order to have 3D smoothed solid and meshed models. These tissues were modeled with different constitutive laws. A transient modal dynamics analysis was applied to simulate the shear wave propagation within the thigh tissues. The effects of MRE experimental parameters (frequency, force) and the muscle material properties (shear modulus: C10) were analyzed through the simulated shear wave displacement within the vastus medialis muscle. The results showed a plausible range of frequencies (from 90Hz to 120 Hz), which could be used for MRE muscle protocol. The wave amplitude increased with the level of the force, revealing the importance of the boundary condition. Moreover, different shear displacement patterns were obtained as a function of the muscle mechanical properties. The present study is the first to analyze the shear wave propagation in skeletal muscles using a 3D subject specific finite element model. This study could be of great value to assist the experimenters in the set-up of MRE protocols.

A magnesium-dependent mreB null mutant: implications for the role of mreB in Bacillus subtilis.

PubMed

Formstone, Alex; Errington, Jeffery

2005-03-01

MreB shares a common prokaryotic ancestor with actin and is present in almost all rod-shaped bacteria. MreB proteins have been implicated in a range of important cell processes, including cell morphogenesis, chromosome segregation and cell polarity. The mreB gene frequently lies at the beginning of a cluster of genes, immediately upstream of the conserved mreC and mreD genes. RNA analysis showed that in Bacillus subtilis mreB is co-transcribed with mreC and that these genes form part of an operon under the control of a promoter(s) upstream of mreB. Construction of an in-frame deletion of mreB and its complementation by mreB(+) only, in trans, established that the gene is important for maintenance of cell width and cell viability under normal growth conditions, independent of polar effects on downstream genes. Remarkably, virtually normal growth was restored to the mreB null mutant in the presence of high concentrations of magnesium, especially when high concentrations of the osmoprotectant, sucrose were also present. Under these conditions, cells could be maintained in the complete absence of an mreB gene, with almost normal morphology. No detectable effect on chromosome segregation was evident in the mutant, nor was there an effect on the topology of nascent peptidoglycan insertion. A GFP-MreB fusion was used to look at the localization of MreB in live cells. The pattern of localization was similar to that previously described, but no tight linkage to nucleoid positioning was evident. Propagation of the mreB null mutant in the absence of magnesium and sucrose led to a progressive increase in cell width, culminating in cell lysis. Cell division was also perturbed but this effect may be secondary to the disturbance in cell width. These results suggest that the major role of MreB in B. subtilis lies in the control of cell diameter.

Motion of single MreB bacterial actin proteins in Caulobacter show treadmilling in vivo

NASA Astrophysics Data System (ADS)

Moerner, W. E.; Kim, Soyeon; Gitai, Zemer; Kinkhabwala, Anika; McAdams, Harley; Shapiro, Lucy

2006-03-01

Ensemble imaging of a bacterial actin homologue, the MreB protein, suggests that the MreB proteins form a dynamic filamentous spiral along the long axis of the cell in Caulobacter crescentus. MreB contracts and expands along the cell axis and plays an important role in cell shape and polarity maintenance, as well as chromosome segregation and translocation of the origin of replication during cell division. In this study we investigated the real-time polymerization of MreB in Caulobacter crescentus using single-molecule fluorescence imaging. With time-lapse imaging, polymerized MreB could be distinguished from cytoplasmic MreB monomers, because single monomeric MreB showed fast motion characteristic of Brownian diffusion, while single polymerized MreB displayed slow, directed motion. This directional movement of labeled MreB in the growing polymer implies that treadmilling is the predominant mechanism in MreB filament formation. These single-molecule imaging experiments provide the first available information on the velocity of bacterial actin polymerization in a living cell.

RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis

PubMed Central

Morgenstein, Randy M.; Bratton, Benjamin P.; Nguyen, Jeffrey P.; Ouzounov, Nikolay; Shaevitz, Joshua W.; Gitai, Zemer

2015-01-01

The rod shape of most bacteria requires the actin homolog, MreB. Whereas MreB was initially thought to statically define rod shape, recent studies found that MreB dynamically rotates around the cell circumference dependent on cell wall synthesis. However, the mechanism by which cytoplasmic MreB is linked to extracytoplasmic cell wall synthesis and the function of this linkage for morphogenesis has remained unclear. Here we demonstrate that the transmembrane protein RodZ mediates MreB rotation by directly or indirectly coupling MreB to cell wall synthesis enzymes. Furthermore, we map the RodZ domains that link MreB to cell wall synthesis and identify mreB mutants that suppress the shape defect of ΔrodZ without restoring rotation, uncoupling rotation from rod-like growth. Surprisingly, MreB rotation is dispensable for rod-like shape determination under standard laboratory conditions but is required for the robustness of rod shape and growth under conditions of cell wall stress. PMID:26396257

RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.

PubMed

Morgenstein, Randy M; Bratton, Benjamin P; Nguyen, Jeffrey P; Ouzounov, Nikolay; Shaevitz, Joshua W; Gitai, Zemer

2015-10-06

The rod shape of most bacteria requires the actin homolog, MreB. Whereas MreB was initially thought to statically define rod shape, recent studies found that MreB dynamically rotates around the cell circumference dependent on cell wall synthesis. However, the mechanism by which cytoplasmic MreB is linked to extracytoplasmic cell wall synthesis and the function of this linkage for morphogenesis has remained unclear. Here we demonstrate that the transmembrane protein RodZ mediates MreB rotation by directly or indirectly coupling MreB to cell wall synthesis enzymes. Furthermore, we map the RodZ domains that link MreB to cell wall synthesis and identify mreB mutants that suppress the shape defect of ΔrodZ without restoring rotation, uncoupling rotation from rod-like growth. Surprisingly, MreB rotation is dispensable for rod-like shape determination under standard laboratory conditions but is required for the robustness of rod shape and growth under conditions of cell wall stress.

Exclusion of assembled MreB by anionic phospholipids at cell poles confers cell polarity for bidirectional growth.

PubMed

Kawazura, Takuma; Matsumoto, Kanon; Kojima, Koki; Kato, Fumiya; Kanai, Tomomi; Niki, Hironori; Shiomi, Daisuke

2017-05-01

Cell polarity determines the direction of cell growth in bacteria. MreB actin spatially regulates peptidoglycan synthesis to enable cells to elongate bidirectionally. MreB densely localizes in the cylindrical part of the rod cell and not in polar regions in Escherichia coli. When treated with A22, which inhibits MreB polymerization, rod-shaped cells became round and MreB was diffusely distributed throughout the cytoplasmic membrane. A22 removal resulted in restoration of the rod shape. Initially, diffuse MreB started to re-assemble, and MreB-free zones were subsequently observed in the cytoplasmic membrane. These MreB-free zones finally became cell poles, allowing the cells to elongate bidirectionally. When MreB was artificially located at the cell poles, an additional pole was created, indicating that artificial localization of MreB at the cell pole induced local peptidoglycan synthesis. It was found that the anionic phospholipids (aPLs), phosphatidylglycerol and cardiolipin, which were enriched in cell poles preferentially interact with monomeric MreB compared with assembled MreB in vitro. MreB tended to localize to cell poles in cells lacking both aPLs, resulting in production of Y-shaped cells. Their findings indicated that aPLs exclude assembled MreB from cell poles to establish cell polarity, thereby allowing cells to elongate in a particular direction. © 2017 John Wiley & Sons Ltd.

Bacillus subtilis MreB orthologs self-organize into filamentous structures underneath the cell membrane in a heterologous cell system.

PubMed

Dempwolff, Felix; Reimold, Christian; Reth, Michael; Graumann, Peter L

2011-01-01

Actin-like bacterial cytoskeletal element MreB has been shown to be essential for the maintenance of rod cell shape in many bacteria. MreB forms rapidly remodelling helical filaments underneath the cell membrane in Bacillus subtilis and in other bacterial cells, and co-localizes with its two paralogs, Mbl and MreBH. We show that MreB localizes as dynamic bundles of filaments underneath the cell membrane in Drosophila S2 Schneider cells, which become highly stable when the ATPase motif in MreB is modified. In agreement with ATP-dependent filament formation, the depletion of ATP in the cells lead to rapid dissociation of MreB filaments. Extended induction of MreB resulted in the formation of membrane protrusions, showing that like actin, MreB can exert force against the cell membrane. Mbl also formed membrane associated filaments, while MreBH formed filaments within the cytosol. When co-expressed, MreB, Mbl and MreBH built up mixed filaments underneath the cell membrane. Membrane protein RodZ localized to endosomes in S2 cells, but localized to the cell membrane when co-expressed with Mbl, showing that bacterial MreB/Mbl structures can recruit a protein to the cell membrane. Thus, MreB paralogs form a self-organizing and dynamic filamentous scaffold underneath the membrane that is able to recruit other proteins to the cell surface.

Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization.

PubMed

Defeu Soufo, Hervé Joël; Graumann, Peter L

2005-03-03

Bacterial actin-like proteins have been shown to perform essential functions in several aspects of cellular physiology. They affect cell growth, cell shape, chromosome segregation and polar localization of proteins, and localize as helical filaments underneath the cell membrane. Bacillus subtilis MreB and Mbl have been shown to perform dynamic motor like movements within cells, extending along helical tracks in a time scale of few seconds. In this work, we show that Bacillus subtilis MreB has a dual role, both in the formation of rod cell shape, and in chromosome segregation, however, its function in cell shape is distinct from that of MreC. Additionally, MreB is important for the localization of the replication machinery to the cell centre, which becomes aberrant soon after depletion of MreB. 3D image reconstructions suggest that frequently, MreB filaments consist of several discontinuous helical filaments with varying length. The localization of MreB was abnormal in cells with decondensed chromosomes, as well as during depletion of Mbl, MreBH and of the MreC/MreD proteins, which we show localize to the cell membrane. Thus, proper positioning of MreB filaments depends on and is affected by a variety of factors in the cell. Our data provide genetic and cytological links between MreB and the membrane, as well as with other actin like proteins, and further supports the connection of MreB with the chromosome. The functional dependence on MreB of the localization of the replication machinery suggests that the replisome is not anchored at the cell centre, but is positioned in a dynamic manner.

Partial functional redundancy of MreB isoforms, MreB, Mbl and MreBH, in cell morphogenesis of Bacillus subtilis.

PubMed

Kawai, Yoshikazu; Asai, Kei; Errington, Jeffery

2009-08-01

MreB proteins are bacterial actin homologues thought to have a role in cell shape determination by positioning the cell wall synthetic machinery. Many bacteria, particularly Gram-positives, have more than one MreB isoform. Bacillus subtilis has three, MreB, Mbl and MreBH, which colocalize in a single helical structure. We now show that the helical pattern of peptidoglycan (PG) synthesis in the cylindrical part of the rod-shaped cell is governed by the redundant action of the three MreB isoforms. Single mutants for any one of mreB isoforms can still incorporate PG in a helical pattern and generate a rod shape. However, after depletion of MreB in an mbl mutant (or depletion of all three isoforms) lateral wall PG synthesis was impaired and the cells became spherical and lytic. Overexpression of any one of the MreB isoforms overcame the lethality as well as the defects in lateral PG synthesis and cell shape. Furthermore, MreB and Mbl can associate with the peptidoglycan biosynthetic machinery independently. However, no single MreB isoform was able to support normal growth under various stress conditions, suggesting that the multiple isoforms are used to allow cells to maintain proper growth and morphogenesis under changing and sometimes adverse conditions.

Assembly of the MreB-associated cytoskeletal ring of Escherichia coli.

PubMed

Vats, Purva; Shih, Yu-Ling; Rothfield, Lawrence

2009-04-01

The Escherichia coli actin homologue MreB is part of a helical cytoskeletal structure that winds around the cell between the two poles. It has been shown that MreB redistributes during the cell cycle to form circumferential ring structures that flank the cytokinetic FtsZ ring and appear to be associated with division and segregation of the helical cytoskeleton. We show here that the MreB cytoskeletal ring also contains the MreC, MreD, Pbp2 and RodA proteins. Assembly of MreB, MreC, MreD and Pbp2 into the ring structure required the FtsZ ring but no other known components of the cell division machinery, whereas assembly of RodA into the cytoskeletal ring required one or more additional septasomal components. Strikingly, MreB, MreC, MreD and RodA were each able to independently assemble into the cytoskeletal ring and coiled cytoskeletal structures in the absence of any of the other ring components. This excludes the possibility that one or more of these proteins acts as a scaffold for incorporation of the other proteins into these structures. In contrast, incorporation of Pbp2 required the presence of MreC, which may provide a docking site for Pbp2 entry.

Dynamic localization and interaction with other Bacillus subtilis actin-like proteins are important for the function of MreB.

PubMed

Defeu Soufo, Hervé Joël; Graumann, Peter L

2006-12-01

Bacterial actin-like proteins play a key role in cell morphology and in chromosome segregation. Many bacteria, like Bacillus subtilis, contain three genes encoding actin-like proteins, called mreB, mbl and mreBH in B. subtilis. We show that MreB and Mbl colocalize extensively within live cells, and that all three B. subtilis actin paralogues interact with each other underneath the cell membrane. A mutation in the phosphate 2 motif of MreB had a dominant negative effect on cell morphology and on chromosome segregation. Expression of this mutant allele of MreB interfered with the dynamic localization of Mbl. These experiments show that the interaction between MreB and Mbl has physiological significance. An mreB deletion strain can grow under special media conditions, however, depletion of Mbl in this mutant background abolished growth, indicating that actin paralogues can partially complement each other. The membrane protein MreC was found to interact with Mbl, but not with MreB, revealing a clear distinction between the function of the two paralogues. The phosphate 2 mutant MreB protein allowed for filament formation of mutant or wild-type MreB, but abolished the dynamic reorganization of the filaments. The latter mutation led to a strong reduction, but not complete loss, of function of MreB, both in terms of chromosome segregation and of cell morphology. Our work shows that that the dynamic localization of MreB is essential for the proper activity of the actin-like protein and that the interactions between MreB paralogues have important physiological significance.

The MreB-Like Protein Mbl of Streptomyces coelicolor A3(2) Depends on MreB for Proper Localization and Contributes to Spore Wall Synthesis▿ †

PubMed Central

Heichlinger, Andrea; Ammelburg, Moritz; Kleinschnitz, Eva-Maria; Latus, Annette; Maldener, Iris; Flärdh, Klas; Wohlleben, Wolfgang; Muth, Günther

2011-01-01

Most bacteria with a rod-shaped morphology contain an actin-like cytoskeleton consisting of MreB polymers, which form helical spirals underneath the cytoplasmic membrane to direct peptidoglycan synthesis for the elongation of the cell wall. In contrast, MreB of Streptomyces coelicolor is not required for vegetative growth but has a role in sporulation. Besides MreB, S. coelicolor encodes two further MreB-like proteins, Mbl and SCO6166, whose function is unknown. Whereas MreB and Mbl are highly similar, SCO6166 is shorter, lacking the subdomains IB and IIB of actin-like proteins. Here, we showed that MreB and Mbl are not functionally redundant but cooperate in spore wall synthesis. Expression analysis by semiquantitative reverse transcription-PCR revealed distinct expression patterns. mreB and mbl are induced predominantly during morphological differentiation. In contrast, sco6166 is strongly expressed during vegetative growth but switched off during sporulation. All genes could be deleted without affecting viability. Even a ΔmreB Δmbl double mutant was viable. Δsco6166 had a wild-type phenotype. ΔmreB, Δmbl, and ΔmreB Δmbl produced swollen, prematurely germinating spores that were sensitive to various kinds of stress, suggesting a defect in spore wall integrity. During aerial mycelium formation, an Mbl-mCherry fusion protein colocalized with an MreB-enhanced green fluorescent protein (MreB-eGFP) fusion protein at the sporulation septa. Whereas MreB-eGFP localized properly in the Δmbl mutant, Mbl-mCherry localization depended on the presence of a functional MreB protein. Our results revealed that MreB and Mbl cooperate in the synthesis of the thickened spore wall, while SCO6166 has a nonessential function during vegetative growth. PMID:21257777

The MreB-like protein Mbl of Streptomyces coelicolor A3(2) depends on MreB for proper localization and contributes to spore wall synthesis.

PubMed

Heichlinger, Andrea; Ammelburg, Moritz; Kleinschnitz, Eva-Maria; Latus, Annette; Maldener, Iris; Flärdh, Klas; Wohlleben, Wolfgang; Muth, Günther

2011-04-01

Most bacteria with a rod-shaped morphology contain an actin-like cytoskeleton consisting of MreB polymers, which form helical spirals underneath the cytoplasmic membrane to direct peptidoglycan synthesis for the elongation of the cell wall. In contrast, MreB of Streptomyces coelicolor is not required for vegetative growth but has a role in sporulation. Besides MreB, S. coelicolor encodes two further MreB-like proteins, Mbl and SCO6166, whose function is unknown. Whereas MreB and Mbl are highly similar, SCO6166 is shorter, lacking the subdomains IB and IIB of actin-like proteins. Here, we showed that MreB and Mbl are not functionally redundant but cooperate in spore wall synthesis. Expression analysis by semiquantitative reverse transcription-PCR revealed distinct expression patterns. mreB and mbl are induced predominantly during morphological differentiation. In contrast, sco6166 is strongly expressed during vegetative growth but switched off during sporulation. All genes could be deleted without affecting viability. Even a ΔmreB Δmbl double mutant was viable. Δsco6166 had a wild-type phenotype. ΔmreB, Δmbl, and ΔmreB Δmbl produced swollen, prematurely germinating spores that were sensitive to various kinds of stress, suggesting a defect in spore wall integrity. During aerial mycelium formation, an Mbl-mCherry fusion protein colocalized with an MreB-enhanced green fluorescent protein (MreB-eGFP) fusion protein at the sporulation septa. Whereas MreB-eGFP localized properly in the Δmbl mutant, Mbl-mCherry localization depended on the presence of a functional MreB protein. Our results revealed that MreB and Mbl cooperate in the synthesis of the thickened spore wall, while SCO6166 has a nonessential function during vegetative growth.

Bacillus subtilis MreB Orthologs Self-Organize into Filamentous Structures underneath the Cell Membrane in a Heterologous Cell System

PubMed Central

Dempwolff, Felix; Reimold, Christian; Reth, Michael; Graumann, Peter L.

2011-01-01

Actin-like bacterial cytoskeletal element MreB has been shown to be essential for the maintenance of rod cell shape in many bacteria. MreB forms rapidly remodelling helical filaments underneath the cell membrane in Bacillus subtilis and in other bacterial cells, and co-localizes with its two paralogs, Mbl and MreBH. We show that MreB localizes as dynamic bundles of filaments underneath the cell membrane in Drosophila S2 Schneider cells, which become highly stable when the ATPase motif in MreB is modified. In agreement with ATP-dependent filament formation, the depletion of ATP in the cells lead to rapid dissociation of MreB filaments. Extended induction of MreB resulted in the formation of membrane protrusions, showing that like actin, MreB can exert force against the cell membrane. Mbl also formed membrane associated filaments, while MreBH formed filaments within the cytosol. When co-expressed, MreB, Mbl and MreBH built up mixed filaments underneath the cell membrane. Membrane protein RodZ localized to endosomes in S2 cells, but localized to the cell membrane when co-expressed with Mbl, showing that bacterial MreB/Mbl structures can recruit a protein to the cell membrane. Thus, MreB paralogs form a self-organizing and dynamic filamentous scaffold underneath the membrane that is able to recruit other proteins to the cell surface. PMID:22069484

Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells.

PubMed

Shiomi, Daisuke; Toyoda, Atsushi; Aizu, Tomoyuki; Ejima, Fumio; Fujiyama, Asao; Shini, Tadasu; Kohara, Yuji; Niki, Hironori

2013-03-01

RodZ interacts with MreB and both factors are required to maintain the rod shape of Escherichia coli. The assembly of MreB into filaments regulates the subcellular arrangement of a group of enzymes that synthesizes the peptidoglycan (PG) layer. However, it is still unknown how polymerization of MreB determines the rod shape of bacterial cells. Regulatory factor(s) are likely to be involved in controlling the function and dynamics of MreB. We isolated suppressor mutations to partially recover the rod shape in rodZ deletion mutants and found that some of the suppressor mutations occurred in mreB. All of the mreB mutations were in or in the vicinity of domain IA of MreB. Those mreB mutations changed the property of MreB filaments in vivo. In addition, suppressor mutations were found in the periplasmic regions in PBP2 and RodA, encoded by mrdA and mrdB genes. Similar to MreB and RodZ, PBP2 and RodA are pivotal to the cell wall elongation process. Thus, we found that mutations in domain IA of MreB and in the periplasmic domain of PBP2 and RodA can restore growth and rod shape to ΔrodZ cells, possibly by changing the requirements of MreB in the process. © 2013 Blackwell Publishing Ltd.

Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells

PubMed Central

Shiomi, Daisuke; Toyoda, Atsushi; Aizu, Tomoyuki; Ejima, Fumio; Fujiyama, Asao; Shini, Tadasu; Kohara, Yuji; Niki, Hironori

2013-01-01

RodZ interacts with MreB and both factors are required to maintain the rod shape of Escherichia coli. The assembly of MreB into filaments regulates the subcellular arrangement of a group of enzymes that synthesizes the peptidoglycan (PG) layer. However, it is still unknown how polymerization of MreB determines the rod shape of bacterial cells. Regulatory factor(s) are likely to be involved in controlling the function and dynamics of MreB. We isolated suppressor mutations to partially recover the rod shape in rodZ deletion mutants and found that some of the suppressor mutations occurred in mreB. All of the mreB mutations were in or in the vicinity of domain IA of MreB. Those mreB mutations changed the property of MreB filaments in vivo. In addition, suppressor mutations were found in the periplasmic regions in PBP2 and RodA, encoded by mrdA and mrdB genes. Similar to MreB and RodZ, PBP2 and RodA are pivotal to the cell wall elongation process. Thus, we found that mutations in domain IA of MreB and in the periplasmic domain of PBP2 and RodA can restore growth and rod shape to ΔrodZ cells, possibly by changing the requirements of MreB in the process. PMID:23301723

Investigations on response time of magnetorheological elastomer under compression mode

NASA Astrophysics Data System (ADS)

Zhu, Mi; Yu, Miao; Qi, Song; Fu, Jie

2018-05-01

For efficient fast control of vibration system with magnetorheological elastomer (MRE)-based smart device, the response time of MRE material is the key parameter which directly affects the control performance of the vibration system. For a step coil current excitation, this paper proposed a Maxwell behavior model with time constant λ to describe the normal force response of MRE, and the response time of MRE was extracted through the separation of coil response time. Besides, the transient responses of MRE under compression mode were experimentally investigated, and the effects of (i) applied current, (ii) particle distribution and (iii) compressive strain on the response time of MRE were addressed. The results revealed that the three factors can affect the response characteristic of MRE quite significantly. Besides the intrinsic importance for contributing to the response evaluation and effective design of MRE device, this study may conduce to the optimal design of controller for MRE control system.

GTPase activity, structure, and mechanical properties of filaments assembled from bacterial cytoskeleton protein MreB.

PubMed

Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

2006-02-01

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.

Large-scale purification and in vitro characterization of the assembly of MreB from Leptospira interrogans.

PubMed

Barkó, Szilvia; Szatmári, Dávid; Bódis, Emőke; Türmer, Katalin; Ujfalusi, Zoltán; Popp, David; Robinson, Robert C; Nyitrai, Miklós

2016-09-01

Weil's syndrome is caused by Leptospira interrogans infections, a Gram negative bacterium with a distinct thin corkscrew cell shape. The molecular basis for this unusual morphology is unknown. In many bacteria, cell wall synthesis is orchestrated by the actin homolog, MreB. Here we have identified the MreB within the L. interrogans genome and expressed the His-tagged protein product of the synthesized gene (Li-MreB) in Escherichia coli. Li-MreB did not purify under standard nucleotide-free conditions used for MreBs from other species, requiring the continual presence of ATP to remain soluble. Covalent modification of Li-MreB free thiols with Alexa488 produced a fluorescent version of Li-MreB. We developed native and denaturing/refolding purification schemes for Li-MreB. The purified product was shown to assemble and disassemble in MgCl2 and KCl dependent manners, as monitored by light scattering and sedimentation studies. The fluorescence spectrum of labeled Li-MreB-Alexa488 showed cation-induced changes in line with an activation process followed by a polymerization phase. The resulting filaments appeared as bundles and sheets under the fluorescence microscope. Finally, since the Li-MreB polymerization was cation dependent, we developed a simple method to measure monovalent cation concentrations within a test case prokaryote, E. coli. We have identified and initially characterized the cation-dependent polymerization properties of a novel MreB from a non-rod shaped bacterium and developed a method to measure cation concentrations within prokaryotes. This initial characterization of Li-MreB will enable future structural determination of the MreB filament from this corkscrew-shaped bacterium. Copyright © 2016 Elsevier B.V. All rights reserved.

MreB Orientation Correlates with Cell Diameter in Escherichia coli.

PubMed

Ouzounov, Nikolay; Nguyen, Jeffrey P; Bratton, Benjamin P; Jacobowitz, David; Gitai, Zemer; Shaevitz, Joshua W

2016-09-06

Bacteria have remarkably robust cell shape control mechanisms. For example, cell diameter only varies by a few percent across a given population. The bacterial actin homolog, MreB, is necessary for establishment and maintenance of rod shape although the detailed properties of MreB that are important for shape control remained unknown. In this study, we perturb MreB in two ways: by treating cells with the polymerization-inhibiting drug A22 and by creating point mutants in mreB. These perturbations modify the steady-state diameter of cells over a wide range, from 790 ± 30 nm to 1700 ± 20 nm. To determine which properties of MreB are important for diameter control, we correlated structural characteristics of fluorescently tagged MreB polymers with cell diameter by simultaneously analyzing three-dimensional images of MreB and cell shape. Our results indicate that the helical pitch angle of MreB inversely correlates with the cell diameter of Escherichia coli. Other correlations between MreB and cell diameter are not found to be significant. These results demonstrate that the physical properties of MreB filaments are important for shape control and support a model in which MreB organizes the cell wall growth machinery to produce a chiral cell wall structure and dictate cell diameter. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The cell shape proteins MreB and MreC control cell morphogenesis by positioning cell wall synthetic complexes.

PubMed

Divakaruni, Arun V; Baida, Cyril; White, Courtney L; Gober, James W

2007-10-01

MreB, the bacterial actin homologue, is thought to function in spatially co-ordinating cell morphogenesis in conjunction with MreC, a protein that wraps around the outside of the cell within the periplasmic space. In Caulobacter crescentus, MreC physically associates with penicillin-binding proteins (PBPs) which catalyse the insertion of intracellularly synthesized precursors into the peptidoglycan cell wall. Here we show that MreC is required for the spatial organization of components of the peptidoglycan-synthesizing holoenzyme in the periplasm and MreB directs the localization of a peptidoglycan precursor synthesis protein in the cytosol. Additionally, fluorescent vancomycin (Van-FL) labelling revealed that the bacterial cytoskeletal proteins MreB and FtsZ, as well as MreC and RodA, were required for peptidoglycan synthetic activity. MreB and FtsZ were found to be required for morphogenesis of the polar stalk. FtsZ was required for a cell cycle-regulated burst of peptidoglycan synthesis early in the cell cycle resulting in the synthesis of cross-band structures, whereas MreB was required for lengthening of the stalk. Thus, the bacterial cytoskeleton and cell shape-determining proteins such as MreC, function in concert to orchestrate the localization of cell wall synthetic complexes resulting in spatially co-ordinated and efficient peptidoglycan synthetic activity.

Dynamic localization of MreB in Vibrio parahaemolyticus and in the ectopic host bacterium Escherichia coli.

PubMed

Chiu, Shen-Wen; Chen, Shau-Yan; Wong, Hin-chung

2008-11-01

MreB, a homolog of eukaryotic actin, participates in morphogenesis, cell division, cell polarity, and chromosome segregation in prokaryotes. In this study, a yellow fluorescent protein conjugate (YFP-MreB(Vp)) was generated to investigate the behavior of MreB in merodiploid strain SC9 of the enteropathogen Vibrio parahaemolyticus. Under normal growth conditions, YFP-MreB(Vp) formed helical filaments with a pitch of 0.64 +/- 0.09 microm in about 85% of exponential-phase cells, and different clusters, relaxed coils, and ring configurations were observed in a small proportion of the cells. Overexpression of YFP-MreB(Vp) substantially altered the structure of the MreB cytoskeleton and resulted in swollen and pleomorphic cells. Disturbing the activities of penicillin-binding proteins or adding magnesium suppressed the morphological distortions. These results indicate that mislocalization of cell wall-synthesizing machinery was responsible for morphological abnormality. By expressing YFP-MreB(Vp) in the ectopic host bacterium Escherichia coli, shrinkage, fragmentation, and annealing of MreB(Vp) filaments were directly observed. This work revealed the dynamic pattern of the localization of YFP-MreB(Vp) in V. parahaemolyticus and its relationship to cell morphogenesis, and the YFP-MreB(Vp)-E. coli system may be used to investigate the dynamic spatial structures of the MreB cytoskeleton in vivo.

The most recent large earthquake on the Rodgers Creek fault, San Francisco bay area

USGS Publications Warehouse

Hecker, S.; Pantosti, D.; Schwartz, D.P.; Hamilton, J.C.; Reidy, L.M.; Powers, T.J.

2005-01-01

The Rodgers Creek fault (RCF) is a principal component of the San Andreas fault system north of San Francisco. No evidence appears in the historical record of a large earthquake on the RCF, implying that the most recent earthquake (MRE) occurred before 1824, when a Franciscan mission was built near the fault at Sonoma, and probably before 1776, when a mission and presidio were built in San Francisco. The first appearance of nonnative pollen in the stratigraphic record at the Triangle G Ranch study site on the south-central reach of the RCF confirms that the MRE occurred before local settlement and the beginning of livestock grazing. Chronological modeling of earthquake age using radiocarbon-dated charcoal from near the top of a faulted alluvial sequence at the site indicates that the MRE occurred no earlier than A.D. 1690 and most likely occurred after A.D. 1715. With these age constraints, we know that the elapsed time since the MRE on the RCF is more than 181 years and less than 315 years and is probably between 229 and 290 years. This elapsed time is similar to published recurrence-interval estimates of 131 to 370 years (preferred value of 230 years) and 136 to 345 years (mean of 205 years), calculated from geologic data and a regional earthquake model, respectively. Importantly, then, the elapsed time may have reached or exceeded the average recurrence time for the fault. The age of the MRE on the RCF is similar to the age of prehistoric surface rupture on the northern and southern sections of the Hayward fault to the south. This suggests possible rupture scenarios that involve simultaneous rupture of the Rodgers Creek and Hayward faults. A buried channel is offset 2.2 (+ 1.2, - 0.8) m along one side of a pressure ridge at the Triangle G Ranch site. This provides a minimum estimate of right-lateral slip during the MRE at this location. Total slip at the site may be similar to, but is probably greater than, the 2 (+ 0.3, - 0.2) m measured previously at the nearby Beebe Ranch site.

Dynamic blocked transfer stiffness method of characterizing the magnetic field and frequency dependent dynamic viscoelastic properties of MRE

NASA Astrophysics Data System (ADS)

Poojary, Umanath R.; Hegde, Sriharsha; Gangadharan, K. V.

2016-11-01

Magneto rheological elastomer (MRE) is a potential resilient element for the semi active vibration isolator. MRE based isolators adapt to different frequency of vibrations arising from the source to isolate the structure over wider frequency range. The performance of MRE isolator depends on the magnetic field and frequency dependent characteristics of MRE. Present study is focused on experimentally evaluating the dynamic stiffness and loss factor of MRE through dynamic blocked transfer stiffness method. The dynamic stiffness variations of MRE exhibit strong magnetic field and mild frequency dependency. Enhancements in dynamic stiffness saturate with the increase in magnetic field and the frequency. The inconsistent variations of loss factor with the magnetic field substantiate the inability of MRE to have independent control over its damping characteristics.

Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein.

PubMed

Defeu Soufo, Hervé Joël; Reimold, Christian; Linne, Uwe; Knust, Tobias; Gescher, Johannes; Graumann, Peter L

2010-02-16

We show that translation initiation factor EF-Tu plays a second important role in cell shape maintenance in the bacterium Bacillus subtilis. EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with MreB, an actin-like cytoskeletal element setting up rod cell shape. The localization of MreB and of EF-Tu is interdependent, but in contrast to the dynamic MreB filaments, EF-Tu structures are more static and may serve as tracks for MreB filaments. In agreement with this idea, EF-Tu and MreB interact in vivo and in vitro. Lowering of the EF-Tu levels had a minor effect on translation but a strong effect on cell shape and on the localization of MreB, and blocking of the function of EF-Tu in translation did not interfere with the localization of MreB, showing that, directly or indirectly, EF-Tu affects the cytoskeletal MreB structure and thus serves two important functions in a bacterium.

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis

PubMed Central

Szwedziak, Piotr; Wong, Felix; Schaefer, Kaitlin; Izoré, Thierry; Renner, Lars D; Holmes, Matthew J; Sun, Yingjie; Bisson-Filho, Alexandre W; Walker, Suzanne; Amir, Ariel; Löwe, Jan

2018-01-01

MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape. PMID:29469806

K-space data processing for magnetic resonance elastography (MRE).

PubMed

Corbin, Nadège; Breton, Elodie; de Mathelin, Michel; Vappou, Jonathan

2017-04-01

Magnetic resonance elastography (MRE) requires substantial data processing based on phase image reconstruction, wave enhancement, and inverse problem solving. The objective of this study is to propose a new, fast MRE method based on MR raw data processing, particularly adapted to applications requiring fast MRE measurement or high elastogram update rate. The proposed method allows measuring tissue elasticity directly from raw data without prior phase image reconstruction and without phase unwrapping. Experimental feasibility is assessed both in a gelatin phantom and in the liver of a porcine model in vivo. Elastograms are reconstructed with the raw MRE method and compared to those obtained using conventional MRE. In a third experiment, changes in elasticity are monitored in real-time in a gelatin phantom during its solidification by using both conventional MRE and raw MRE. The raw MRE method shows promising results by providing similar elasticity values to the ones obtained with conventional MRE methods while decreasing the number of processing steps and circumventing the delicate step of phase unwrapping. Limitations of the proposed method are the influence of the magnitude on the elastogram and the requirement for a minimum number of phase offsets. This study demonstrates the feasibility of directly reconstructing elastograms from raw data.

Motion of variable-length MreB filaments at the bacterial cell membrane influences cell morphology

PubMed Central

Reimold, Christian; Defeu Soufo, Herve Joel; Dempwolff, Felix; Graumann, Peter L.

2013-01-01

The maintenance of rod-cell shape in many bacteria depends on actin-like MreB proteins and several membrane proteins that interact with MreB. Using superresolution microscopy, we show that at 50-nm resolution, Bacillus subtilis MreB forms filamentous structures of length up to 3.4 μm underneath the cell membrane, which run at angles diverging up to 40° relative to the cell circumference. MreB from Escherichia coli forms at least 1.4-μm-long filaments. MreB filaments move along various tracks with a maximal speed of 85 nm/s, and the loss of ATPase activity leads to the formation of extended and static filaments. Suboptimal growth conditions lead to formation of patch-like structures rather than extended filaments. Coexpression of wild-type MreB with MreB mutated in the subunit interface leads to formation of shorter MreB filaments and a strong effect on cell shape, revealing a link between filament length and cell morphology. Thus MreB has an extended-filament architecture with the potential to position membrane proteins over long distances, whose localization in turn may affect the shape of the cell wall. PMID:23783036

Motion of variable-length MreB filaments at the bacterial cell membrane influences cell morphology.

PubMed

Reimold, Christian; Defeu Soufo, Herve Joel; Dempwolff, Felix; Graumann, Peter L

2013-08-01

The maintenance of rod-cell shape in many bacteria depends on actin-like MreB proteins and several membrane proteins that interact with MreB. Using superresolution microscopy, we show that at 50-nm resolution, Bacillus subtilis MreB forms filamentous structures of length up to 3.4 μm underneath the cell membrane, which run at angles diverging up to 40° relative to the cell circumference. MreB from Escherichia coli forms at least 1.4-μm-long filaments. MreB filaments move along various tracks with a maximal speed of 85 nm/s, and the loss of ATPase activity leads to the formation of extended and static filaments. Suboptimal growth conditions lead to formation of patch-like structures rather than extended filaments. Coexpression of wild-type MreB with MreB mutated in the subunit interface leads to formation of shorter MreB filaments and a strong effect on cell shape, revealing a link between filament length and cell morphology. Thus MreB has an extended-filament architecture with the potential to position membrane proteins over long distances, whose localization in turn may affect the shape of the cell wall.

Polymerization properties of the Thermotoga maritima actin MreB: roles of temperature, nucleotides, and ions.

PubMed

Bean, Greg J; Amann, Kurt J

2008-01-15

MreB is a bacterial orthologue of actin that affects cell shape, polarity, and chromosome segregation. Although a significant body of work has explored its cellular functions, we know very little about the biochemical behavior of MreB. We have cloned, overexpressed in Escherichia coli, and purified untagged MreB1 from Thermotoga maritima. We have characterized the conditions that regulate its monomer-to-polymer assembly reaction, the critical concentrations of that reaction, the manner in which MreB uses nucleotides, its stability, and the structure of the assembled polymer. MreB requires a bound purine nucleotide for polymerization and rapidly hydrolyzes it following assembly. MreB assembly contains two distinct components, one that does not require divalent cations and one that does, which may comprise the nucleation and elongation phases of assembly, respectively. MreB assembly is strongly favored by increasing temperature or protein concentration but inhibited differentially by high concentrations of monovalent salts. The polymerization rate increases and the bulk critical concentration decreases with increasing temperature, but in contrast to previous reports, MreB is capable of polymerizing across a broad range of temperatures. MreB polymers are shorter and stiffer and scatter more light than eukaryotic actin filaments. Due to rapid ATP hydrolysis and phosphate release, we suggest that most assembled MreB in cells is in the ADP-bound state. Because of only moderate differences between the ATP and ADP critical concentrations, treadmilling may occur, but we do not predict dynamic instability in cells. Because of the relatively low cellular concentration of MreB and the observed structural properties of the polymer, a single MreB assembly may exist in cells.

The bacterial Sec system is required for the organization and function of the MreB cytoskeleton

PubMed Central

2017-01-01

The Sec system is responsible for protein insertion, translocation and secretion across membranes in all cells. The bacterial actin homolog MreB controls various processes, including cell wall synthesis, membrane organization and polarity establishment. Here we show that the two systems genetically interact and that components of the Sec system, especially the SecA motor protein, are essential for spatiotemporal organization of MreB in E. coli, as evidenced by the accumulation of MreB at irregular sites in Sec-impaired cells. MreB mislocalization in SecA-defective cells significantly affects MreB-coordinated processes, such as cell wall synthesis, and induce formation of membrane invaginations enriched in high fluidity domains. Additionally, MreB is not recruited to the FtsZ ring in secA mutant cells, contributing to division arrest and cell filamentation. Our results show that all these faults are due to improper targeting of MreB to the membrane in the absence of SecA. Thus, when we reroute RodZ, MreB membrane-anchor, by fusing it to a SecA-independent integral membrane protein and overproducing it, MreB localization is restored and the defect in cell division is corrected. Notably, the RodZ moiety is not properly inserted into the membrane, strongly suggesting that it only serves as a bait for placing MreB around the cell circumference. Finally, we show that MreB localization depends on SecA also in C. crescentus, suggesting that regulation of MreB by the Sec system is conserved in bacteria. Taken together, our data reveal that the secretion system plays an important role in determining the organization and functioning of the cytoskeletal system in bacteria. PMID:28945742

The bacterial Sec system is required for the organization and function of the MreB cytoskeleton.

PubMed

Govindarajan, Sutharsan; Amster-Choder, Orna

2017-09-01

The Sec system is responsible for protein insertion, translocation and secretion across membranes in all cells. The bacterial actin homolog MreB controls various processes, including cell wall synthesis, membrane organization and polarity establishment. Here we show that the two systems genetically interact and that components of the Sec system, especially the SecA motor protein, are essential for spatiotemporal organization of MreB in E. coli, as evidenced by the accumulation of MreB at irregular sites in Sec-impaired cells. MreB mislocalization in SecA-defective cells significantly affects MreB-coordinated processes, such as cell wall synthesis, and induce formation of membrane invaginations enriched in high fluidity domains. Additionally, MreB is not recruited to the FtsZ ring in secA mutant cells, contributing to division arrest and cell filamentation. Our results show that all these faults are due to improper targeting of MreB to the membrane in the absence of SecA. Thus, when we reroute RodZ, MreB membrane-anchor, by fusing it to a SecA-independent integral membrane protein and overproducing it, MreB localization is restored and the defect in cell division is corrected. Notably, the RodZ moiety is not properly inserted into the membrane, strongly suggesting that it only serves as a bait for placing MreB around the cell circumference. Finally, we show that MreB localization depends on SecA also in C. crescentus, suggesting that regulation of MreB by the Sec system is conserved in bacteria. Taken together, our data reveal that the secretion system plays an important role in determining the organization and functioning of the cytoskeletal system in bacteria.

MreB-Dependent Inhibition of Cell Elongation during the Escape from Competence in Bacillus subtilis

PubMed Central

Mirouze, Nicolas; Ferret, Cécile; Yao, Zhizhong; Chastanet, Arnaud; Carballido-López, Rut

2015-01-01

During bacterial exponential growth, the morphogenetic actin-like MreB proteins form membrane-associated assemblies that move processively following trajectories perpendicular to the long axis of the cell. Such MreB structures are thought to scaffold and restrict the movement of peptidoglycan synthesizing machineries, thereby coordinating sidewall elongation. In Bacillus subtilis, this function is performed by the redundant action of three MreB isoforms, namely MreB, Mbl and MreBH. mreB and mbl are highly transcribed from vegetative promoters. We have found that their expression is maximal at the end of exponential phase, and rapidly decreases to a low basal level upon entering stationary phase. However, in cells developing genetic competence, a stationary phase physiological adaptation, expression of mreB was specifically reactivated by the central competence regulator ComK. In competent cells, MreB was found in complex with several competence proteins by in vitro pull-down assays. In addition, it co-localized with the polar clusters formed by the late competence peripheral protein ComGA, in a ComGA-dependent manner. ComGA has been shown to be essential for the inhibition of cell elongation characteristic of cells escaping the competence state. We show here that the pathway controlling this elongation inhibition also involves MreB. Our findings suggest that ComGA sequesters MreB to prevent cell elongation and therefore the escape from competence. PMID:26091431

Localization and expression of MreB in Vibrio parahaemolyticus under different stresses.

PubMed

Chiu, Shen-Wen; Chen, Shau-Yan; Wong, Hin-chung

2008-11-01

MreB, the homolog of eukaryotic actin, may play a vital role when prokaryotes cope with stress by altering their spatial organization, including their morphology, subcellular architecture, and localization of macromolecules. This study investigates the behavior of MreB in Vibrio parahaemolyticus under various stresses. The behavior of MreB was probed using a yellow fluorescent protein-MreB conjugate in merodiploid strain SC9. Under normal growth conditions, MreB formed helical filaments in exponential-phase cells. The shape of starved or stationary-phase cells changed from rods to small spheroids. The cells differentiated into the viable but nonculturable (VBNC) state with small spherical cells via a "swelling-waning" process. In all cases, drastic remodeling of the MreB cytoskeleton was observed. MreB helices typically were loosened and fragmented into short filaments, arcs, and spots in bacteria under these stresses. The disintegrated MreB exhibited a strong tendency to attach to the cytoplasmic membrane. The expression of mreB generally declined in bacteria in the stationary phase and under starvation but was upregulated during the initial periods of cold shock and VBNC state differentiation and decreased afterwards. Our findings demonstrated the behavior of MreB in the morphological changes of V. parahaemolyticus under intrinsic or extrinsic stresses and may have important implications for studying the cellular stress response and aging.

MreB-Dependent Inhibition of Cell Elongation during the Escape from Competence in Bacillus subtilis.

PubMed

Mirouze, Nicolas; Ferret, Cécile; Yao, Zhizhong; Chastanet, Arnaud; Carballido-López, Rut

2015-06-01

During bacterial exponential growth, the morphogenetic actin-like MreB proteins form membrane-associated assemblies that move processively following trajectories perpendicular to the long axis of the cell. Such MreB structures are thought to scaffold and restrict the movement of peptidoglycan synthesizing machineries, thereby coordinating sidewall elongation. In Bacillus subtilis, this function is performed by the redundant action of three MreB isoforms, namely MreB, Mbl and MreBH. mreB and mbl are highly transcribed from vegetative promoters. We have found that their expression is maximal at the end of exponential phase, and rapidly decreases to a low basal level upon entering stationary phase. However, in cells developing genetic competence, a stationary phase physiological adaptation, expression of mreB was specifically reactivated by the central competence regulator ComK. In competent cells, MreB was found in complex with several competence proteins by in vitro pull-down assays. In addition, it co-localized with the polar clusters formed by the late competence peripheral protein ComGA, in a ComGA-dependent manner. ComGA has been shown to be essential for the inhibition of cell elongation characteristic of cells escaping the competence state. We show here that the pathway controlling this elongation inhibition also involves MreB. Our findings suggest that ComGA sequesters MreB to prevent cell elongation and therefore the escape from competence.

Bacillus subtilis MreB paralogues have different filament architectures and lead to shape remodelling of a heterologous cell system.

PubMed

Soufo, Hervé Joël Defeu; Graumann, Peter L

2010-12-01

Like many bacteria, Bacillus subtilis cells contain three actin-like MreB proteins. We show that the three paralogues, MreB, Mbl and MreBH, have different filament architectures in a heterologous cell system, and form straight filaments, helices or ring structures, different from the regular helical arrangement in B. subtilis cells. However, when coexpressed, they colocalize into a single filamentous helical structure, showing that the paralogues influence each other's filament architecture. Ring-like MreBH structures can be converted into MreB-like helical filaments by a single point mutation affecting subunit contacts, showing that MreB paralogues feature flexible filament arrangements. Time-lapse and FRAP experiments show that filaments can extend as well as shrink at both ends, and also show internal rearrangement, suggesting that filaments consist of overlapping bundles of shorter filaments that continuously turn over. Upon induction in Escherichia coli cells, B. subtilis MreB (BsMreB) filaments push the cells into strikingly altered cell morphology, showing that MreB filaments can change cell shape. E. coli cells with a weakened cell wall were ruptured upon induction of BsMreB filaments, suggesting that the bacterial actin orthologue may exert force against the cell membrane and envelope, and thus possibly plays an additional mechanical role in bacteria. © 2010 Blackwell Publishing Ltd.

Assembly of MreB filaments on liposome membranes: a synthetic biology approach.

PubMed

Maeda, Yusuke T; Nakadai, Tomoyoshi; Shin, Jonghyeon; Uryu, Kunihiro; Noireaux, Vincent; Libchaber, Albert

2012-02-17

The physical interaction between the cytoskeleton and the cell membrane is essential in defining the morphology of living organisms. In this study, we use a synthetic approach to polymerize bacterial MreB filaments inside phospholipid vesicles. When the proteins MreB and MreC are expressed inside the liposomes, the MreB cytoskeleton structure develops at the inner membrane. Furthermore, when purified MreB is used inside the liposomes, MreB filaments form a 4-10 μm rigid bundle structure and deform the lipid vesicles in physical contact with the vesicle inner membrane. These results indicate that the fibrillation of MreB filaments can take place either in close proximity of deformable lipid membrane or in the presence of associated protein. Our finding might be relevant for the self-assembly of cytoskeleton filaments toward the construction of artificial cell systems.

The actin homologue MreB organizes the bacterial cell membrane

PubMed Central

Strahl, Henrik; Bürmann, Frank; Hamoen, Leendert W.

2014-01-01

The eukaryotic cortical actin cytoskeleton creates specific lipid domains, including lipid rafts, which determine the distribution of many membrane proteins. Here we show that the bacterial actin homologue MreB displays a comparable activity. MreB forms membrane-associated filaments that coordinate bacterial cell wall synthesis. We noticed that the MreB cytoskeleton influences fluorescent staining of the cytoplasmic membrane. Detailed analyses combining an array of mutants, using specific lipid staining techniques and spectroscopic methods, revealed that MreB filaments create specific membrane regions with increased fluidity (RIFs). Interference with these fluid lipid domains (RIFs) perturbs overall lipid homeostasis and affects membrane protein localization. The influence of MreB on membrane organization and fluidity may explain why the active movement of MreB stimulates membrane protein diffusion. These novel MreB activities add additional complexity to bacterial cell membrane organization and have implications for many membrane-associated processes. PMID:24603761

Direct membrane binding by bacterial actin MreB.

PubMed

Salje, Jeanne; van den Ent, Fusinita; de Boer, Piet; Löwe, Jan

2011-08-05

Bacterial actin MreB is one of the key components of the bacterial cytoskeleton. It assembles into short filaments that lie just underneath the membrane and organize the cell wall synthesis machinery. Here we show that MreB from both T. maritima and E. coli binds directly to cell membranes. This function is essential for cell shape determination in E. coli and is proposed to be a general property of many, if not all, MreBs. We demonstrate that membrane binding is mediated by a membrane insertion loop in TmMreB and by an N-terminal amphipathic helix in EcMreB and show that purified TmMreB assembles into double filaments on a membrane surface that can induce curvature. This, the first example of a membrane-binding actin filament, prompts a fundamental rethink of the structure and dynamics of MreB filaments within cells. Copyright © 2011 Elsevier Inc. All rights reserved.

BolA inhibits cell elongation and regulates MreB expression levels.

PubMed

Freire, Patrick; Moreira, Ricardo Neves; Arraiano, Cecília Maria

2009-02-06

The morphogene bolA is a general stress response gene in Escherichia coli that induces a round morphology when overexpressed. Results presented in this report show that increased BolA levels can inhibit cell elongation mechanisms. MreB polymerization is crucial for the bacterial cell cytoskeleton, and this protein is essential for the maintenance of a cellular rod shape. In this report, we demonstrate that bolA overexpression affects the architecture of MreB filaments. An increase in BolA leads to a significant reduction in MreB protein levels and mreB transcripts. BolA affects the mreBCD operon in vivo at the level of transcription. Furthermore, our results show that BolA is a new transcriptional repressor of MreB. The alterations in cell morphology induced by bolA seem to be mediated by a complex pathway that integrates PBP5, PBP6, MreB, and probably other regulators of cell morphology/elongation.

The actin homologue MreB organizes the bacterial cell membrane.

PubMed

Strahl, Henrik; Bürmann, Frank; Hamoen, Leendert W

2014-03-07

The eukaryotic cortical actin cytoskeleton creates specific lipid domains, including lipid rafts, which determine the distribution of many membrane proteins. Here we show that the bacterial actin homologue MreB displays a comparable activity. MreB forms membrane-associated filaments that coordinate bacterial cell wall synthesis. We noticed that the MreB cytoskeleton influences fluorescent staining of the cytoplasmic membrane. Detailed analyses combining an array of mutants, using specific lipid staining techniques and spectroscopic methods, revealed that MreB filaments create specific membrane regions with increased fluidity (RIFs). Interference with these fluid lipid domains (RIFs) perturbs overall lipid homeostasis and affects membrane protein localization. The influence of MreB on membrane organization and fluidity may explain why the active movement of MreB stimulates membrane protein diffusion. These novel MreB activities add additional complexity to bacterial cell membrane organization and have implications for many membrane-associated processes.

Effects of MreB paralogs on poly-γ-glutamic acid synthesis and cell morphology in Bacillus amyloliquefaciens.

PubMed

Gao, Weixia; Zhang, Zhongxiong; Feng, Jun; Dang, Yulei; Quan, Yufen; Gu, Yanyan; Wang, Shufang; Song, Cunjiang

2016-09-01

Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly-γ-glutamic acid (γ-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens, CwlO and LytE can degrade γ-PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of γ-PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the γ-PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the γ-PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, γ-PGA molecular weight and titer. In the mreBH inhibition mutant, γ-PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce γ-PGA degradation, and that improving the cell size could strengthen γ-PGA synthesis. This is the first report of enhanced γ-PGA production via suppression of actin-like MreB paralogs. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

PubMed

Defeu Soufo, Hervé Joël; Reimold, Christian; Breddermann, Hannes; Mannherz, Hans G; Graumann, Peter L

2015-04-24

EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds after addition of magnesium. Purified EF-Tu enhanced the amount of MreB filaments, as seen by sedimentation assays, the speed of filament formation and the length of MreB filaments in vitro. EF-Tu had the strongest impact on MreB filaments in a 1:1 ratio, and EF-Tu co-sedimented with MreB filaments, revealing a stoichiometric interaction between both proteins. This was supported by cross-linking assays where 1:1 species were well detectable. When expressed in E. coli cells, B. subtilis MreB formed filaments and induced the formation of co-localizing B. subtilis EF-Tu structures, indicating that MreB can direct the positioning of EF-Tu structures in a heterologous cell system. Fluorescence recovery after photobleaching analysis showed that MreB filaments have a higher turnover in B. subtilis cells than in E. coli cells, indicating different filament kinetics in homologous or heterologous cell systems. The data show that MreB can direct the localization of EF-Tu in vivo, which in turn positively affects the formation and dynamics of MreB filaments. Thus, EF-Tu is a modulator of the activity of a bacterial actin-like protein. Copyright © 2015. Published by Elsevier Ltd.

Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA.

PubMed

Cayrol, Bastien; Fortas, Emilie; Martret, Claire; Cech, Grzegorz; Kloska, Anna; Caulet, Stephane; Barbet, Marion; Trépout, Sylvain; Marco, Sergio; Taghbalout, Aziz; Busi, Florent; Wegrzyn, Grzegorz; Arluison, Véronique

2015-01-01

The bacterial actin-homolog MreB is a key player in bacterial cell-wall biosynthesis and is required for the maintenance of the rod-like morphology of Escherichia coli. However, how MreB cellular levels are adjusted to growth conditions is poorly understood. Here, we show that DsrA, an E. coli small noncoding RNA (sRNA), is involved in the post-transcriptional regulation of mreB. DsrA is required for the downregulation of MreB cellular concentration during environmentally induced slow growth-rates, mainly growth at low temperature and during the stationary phase. DsrA interacts in an Hfq-dependent manner with the 5' region of mreB mRNA, which contains signals for translation initiation and thereby affects mreB translation and stability. Moreover, as DsrA is also involved in the regulation of two transcriptional regulators, σ(S) and the nucleoid associated protein H-NS, which negatively regulate mreB transcription, it also indirectly contributes to mreB transcriptional down-regulation. By using quantitative analyses, our results evidence the complexity of this regulation and the tangled interplay between transcriptional and post-transcriptional control. As transcription factors and sRNA-mediated post-transcriptional regulators use different timescales, we propose that the sRNA pathway helps to adapt to changes in temperature, but also indirectly mediates long-term regulation of MreB concentration. The tight regulation and fine-tuning of mreB gene expression in response to cellular stresses is discussed in regard to the effect of the MreB protein on cell elongation.

Automated liver elasticity calculation for 3D MRE

NASA Astrophysics Data System (ADS)

Dzyubak, Bogdan; Glaser, Kevin J.; Manduca, Armando; Ehman, Richard L.

2017-03-01

Magnetic Resonance Elastography (MRE) is a phase-contrast MRI technique which calculates quantitative stiffness images, called elastograms, by imaging the propagation of acoustic waves in tissues. It is used clinically to diagnose liver fibrosis. Automated analysis of MRE is difficult as the corresponding MRI magnitude images (which contain anatomical information) are affected by intensity inhomogeneity, motion artifact, and poor tissue- and edge-contrast. Additionally, areas with low wave amplitude must be excluded. An automated algorithm has already been successfully developed and validated for clinical 2D MRE. 3D MRE acquires substantially more data and, due to accelerated acquisition, has exacerbated image artifacts. Also, the current 3D MRE processing does not yield a confidence map to indicate MRE wave quality and guide ROI selection, as is the case in 2D. In this study, extension of the 2D automated method, with a simple wave-amplitude metric, was developed and validated against an expert reader in a set of 57 patient exams with both 2D and 3D MRE. The stiffness discrepancy with the expert for 3D MRE was -0.8% +/- 9.45% and was better than discrepancy with the same reader for 2D MRE (-3.2% +/- 10.43%), and better than the inter-reader discrepancy observed in previous studies. There were no automated processing failures in this dataset. Thus, the automated liver elasticity calculation (ALEC) algorithm is able to calculate stiffness from 3D MRE data with minimal bias and good precision, while enabling stiffness measurements to be fully reproducible and to be easily performed on the large 3D MRE datasets.

The cellular Mre11 protein interferes with adenovirus E4 mutant DNA replication.

PubMed

Mathew, Shomita S; Bridge, Eileen

2007-09-01

Adenovirus type 5 (Ad5) relocalizes and degrades the host DNA repair protein Mre11, and efficiently initiates viral DNA replication. Mre11 associates with Ad E4 mutant DNA replication centers and is important for concatenating viral genomes. We have investigated the role of Mre11 in the E4 mutant DNA replication defect. RNAi-mediated knockdown of Mre11 dramatically rescues E4 mutant DNA replication in cells that do or do not concatenate viral genomes, suggesting that Mre11 inhibits DNA replication independent of genome concatenation. The mediator of DNA damage checkpoint 1 (Mdc1) protein is involved in recruiting and sustaining Mre11 at sites of DNA damage following ionizing radiation. We observe foci formation by Mdc1 in response to viral infection, indicating that this damage response protein is activated. However, knockdown of Mdc1 does not prevent Mre11 from localizing at viral DNA replication foci or rescue E4 mutant DNA replication. Our results are consistent with a model in which Mre11 interferes with DNA replication when it is localized at viral DNA replication foci.

Genetic variants in ATM, H2AFX and MRE11 genes and susceptibility to breast cancer in the polish population.

PubMed

Podralska, Marta; Ziółkowska-Suchanek, Iwona; Żurawek, Magdalena; Dzikiewicz-Krawczyk, Agnieszka; Słomski, Ryszard; Nowak, Jerzy; Stembalska, Agnieszka; Pesz, Karolina; Mosor, Maria

2018-04-20

DNA damage repair is a complex process, which can trigger the development of cancer if disturbed. In this study, we hypothesize a role of variants in the ATM, H2AFX and MRE11 genes in determining breast cancer (BC) susceptibility. We examined the whole sequence of the ATM kinase domain and estimated the frequency of founder mutations in the ATM gene (c.5932G > T, c.6095G > A, and c.7630-2A > C) and single nucleotide polymorphisms (SNPs) in H2AFX (rs643788, rs8551, rs7759, and rs2509049) and MRE11 (rs1061956 and rs2155209) among 315 breast cancer patients and 515 controls. The analysis was performed using high-resolution melting for new variants and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for recurrent ATM mutations. H2AFX and MRE11 polymorphisms were analyzed using TaqMan assays. The cumulative genetic risk scores (CGRS) were calculated using unweighted and weighted approaches. We identified four mutations (c.6067G > A, c.8314G > A, c.8187A > T, and c.6095G > A) in the ATM gene in three BC cases and two control subjects. We observed a statistically significant association of H2AFX variants with BC. Risk alleles (the G of rs7759 and the T of rs8551 and rs2509049) were observed more frequently in BC cases compared to the control group, with P values, odds ratios (OR) and 95% confidence intervals (CIs) of 0.0018, 1.47 (1.19 to 1.82); 0.018, 1.33 (1.09 to 1.64); and 0.024, 1.3 (1.06 to 1.59), respectively. Haplotype-based tests identified a significant association of the H2AFX CACT haplotype with BC (P <  0.0001, OR = 27.29, 95% CI 3.56 to 209.5). The risk of BC increased with the growing number of risk alleles. The OR (95% CI) for carriers of ≥ four risk alleles was 1.71 (1.11 to 2.62) for the CGRS. This study confirms that H2AFX variants are associated with an increased risk of BC. The above-reported sequence variants of MRE11 genes may not constitute a risk factor of breast cancer in the Polish population. The contribution of mutations detected in the ATM gene to the development of breast cancer needs further detailed study.

Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix.

PubMed

Kawai, Yoshikazu; Daniel, Richard A; Errington, Jeffery

2009-03-01

The bacterial actin homologue MreB plays a key role in cell morphogenesis. In Bacillus subtilis MreB is essential under normal growth conditions and mreB mutants are defective in the control of cell diameter. However, the precise role of MreB is still unclear. Analysis of the lethal phenotypic consequences of mreB disruption revealed an unusual bulging phenotype that precedes cell death. A similar phenotype was seen in wild-type cells at very low Mg(2+) concentrations. We found that inactivation of the major bi-functional penicillin-binding protein (PBP) PBP1 of B. subtilis restored the viability of an mreB null mutant as well as preventing bulging in both mutant and wild-type backgrounds. Bulging was associated with delocalization of PBP1. We show that the normal pattern of localization of PBP1 is dependent on MreB and that the proteins can physically interact using in vivo pull-down and bacterial two-hybrid approaches. Interactions between MreB and several other PBPs were also detected. Our results suggest that MreB filaments associate directly with the peptidoglycan biosynthetic machinery in B. subtilis as part of the mechanism that brings about controlled cell elongation.

Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD.

PubMed

White, Courtney L; Kitich, Aleksandar; Gober, James W

2010-05-01

In Caulobacter crescentus, intact cables of the actin homologue, MreB, are required for the proper spatial positioning of MurG which catalyses the final step in peptidoglycan precursor synthesis. Similarly, in the periplasm, MreC controls the spatial orientation of the penicillin binding proteins and a lytic transglycosylase. We have now found that MreB cables are required for the organization of several other cytosolic murein biosynthetic enzymes such as MraY, MurB, MurC, MurE and MurF. We also show these proteins adopt a subcellular pattern of localization comparable to MurG, suggesting the existence of cytoskeletal-dependent interactions. Through extensive two-hybrid analyses, we have now generated a comprehensive interaction map of components of the bacterial morphogenetic complex. In the cytosol, this complex contains both murein biosynthetic enzymes and morphogenetic proteins, including RodA, RodZ and MreD. We show that the integral membrane protein, MreD, is essential for lateral peptidoglycan synthesis, interacts with the precursor synthesizing enzymes MurG and MraY, and additionally, determines MreB localization. Our results suggest that the interdependent localization of MreB and MreD functions to spatially organize a complex of peptidoglycan precursor synthesis proteins, which is required for propagation of a uniform cell shape and catalytically efficient peptidoglycan synthesis.

The assembly of MreB, a prokaryotic homolog of actin.

PubMed

Esue, Osigwe; Cordero, Maria; Wirtz, Denis; Tseng, Yiider

2005-01-28

MreB, a major component of the bacterial cytoskeleton, exhibits high structural homology to its eukaryotic counterpart actin. Live cell microscopy studies suggest that MreB molecules organize into large filamentous spirals that support the cell membrane and play a key shape-determining function. However, the basic properties of MreB filament assembly remain unknown. Here, we studied the assembly of Thermotoga maritima MreB triggered by ATP in vitro and compared it to the well-studied assembly of actin. These studies show that MreB filament ultrastructure and polymerization depend crucially on temperature as well as the ions present on solution. At the optimal growth temperature of T. maritima, MreB assembly proceeded much faster than that of actin, without nucleation (or nucleation is highly favorable and fast) and with little or no contribution from filament end-to-end annealing. MreB exhibited rates of ATP hydrolysis and phosphate release similar to that of F-actin, however, with a critical concentration of approximately 3 nm, which is approximately 100-fold lower than that of actin. Furthermore, MreB assembled into filamentous bundles that have the ability to spontaneously form ring-like structures without auxiliary proteins. These findings suggest that despite high structural homology, MreB and actin display significantly different assembly properties.

Characterization of MreB polymers in E. coli and their correlations to cell shape

NASA Astrophysics Data System (ADS)

Nguyen, Jeffrey; Ouzonov, Nikolay; Gitai, Zemer; Shaevitz, Joshua

2015-03-01

Shape influences all facets of how bacteria interact with their environment. The size of E. coli is determined by the peptidoglycan cell wall and internal turgor pressure. The cell wall is patterned by MreB, an actin homolog that forms short polymers on the cytoplasmic membrane. MreB coordinates the breaking of old material and the insertion of new material for growth, but it is currently unknown what mechanism sets the absolute diameter of the cell. Using new techniques in fluorescence microscopy and image processing, we are able to quantify cell shape in 3- dimensions and access previously unattainable data on the conformation of MreB polymers. To study how MreB affects the diameter of bacteria, we analyzed the shapes and polymers of cells that have had MreB perturbed by one of two methods. We first treated cells with the MreB polymerization-inhibiting drug A22. Secondly, we created point mutants in MreB that change MreB polymer conformation and the cell shape. By analyzing the correlations between different shape and polymer metrics, we find that under both treatments, the average helical pitch angle of the polymers correlates strongly with the cell diameter. This observation links the micron scale shape of the cell to the nanometer scale MreB cytoskeleton.

MreB drives de novo rod morphogenesis in Caulobacter crescentus via remodeling of the cell wall.

PubMed

Takacs, Constantin N; Poggio, Sebastian; Charbon, Godefroid; Pucheault, Mathieu; Vollmer, Waldemar; Jacobs-Wagner, Christine

2010-03-01

MreB, the bacterial actin-like cytoskeleton, is required for the rod morphology of many bacterial species. Disruption of MreB function results in loss of rod morphology and cell rounding. Here, we show that the widely used MreB inhibitor A22 causes MreB-independent growth inhibition that varies with the drug concentration, culture medium conditions, and bacterial species tested. MP265, an A22 structural analog, is less toxic than A22 for growth yet equally efficient for disrupting the MreB cytoskeleton. The action of A22 and MP265 is enhanced by basic pH of the culture medium. Using this knowledge and the rapid reversibility of drug action, we examined the restoration of rod shape in lemon-shaped Caulobacter crescentus cells pretreated with MP265 or A22 under nontoxic conditions. We found that reversible restoration of MreB function after drug removal causes extensive morphological changes including a remarkable cell thinning accompanied with elongation, cell branching, and shedding of outer membrane vesicles. We also thoroughly characterized the composition of C. crescentus peptidoglycan by high-performance liquid chromatography and mass spectrometry and showed that MreB disruption and recovery of rod shape following restoration of MreB function are accompanied by considerable changes in composition. Our results provide insight into MreB function in peptidoglycan remodeling and rod shape morphogenesis and suggest that MreB promotes the transglycosylase activity of penicillin-binding proteins.

High Rate of Acquisition but Short Duration of Carriage of Multidrug-Resistant Enterobacteriaceae After Travel to the Tropics.

PubMed

Ruppé, Etienne; Armand-Lefèvre, Laurence; Estellat, Candice; Consigny, Paul-Henri; El Mniai, Assiya; Boussadia, Yacine; Goujon, Catherine; Ralaimazava, Pascal; Campa, Pauline; Girard, Pierre-Marie; Wyplosz, Benjamin; Vittecoq, Daniel; Bouchaud, Olivier; Le Loup, Guillaume; Pialoux, Gilles; Perrier, Marion; Wieder, Ingrid; Moussa, Nabila; Esposito-Farèse, Marina; Hoffmann, Isabelle; Coignard, Bruno; Lucet, Jean-Christophe; Andremont, Antoine; Matheron, Sophie

2015-08-15

Multidrug-resistant Enterobacteriaceae (MRE) are widespread in the community, especially in tropical regions. Travelers are at risk of acquiring MRE in these regions, but the precise extent of the problem is not known. From February 2012 to April 2013, travelers attending 6 international vaccination centers in the Paris area prior to traveling to tropical regions were asked to provide a fecal sample before and after their trip. Those found to have acquired MRE were asked to send fecal samples 1, 2, 3, 6, and 12 months after their return, or until MRE was no longer detected. The fecal relative abundance of MRE among all Enterobacteriaceae was determined in each carrier. Among 824 participating travelers, 574 provided fecal samples before and after travel and were not MRE carriers before departure. Of these, 292 (50.9%) acquired an average of 1.8 MRE. Three travelers (0.5%) acquired carbapenemase-producing Enterobacteriaceae. The acquisition rate was higher in Asia (142/196 [72.4%]) than in sub-Saharan Africa (93/195 [47.7%]) or Latin America (57/183 [31.1%]). MRE acquisition was associated with the type of travel, diarrhea, and exposure to β-lactams during the travel. Three months after return, 4.7% of the travelers carried MRE. Carriage lasted longer in travelers returning from Asia and in travelers with a high relative abundance of MRE at return. MRE acquisition is very frequent among travelers to tropical regions. Travel to these regions should be considered a risk factor of MRE carriage during the first 3 months after return, but not beyond. NCT01526187. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automated Liver Elasticity Calculation for 3D MRE

PubMed Central

Dzyubak, Bogdan; Glaser, Kevin J.; Manduca, Armando; Ehman, Richard L.

2017-01-01

Magnetic Resonance Elastography (MRE) is a phase-contrast MRI technique which calculates quantitative stiffness images, called elastograms, by imaging the propagation of acoustic waves in tissues. It is used clinically to diagnose liver fibrosis. Automated analysis of MRE is difficult as the corresponding MRI magnitude images (which contain anatomical information) are affected by intensity inhomogeneity, motion artifact, and poor tissue- and edge-contrast. Additionally, areas with low wave amplitude must be excluded. An automated algorithm has already been successfully developed and validated for clinical 2D MRE. 3D MRE acquires substantially more data and, due to accelerated acquisition, has exacerbated image artifacts. Also, the current 3D MRE processing does not yield a confidence map to indicate MRE wave quality and guide ROI selection, as is the case in 2D. In this study, extension of the 2D automated method, with a simple wave-amplitude metric, was developed and validated against an expert reader in a set of 57 patient exams with both 2D and 3D MRE. The stiffness discrepancy with the expert for 3D MRE was −0.8% ± 9.45% and was better than discrepancy with the same reader for 2D MRE (−3.2% ± 10.43%), and better than the inter-reader discrepancy observed in previous studies. There were no automated processing failures in this dataset. Thus, the automated liver elasticity calculation (ALEC) algorithm is able to calculate stiffness from 3D MRE data with minimal bias and good precision, while enabling stiffness measurements to be fully reproducible and to be easily performed on the large 3D MRE datasets. PMID:29033488

MRE11-deficiency associated with improved long-term disease free survival and overall survival in a subset of stage III colon cancer patients in randomized CALGB 89803 trial.

PubMed

Pavelitz, Thomas; Renfro, Lindsay; Foster, Nathan R; Caracol, Amber; Welsch, Piri; Lao, Victoria Valinluck; Grady, William B; Niedzwiecki, Donna; Saltz, Leonard B; Bertagnolli, Monica M; Goldberg, Richard M; Rabinovitch, Peter S; Emond, Mary; Monnat, Raymond J; Maizels, Nancy

2014-01-01

Colon cancers deficient in mismatch repair (MMR) may exhibit diminished expression of the DNA repair gene, MRE11, as a consequence of contraction of a T11 mononucleotide tract. This study investigated MRE11 status and its association with prognosis, survival and drug response in patients with stage III colon cancer. Cancer and Leukemia Group B 89803 (Alliance) randomly assigned 1,264 patients with stage III colon cancer to postoperative weekly adjuvant bolus 5-fluorouracil/leucovorin (FU/LV) or irinotecan+FU/LV (IFL), with 8 year follow-up. Tumors from these patients were analyzed to determine stability of a T11 tract in the MRE11 gene. The primary endpoint was overall survival (OS), and a secondary endpoint was disease-free survival (DFS). Non-proportional hazards were addressed using time-dependent covariates in Cox analyses. Of 625 tumor cases examined, 70 (11.2%) exhibited contraction at the T11 tract in one or both MRE11 alleles and were thus predicted to be deficient in MRE11 (dMRE11). In pooled treatment analyses, dMRE11 patients showed initially reduced DFS and OS but improved long-term DFS and OS compared with patients with an intact MRE11 T11 tract. In the subgroup of dMRE11 patients treated with IFL, an unexplained early increase in mortality but better long-term DFS than IFL-treated pMRE11 patients was observed. Analysis of this relatively small number of patients and events showed that the dMRE11 marker predicts better prognosis independent of treatment in the long-term. In subgroup analyses, dMRE11 patients treated with irinotecan exhibited unexplained short-term mortality. MRE11 status is readily assayed and may therefore prove to be a useful prognostic marker, provided that the results reported here for a relatively small number of patients can be generalized in independent analyses of larger numbers of samples. ClinicalTrials.gov NCT00003835.

MRE11-Deficiency Associated with Improved Long-Term Disease Free Survival and Overall Survival in a Subset of Stage III Colon Cancer Patients in Randomized CALGB 89803 Trial

PubMed Central

Pavelitz, Thomas; Renfro, Lindsay; Foster, Nathan R.; Caracol, Amber; Welsch, Piri; Lao, Victoria Valinluck; Grady, William B.; Niedzwiecki, Donna; Saltz, Leonard B.; Bertagnolli, Monica M.; Goldberg, Richard M.; Rabinovitch, Peter S.; Emond, Mary; Monnat, Raymond J.; Maizels, Nancy

2014-01-01

Purpose Colon cancers deficient in mismatch repair (MMR) may exhibit diminished expression of the DNA repair gene, MRE11, as a consequence of contraction of a T11 mononucleotide tract. This study investigated MRE11 status and its association with prognosis, survival and drug response in patients with stage III colon cancer. Patients and Methods Cancer and Leukemia Group B 89803 (Alliance) randomly assigned 1,264 patients with stage III colon cancer to postoperative weekly adjuvant bolus 5-fluorouracil/leucovorin (FU/LV) or irinotecan+FU/LV (IFL), with 8 year follow-up. Tumors from these patients were analyzed to determine stability of a T11 tract in the MRE11 gene. The primary endpoint was overall survival (OS), and a secondary endpoint was disease-free survival (DFS). Non-proportional hazards were addressed using time-dependent covariates in Cox analyses. Results Of 625 tumor cases examined, 70 (11.2%) exhibited contraction at the T11 tract in one or both MRE11 alleles and were thus predicted to be deficient in MRE11 (dMRE11). In pooled treatment analyses, dMRE11 patients showed initially reduced DFS and OS but improved long-term DFS and OS compared with patients with an intact MRE11 T11 tract. In the subgroup of dMRE11 patients treated with IFL, an unexplained early increase in mortality but better long-term DFS than IFL-treated pMRE11 patients was observed. Conclusions Analysis of this relatively small number of patients and events showed that the dMRE11 marker predicts better prognosis independent of treatment in the long-term. In subgroup analyses, dMRE11 patients treated with irinotecan exhibited unexplained short-term mortality. MRE11 status is readily assayed and may therefore prove to be a useful prognostic marker, provided that the results reported here for a relatively small number of patients can be generalized in independent analyses of larger numbers of samples. Trial Registration ClinicalTrials.gov NCT00003835 PMID:25310185

Assembly properties of the Bacillus subtilis actin, MreB.

PubMed

Mayer, Joshua A; Amann, Kurt J

2009-02-01

The bacterial actin MreB has been implicated in a variety of cellular roles including cell shape determination, cell wall synthesis, chromosome condensation and segregation, and the establishment and maintenance of cell polarity. Toward elucidating a clearer understanding of how MreB functions inside the bacterial cell, we investigated biochemically the polymerization of MreB from Bacillus subtilis. Light scattering and sedimentation assays revealed pH-, ionic-, cationic-, and temperature-dependent behavior. B. subtilis MreB polymerizes in the presence of millimolar divalent cations in a protein concentration-dependent manner. Polymerization is favored by decreasing pH and inhibited by monovalent salts and low temperatures. Although B. subtilis MreB binds and hydrolyzes both ATP and GTP, it does not require a bound nucleotide for assembly and polymerizes indistinguishably regardless of the nucleotide species bound, with a critical concentration of approximately 900 nM. A number of the presently reported properties of B. subtilis MreB differ significantly from those of T. maritima MreB1 (Bean and Amann [2008]: Biochemistry 47: 826-835), including the nucleotide requirements and temperature and ionic effects on polymerization state. These observations collectively suggest that additional factors interact with MreB to account for its complex dynamic behavior in cells.

Vibration safety limits for magnetic resonance elastography.

PubMed

Ehman, E C; Rossman, P J; Kruse, S A; Sahakian, A V; Glaser, K J

2008-02-21

Magnetic resonance elastography (MRE) has been demonstrated to have potential as a clinical tool for assessing the stiffness of tissue in vivo. An essential step in MRE is the generation of acoustic mechanical waves within a tissue via a coupled mechanical driver. Motivated by an increasing volume of human imaging trials using MRE, the objectives of this study were to audit the vibration amplitude of exposure for our IRB-approved human MRE studies, to compare these values to a conservative regulatory standard for vibrational exposure and to evaluate the applicability and implications of this standard for MRE. MRE displacement data were examined from 29 MRE exams, including the liver, brain, kidney, breast and skeletal muscle. Vibrational acceleration limits from a European Union directive limiting occupational exposure to whole-body and extremity vibrations (EU 2002/44/EC) were adjusted for time and frequency of exposure, converted to maximum displacement values and compared to the measured in vivo displacements. The results indicate that the vibrational amplitudes used in MRE studies are below the EU whole-body vibration limit, and the EU guidelines represent a useful standard that could be readily accepted by Institutional Review Boards to define standards for vibrational exposures for MRE studies in humans.

Vibration safety limits for magnetic resonance elastography

PubMed Central

Ehman, E C; Rossman, P J; Kruse, S A; Sahakian, A V; Glaser, K J

2010-01-01

Magnetic resonance elastography (MRE) has been demonstrated to have potential as a clinical tool for assessing the stiffness of tissue in vivo. An essential step in MRE is the generation of acoustic mechanical waves within tissue via a coupled mechanical driver. Motivated by an increasing volume of human imaging trials using MRE, the objectives of this study were to audit the vibration amplitude of exposure for our IRB-approved human MRE studies, to compare these values to a conservative regulatory standard for vibrational exposure, and to evaluate the applicability and implications of this standard for MRE. MRE displacement data were examined from 29 MRE exams, including the liver, brain, kidney, breast, and skeletal muscle. Vibrational acceleration limits from a European Union directive limiting occupational exposure to whole-body and extremity vibrations (EU 2002/44/EC) were adjusted for time and frequency of exposure, converted to maximum displacement values, and compared to the measured in vivo displacements. The results indicate that the vibrational amplitudes used in MRE studies are below the EU whole-body vibration limit and the EU guidelines represent a useful standard that could be readily accepted by Institutional Review Boards to define standards for vibrational exposures for MRE studies in humans. PMID:18263949

Association Between Obesity and Discordance in Fibrosis Stage Determination by Magnetic Resonance vs Transient Elastography in Patients With Nonalcoholic Liver Disease.

PubMed

Caussy, Cyrielle; Chen, Jun; Alquiraish, Mosab H; Cepin, Sandra; Nguyen, Phirum; Hernandez, Carolyn; Yin, Meng; Bettencourt, Ricki; Cachay, Edward R; Jayakumar, Saumya; Fortney, Lynda; Hooker, Jonathan; Sy, Ethan; Valasek, Mark A; Rizo, Emily; Richards, Lisa; Brenner, David A; Sirlin, Claude B; Ehman, Richard L; Loomba, Rohit

2018-01-17

Magnetic resonance elastography (MRE) and transient elastography (TE) are noninvasive techniques used to detect liver fibrosis in nonalcoholic fatty liver disease. MRE detects fibrosis more accurately than TE, but MRE is more expensive, and the concordance between MRE and TE have not been optimally assessed in obese patients. It is important to determine under which conditions TE and MRE produce the same readings, so that some patients can simply undergo TE evaluation to detect fibrosis. We aimed to assess the association between body mass index (BMI) and discordancy between MRE and TE findings, using liver biopsy as the reference, and validated our findings in a separate cohort. We performed a cross-sectional study of 119 adults with nonalcoholic fatty liver disease who underwent MRE, TE with M and XL probe, and liver biopsy analysis from October 2011 through January 2017 (training cohort). MRE and TE results were considered to be concordant if they found patients to have the same stage fibrosis as liver biopsy analysis. We validated our findings in 75 adults with nonalcoholic fatty liver disease who underwent contemporaneous MRE, TE, and liver biopsy at a separate institution from March 2010 through May 2013. The primary outcome was rate of discordance between MRE and TE in determining stage of fibrosis (stage 2-4 vs 0-1). Secondary outcomes were the rate of discordance between MRE and TE in determining dichotomized stage of fibrosis (1-4 vs 0, 3-4 vs 0-2, and 4 vs 0-3). In the training cohort, there was 43.7% discordance in findings from MRE versus TE. BMI associated significantly with discordance in findings from MRE versus TE (odds ratio, 1.69; 95% confidence interval, 1.15-2.51; P = .008) after multivariable adjustment by age and sex. The findings were confirmed in the validation cohort: there was 45.3% discordance in findings from MRE versus TE. BMI again associated significantly with discordance in findings from MRE versus TE (odds ratio, 1.52; 95% confidence interval, 1.04-2.21; P = .029) after multivariable adjustment by age and sex. We identified and validated BMI as a factor significantly associated with discordance of findings from MRE versus TE in assessment of fibrosis stage. The degree of discordancy increases with BMI. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

Differential conformational modulations of MreB folding upon interactions with GroEL/ES and TRiC chaperonin components

PubMed Central

Moparthi, Satish Babu; Carlsson, Uno; Vincentelli, Renaud; Jonsson, Bengt-Harald; Hammarström, Per; Wenger, Jérôme

2016-01-01

Here, we study and compare the mechanisms of action of the GroEL/GroES and the TRiC chaperonin systems on MreB client protein variants extracted from E. coli. MreB is a homologue to actin in prokaryotes. Single-molecule fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence polarization anisotropy report the binding interaction of folding MreB with GroEL, GroES and TRiC. Fluorescence resonance energy transfer (FRET) measurements on MreB variants quantified molecular distance changes occurring during conformational rearrangements within folding MreB bound to chaperonins. We observed that the MreB structure is rearranged by a binding-induced expansion mechanism in TRiC, GroEL and GroES. These results are quantitatively comparable to the structural rearrangements found during the interaction of β-actin with GroEL and TRiC, indicating that the mechanism of chaperonins is conserved during evolution. The chaperonin-bound MreB is also significantly compacted after addition of AMP-PNP for both the GroEL/ES and TRiC systems. Most importantly, our results showed that GroES may act as an unfoldase by inducing a dramatic initial expansion of MreB (even more than for GroEL) implicating a role for MreB folding, allowing us to suggest a delivery mechanism for GroES to GroEL in prokaryotes. PMID:27328749

Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis.

PubMed

Garner, Ethan C; Bernard, Remi; Wang, Wenqin; Zhuang, Xiaowei; Rudner, David Z; Mitchison, Tim

2011-07-08

Rod-shaped bacteria elongate by the action of cell wall synthesis complexes linked to underlying dynamic MreB filaments. To understand how the movements of these filaments relate to cell wall synthesis, we characterized the dynamics of MreB and the cell wall elongation machinery using high-precision particle tracking in Bacillus subtilis. We found that MreB and the elongation machinery moved circumferentially around the cell, perpendicular to its length, with nearby synthesis complexes and MreB filaments moving independently in both directions. Inhibition of cell wall synthesis by various methods blocked the movement of MreB. Thus, bacteria elongate by the uncoordinated, circumferential movements of synthetic complexes that insert radial hoops of new peptidoglycan during their transit, possibly driving the motion of the underlying MreB filaments.

Steady-state configurations and dynamics of the MreB helix within bacteria

NASA Astrophysics Data System (ADS)

Rutenberg, Andrew; Allard, Jun

2007-03-01

We present a quantitative model of the actin-like MreB cytoskeleton that is present in many prokaryotes. Individual MreB polymers are bundled into a supra-molecular array to make up helical cables. The cell wall imposes constraint forces through a global elasticity model. With variational techniques and stochastic simulations we obtain relationships between observable quantities such as the pitch of the helix, the total abundance of MreB molecules, and the thickness of the MreB cables. We address changes expected with slow cell growth, as well as turnover dynamics that are relevant to FRAP studies. We also address polarized macromolecular trafficking along the MreB cables without motor proteins.

MreB: pilot or passenger of cell wall synthesis?

PubMed

White, Courtney L; Gober, James W

2012-02-01

The discovery that the bacterial cell shape determinant MreB is related to actin spurred new insights into bacterial morphogenesis and development. The trafficking and mechanical roles of the eukaryotic cytoskeleton were hypothesized to have a functional ancestor in MreB based on evidence implicating MreB as an organizer of cell wall synthesis. Genetic, biochemical and cytological studies implicate MreB as a coordinator of a large multi-protein peptidoglycan (PG) synthesizing holoenzyme. Recent advances in microscopy and new biochemical evidence, however, suggest that MreB may function differently than previously envisioned. This review summarizes our evolving knowledge of MreB and attempts to refine the generalized model of the proteins organizing PG synthesis in bacteria. This is generally thought to be conserved among eubacteria and the majority of the discussion will focus on studies from a few well-studied model organisms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bacterial actin MreB forms antiparallel double filaments

PubMed Central

van den Ent, Fusinita; Izoré, Thierry; Bharat, Tanmay AM; Johnson, Christopher M; Löwe, Jan

2014-01-01

Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments. DOI: http://dx.doi.org/10.7554/eLife.02634.001 PMID:24843005

Bacterial actin MreB forms antiparallel double filaments.

PubMed

van den Ent, Fusinita; Izoré, Thierry; Bharat, Tanmay Am; Johnson, Christopher M; Löwe, Jan

2014-05-02

Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments.DOI: http://dx.doi.org/10.7554/eLife.02634.001. Copyright © 2014, van den Ent et al.

Quantification, validation, and follow-up of small bowel motility in Crohn's disease

NASA Astrophysics Data System (ADS)

Cerrolaza, Juan J.; Peng, Jennifer Q.; Safdar, Nabile M.; Conklin, Laurie; Sze, Raymond; Linguraru, Marius George

2015-03-01

The use of magnetic resonance enterography (MRE) has become a mainstay in the evaluation, assessment and follow up of inflammatory bowel diseases, such as Crohn's disease (CD), thanks to its high image quality and its non-ionizing nature. In particular, the advent of faster MRE sequences less sensitive to image-motion artifacts offers the possibility to obtain visual, structural and functional information of the patient's small bowel. However, the inherent subjectivity of the mere visual inspection of these images often hinders the accurate identification and monitoring of the pathological areas. In this paper, we present a framework that provides quantitative and objective motility information of the small bowel from free-breathing MRE dynamic sequences. After compensating for the breathing motion of the patient, we create personalized peristaltic activity maps via optical flow analysis. The result is the creation of a new set of images providing objective and precise functional information of the small bowel. The accuracy of the new method was also evaluated from two different perspectives: objective accuracy (1.1 ± 0.6 mm/s of error), i.e., the ability of the system to provide quantitative and accurate information about the motility of moving bowel landmarks, and subjective accuracy (avg. difference of 0.7 ± 0.7 in a range of 1 to 5), i.e., the degree of agreement with the subjective evaluation of an expert. Finally, the practical utility of the new method was successfully evaluated in a preliminary study with 32 studies of healthy and CD cases, showing its potential for the fast and accurate assessment and follow up of CD in the small bowel.

Exploring the A22-Bacterial Actin MreB Interaction through Molecular Dynamics Simulations.

PubMed

Awuni, Yaw; Jiang, Shimin; Robinson, Robert C; Mu, Yuguang

2016-09-22

MreB is an actin-like cytoskeleton protein that plays a vital role in the maintenance of the rod-shaped morphology of many bacteria. S-(3,4-Dichlorobenzyl) isothiourea (A22) is an antibiotic-like small molecule that perturbs the rod cell shape and has been suggested to inhibit MreB by targeting ATP hydrolysis. However, without the elucidation of the structure of the ATP-bound state of MreB in the presence of A22, the mechanism of A22 inhibition is still not clear. Here we apply conventional molecular dynamics simulations to explore the dynamics of the active site of MreB in complex with A22 and different nucleotides. We observe that hydrogen bonding between A22 and the catalytic Glu140 residue is not favored in the ATP-A22-bound state of MreB. Water dynamics analysis in the MreB active site reveals that in the presence of A22 water molecules are able to occupy positions suitable for ATP hydrolysis. Overall, our results are consistent with a mechanism in which A22 affects MreB polymerization/depolymerization dynamics in part through slowing phosphate release rather than by inhibiting ATP hydrolysis. These data can be incorporated in the design/development of the next generation of MreB inhibitors.

Filament structure, organization, and dynamics in MreB sheets.

PubMed

Popp, David; Narita, Akihiro; Maeda, Kayo; Fujisawa, Tetsuro; Ghoshdastider, Umesh; Iwasa, Mitsusada; Maéda, Yuichiro; Robinson, Robert C

2010-05-21

In vivo fluorescence microscopy studies of bacterial cells have shown that the bacterial shape-determining protein and actin homolog, MreB, forms cable-like structures that spiral around the periphery of the cell. The molecular structure of these cables has yet to be established. Here we show by electron microscopy that Thermatoga maritime MreB forms complex, several mum long multilayered sheets consisting of diagonally interwoven filaments in the presence of either ATP or GTP. This architecture, in agreement with recent rheological measurements on MreB cables, may have superior mechanical properties and could be an important feature for maintaining bacterial cell shape. MreB polymers within the sheets appear to be single-stranded helical filaments rather than the linear protofilaments found in the MreB crystal structure. Sheet assembly occurs over a wide range of pH, ionic strength, and temperature. Polymerization kinetics are consistent with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation. Steady-state TIRF microscopy studies of MreB suggest filament treadmilling while high pressure small angle x-ray scattering measurements indicate that the stability of MreB polymers is similar to that of F-actin filaments. In the presence of ADP or GDP, long, thin cables formed in which MreB was arranged in parallel as linear protofilaments. This suggests that the bacterial cell may exploit various nucleotides to generate different filament structures within cables for specific MreB-based functions.

Quantification of Regional Aortic Stiffness Using MR Elastography: A Phantom and Ex-vivo Porcine Aorta Study

PubMed Central

Zhang, Nan; Chen, Jun; Yin, Meng; Glaser, Kevin J.; Xu, Lei; Ehman, Richard L.

2015-01-01

MR Elastography (MRE) is a noninvasive technique for measuring tissue stiffness that has been used to assess the average stiffness of the abdominal aorta. The utility of aortic MRE would be improved if it could provide information about local variations in aortic stiffness. We hypothesize that regional variations in aortic stiffness can also be measured with MRE and the purpose of this work was to demonstrate that MRE can measure regional stiffness variations in a vascular phantom and in ex vivo porcine aortas. A vascular phantom was fabricated, containing two silicone tubes embedded in gel. A segment of one of the tubes was modified to increase its stiffness. MRE was performed on the phantom with a continuous flow of water through the tubes. The stiffness distribution along the modified tube was measured and compared to the reference tube. MRE was also performed in porcine aortas embedded in gel with segments treated with saline or formalin for 4 days. The stiffness difference between saline- and formalin-treated aortic segments was measured by MRE and mechanical tests. A positive correlation was found between the regional stiffnesses measured by MRE and mechanical tests. The results indicate that MRE can be used to evaluate the local stiffness distribution in silicone tubes and ex vivo porcine aortas. It may therefore be possible to apply MRE to measure regional stiffness variations of the aorta in vivo. PMID:26597836

mre11S—a yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis

PubMed Central

Nairz, Knud; Klein, Franz

1997-01-01

During meiotic prophase the repair of self-inflicted DNA double-strand break (DSB) damage leads to meiotic recombination in yeast. We employed a genetic screen to specifically characterize cellular functions that become essential after this DSB formation. As a result a new allele of MRE11, termed mre11S (for Separation of functions) was isolated that allows initiation but not processing and repair of meiotic DSBs similar to the well-characterized rad50S allele. In contrast, the mre11-1 allele blocks initiation of meiotic DSBs as reported previously by others. The mre11S allele, which is mutated in the 5′ part of the gene, can partially complement mre11 alleles disrupted close to the 3′ end that cannot initiate DSBs when homozygous. This suggests homodimerization of the Mre11 protein and the presence of separate domains for DSB initiation and 5′ resection. The fact that two genes, RAD50 and MRE11, required for DSB processing are also essential for DSB initiation dictates a model in which a bifunctional initiation/repair complex is required to initiate meiotic recombination. A subset of mre11S nuclei was shown to perform extensive but partially nonhomologous synapsis. We propose that the unprocessed DSBs present in mre11S allow for synapsis, but that homologous synapsis is only ensured at a later stage of recombination. PMID:9303542

Magnetic resonance enterography has good inter-rater agreement and diagnostic accuracy for detecting inflammation in pediatric Crohn disease.

PubMed

Church, Peter C; Greer, Mary-Louise C; Cytter-Kuint, Ruth; Doria, Andrea S; Griffiths, Anne M; Turner, Dan; Walters, Thomas D; Feldman, Brian M

2017-05-01

Magnetic resonance enterography (MRE) is increasingly relied upon for noninvasive assessment of intestinal inflammation in Crohn disease. However very few studies have examined the diagnostic accuracy of individual MRE signs in children. We have created an MR-based multi-item measure of intestinal inflammation in children with Crohn disease - the Pediatric Inflammatory Crohn's MRE Index (PICMI). To inform item selection for this instrument, we explored the inter-rater agreement and diagnostic accuracy of individual MRE signs of inflammation in pediatric Crohn disease and compared our findings with the reference standards of the weighted Pediatric Crohn's Disease Activity Index (wPCDAI) and C-reactive protein (CRP). In this cross-sectional single-center study, MRE studies in 48 children with diagnosed Crohn disease (66% male, median age 15.5 years) were reviewed by two independent radiologists for the presence of 15 MRE signs of inflammation. Using kappa statistics we explored inter-rater agreement for each MRE sign across 10 anatomical segments of the gastrointestinal tract. We correlated MRE signs with the reference standards using correlation coefficients. Radiologists measured the length of inflamed bowel in each segment of the gastrointestinal tract. In each segment, MRE signs were scored as either binary (0-absent, 1-present), or ordinal (0-absent, 1-mild, 2-marked). These segmental scores were weighted by the length of involved bowel and were summed to produce a weighted score per patient for each MRE sign. Using a combination of wPCDAI≥12.5 and CRP≥5 to define active inflammation, we calculated area under the receiver operating characteristic curve (AUC) for each weighted MRE sign. Bowel wall enhancement, wall T2 hyperintensity, wall thickening and wall diffusion-weighted imaging (DWI) hyperintensity were most commonly identified. Inter-rater agreement was best for decreased motility and wall DWI hyperintensity (kappa≥0.64). Correlation between MRE signs and wPCDAI was higher than with CRP. AUC was highest (≥0.75) for ulcers, wall enhancement, wall thickening, wall T2 hyperintensity and wall DWI hyperintensity. Some MRE signs had good inter-rater agreement and AUC for detection of inflammation in children with Crohn disease.

YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl.

PubMed

Duan, Yi; Sperber, Anthony M; Herman, Jennifer K

2016-08-01

Many bacteria utilize actin-like proteins to direct peptidoglycan (PG) synthesis. MreB and MreB-like proteins are thought to act as scaffolds, guiding the localization and activity of key PG-synthesizing proteins during cell elongation. Despite their critical role in viability and cell shape maintenance, very little is known about how the activity of MreB family proteins is regulated. Using a Bacillus subtilis misexpression screen, we identified two genes, yodL and yisK, that when misexpressed lead to loss of cell width control and cell lysis. Expression analysis suggested that yodL and yisK are previously uncharacterized Spo0A-regulated genes, and consistent with these observations, a ΔyodL ΔyisK mutant exhibited reduced sporulation efficiency. Suppressors resistant to YodL's killing activity occurred primarily in mreB mutants and resulted in amino acid substitutions at the interface between MreB and the highly conserved morphogenic protein RodZ, whereas suppressors resistant to YisK occurred primarily in mbl mutants and mapped to Mbl's predicted ATP-binding pocket. YodL's shape-altering activity appears to require MreB, as a ΔmreB mutant was resistant to the effects of YodL but not YisK. Similarly, YisK appears to require Mbl, as a Δmbl mutant was resistant to the cell-widening effects of YisK but not of YodL. Collectively, our results suggest that YodL and YisK likely modulate MreB and Mbl activity, possibly during the early stages of sporulation. The peptidoglycan (PG) component of the cell envelope confers structural rigidity to bacteria and protects them from osmotic pressure. MreB and MreB-like proteins are thought to act as scaffolds for PG synthesis and are essential in bacteria exhibiting nonpolar growth. Despite the critical role of MreB-like proteins, we lack mechanistic insight into how their activities are regulated. Here, we describe the discovery of two B. subtilis proteins, YodL and YisK, which modulate MreB and Mbl activities. Our data suggest that YodL specifically targets MreB, whereas YisK targets Mbl. The apparent specificities with which YodL and YisK are able to differentially target MreB and Mbl make them potentially powerful tools for probing the mechanics of cytoskeletal function in bacteria. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl

PubMed Central

Duan, Yi; Sperber, Anthony M.

2016-01-01

ABSTRACT Many bacteria utilize actin-like proteins to direct peptidoglycan (PG) synthesis. MreB and MreB-like proteins are thought to act as scaffolds, guiding the localization and activity of key PG-synthesizing proteins during cell elongation. Despite their critical role in viability and cell shape maintenance, very little is known about how the activity of MreB family proteins is regulated. Using a Bacillus subtilis misexpression screen, we identified two genes, yodL and yisK, that when misexpressed lead to loss of cell width control and cell lysis. Expression analysis suggested that yodL and yisK are previously uncharacterized Spo0A-regulated genes, and consistent with these observations, a ΔyodL ΔyisK mutant exhibited reduced sporulation efficiency. Suppressors resistant to YodL's killing activity occurred primarily in mreB mutants and resulted in amino acid substitutions at the interface between MreB and the highly conserved morphogenic protein RodZ, whereas suppressors resistant to YisK occurred primarily in mbl mutants and mapped to Mbl's predicted ATP-binding pocket. YodL's shape-altering activity appears to require MreB, as a ΔmreB mutant was resistant to the effects of YodL but not YisK. Similarly, YisK appears to require Mbl, as a Δmbl mutant was resistant to the cell-widening effects of YisK but not of YodL. Collectively, our results suggest that YodL and YisK likely modulate MreB and Mbl activity, possibly during the early stages of sporulation. IMPORTANCE The peptidoglycan (PG) component of the cell envelope confers structural rigidity to bacteria and protects them from osmotic pressure. MreB and MreB-like proteins are thought to act as scaffolds for PG synthesis and are essential in bacteria exhibiting nonpolar growth. Despite the critical role of MreB-like proteins, we lack mechanistic insight into how their activities are regulated. Here, we describe the discovery of two B. subtilis proteins, YodL and YisK, which modulate MreB and Mbl activities. Our data suggest that YodL specifically targets MreB, whereas YisK targets Mbl. The apparent specificities with which YodL and YisK are able to differentially target MreB and Mbl make them potentially powerful tools for probing the mechanics of cytoskeletal function in bacteria. PMID:27215790

Between-Meal Food Intake for Reservists Training in the Field

DTIC Science & Technology

1989-04-06

GUM, MRE MR6816 58 HAM/CHICKEN LOAF, MRE MR6302 13 JELLY, MRE MR6903 45 MAPLE NUT CAKE, MRE MR6805 23 MEATBALLS W/BBQ SAUCE, MRE MR6310 28 PEACHES...0530-1630 HR) (cont’d) FOOD ITEM FREQUENCY DEVILED HAM 5 DINNER ROLL 1 DONUT, FILLED, PLAIN 4 DRESSING, ASST, REG 10 EGG , BOILED or SCRAMBLED 4 FRUIT...MARGARINE, PATTIE 1 MCDONALD’S SAUSAGE & EGG MCMUFFIN 1 MELBA TOAST, 1 PIECE 4 MILK, CHOCOLATE, UHT 9 MILK, WHITE, UHT 2% 18 MILK, SKIM, PROTEIN 3 18 BETWEEN

Duplication and segregation of the actin (MreB) cytoskeleton during the prokaryotic cell cycle.

PubMed

Vats, Purva; Rothfield, Lawrence

2007-11-06

The bacterial actin homolog MreB exists as a single-copy helical cytoskeletal structure that extends between the two poles of rod-shaped bacteria. In this study, we show that equipartition of the MreB cytoskeleton into daughter cells is accomplished by division and segregation of the helical MreB array into two equivalent structures located in opposite halves of the predivisional cell. This process ensures that each daughter cell inherits one copy of the MreB cytoskeleton. The process is triggered by the membrane association of the FtsZ cell division protein. The cytoskeletal division and segregation events occur before and independently of cytokinesis and involve specialized MreB structures that appear to be intermediates in this process.

Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria.

PubMed

Domínguez-Escobar, Julia; Chastanet, Arnaud; Crevenna, Alvaro H; Fromion, Vincent; Wedlich-Söldner, Roland; Carballido-López, Rut

2011-07-08

The peptidoglycan cell wall and the actin-like MreB cytoskeleton are major determinants of cell shape in rod-shaped bacteria. The prevailing model postulates that helical, membrane-associated MreB filaments organize elongation-specific peptidoglycan-synthesizing complexes along sidewalls. We used total internal reflection fluorescence microscopy to visualize the dynamic relation between MreB isoforms and cell wall synthesis in live Bacillus subtilis cells. During exponential growth, MreB proteins did not form helical structures. Instead, together with other morphogenetic factors, they assembled into discrete patches that moved processively along peripheral tracks perpendicular to the cell axis. Patch motility was largely powered by cell wall synthesis, and MreB polymers restricted diffusion of patch components in the membrane and oriented patch motion.

A22 disrupts the bacterial actin cytoskeleton by directly binding and inducing a low-affinity state in MreB.

PubMed

Bean, G J; Flickinger, S T; Westler, W M; McCully, M E; Sept, D; Weibel, D B; Amann, K J

2009-06-09

S-(3,4-Dichlorobenzyl)isothiourea (A22) disrupts the actin cytoskeleton of bacteria, causing defects of morphology and chromosome segregation. Previous studies have suggested that the actin homologue MreB itself is the target of A22, but there has been no direct observation of A22 binding to MreB and no mechanistic explanation of its mode of action. We show that A22 binds MreB with at least micromolar affinity in its nucleotide-binding pocket in a manner that is sterically incompatible with simultaneous ATP binding. A22 negatively affects both the time course and extent of MreB polymerization in vitro in the presence of ATP. A22 prevents assembly of MreB into long, rigid polymers, as determined by both fluorescence microscopy and sedimentation assays. A22 increases the critical concentration of ATP-bound MreB assembly from 500 nM to approximately 2000 nM. We therefore conclude that A22 is a competitive inhibitor of ATP binding to MreB. A22-bound MreB is capable of polymerization, but with assembly properties that more closely resemble those of the ADP-bound state. Because the cellular concentration of MreB is in the low micromolar range, this mechanism explains the ability of A22 to largely disassemble the actin cytoskeleton in bacterial cells. It also represents a novel mode of action for a cytoskeletal drug and the first biochemical characterization of the interaction between a small molecule inhibitor of the bacterial cytoskeleton and its target.

Detecting inflammation in inflammatory bowel disease - how does ultrasound compare to magnetic resonance enterography using standardised scoring systems?

PubMed

Barber, Joy L; Zambrano-Perez, Alexsandra; Olsen, Øystein E; Kiparissi, Fevronia; Baycheva, Mila; Knaflez, Daniela; Shah, Neil; Watson, Tom A

2018-06-01

Magnetic resonance enterography (MRE) is the current gold standard for imaging in inflammatory bowel disease, but ultrasound (US) is a potential alternative. To determine whether US is as good as MRE for the detecting inflamed bowel, using a combined consensus score as the reference standard. We conducted a retrospective cohort study in children and adolescents <18 years with inflammatory bowel disease (IBD) at a tertiary and quaternary centre. We included children who underwent MRE and US within 4 weeks. We scored MRE using the London score and US using a score adapted from the METRIC (MR Enterography or Ultrasound in Crohn's Disease) trial. Four gastroenterologists assessed an independent clinical consensus score. A combined consensus score using the imaging and clinical scores was agreed upon and used as the reference standard to compare MRE with US. We included 53 children. At a whole-patient level, MRE scores were 2% higher than US scores. We used Lin coefficient to assess inter-observer variability. The repeatability of MRE scores was poor (Lin 0.6). Agreement for US scoring was substantial (Lin 0.95). There was a significant positive correlation between MRE and clinical consensus scores (Spearman's rho = 0.598, P=0.0053) and US and clinical consensus scores (Spearman's rho = 0.657, P=0.0016). US detects as much clinically significant bowel disease as MRE. It is possible that MRE overestimates the presence of disease when using a scoring system. This study demonstrates the feasibility of using a clinical consensus reference standard in paediatric IBD imaging studies.

CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae.

PubMed

Fenton, Andrew K; El Mortaji, Lamya; Lau, Derek T C; Rudner, David Z; Bernhardt, Thomas G

2016-12-12

Most bacterial cells are surrounded by a peptidoglycan cell wall that is essential for their integrity. The major synthases of this exoskeleton are called penicillin-binding proteins (PBPs) 1,2 . Surprisingly little is known about how cells control these enzymes, given their importance as drug targets. In the model Gram-negative bacterium Escherichia coli, outer membrane lipoproteins are critical activators of the class A PBPs (aPBPs) 3,4 , bifunctional synthases capable of polymerizing and crosslinking peptidoglycan to build the exoskeletal matrix 1 . Regulators of PBP activity in Gram-positive bacteria have yet to be discovered but are likely to be distinct due to the absence of an outer membrane. To uncover Gram-positive PBP regulatory factors, we used transposon-sequencing (Tn-Seq) 5 to screen for mutations affecting the growth of Streptococcus pneumoniae cells when the aPBP synthase PBP1a was inactivated. Our analysis revealed a set of genes that were essential for growth in wild-type cells yet dispensable when pbp1a was deleted. The proteins encoded by these genes include the conserved cell wall elongation factors MreC and MreD 2,6,7 , as well as a membrane protein of unknown function (SPD_0768) that we have named CozE (coordinator of zonal elongation). Our results indicate that CozE is a member of the MreCD complex of S. pneumoniae that directs the activity of PBP1a to the midcell plane where it promotes zonal cell elongation and normal morphology. CozE homologues are broadly distributed among bacteria, suggesting that they represent a widespread family of morphogenic proteins controlling cell wall biogenesis by the PBPs.

Novel protein interactions with an actin homolog (MreB) of Helicobacter pylori determined by bacterial two-hybrid system.

PubMed

Zepeda Gurrola, Reyna Cristina; Fu, Yajuan; Rodríguez Luna, Isabel Cristina; Benítez Cardoza, Claudia Guadalupe; López López, María de Jesús; López Vidal, Yolanda; Gutíerrez, Germán Rubén Aguilar; Rodríguez Pérez, Mario A; Guo, Xianwu

2017-08-01

The bacterium Helicobacter pylori infects more than 50% of the world population and causes several gastroduodenal diseases, including gastric cancer. Nevertheless, we still need to explore some protein interactions that may be involved in pathogenesis. MreB, an actin homolog, showed some special characteristics in previous studies, indicating that it could have different functions. Protein functions could be realized via protein-protein interactions. In the present study, the MreB protein from H. pylori 26695 fused with two tags 10×His and GST in tandem was overexpressed and purified from Escherchia coli. The purified recombinant protein was used to perform a pull-down assay with H. pylori 26695 cell lysate. The pulled-down proteins were identified by mass spectrometry (MALDI-TOF), in which the known important proteins related to morphogenesis were absent but several proteins related to pathogenesis process were observed. The bacterial two-hybrid system was further used to evaluate the protein interactions and showed that new interactions of MreB respectively with VacA, UreB, HydB, HylB and AddA were confirmed but the interaction MreB-MreC was not validated. These results indicated that the protein MreB in H. pylori has a distinct interactome, does not participate in cell morphogenesis via MreB-MreC but could be related to pathogenesis. Copyright © 2017 Elsevier GmbH. All rights reserved.

Mutations in the nucleotide binding pocket of MreB can alter cell curvature and polar morphology in Caulobacter.

PubMed

Dye, Natalie A; Pincus, Zachary; Fisher, Isabelle C; Shapiro, Lucy; Theriot, Julie A

2011-07-01

The maintenance of cell shape in Caulobacter crescentus requires the essential gene mreB, which encodes a member of the actin superfamily and the target of the antibiotic, A22. We isolated 35 unique A22-resistant Caulobacter strains with single amino acid substitutions near the nucleotide binding site of MreB. Mutations that alter cell curvature and mislocalize the intermediate filament crescentin cluster on the back surface of MreB's structure. Another subset have variable cell widths, with wide cell bodies and actively growing thin extensions of the cell poles that concentrate fluorescent MreB. We found that the extent to which MreB localization is perturbed is linearly correlated with the development of pointed cell poles and variable cell widths. Further, we find that a mutation to glycine of two conserved aspartic acid residues that are important for nucleotide hydrolysis in other members of the actin superfamily abolishes robust midcell recruitment of MreB but supports a normal rate of growth. These mutant strains provide novel insight into how MreB's protein structure, subcellular localization, and activity contribute to its function in bacterial cell shape. © 2011 Blackwell Publishing Ltd.

Mutations in the nucleotide binding pocket of MreB can alter cell curvature and polar morphology in Caulobacter

PubMed Central

Dye, Natalie A; Pincus, Zachary; Fisher, Isabelle C; Shapiro, Lucy; Theriot, Julie A

2011-01-01

Summary The maintenance of cell shape in Caulobacter crescentus requires the essential gene mreB, which encodes a member of the actin superfamily and the target of the antibiotic, A22. We isolated 35 unique A22-resistant Caulobacter strains with single amino acid substitutions near the nucleotide binding site of MreB. Mutations that alter cell curvature and mislocalize the intermediate filament crescentin cluster on the back surface of MreB's structure. Another subset have variable cell widths, with wide cell bodies and actively growing thin extensions of the cell poles that concentrate fluorescent MreB. We found that the extent to which MreB localization is perturbed is linearly correlated with the development of pointed cell poles and variable cell widths. Further, we find that a mutation to glycine of two conserved aspartic acid residues that are important for nucleotide hydrolysis in other members of the actin superfamily abolishes robust midcell recruitment of MreB but supports a normal rate of growth. These mutant strains provide novel insight into how MreB's protein structure, subcellular localization, and activity contribute to its function in bacterial cell shape. PMID:21564339

Carbonyl iron powder surface modification of magnetorheological elastomers for vibration absorbing application

NASA Astrophysics Data System (ADS)

Chen, Dong; Yu, Miao; Zhu, Mi; Qi, Song; Fu, Jie

2016-11-01

With excellent characteristic of magnetic-control stiffness, magnetorheological elastomer (MRE) is well suited as a spring element of vibration absorber. To improve the vibration attenuation performance of MRE vibration absorbers, this paper expects to improve the mechanical strength and reduce the loss factor of MRE by interface modification. The surface of carbonyl iron powder (CIP) was modified with silica coating by a simple and convenient approach. Several MRE samples, with different proportions of modified CIPs were fabricated under a constant magnetic field. The morphology and composition of modified CIP were characterized by scanning electron microscope and Fourier transform infrared spectra. The results indicated that the modified CIPs were coated with uniform and continuous silica, which can make a better combination between particle and matrix. The tensile strength, magnetorheological properties and the damping properties of the MRE samples were tested by material testing machine and rheometer. The experimental results demonstrated that the loss factor of the MRE which incorporated with modified CIPs decreased markedly, and the tensile strength of such material has been much improved, at the same time this kind of MRE kept high MR effect. It is expected that this MRE material will meet the requirements of vibration absorber.

Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB

PubMed Central

Schirner, Kathrin; Eun, Ye-Jin; Dion, Mike; Luo, Yun; Helmann, John D.; Garner, Ethan C.; Walker, Suzanne

2014-01-01

Summary The bacterial actin homolog MreB, which is critical for rod shape determination, forms filaments that rotate around the cell width on the inner surface of the cytoplasmic membrane. What determines filament association with the membranes or with other cell wall elongation proteins is not known. Using specific chemical and genetic perturbations while following MreB filament motion, we find that MreB membrane association is an actively regulated process that depends on the presence of lipid-linked peptidoglycan precursors. When precursors are depleted, MreB filaments disassemble into the cytoplasm and peptidoglycan synthesis becomes disorganized. In cells that lack wall teichoic acids, but continue to make peptidoglycan, dynamic MreB filaments are observed, although their presence is not sufficient to establish a rod shape. We propose that the cell regulates MreB filament association with the membrane, allowing rapid and reversible inactivation of cell wall enzyme complexes in response to the inhibition of cell wall synthesis. PMID:25402772

Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB.

PubMed

Schirner, Kathrin; Eun, Ye-Jin; Dion, Mike; Luo, Yun; Helmann, John D; Garner, Ethan C; Walker, Suzanne

2015-01-01

The bacterial actin homolog MreB, which is crucial for rod shape determination, forms filaments that rotate around the cell width on the inner surface of the cytoplasmic membrane. What determines filament association with the membranes or with other cell wall elongation proteins is not known. Using specific chemical and genetic perturbations while following MreB filament motion, we find that MreB membrane association is an actively regulated process that depends on the presence of lipid-linked peptidoglycan precursors. When precursors are depleted, MreB filaments disassemble into the cytoplasm, and peptidoglycan synthesis becomes disorganized. In cells that lack wall teichoic acids but continue to make peptidoglycan, dynamic MreB filaments are observed, although their presence is not sufficient to establish a rod shape. We propose that the cell regulates MreB filament association with the membrane, allowing rapid and reversible inactivation of cell wall enzyme complexes in response to the inhibition of cell wall synthesis.

Synchronous Measuring Techniques in Parallel to MRE: Study of Pressure, Pre-Tension, and Surface Dynamics

NASA Astrophysics Data System (ADS)

Brinker, Spencer Thomas

The contents of this dissertation include investigations in Magnetic Resonance Elastography (MRE) using a preclinical 9.4 Tesla small animal Magnetic Resonance Imaging (MRI) system along with synthetic materials that mimic the mechanical properties of soft human tissue. MRE is used for studying the mechanical behavior of soft tissue particularly applicable to medical applications. Wave motion induced by a mechanical driver is measured with MRI to acquire internal displacement fields over time and space within a material media. Complex shear modulus of the media is calculated from the response of mechanical wave transmission through the material. Changes in soft tissue stiffness is associated with disease progression and thus, is why assessing tissue mechanical properties with MRE has powerful diagnostic potential due to the noninvasive procedure of MRI. The experiments performed in this dissertation used elastic phantoms and specimens to observe the influence of pre-stress on MRE derived mechanical properties while additional mechanical measurements from other related material testing methods were synchronously collected alongside MRI scanning. An organ simulating phantom was used to explore changes in MRE stiffness in response to gas and liquid cyclic pressure loading. MRE stiffness increased with pressure and hysteresis was observed in cyclic pressure loading. The results suggest MRE is applicable to pressure related disease assessment. In addition, an interconnected porosity pressure phantom was constructed for future porous media investigations. A custom system was also built to demonstrate concurrent tensile testing during MRE for investigating homogeneous soft material media undergoing pre-tension. Stiffness increased with uniaxial tensile stress and strain. The tension and stiffness relationship explored can be related to the stress analysis of voluntary muscle. The results also offer prospective experimental strategies for community wide standards on MRE calibration methods. Lastly, a novel platform was developed for synchronous acquisition of Scanning Laser Doppler Vibrometry (SLDV) and MRE for examining surface wave dynamics related to internal media wave propagation in soft material experiencing sinusoidal mechanical excitation. The results indicate that optical displacement measurements of media on the surface are similar in nature to internal displacement measured from MRE. It is concluded that optical and MRI based elastography yield similar values of complex shear modulus.

MR enterography in nonresponsive adult celiac disease: Correlation with endoscopic, pathologic, serologic, and genetic features.

PubMed

Radmard, Amir Reza; Hashemi Taheri, Amir Pejman; Salehian Nik, Elham; Kooraki, Soheil; Kolahdoozan, Shadi; Mirminachi, Babak; Sotoudeh, Masoud; Ekhlasi, Golnaz; Malekzadeh, Reza; Shahbazkhani, Bijan

2017-10-01

To assess small bowel abnormalities on magnetic resonance enterography (MRE) in adult patients with nonresponsive celiac disease (CD) and investigate their associations with endoscopic, histopathologic, serologic, and genetic features. This prospective study was carried out between September 2012 and August 2013. After approval by the Ethics Committee of our institution, informed consent was acquired from all participants. Forty consecutive patients with nonresponsive CD, aged 17-76 years, underwent MRE using a 1.5T unit. Sequences included T 2 -HASTE, True-FISP, pre- and postcontrast VIBE to assess the quantitative (number of ileal and jejunal folds) and qualitative (fold pattern abnormalities, mural thickening, increased enhancement, bowel dilatation, or intussusception) measures. Endoscopic manifestations were categorized as normal/mild vs. severe. Histopathological results were divided into mild and severe. Genotyping of HLA-DQ2 and DQ8 was performed. Serum levels of tissue-transglutaminase, endomysial, and gliadin antibodies were also determined. Logistic regression analysis and receiver operating characteristic (ROC) curve were used. Twenty-nine (72.5%) cases showed abnormal MRE. Reversed jejunoileal fold pattern had significant association with severe endoscopic (odds ratio [OR] = 8.38, 95% confidence interval [CI] 1.73-40.5) and pathologic features (OR = 7.36, 95% CI 1.33-40.54). An increased number of ileal folds/inch was significantly associated with severe MARSH score and positive HLA-DQ8. (P < 0.001 and P = 0.026, respectively). Ileal fold number had the highest areas under the curve for prediction of severe endoscopic (AUC: 0.75, P = 0.009) and pathologic (AUC: 0.84, P < 0.001) findings and positive anti-transglutaminase antibody (AUC: 0.85, P = 0.027). Fold pattern reversal on MRE is highly associated with endoscopic and pathologic features of refractory celiac disease (RCD). Increased ileal folds showed higher correlation with endoscopic-pathologic features, HLA-DQ8, and anti-transglutaminase level. MRE might be more sensitive for detection of increased ileal folds in CD rather than reduction of duodenal and jejunal folds due to better distension of ileal loops. 2 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1096-1106. © 2017 International Society for Magnetic Resonance in Medicine.

Requirement of the Mre11 complex and exonuclease 1 for activation of the Mec1 signaling pathway.

PubMed

Nakada, Daisuke; Hirano, Yukinori; Sugimoto, Katsunori

2004-11-01

The large protein kinases, ataxia-telangiectasia mutated (ATM) and ATM-Rad3-related (ATR), orchestrate DNA damage checkpoint pathways. In budding yeast, ATM and ATR homologs are encoded by TEL1 and MEC1, respectively. The Mre11 complex consists of two highly related proteins, Mre11 and Rad50, and a third protein, Xrs2 in budding yeast or Nbs1 in mammals. The Mre11 complex controls the ATM/Tel1 signaling pathway in response to double-strand break (DSB) induction. We show here that the Mre11 complex functions together with exonuclease 1 (Exo1) in activation of the Mec1 signaling pathway after DNA damage and replication block. Mec1 controls the checkpoint responses following UV irradiation as well as DSB induction. Correspondingly, the Mre11 complex and Exo1 play an overlapping role in activation of DSB- and UV-induced checkpoints. The Mre11 complex and Exo1 collaborate in producing long single-stranded DNA (ssDNA) tails at DSB ends and promote Mec1 association with the DSBs. The Ddc1-Mec3-Rad17 complex associates with sites of DNA damage and modulates the Mec1 signaling pathway. However, Ddc1 association with DSBs does not require the function of the Mre11 complex and Exo1. Mec1 controls checkpoint responses to stalled DNA replication as well. Accordingly, the Mre11 complex and Exo1 contribute to activation of the replication checkpoint pathway. Our results provide a model in which the Mre11 complex and Exo1 cooperate in generating long ssDNA tracts and thereby facilitate Mec1 association with sites of DNA damage or replication block.

MR (Mre11-Rad50) complex in Giardia duodenalis: In vitro characterization and its response upon DNA damage.

PubMed

Sandoval-Cabrera, A; Zarzosa-Álvarez, A L; Martínez-Miguel, R M; Bermúdez-Cruz, R M

2015-04-01

Giardia duodenalis is a well-known protozoan parasite of humans and other mammals. The repair of DNA double strand breaks (DSBs) is crucial for genomic stability and homologous recombination is one of the primary mechanisms used by cells to repair DNA. The Mre11 complex is comprised by Mre11, an endonuclease and 3'-5' exonuclease known to resect ends during homologous recombination, and Rad50, a member of the structural maintenance of chromosomes (SMC) family of ATPases. In this work we cloned, expressed and characterized the catalytic activities of the giardial Mre11 (GdMre11) and Rad50 (GdRad50) proteins. Our results show that while purified recombinant GdMre11 and GdRad50 proteins bind DNA, GdMre11 contains a 3'-5' exonuclease and purified recombinant GdRad50 has ATPase activity. The predicted structure for GdMre11 revealed a conserved Mn(2+) dependent binding pocket. We also explored the expression of giardial mre11 and rad50 genes after ionizing radiation, and our results indicate that both specific transcripts were increased after 1-2 h while their protein levels were found to be significantly increased 4 h after gamma radiation treatment. These proteins were localized in the nuclei before and after irradiation. The implication of these observations is discussed. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Morphogenes bolA and mreB mediate the photoregulation of cellular morphology during complementary chromatic acclimation in Fremyella diplosiphon.

PubMed

Singh, Shailendra P; Montgomery, Beronda L

2014-07-01

Photoregulation of pigmentation during complementary chromatic acclimation (CCA) is well studied in Fremyella diplosiphon; however, mechanistic insights into the CCA-associated morphological changes are still emerging. F. diplosiphon cells are rectangular under green light (GL), whereas cells are smaller and spherical under red light (RL). Here, we investigate the role of morphogenes bolA and mreB during CCA using gene expression and gene function analyses. The F. diplosiphon bolA gene is essential as its complete removal from the genome was unsuccessful. Depletion of bolA resulted in slow growth, morphological defects and the accumulation of high levels of reactive oxygen species in a partially segregated ΔbolA strain. Higher expression of bolA was observed under RL and was correlated with lower expression of mreB and mreC genes in wild type. In a ΔrcaE strain that lacks the red-/green-responsive RcaE photoreceptor, the expression of bolA and mre genes was altered under both RL and GL. Observed gene expression relationships suggest that mreB and mreC expression is controlled by RcaE-dependent photoregulation of bolA expression. Expression of F. diplosiphon bolA and mreB homologues in Escherichia coli demonstrated functional conservation of the encoded proteins. Together, these studies establish roles for bolA and mreB in RcaE-dependent regulation of cellular morphology. © 2014 John Wiley & Sons Ltd.

Presence of multiple sites containing polar material in spherical Escherichia coli cells that lack MreB.

PubMed

Nilsen, Trine; Yan, Arthur W; Gale, Gregory; Goldberg, Marcia B

2005-09-01

In rod-shaped bacteria, certain proteins are specifically localized to the cell poles. The nature of the positional information that leads to the proper localization of these proteins is unclear. In a screen for factors required for the localization of the Shigella sp. actin assembly protein IcsA to the bacterial pole, a mutant carrying a transposon insertion in mreB displayed altered targeting of IcsA. The phenotype of cells containing a transposon insertion in mreB was indistinguishable from that of cells containing a nonpolar mutation in mreB or that of wild-type cells treated with the MreB inhibitor A22. In cells lacking MreB, a green fluorescent protein (GFP) fusion to a cytoplasmic derivative of IcsA localized to multiple sites. Secreted full-length native IcsA was present in multiple faint patches on the surfaces of these cells in a pattern similar to that seen for the cytoplasmic IcsA-GFP fusion. EpsM, the polar Vibrio cholerae inner membrane protein, also localized to multiple sites in mreB cells and colocalized with IcsA, indicating that localization to multiple sites is not unique to IcsA. Our results are consistent with the requirement, either direct or indirect, for MreB in the restriction of certain polar material to defined sites within the cell and, in the absence of MreB, with the formation of ectopic sites containing polar material.

Chlamydia co-opts the rod shape-determining proteins MreB and Pbp2 for cell division.

PubMed

Ouellette, Scot P; Karimova, Gouzel; Subtil, Agathe; Ladant, Daniel

2012-07-01

Chlamydiae are obligate intracellular bacterial pathogens that have extensively reduced their genome in adapting to the intracellular environment. The chlamydial genome contains only three annotated cell division genes and lacks ftsZ. How this obligate intracellular pathogen divides is uncharacterized. Chlamydiae contain two high-molecular-weight (HMW) penicillin binding proteins (Pbp) implicated in peptidoglycan synthesis, Pbp2 and Pbp3/FtsI. We show here, using HMW Pbp-specific penicillin derivatives, that both Pbp2 and Pbp3 are essential for chlamydial cell division. Ultrastructural analyses of antibiotic-treated cultures revealed distinct phenotypes: Pbp2 inhibition induced internal cell bodies within a single outer membrane whereas Pbp3 inhibition induced elongated phenotypes with little internal division. Each HMW Pbp interacts with the Chlamydia cell division protein FtsK. Chlamydiae are coccoid yet contain MreB, a rod shape-determining protein linked to Pbp2 in bacilli. Using MreB-specific antibiotics, we show that MreB is essential for chlamydial growth and division. Importantly, co-treatment with MreB-specific and Pbp-specific antibiotics resulted in the MreB-inhibited phenotype, placing MreB upstream of Pbp function in chlamydial cell division. Finally, we showed that MreB also interacts with FtsK. We propose that, in Chlamydia, MreB acts as a central co-ordinator at the division site to substitute for the lack of FtsZ in this bacterium. © 2012 Blackwell Publishing Ltd.

Characterization of binding preference of polyhydroxyalkanoate biosynthesis-related multifunctional protein PhaM from Ralstonia eutropha.

PubMed

Ushimaru, Kazunori; Tsuge, Takeharu

2016-05-01

The binding preference of a polyhydroxyalkanoate (PHA) biosynthesis-related multifunctional protein from Ralstonia eutropha (PhaMRe) was characterized. In vitro activity assay showed that PHA synthase from R. eutropha (PhaCRe) was activated by the presence of PhaMRe but PHA synthase from Aeromonas caviae (PhaCAc) was not. Additionally, in vitro assays of protein-protein interactions demonstrated that PhaMRe interacted with PhaCRe directly, but did not interact with PhaCAc. These results suggest that the protein-protein interaction is important for the activation of PhaC by PhaMRe. Further analyses indicated that PhaMRe has little or no direct interaction with the PHA polymer chain. Subsequently, PHA biosynthesis genes (phaA Re, phaB Re, and phaC Re/phaC Ac) and the phaM Re gene were introduced into recombinant Escherichia coli and cultivated for PHA accumulation. Contrary to our expectations, the expression of PhaMRe decreased PHA accumulation and changed the morphology of PHA granules to be microscopically obscure shape in PhaCRe-expressing E. coli. No change in the amount of P(3HB) or the morphology of granules by PhaMRe expression was observed in PhaCAc-expressing E. coli. These observations suggest that PhaMRe affects cellular physiology through the PhaM-PhaC interaction.

The effect of inhibition of host MreB on the infection of thermophilic phage GVE2 in high temperature environment.

PubMed

Jin, Min; Chen, Yanjiang; Xu, Chenxi; Zhang, Xiaobo

2014-04-28

In eukaryotes, the manipulation of the host actin cytoskeleton is a necessary strategy for viral pathogens to invade host cells. Increasing evidence indicates that the actin homolog MreB of bacteria plays key roles in cell shape formation, cell polarity, cell wall biosynthesis, and chromosome segregation. However, the role of bacterial MreB in the bacteriophage infection is not extensively investigated. To address this issue, in this study, the MreB of thermophilic Geobacillus sp. E263 from a deep-sea hydrothermal field was characterized by inhibiting the MreB polymerization and subsequently evaluating the bacteriophage GVE2 infection. The results showed that the host MreB played important roles in the bacteriophage infection at high temperature. After the host cells were treated with small molecule drug A22 or MP265, the specific inhibitors of MreB polymerization, the adsorption of GVE2 and the replication of GVE2 genome were significantly repressed. The confocal microscopy data revealed that MreB facilitated the GVE2 infection by inducing the polar distribution of virions during the phage infection. Our study contributed novel information to understand the molecular events of the host in response to bacteriophage challenge and extended our knowledge about the host-virus interaction in deep-sea vent ecosystems.

Antioxidant and Proapoptotic Activities of Sclerocarya birrea [(A. Rich.) Hochst.] Methanolic Root Extract on the Hepatocellular Carcinoma Cell Line HepG2

PubMed Central

Armentano, Maria Francesca; Bisaccia, Faustino; Miglionico, Rocchina; Russo, Daniela; Nolfi, Nicoletta; Carmosino, Monica; Andrade, Paula B.; Valentão, Patrícia; Diop, Moussoukhoye Sissokho

2015-01-01

The main goal of this study was to characterize the in vitro antioxidant activity and the apoptotic potential of S. birrea methanolic root extract (MRE). Among four tested extracts, obtained with different solvents, MRE showed the highest content of polyphenols, flavonoids, and tannins together with antioxidant activities tested with superoxide, nitric oxide, ABTS, and beta-carotene bleaching assays. Moreover, the cytotoxic effect of MRE was evaluated on the hepatocarcinoma cell line HepG2. In these cells, MRE treatment induced apoptosis and generated reactive oxygen species (ROS) in dose-dependent manner. The cytotoxic effect promoted by MRE was prevented by pretreatment of HepG2 cells with N-acetyl-L-cysteine (NAC), suggesting that oxidative stress was pivotal in MRE-mediated cell death. Moreover, we showed that the MRE treatment induced the mitochondrial membrane depolarization and the cytochrome c release from mitochondria into the cytosol. It suggests that the apoptosis occurred in a mitochondrial-dependent pathway. Interestingly, MRE showed a sensibly lower cytotoxicity, associated with a low increase of ROS, in normal human dermal fibroblasts compared to HepG2 cells. It is suggested that the methanolic root extract of S. Birrea is able to selectively increase intracellular ROS levels in cancer cells, promoting cell death. PMID:26075245

Antioxidant and proapoptotic activities of Sclerocarya birrea [(A. Rich.) Hochst.] methanolic root extract on the hepatocellular carcinoma cell line HepG2.

PubMed

Armentano, Maria Francesca; Bisaccia, Faustino; Miglionico, Rocchina; Russo, Daniela; Nolfi, Nicoletta; Carmosino, Monica; Andrade, Paula B; Valentão, Patrícia; Diop, Moussoukhoye Sissokho; Milella, Luigi

2015-01-01

The main goal of this study was to characterize the in vitro antioxidant activity and the apoptotic potential of S. birrea methanolic root extract (MRE). Among four tested extracts, obtained with different solvents, MRE showed the highest content of polyphenols, flavonoids, and tannins together with antioxidant activities tested with superoxide, nitric oxide, ABTS, and beta-carotene bleaching assays. Moreover, the cytotoxic effect of MRE was evaluated on the hepatocarcinoma cell line HepG2. In these cells, MRE treatment induced apoptosis and generated reactive oxygen species (ROS) in dose-dependent manner. The cytotoxic effect promoted by MRE was prevented by pretreatment of HepG2 cells with N-acetyl-L-cysteine (NAC), suggesting that oxidative stress was pivotal in MRE-mediated cell death. Moreover, we showed that the MRE treatment induced the mitochondrial membrane depolarization and the cytochrome c release from mitochondria into the cytosol. It suggests that the apoptosis occurred in a mitochondrial-dependent pathway. Interestingly, MRE showed a sensibly lower cytotoxicity, associated with a low increase of ROS, in normal human dermal fibroblasts compared to HepG2 cells. It is suggested that the methanolic root extract of S. Birrea is able to selectively increase intracellular ROS levels in cancer cells, promoting cell death.

Testing the shorter and variable recurrence interval hypothesis along the Cholame segment of the San Andreas Fault

NASA Astrophysics Data System (ADS)

Williams, A.; Arrowsmith, R.; Rockwell, T. K.; Akciz, S. O.; Grant Ludwig, L.

2016-12-01

The Cholame segment of the San Andreas Fault interacts with the Parkfield segment to the northwest with its creep and M6 earthquakes and the locked Carrizo segment to the southeast. Although offset reconstructions exist for this 75 km reach, rupture behavior is poorly characterized, limiting seismic hazard evaluation. Here we present new paleoseismic results from 2 fault perpendicular 26 m long trenches connected by a 15 m long fault parallel trench. The site is located south of the Parkfield segment 20 km southeast of Highway 46. Site geomorphology is characterized by several 50 m offset drainages northwest of the trenches, small shutter ridges and sag ponds, and alluvial fans crossing the fault. Fault zone stratigraphy consists of alternating finely bedded sands, silts, and gravels, and bioturbated soil horizons. The strata record 3-4 earthquakes and possible deformation post-1857, similar to the LY4 site 38 km southeast. E4, E3 and the most recent earthquake (MRE) are well supported by evidence of decreasing vertical offset up-sequence, capped fissure fill and colluvial wedges, which create small horst and graben structures. Units display vertical offsets ranging from 60 cm at the base to 12 cm near the MRE horizon, small colluvial wedges, and sag deposits within the 4 m wide fault zone. E2—the penultimate-is less certain, supported only by the decreasing offset in the stratigraphic sequence. The E4 event horizon is a gradational clayey silt sag deposit capped by discontinuous gravel, 18 cm at its thickest point and extending 4.8 m across the fault zone. The E3 and E2 event horizons are capped by thin bedded silty clay, and bounded by discontinuous burn horizons. The MRE horizon extends 6 m across the main fault zone, and consists of a silty clay sag deposit capped by very fine, bedded sand and coarse gravel, 22 cm at its thickest point and overlying a burn horizon. If the MRE is indeed the 1857 event, it has significant potential in correlation with the high quality rupture records at Bidart (70 km southeast), and Frazier Mountain (180 km southeast). This site contains abundant detrital charcoal in many of the units and burn horizons at or near event horizons providing great potential for bracketing the age of these paleoearthquakes.

The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-Terminal yellow fluorescent protein tag.

PubMed

Swulius, Matthew T; Jensen, Grant J

2012-12-01

Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.

An early cytoplasmic step of peptidoglycan synthesis is associated to MreB in Bacillus subtilis.

PubMed

Rueff, Anne-Stéphanie; Chastanet, Arnaud; Domínguez-Escobar, Julia; Yao, Zhizhong; Yates, James; Prejean, Maria-Victoria; Delumeau, Olivier; Noirot, Philippe; Wedlich-Söldner, Roland; Filipe, Sergio R; Carballido-López, Rut

2014-01-01

MreB proteins play a major role during morphogenesis of rod-shaped bacteria by organizing biosynthesis of the peptidoglycan cell wall. However, the mechanisms underlying this process are not well understood. In Bacillus subtilis, membrane-associated MreB polymers have been shown to be associated to elongation-specific complexes containing transmembrane morphogenetic factors and extracellular cell wall assembly proteins. We have now found that an early intracellular step of cell wall synthesis is also associated to MreB. We show that the previously uncharacterized protein YkuR (renamed DapI) is required for synthesis of meso-diaminopimelate (m-DAP), an essential constituent of the peptidoglycan precursor, and that it physically interacts with MreB. Highly inclined laminated optical sheet microscopy revealed that YkuR forms uniformly distributed foci that exhibit fast motion in the cytoplasm, and are not detected in cells lacking MreB. We propose a model in which soluble MreB organizes intracellular steps of peptidoglycan synthesis in the cytoplasm to feed the membrane-associated cell wall synthesizing machineries. © 2013 John Wiley & Sons Ltd.

Magnetic resonance elastography (MRE) in cancer: Technique, analysis, and applications

PubMed Central

Pepin, Kay M.; Ehman, Richard L.; McGee, Kiaran P.

2015-01-01

Tissue mechanical properties are significantly altered with the development of cancer. Magnetic resonance elastography (MRE) is a noninvasive technique capable of quantifying tissue mechanical properties in vivo. This review describes the basic principles of MRE and introduces some of the many promising MRE methods that have been developed for the detection and characterization of cancer, evaluation of response to therapy, and investigation of the underlying mechanical mechanisms associated with malignancy. PMID:26592944

Steady-state helices of the actin homolog MreB inside bacteria: dynamics without motors.

PubMed

Allard, Jun F; Rutenberg, Andrew D

2007-09-01

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasistatic evolution of the helical pitch with cell growth, as well as time scales of helix turnover and de novo establishment. We find that while the body of a polarized MreB helix treadmills toward its slow-growing end, the fast-growing tips of laterally associated protofilaments move toward the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.

Steady-state helices of the actin homolog MreB inside bacteria: Dynamics without motors

NASA Astrophysics Data System (ADS)

Allard, Jun F.; Rutenberg, Andrew D.

2007-09-01

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasistatic evolution of the helical pitch with cell growth, as well as time scales of helix turnover and de novo establishment. We find that while the body of a polarized MreB helix treadmills toward its slow-growing end, the fast-growing tips of laterally associated protofilaments move toward the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.

Fabrication and investigation on field-dependent properties of natural rubber based magneto-rheological elastomer isolator

NASA Astrophysics Data System (ADS)

Ain Abd Wahab, Nurul; Amri Mazlan, Saiful; Ubaidillah; Kamaruddin, Shamsul; Intan Nik Ismail, Nik; Choi, Seung-Bok; Haziq Rostam Sharif, Amirul

2016-10-01

This study presents a laminated magnetorheological elastomer (MRE) isolator which applies to vibration control in practice. The proposed isolator is fabricated with multilayer MRE sheets associated with the natural rubber (NR) as a matrix, and steel plates. The fabricated MRE isolator is then magnetically analysed to achieve high magnetic field intensity which can produce high damping force required for effective vibration control. Subsequently, the NR-based MRE specimen is tested to identify the field-dependent rheological properties such as storage modulus with 60 weight percentage of carbonyl iron particles. It is shown from this test that the MR effect of MRE specimen is quantified to reach up to 120% at 0.8 T. Following the design stage, the electromagnetic simulation using the finite element method magnetic (FEMM) software is carried out for analysing the magnetic flux distribution in the laminated MRE isolator. The laminated MRE isolator is then examined to a series of compression for static and dynamic test under various applied currents using the dynamic fatigue machine and biaxial dynamic testing machine. It is shown that the static compression force is increased by 14.5% under strong magnetic field compared to its off-state. Meanwhile, the dynamic compression test results show that the force increase of the laminated MRE isolator is up to 16% and 7% for low and high frequency respectively. From the results presented in this work, it is demonstrated that the full-scale concept of the MRE isolator can be one of the potential candidates for vibration control applications by tunability of the dynamic stiffness.

The effect of inhibition of host MreB on the infection of thermophilic phage GVE2 in high temperature environment

PubMed Central

Jin, Min; Chen, Yanjiang; Xu, Chenxi; Zhang, Xiaobo

2014-01-01

In eukaryotes, the manipulation of the host actin cytoskeleton is a necessary strategy for viral pathogens to invade host cells. Increasing evidence indicates that the actin homolog MreB of bacteria plays key roles in cell shape formation, cell polarity, cell wall biosynthesis, and chromosome segregation. However, the role of bacterial MreB in the bacteriophage infection is not extensively investigated. To address this issue, in this study, the MreB of thermophilic Geobacillus sp. E263 from a deep-sea hydrothermal field was characterized by inhibiting the MreB polymerization and subsequently evaluating the bacteriophage GVE2 infection. The results showed that the host MreB played important roles in the bacteriophage infection at high temperature. After the host cells were treated with small molecule drug A22 or MP265, the specific inhibitors of MreB polymerization, the adsorption of GVE2 and the replication of GVE2 genome were significantly repressed. The confocal microscopy data revealed that MreB facilitated the GVE2 infection by inducing the polar distribution of virions during the phage infection. Our study contributed novel information to understand the molecular events of the host in response to bacteriophage challenge and extended our knowledge about the host-virus interaction in deep-sea vent ecosystems. PMID:24769758

Multiple Arginine Residues Are Methylated in Drosophila Mre11 and Required for Survival Following Ionizing Radiation.

PubMed

Yuan, Qing; Tian, Ran; Zhao, Haiying; Li, Lijuan; Bi, Xiaolin

2018-05-31

Mre11 is a key player for DNA double strand break repair. Previous studies have shown that mammalian Mre11 is methylated at multiple arginines in its C-terminal Glycine-Arginine-Rich motif (GAR) by protein arginine methyltransferase PRMT1. Here, we found that the Drosophila Mre11 is methylated at arginines 559, 563, 565, and 569 in the GAR motif by DART1, the Drosophila homolog of PRMT1. Mre11 interacts with DART1 in S2 cells, and this interaction does not require the GAR motif. Arginines methylated Mre11 localizes exclusively in the nucleus as soluble nuclear protein or chromatin-binding protein. To study the in vivo functions of methylation, we generated the single Arg-Ala and all Arginines mutated flies. We found these mutants were sensitive to ionizing radiation. Furthermore, Arg-Ala mutated flies had no irradiation induced G2/M checkpoint defect in wing disc and eye disc. Thus, we provided evidence that arginines in Drosophila Mre11 are methylated by DART1 methytransferase and flies loss of arginine methylation are sensitive to irradiation. Copyright © 2018 Yuan et al.

DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22.

PubMed

Karczmarek, Aneta; Martínez-Arteaga, Rocío; Baselga, Rocío Martínez-Arteaga; Alexeeva, Svetlana; Hansen, Flemming G; Vicente, Miguel; Nanninga, Nanne; den Blaauwen, Tanneke

2007-07-01

The bacterial actin homologue MreB forms a helix underneath the cytoplasmic membrane and was shown to be essential in the morphogenesis of the rod-shaped cells. Additionally, MreB was implicated to be involved in DNA segregation. However, in our hands the mreBCD deletion strain (PA340-678) grew without apparent DNA segregation defect, suggesting that the reported chromosome segregation inhibition could be caused by a temporarily effect of MreB inhibition or depletion. To assess the involvement of MreB in DNA segregation during the transition from rod to sphere, we compared the effect of A22 and the PBP2 inhibitor mecillinam on the percentage of cells with segregated nucleoids and the number of oriC foci in wild-type Escherichia coli cells. Cells became spherical in the same time window during both treatments and we could not detect any difference in the chromosome or oriC segregation between these two treatments. Additionally, flow cytometric analyses showed that A22 and mecillinam treatment gave essentially the same chromosome segregation pattern. We conclude that MreB is not directly involved in DNA segregation of E. coli.

The actin-like MreB proteins in Bacillus subtilis: a new turn.

PubMed

Chastanet, Arnaud; Carballido-Lopez, Rut

2012-06-01

A decade ago, two breakthrough descriptions were reported: 1) the first helix-like protein localization pattern of MreB and its paralog Mbl in Bacillus subtilis and 2) the crystal structure of Thermotoga maritima MreB1, which was remarkably similar to that of actin. These discoveries strongly stimulated the field of bacterial development, leading to the identification of many new cytoskeletal proteins (1) and the publication of many studies describing the helical patterns of protein, DNA and even lipid domains. However, today, new breakthroughs are shaking up what had become a dogma. Instead of helical structures, MreBs appear to form discrete patches that move circumferentially around the cell, questioning the idea of MreB cables forming an actin-like cytoskeleton. Furthermore, increasing evidence of biochemical properties that are unlike the properties of actin suggest that the molecular behavior of MreB proteins may be different. The aim of this review is to summarize the current knowledge of the so-called "actin-like" MreB cytoskeleton through a discussion of the model Gram-positive bacterium B. subtilis and the most recent findings in this rapidly evolving research field.

Engineering the bacterial shapes for enhanced inclusion bodies accumulation.

PubMed

Jiang, Xiao-Ran; Wang, Huan; Shen, Rui; Chen, Guo-Qiang

2015-05-01

Many bacteria can accumulate inclusion bodies such as sulfur, polyphosphate, glycogen, proteins or polyhydroxyalkanoates. To exploit bacteria as factories for effective production of inclusion bodies, a larger intracellular space is needed for more inclusion body accumulation. In this study, polyhydroxybutyrate (PHB) was investigated as an inclusion bodies representative to be accumulated by Escherichia coli JM109SG. Various approaches were taken to increase the bacterial cell sizes including deletion on actin-like protein gene mreB, weak expression of mreB in mreB deletion mutant, and weak expression of mreB in mreB deletion mutant under inducible expression of SulA, the inhibitor of division ring protein FtsZ. All of the methods resulted in different levels of increases in bacterial sizes and PHB granules accumulation. Remarkably, an increase of over 100% PHB accumulation was observed in recombinant E. coli overexpressing mreB in an mreB deletion mutant under inducible expression of FtsZ inhibiting protein SulA. The molecular mechanism of enlarged bacterial size was found to be directly relate to weakened cytoskeleton which was the result of broken skeleton helix. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Viscoelastic properties of soft gels: comparison of magnetic resonance elastography and dynamic shear testing in the shear wave regime

NASA Astrophysics Data System (ADS)

Okamoto, R. J.; Clayton, E. H.; Bayly, P. V.

2011-10-01

Magnetic resonance elastography (MRE) is used to quantify the viscoelastic shear modulus, G*, of human and animal tissues. Previously, values of G* determined by MRE have been compared to values from mechanical tests performed at lower frequencies. In this study, a novel dynamic shear test (DST) was used to measure G* of a tissue-mimicking material at higher frequencies for direct comparison to MRE. A closed-form solution, including inertial effects, was used to extract G* values from DST data obtained between 20 and 200 Hz. MRE was performed using cylindrical 'phantoms' of the same material in an overlapping frequency range of 100-400 Hz. Axial vibrations of a central rod caused radially propagating shear waves in the phantom. Displacement fields were fit to a viscoelastic form of Navier's equation using a total least-squares approach to obtain local estimates of G*. DST estimates of the storage G' (Re[G*]) and loss modulus G'' (Im[G*]) for the tissue-mimicking material increased with frequency from 0.86 to 0.97 kPa (20-200 Hz, n = 16), while MRE estimates of G' increased from 1.06 to 1.15 kPa (100-400 Hz, n = 6). The loss factor (Im[G*]/Re[G*]) also increased with frequency for both test methods: 0.06-0.14 (20-200 Hz, DST) and 0.11-0.23 (100-400 Hz, MRE). Close agreement between MRE and DST results at overlapping frequencies indicates that G* can be locally estimated with MRE over a wide frequency range. Low signal-to-noise ratio, long shear wavelengths and boundary effects were found to increase residual fitting error, reinforcing the use of an error metric to assess confidence in local parameter estimates obtained by MRE.

Functional Analysis of the Cytoskeleton Protein MreB from Chlamydophila pneumoniae

PubMed Central

Gaballah, Ahmed; Kloeckner, Anna; Otten, Christian; Sahl, Hans-Georg; Henrichfreise, Beate

2011-01-01

In rod-shaped bacteria, the bacterial actin ortholog MreB is considered to organize the incorporation of cell wall precursors into the side-wall, whereas the tubulin homologue FtsZ is known to tether incorporation of cell wall building blocks at the developing septum. For intracellular bacteria, there is no need to compensate osmotic pressure by means of a cell wall, and peptidoglycan has not been reliably detected in Chlamydiaceae. Surprisingly, a nearly complete pathway for the biosynthesis of the cell wall building block lipid II has been found in the genomes of Chlamydiaceae. In a previous study, we discussed the hypothesis that conservation of lipid II biosynthesis in cell wall-lacking bacteria may reflect the intimate molecular linkage of cell wall biosynthesis and cell division and thus an essential role of the precursor in cell division. Here, we investigate why spherical-shaped chlamydiae harbor MreB which is almost exclusively found in elongated bacteria (i.e. rods, vibrios, spirilla) whereas they lack the otherwise essential division protein FtsZ. We demonstrate that chlamydial MreB polymerizes in vitro and that polymerization is not inhibited by the blocking agent A22. As observed for MreB from Bacillus subtilis, chlamydial MreB does not require ATP for polymerization but is capable of ATP hydrolysis in phosphate release assays. Co-pelleting and bacterial two-hybrid experiments indicate that MreB from Chlamydophila (Chlamydia) pneumoniae interacts with MurF, MraY and MurG, three key components in lipid II biosynthesis. In addition, MreB polymerization is improved in the presence of MurF. Our findings suggest that MreB is involved in tethering biosynthesis of lipid II and as such may be necessary for maintaining a functional divisome machinery in Chlamydiaceae. PMID:22022378

Functional analysis of the cytoskeleton protein MreB from Chlamydophila pneumoniae.

PubMed

Gaballah, Ahmed; Kloeckner, Anna; Otten, Christian; Sahl, Hans-Georg; Henrichfreise, Beate

2011-01-01

In rod-shaped bacteria, the bacterial actin ortholog MreB is considered to organize the incorporation of cell wall precursors into the side-wall, whereas the tubulin homologue FtsZ is known to tether incorporation of cell wall building blocks at the developing septum. For intracellular bacteria, there is no need to compensate osmotic pressure by means of a cell wall, and peptidoglycan has not been reliably detected in Chlamydiaceae. Surprisingly, a nearly complete pathway for the biosynthesis of the cell wall building block lipid II has been found in the genomes of Chlamydiaceae. In a previous study, we discussed the hypothesis that conservation of lipid II biosynthesis in cell wall-lacking bacteria may reflect the intimate molecular linkage of cell wall biosynthesis and cell division and thus an essential role of the precursor in cell division. Here, we investigate why spherical-shaped chlamydiae harbor MreB which is almost exclusively found in elongated bacteria (i.e. rods, vibrios, spirilla) whereas they lack the otherwise essential division protein FtsZ. We demonstrate that chlamydial MreB polymerizes in vitro and that polymerization is not inhibited by the blocking agent A22. As observed for MreB from Bacillus subtilis, chlamydial MreB does not require ATP for polymerization but is capable of ATP hydrolysis in phosphate release assays. Co-pelleting and bacterial two-hybrid experiments indicate that MreB from Chlamydophila (Chlamydia) pneumoniae interacts with MurF, MraY and MurG, three key components in lipid II biosynthesis. In addition, MreB polymerization is improved in the presence of MurF. Our findings suggest that MreB is involved in tethering biosynthesis of lipid II and as such may be necessary for maintaining a functional divisome machinery in Chlamydiaceae.

Viscoelastic properties of soft gels: comparison of magnetic resonance elastography and dynamic shear testing in the shear wave regime.

PubMed

Okamoto, R J; Clayton, E H; Bayly, P V

2011-10-07

Magnetic resonance elastography (MRE) is used to quantify the viscoelastic shear modulus, G*, of human and animal tissues. Previously, values of G* determined by MRE have been compared to values from mechanical tests performed at lower frequencies. In this study, a novel dynamic shear test (DST) was used to measure G* of a tissue-mimicking material at higher frequencies for direct comparison to MRE. A closed-form solution, including inertial effects, was used to extract G* values from DST data obtained between 20 and 200 Hz. MRE was performed using cylindrical 'phantoms' of the same material in an overlapping frequency range of 100-400 Hz. Axial vibrations of a central rod caused radially propagating shear waves in the phantom. Displacement fields were fit to a viscoelastic form of Navier's equation using a total least-squares approach to obtain local estimates of G*. DST estimates of the storage G' (Re[G*]) and loss modulus G″ (Im[G*]) for the tissue-mimicking material increased with frequency from 0.86 to 0.97 kPa (20-200 Hz, n = 16), while MRE estimates of G' increased from 1.06 to 1.15 kPa (100-400 Hz, n = 6). The loss factor (Im[G*]/Re[G*]) also increased with frequency for both test methods: 0.06-0.14 (20-200 Hz, DST) and 0.11-0.23 (100-400 Hz, MRE). Close agreement between MRE and DST results at overlapping frequencies indicates that G* can be locally estimated with MRE over a wide frequency range. Low signal-to-noise ratio, long shear wavelengths and boundary effects were found to increase residual fitting error, reinforcing the use of an error metric to assess confidence in local parameter estimates obtained by MRE.

A new class of magnetorheological elastomers based on waste tire rubber and the characterization of their properties

NASA Astrophysics Data System (ADS)

Ubaidillah; Imaduddin, Fitrian; Li, Yancheng; Amri Mazlan, Saiful; Sutrisno, Joko; Koga, Tsuyoshi; Yahya, Iwan; Choi, Seung-Bok

2016-11-01

This paper proposes a new type of magnetorheological elastomer (MRE) using rubber from waste tires and describes its performance characteristics. In this work, scrap tires were utilized as a primary matrix for the MRE without incorporation of virgin elastomers. The synthesis of the scrap tire based MRE adopted a high-temperature high-pressure sintering technique to achieve the reclaiming of vulcanized rubber. The material properties of the MRE samples were investigated through physical and viscoelastic examinations. The physical tests confirmed several material characteristics—microstructure, magnetic, and thermal properties-while the viscoelastic examination was conducted with a laboratory-made dynamic compression apparatus. It was observed from the viscoelastic examination that the proposed MRE has magnetic-field-dependent properties of the storage modulus, loss modulus, and loss tangent at different excitation frequencies and strain amplitudes. Specifically, the synthesized MRE showed a high zero field modulus, a reasonable MR effect under maximum applied current, and remarkable damping properties.

In Escherichia coli, MreB and FtsZ direct the synthesis of lateral cell wall via independent pathways that require PBP 2.

PubMed

Varma, Archana; Young, Kevin D

2009-06-01

In Escherichia coli, the cytoplasmic proteins MreB and FtsZ play crucial roles in ensuring that new muropeptide subunits are inserted into the cell wall in a spatially correct way during elongation and division. In particular, to retain a constant diameter and overall shape, new material must be inserted into the wall uniformly around the cell's perimeter. Current thinking is that MreB accomplishes this feat through intermediary proteins that tether peptidoglycan synthases to the outer face of the inner membrane. We tested this idea in E. coli by using a DD-carboxypeptidase mutant that accumulates pentapeptides in its peptidoglycan, allowing us to visualize new muropeptide incorporation. Surprisingly, inhibiting MreB with the antibiotic A22 did not result in uneven insertion of new wall, although the cells bulged and lost their rod shapes. Instead, uneven (clustered) incorporation occurred only if MreB and FtsZ were inactivated simultaneously, providing the first evidence in E. coli that FtsZ can direct murein incorporation into the lateral cell wall independently of MreB. Inhibiting penicillin binding protein 2 (PBP 2) alone produced the same clustered phenotype, implying that MreB and FtsZ tether peptidoglycan synthases via a common mechanism that includes PBP 2. However, cell shape was determined only by the presence or absence of MreB and not by the even distribution of new wall material as directed by FtsZ.

The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity.

PubMed

Yang, Lingna; Wang, Chongyuan; Li, Fudong; Zhang, Jiahai; Nayab, Anam; Wu, Jihui; Shi, Yunyu; Gong, Qingguo

2017-09-29

MEX-3 is a K-homology (KH) domain-containing RNA-binding protein first identified as a translational repressor in Caenorhabditis elegans , and its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3'-UTR and post-transcriptional regulation of MEX-3 target transcripts. However, the molecular mechanisms of translational repression and the consensus RNA sequence recognized by the MEX-3C KH domain are unknown. Here, using X-ray crystallography and isothermal titration calorimetry, we investigated the RNA-binding activity and selectivity of human MEX-3C dual KH domains. Our high-resolution crystal structures of individual KH domains complexed with a noncanonical U-rich and a GA-rich RNA sequence revealed that the KH1/2 domains of human MEX-3C bound MRE10, a 10-mer RNA (5'-CAGAGUUUAG-3') consisting of an eight-nucleotide MEX-3-recognition element (MRE) motif, with high affinity. Of note, we also identified a consensus RNA motif recognized by human MEX-3C. The potential RNA-binding sites in the 3'-UTR of the human leukocyte antigen serotype ( HLA-A2 ) mRNA were mapped with this RNA-binding motif and further confirmed by fluorescence polarization. The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

7 CFR 98.5 - Fees and charges.

Code of Federal Regulations, 2013 CFR

2013-01-01

... MEALS, READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.5 Fees and charges. (a) The fee charged for any single laboratory analysis of meat, meat food... charge for any requested laboratory analysis of meat, meat food products, and MRE's not listed shall be...

7 CFR 98.5 - Fees and charges.

Code of Federal Regulations, 2010 CFR

2010-01-01

... MEALS, READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.5 Fees and charges. (a) The fee charged for any single laboratory analysis of meat, meat food... charge for any requested laboratory analysis of meat, meat food products, and MRE's not listed shall be...

7 CFR 98.5 - Fees and charges.

Code of Federal Regulations, 2012 CFR

2012-01-01

... MEALS, READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.5 Fees and charges. (a) The fee charged for any single laboratory analysis of meat, meat food... charge for any requested laboratory analysis of meat, meat food products, and MRE's not listed shall be...

PBP deletion mutants of Escherichia coli exhibit irregular distribution of MreB at the deformed zones.

PubMed

Vijayan, Saptha; Mallick, Sathi; Dutta, Mouparna; Narayani, M; Ghosh, Anindya S

2014-02-01

MreB is a cytoskeletal protein, which is responsible for maintaining proper cellular morphology and is essential for cell survival. Likewise, penicillin-binding protein 5 (PBP5) helps in maintaining cell shape, though non-essential for survival. The contradicting feature of these two proteins paves the way for this study, wherein we attempt to draw a relation on the nature of distribution of MreB in PBP deletion mutants. The study revealed that the uniform MreB helices/patches were destabilized/disturbed at the zone of deformities of the PBP mutants, whereas the helical patterns were retained at the regions maintaining a rod shape. We interpret that MreB remains functional irrespective of its distribution being misguided by the aberrant shapes of PBP mutants.

Pre-clinical MR elastography: Principles, techniques, and applications

NASA Astrophysics Data System (ADS)

Bayly, P. V.; Garbow, J. R.

2018-06-01

Magnetic resonance elastography (MRE) is a method for measuring the mechanical properties of soft tissue in vivo, non-invasively, by imaging propagating shear waves in the tissue. The speed and attenuation of waves depends on the elastic and dissipative properties of the underlying material. Tissue mechanical properties are essential for biomechanical models and simulations, and may serve as markers of disease, injury, development, or recovery. MRE is already established as a clinical technique for detecting and characterizing liver disease. The potential of MRE for diagnosing or characterizing disease in other organs, including brain, breast, and heart is an active research area. Studies involving MRE in the pre-clinical setting, in phantoms and artificial biomaterials, in the mouse, and in other mammals, are critical to the development of MRE as a robust, reliable, and useful modality.

Natural transformation occurs independently of the essential actin-like MreB cytoskeleton in Legionella pneumophila

PubMed Central

Juan, Pierre-Alexandre; Attaiech, Laetitia; Charpentier, Xavier

2015-01-01

Natural transformation is the process by which bacteria can actively take up and integrate exogenous DNA thereby providing a source of genetic diversity. Under specific growth conditions the coordinated expression of several genes – a situation referred to as “competence” – allows bacteria to assemble a highly processive and dedicated system that can import high molecular weight DNA. Within the cell these large imported DNA molecules are protected from degradation and brought to the chromosome for recombination. Here, we report elevated expression of mreB during competence in the Gram-negative pathogen Legionella pneumophila. Interestingly a similar observation had previously been reported in the distantly-related Gram-positive organism Bacillus subtilis. MreB is often viewed as the bacterial actin homolog contributing to bacterial morphogenesis by coordinating peptidoglycan-synthesising complexes. In addition MreB is increasingly found to be involved in a growing number of processes including chromosome segregation and motor-driven motility. Using genetic and pharmacological approaches, we examined the possible role of MreB during natural transformation in L. pneumophila. Our data show that natural transformation does not require MreB dynamics and exclude a direct role of MreB filaments in the transport of foreign DNA and its recombination in the chromosome. PMID:26526572

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.

PubMed

van Teeffelen, Sven; Wang, Siyuan; Furchtgott, Leon; Huang, Kerwyn Casey; Wingreen, Ned S; Shaevitz, Joshua W; Gitai, Zemer

2011-09-20

Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.

Natural transformation occurs independently of the essential actin-like MreB cytoskeleton in Legionella pneumophila.

PubMed

Juan, Pierre-Alexandre; Attaiech, Laetitia; Charpentier, Xavier

2015-11-03

Natural transformation is the process by which bacteria can actively take up and integrate exogenous DNA thereby providing a source of genetic diversity. Under specific growth conditions the coordinated expression of several genes--a situation referred to as "competence"--allows bacteria to assemble a highly processive and dedicated system that can import high molecular weight DNA. Within the cell these large imported DNA molecules are protected from degradation and brought to the chromosome for recombination. Here, we report elevated expression of mreB during competence in the Gram-negative pathogen Legionella pneumophila. Interestingly a similar observation had previously been reported in the distantly-related Gram-positive organism Bacillus subtilis. MreB is often viewed as the bacterial actin homolog contributing to bacterial morphogenesis by coordinating peptidoglycan-synthesising complexes. In addition MreB is increasingly found to be involved in a growing number of processes including chromosome segregation and motor-driven motility. Using genetic and pharmacological approaches, we examined the possible role of MreB during natural transformation in L. pneumophila. Our data show that natural transformation does not require MreB dynamics and exclude a direct role of MreB filaments in the transport of foreign DNA and its recombination in the chromosome.

In Vivo, High-Frequency Three-Dimensional Cardiac MR Elastography: Feasibility in Normal Volunteers

PubMed Central

Arani, Arvin; Glaser, Kevin L.; Arunachalam, Shivaram P.; Rossman, Phillip J.; Lake, David S.; Trzasko, Joshua D.; Manduca, Armando; McGee, Kiaran P.; Ehman, Richard L.; Araoz, Philip A.

2016-01-01

Purpose Noninvasive stiffness imaging techniques (elastography) can image myocardial tissue biomechanics in vivo. For cardiac MR elastography (MRE) techniques, the optimal vibration frequency for in vivo experiments is unknown. Furthermore, the accuracy of cardiac MRE has never been evaluated in a geometrically accurate phantom. Therefore, the purpose of this study was to determine the necessary driving frequency to obtain accurate three-dimensional (3D) cardiac MRE stiffness estimates in a geometrically accurate diastolic cardiac phantom and to determine the optimal vibration frequency that can be introduced in healthy volunteers. Methods The 3D cardiac MRE was performed on eight healthy volunteers using 80 Hz, 100 Hz, 140 Hz, 180 Hz, and 220 Hz vibration frequencies. These frequencies were tested in a geometrically accurate diastolic heart phantom and compared with dynamic mechanical analysis (DMA). Results The 3D Cardiac MRE was shown to be feasible in volunteers at frequencies as high as 180 Hz. MRE and DMA agreed within 5% at frequencies greater than 180 Hz in the cardiac phantom. However, octahedral shear strain signal to noise ratios and myocardial coverage was shown to be highest at a frequency of 140 Hz across all subjects. Conclusion This study motivates future evaluation of high-frequency 3D MRE in patient populations. PMID:26778442

Design of magnetic Circuit Simulation for Curing Device of Anisotropic MRE

NASA Astrophysics Data System (ADS)

Hapipi, N.; Ubaidillah; Mazlan, S. A.; Widodo, P. J.

2018-03-01

The strength of magnetic field during fabrication of magnetorheological elastomer (MRE) plays a crucial role in order to form a pre-structured MRE. So far, gaussmeter were used to determine the magnetic intensity subjected to the MRE during curing. However, the magnetic flux reading through that measurement considered less accurate. Therefore, a simulation should be done to figure out the magnetic flux concentration around the sample. This paper investigates the simulation of magnetic field distribution in a curing device used during curing stage of anisotropic magnetorheological elastomer (MRE). The target in designing the magnetic circuit is to ensure a sufficient and uniform magnetic field to all the MRE surfaces during the curing process. The magnetic circuit design for the curing device was performed using Finite Element Method Magnetic (FEMM) to examine the magnetic flux density distribution in the device. The material selection was first done instantaneously during a magnetic simulation process. Then, the experimental validation of simulation was performed by measuring and comparing the actual flux generated within the specimen type and the one from the FEMM simulation. İt apparent that the data from FEMM simulation shows an agreement with the actual measurement. Furthermore, the FEMM results showed that the magnetic design is able to provide sufficient and uniform magnetic field all over the surfaces of the MRE.

Investigation on the effect of MR elastomer based adaptive vibration absorbers on the radiated sound from circular elastic plates

NASA Astrophysics Data System (ADS)

Hemmatian, M.; Sedaghati, R.

2016-04-01

This study aims to investigate the effect of using magnetorheological elastomer (MRE)-based adaptive tuned vibration absorbers (ATVA) on the sound transmission in an elastic plate. Sound transmission loss (STL) of an elastic circular thin plate is analytically studied. The plate is excited by a plane acoustic wave as an incident sound and the displacement of the plate is calculated using corresponding mode shapes of the system for clamped boundary condition. Rayleigh integral approach is used to express the transmitted sound pressure in terms of the plate's displacement modal amplitude. In order to increase sound transmission loss of the plate, the MRE-based ATVA is considered. The basic idea is to be able to change the stiffness of the ATVA by varying magnetic field in order to reduce the transmitted acoustic energy of the host structure in a wide frequency range. Here, a MRE-based ATVA under the shear mode consisting of an oscillator mass, magnetic conductor, coils and MRE is investigated. In order to predict the viscoelastic characteristics of the field-dependent MRE based on the applied magnetic field, the double pole model is used. Finally, MRE-based ATVAs are integrated with the plate to absorb the plate energy with the aim of decreasing the transmitted sound power. Results show that plate with integrated MRE-based ATVAs suppresses the axisymmetric vibration of the plate and thus considerably improves the STL. Parametric studies on the influence of the position of MRE-based ATVAs and the effects of applied current on their performance are also presented.

77 FR 15053 - Manual for Courts-Martial; Proposed Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-14

... the M.R.E. and a Word document using color-coded text and comments to explain amendments. Updated... evidence. f. Commenter recommended using the words ``pursuant to statutory authority'' in M.R.E. 807. JSC... the rule to findings. i. Commenter recommended removing the word ``allegedly'' from proposed M.R.E...

Expression of membrane-associated proteins within single emulsion cell facsimiles.

PubMed

Chanasakulniyom, Mayuree; Martino, Chiara; Paterson, David; Horsfall, Louise; Rosser, Susan; Cooper, Jonathan M

2012-07-07

MreB is a structural membrane-associated protein which is one of the key components of the bacterial cytoskeleton. Although it plays an important role in shape maintenance of rod-like bacteria, the understanding of its mechanism of action is still not fully understood. This study shows how segmented flow and microdroplet technology can be used as a new tool for biological in vitro investigation of this protein. In this paper, we demonstrate cell-free expression in a single emulsion system to express red fluorescence protein (RFP) and MreB linked RFP (MreB-RFP). We follow the aggregation and localisation of the fusion protein MreB-RFP in this artificial cell-like environment. The expression of MreB-RFP in single emulsion droplets leads to the formation of micrometer-scale protein patches distributed at the water/oil interface.

A Novel indole compound that inhibits Pseudomonas aeruginosa growth by targeting MreB is a substrate for MexAB-OprM.

PubMed

Robertson, Gregory T; Doyle, Timothy B; Du, Qun; Duncan, Leonard; Mdluli, Khisimuzi E; Lynch, A Simon

2007-10-01

Drug efflux systems contribute to the intrinsic resistance of Pseudomonas aeruginosa to many antibiotics and biocides and hamper research focused on the discovery and development of new antimicrobial agents targeted against this important opportunistic pathogen. Using a P. aeruginosa PAO1 derivative bearing deletions of opmH, encoding an outer membrane channel for efflux substrates, and four efflux pumps belonging to the resistance nodulation/cell division class including mexAB-oprM, we identified a small-molecule indole-class compound (CBR-4830) that is inhibitory to growth of this efflux-compromised strain. Genetic studies established MexAB-OprM as the principal pump for CBR-4830 and revealed MreB, a prokaryotic actin homolog, as the proximal cellular target of CBR-4830. Additional studies establish MreB as an essential protein in P. aeruginosa, and efflux-compromised strains treated with CBR-4830 transition to coccoid shape, consistent with MreB inhibition or depletion. Resistance genetics further suggest that CBR-4830 interacts with the putative ATP-binding pocket in MreB and demonstrate significant cross-resistance with A22, a structurally unrelated compound that has been shown to promote rapid dispersion of MreB filaments in vivo. Interestingly, however, ATP-dependent polymerization of purified recombinant P. aeruginosa MreB is blocked in vitro in a dose-dependent manner by CBR-4830 but not by A22. Neither compound exhibits significant inhibitory activity against mutant forms of MreB protein that bear mutations identified in CBR-4830-resistant strains. Finally, employing the strains and reagents prepared and characterized during the course of these studies, we have begun to investigate the ability of analogues of CBR-4830 to inhibit the growth of both efflux-proficient and efflux-compromised P. aeruginosa through specific inhibition of MreB function.

Novel technique for MR elastography of the prostate using a modified standard endorectal coil as actuator.

PubMed

Thörmer, Gregor; Reiss-Zimmermann, Martin; Otto, Josephin; Hoffmann, Karl-Titus; Moche, Michael; Garnov, Nikita; Kahn, Thomas; Busse, Harald

2013-06-01

To present a novel method for MR elastography (MRE) of the prostate at 3 Tesla using a modified endorectal imaging coil. A commercial endorectal coil was modified to dynamically generate mechanical stress (contraction and dilation) in a prostate phantom with embedded phantom "lesions" (6 mm diameter) and in a porcine model. Resulting tissue displacements were measured with a motion-sensitive EPI sequence at actuation frequencies of 50-200 Hz. Maps of shear modulus G were calculated from the measured phase-difference shear-wave patterns. In the G maps of the phantom, "lesions" were easily discernible against the background. The average G values of regions of interest placed in the "lesion" (8.2 ± 1.9 kPa) were much higher than those in the background (3.6 ± 1.4 kPa) but systematically lower than values reported by the vendor (13.0 ± 1.0 and 6.7 ± 0.7 kPa, respectively). In the porcine model, shear waves could be generated and measured shear moduli were substantially different for muscle (7.1 ± 2.0 kPa), prostate (3.0 ± 1.4 kPa), and bulbourethral gland (5.6 ± 1.9 kPa). An endorectal MRE concept is technically feasible. The presented technique will allow for simultaneous MRE and MRI acquisitions using a commercial base device with minor, MR-conditional modifications. The diagnostic value needs to be determined in further trials. Copyright © 2012 Wiley Periodicals, Inc.

Minimum relative entropy, Bayes and Kapur

NASA Astrophysics Data System (ADS)

Woodbury, Allan D.

2011-04-01

The focus of this paper is to illustrate important philosophies on inversion and the similarly and differences between Bayesian and minimum relative entropy (MRE) methods. The development of each approach is illustrated through the general-discrete linear inverse. MRE differs from both Bayes and classical statistical methods in that knowledge of moments are used as ‘data’ rather than sample values. MRE like Bayes, presumes knowledge of a prior probability distribution and produces the posterior pdf itself. MRE attempts to produce this pdf based on the information provided by new moments. It will use moments of the prior distribution only if new data on these moments is not available. It is important to note that MRE makes a strong statement that the imposed constraints are exact and complete. In this way, MRE is maximally uncommitted with respect to unknown information. In general, since input data are known only to within a certain accuracy, it is important that any inversion method should allow for errors in the measured data. The MRE approach can accommodate such uncertainty and in new work described here, previous results are modified to include a Gaussian prior. A variety of MRE solutions are reproduced under a number of assumed moments and these include second-order central moments. Various solutions of Jacobs & van der Geest were repeated and clarified. Menke's weighted minimum length solution was shown to have a basis in information theory, and the classic least-squares estimate is shown as a solution to MRE under the conditions of more data than unknowns and where we utilize the observed data and their associated noise. An example inverse problem involving a gravity survey over a layered and faulted zone is shown. In all cases the inverse results match quite closely the actual density profile, at least in the upper portions of the profile. The similar results to Bayes presented in are a reflection of the fact that the MRE posterior pdf, and its mean are constrained not by d=Gm but by its first moment E(d=Gm), a weakened form of the constraints. If there is no error in the data then one should expect a complete agreement between Bayes and MRE and this is what is shown. Similar results are shown when second moment data is available (e.g. posterior covariance equal to zero). But dissimilar results are noted when we attempt to derive a Bayesian like result from MRE. In the various examples given in this paper, the problems look similar but are, in the final analysis, not equal. The methods of attack are different and so are the results even though we have used the linear inverse problem as a common template.

Semi-active control of magnetorheological elastomer base isolation system utilising learning-based inverse model

NASA Astrophysics Data System (ADS)

Gu, Xiaoyu; Yu, Yang; Li, Jianchun; Li, Yancheng

2017-10-01

Magnetorheological elastomer (MRE) base isolations have attracted considerable attention over the last two decades thanks to its self-adaptability and high-authority controllability in semi-active control realm. Due to the inherent nonlinearity and hysteresis of the devices, it is challenging to obtain a reasonably complicated mathematical model to describe the inverse dynamics of MRE base isolators and hence to realise control synthesis of the MRE base isolation system. Two aims have been achieved in this paper: i) development of an inverse model for MRE base isolator based on optimal general regression neural network (GRNN); ii) numerical and experimental validation of a real-time semi-active controlled MRE base isolation system utilising LQR controller and GRNN inverse model. The superiority of GRNN inverse model lays in fewer input variables requirement, faster training process and prompt calculation response, which makes it suitable for online training and real-time control. The control system is integrated with a three-storey shear building model and control performance of the MRE base isolation system is compared with bare building, passive-on isolation system and passive-off isolation system. Testing results show that the proposed GRNN inverse model is able to reproduce desired control force accurately and the MRE base isolation system can effectively suppress the structural responses when compared to the passive isolation system.

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly

PubMed Central

van Teeffelen, Sven; Wang, Siyuan; Furchtgott, Leon; Huang, Kerwyn Casey; Wingreen, Ned S.; Shaevitz, Joshua W.; Gitai, Zemer

2011-01-01

Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis. PMID:21903929

Simultaneous 3D MR elastography of the in vivo mouse brain

NASA Astrophysics Data System (ADS)

Kearney, Steven P.; Majumdar, Shreyan; Royston, Thomas J.; Klatt, Dieter

2017-10-01

The feasibility of sample interval modulation (SLIM) magnetic resonance elastography (MRE) for the in vivo mouse brain is assessed, and an alternative SLIM-MRE encoding method is introduced. In SLIM-MRE, the phase accumulation for each motion direction is encoded simultaneously by varying either the start time of the motion encoding gradient (MEG), SLIM-phase constant (SLIM-PC), or the initial phase of the MEG, SLIM-phase varying (SLIM-PV). SLIM-PC provides gradient moment nulling, but the mutual gradient shift necessitates increased echo time (TE). SLIM-PV requires no increased TE, but exhibits non-uniform flow compensation. Comparison was to conventional MRE using six C57BL/6 mice. For SLIM-PC, the Spearman’s rank correlation to conventional MRE for the shear storage and loss modulus images were 80% and 76%, respectively, and likewise for SLIM-PV, 73% and 69%, respectively. The results of the Wilcoxon rank sum test showed that there were no statistically significant differences between the spatially averaged shear moduli derived from conventional-MRE, SLIM-PC, and SLIM-PV acquisitions. Both SLIM approaches were comparable to conventional MRE scans with Spearman’s rank correlation of 69%-80% and with 3 times reduction in scan time. The SLIM-PC method had the best correlation, and SLIM-PV may be a useful tool in experimental conditions, where both measurement time and T2 relaxation is critical.

In vivo, high-frequency three-dimensional cardiac MR elastography: Feasibility in normal volunteers.

PubMed

Arani, Arvin; Glaser, Kevin L; Arunachalam, Shivaram P; Rossman, Phillip J; Lake, David S; Trzasko, Joshua D; Manduca, Armando; McGee, Kiaran P; Ehman, Richard L; Araoz, Philip A

2017-01-01

Noninvasive stiffness imaging techniques (elastography) can image myocardial tissue biomechanics in vivo. For cardiac MR elastography (MRE) techniques, the optimal vibration frequency for in vivo experiments is unknown. Furthermore, the accuracy of cardiac MRE has never been evaluated in a geometrically accurate phantom. Therefore, the purpose of this study was to determine the necessary driving frequency to obtain accurate three-dimensional (3D) cardiac MRE stiffness estimates in a geometrically accurate diastolic cardiac phantom and to determine the optimal vibration frequency that can be introduced in healthy volunteers. The 3D cardiac MRE was performed on eight healthy volunteers using 80 Hz, 100 Hz, 140 Hz, 180 Hz, and 220 Hz vibration frequencies. These frequencies were tested in a geometrically accurate diastolic heart phantom and compared with dynamic mechanical analysis (DMA). The 3D Cardiac MRE was shown to be feasible in volunteers at frequencies as high as 180 Hz. MRE and DMA agreed within 5% at frequencies greater than 180 Hz in the cardiac phantom. However, octahedral shear strain signal to noise ratios and myocardial coverage was shown to be highest at a frequency of 140 Hz across all subjects. This study motivates future evaluation of high-frequency 3D MRE in patient populations. Magn Reson Med 77:351-360, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines.

PubMed

Eryilmaz, Marion; Schmitt, Eberhard; Krufczik, Matthias; Theda, Franziska; Lee, Jin-Ho; Cremer, Christoph; Bestvater, Felix; Schaufler, Wladimir; Hausmann, Michael; Hildenbrand, Georg

2018-01-22

In radiation biophysics, it is a subject of nowadays research to investigate DNA strand break repair in detail after damage induction by ionizing radiation. It is a subject of debate as to what makes up the cell's decision to use a certain repair pathway and how the repair machinery recruited in repair foci is spatially and temporarily organized. Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by γH2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair.

Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines

PubMed Central

Eryilmaz, Marion; Schmitt, Eberhard; Krufczik, Matthias; Theda, Franziska; Lee, Jin-Ho; Cremer, Christoph; Bestvater, Felix; Schaufler, Wladimir; Hildenbrand, Georg

2018-01-01

In radiation biophysics, it is a subject of nowadays research to investigate DNA strand break repair in detail after damage induction by ionizing radiation. It is a subject of debate as to what makes up the cell’s decision to use a certain repair pathway and how the repair machinery recruited in repair foci is spatially and temporarily organized. Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by γH2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair. PMID:29361783

Magnetic resonance enterography or video capsule endoscopy – what do Crohn’s disease patients prefer?

PubMed Central

Lahat, Adi; Kopylov, Uri; Amitai, Marianne M; Neuman, Sandra; Levhar, Nina; Yablecovitch, Doron; Avidan, Benjamin; Yanai, Henit; Dotan, Iris; Chowers, Yehuda; Weiss, Batya; Ben-Horin, Shomron; Eliakim, Rami

2016-01-01

Background Despite differences in the information obtained by capsule endoscopy (CE) and magnetic resonance enterography (MRE), one of these modalities is usually needed when evaluating disease activity. There are no data on patients’ preference that would help guide the choice between these two modalities in these instances. Aim To compare patients’ tolerance and preference to MRE versus CE. Patients and methods Patients with known small bowel Crohn’s disease (CD) in clinical remission (Crohn’s disease activity index [CDAI] <150) or with mild symptoms (CDAI <220) were prospectively recruited. All patients underwent MRE followed by CE. Patients were asked to fill out a questionnaire addressing specific points regarding inconvenience during the preparation for the procedures, the procedures, and postprocedures. Side effects and procedure preference were addressed. Questionnaires were included for analysis only when more than 95% of the items were addressed. Results Fifty-six patients fulfilled inclusion criteria. Pre-exam discomfort, during-exam discomfort, nausea, vomiting, bloating, and abdominal pain were all significantly more prominent in MRE as compared to CE (P<0.0001, P<0.0001, P<0.0001, P=0.009, P=0.0002, P<0.0001, respectively). MRE was perceived as a more difficult procedure (P<0.0001). Furthermore, MRE was associated with a specific adverse event – claustrophobia. Seventy-eight percent of patients (44 patients) preferred to repeat CE as compared to 22% (P<0.0001) who preferred MRE. Conclusion CE was better tolerated by CD patients compared to MRE and was preferred by 78% of patients. The superior tolerability of CE should be considered along with the diagnostic features, and more data sought when choosing between these two modalities for CD patients for long-term follow-up. PMID:27354774

The actin-like MreB cytoskeleton organizes viral DNA replication in bacteria.

PubMed

Muñoz-Espín, Daniel; Daniel, Richard; Kawai, Yoshikazu; Carballido-López, Rut; Castilla-Llorente, Virginia; Errington, Jeff; Meijer, Wilfried J J; Salas, Margarita

2009-08-11

Little is known about the organization or proteins involved in membrane-associated replication of prokaryotic genomes. Here we show that the actin-like MreB cytoskeleton of the distantly related bacteria Escherichia coli and Bacillus subtilis is required for efficient viral DNA replication. Detailed analyses of B. subtilis phage ϕ29 showed that the MreB cytoskeleton plays a crucial role in organizing phage DNA replication at the membrane. Thus, phage double-stranded DNA and components of the ϕ29 replication machinery localize in peripheral helix-like structures in a cytoskeleton-dependent way. Importantly, we show that MreB interacts directly with the ϕ29 membrane-protein p16.7, responsible for attaching viral DNA at the cell membrane. Altogether, the results reveal another function for the MreB cytoskeleton and describe a mechanism by which viral DNA replication is organized at the bacterial membrane.

Super-resolution imaging and tracking of protein-protein interactions in sub-diffraction cellular space

NASA Astrophysics Data System (ADS)

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-07-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein-protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB-EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB-EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB-EF-Tu interactions.

Super-resolution imaging and tracking of protein–protein interactions in sub-diffraction cellular space

PubMed Central

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-01-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein–protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB–EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB–EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB–EF-Tu interactions. PMID:25030837

Actin homolog MreB affects chromosome segregation by regulating topoisomerase IV in Escherichia coli.

PubMed

Madabhushi, Ram; Marians, Kenneth J

2009-01-30

In Escherichia coli, topoisomerase IV, a type II topoisomerase, mediates the resolution of topological linkages between replicated daughter chromosomes and is essential for chromosome segregation. Topo IV activity is restricted to only a short interval late in the cell cycle. However, the mechanism that confers this temporal regulation is unknown. Here we report that the bacterial actin homolog MreB participates in the temporal oscillation of Topo IV activity. We show that mreB mutant strains are deficient in Topo IV activity. In addition, we demonstrate that, depending upon whether it is in a monomeric or polymerized state, MreB affects Topo IV activity differentially. In addition, MreB physically interacts with the ParC subunit of Topo IV. Together, these results may explain how dynamics of the bacterial cytoskeleton are coordinated with the timing of chromosome segregation.

A MATLAB implementation of the minimum relative entropy method for linear inverse problems

NASA Astrophysics Data System (ADS)

Neupauer, Roseanna M.; Borchers, Brian

2001-08-01

The minimum relative entropy (MRE) method can be used to solve linear inverse problems of the form Gm= d, where m is a vector of unknown model parameters and d is a vector of measured data. The MRE method treats the elements of m as random variables, and obtains a multivariate probability density function for m. The probability density function is constrained by prior information about the upper and lower bounds of m, a prior expected value of m, and the measured data. The solution of the inverse problem is the expected value of m, based on the derived probability density function. We present a MATLAB implementation of the MRE method. Several numerical issues arise in the implementation of the MRE method and are discussed here. We present the source history reconstruction problem from groundwater hydrology as an example of the MRE implementation.

Determining Permissible Oxygen and Water Vapor Transmission Rate for Non-Retort Military Ration Packaging

DTIC Science & Technology

2011-11-01

OXYGEN AND WATER VAPOR TRANSMISSION RATE FOR NON- RETORT MILITARY RATION PACKAGING by Danielle Froio Alan Wright Nicole Favreau and Sarah...ANSI Std. Z39.18 RETORT STORAGE SHELF LIFE RETORT POUCHES SENSORY ANALYSIS OXYGEN CRACKERS PACKAGING SENSORY... Packaging for MRE. (a) MRE Retort Pouch Quad-Laminate Structure; (b) MRE Non- retort Pouch Tri-Laminate Structure

Breast magnetic resonance elastography: a review of clinical work and future perspectives.

PubMed

Bohte, A E; Nelissen, J L; Runge, J H; Holub, O; Lambert, S A; de Graaf, L; Kolkman, S; van der Meij, S; Stoker, J; Strijkers, G J; Nederveen, A J; Sinkus, R

2018-05-30

This review on magnetic resonance elastography (MRE) of the breast provides an overview of available literature and describes current developments in the field of breast MRE, including new transducer technology for data acquisition and multi-frequency-derived power-law behaviour of tissue. Moreover, we discuss the future potential of breast MRE, which goes beyond its original application as an additional tool in differentiating benign from malignant breast lesions. These areas of ongoing and future research include MRE for pre-operative tumour delineation, staging, monitoring and predicting response to treatment, as well as prediction of the metastatic potential of primary tumours. Copyright © 2018 John Wiley & Sons, Ltd.

The small G-protein MglA connects to the MreB actin cytoskeleton at bacterial focal adhesions.

PubMed

Treuner-Lange, Anke; Macia, Eric; Guzzo, Mathilde; Hot, Edina; Faure, Laura M; Jakobczak, Beata; Espinosa, Leon; Alcor, Damien; Ducret, Adrien; Keilberg, Daniela; Castaing, Jean Philippe; Lacas Gervais, Sandra; Franco, Michel; Søgaard-Andersen, Lotte; Mignot, Tâm

2015-07-20

In Myxococcus xanthus the gliding motility machinery is assembled at the leading cell pole to form focal adhesions, translocated rearward to propel the cell, and disassembled at the lagging pole. We show that MglA, a Ras-like small G-protein, is an integral part of this machinery. In this function, MglA stimulates the assembly of the motility complex by directly connecting it to the MreB actin cytoskeleton. Because the nucleotide state of MglA is regulated spatially and MglA only binds MreB in the guanosine triphosphate-bound form, the motility complexes are assembled at the leading pole and dispersed at the lagging pole where the guanosine triphosphatase activating protein MglB disrupts the MglA-MreB interaction. Thus, MglA acts as a nucleotide-dependent molecular switch to regulate the motility machinery spatially. The function of MreB in motility is independent of its function in peptidoglycan synthesis, representing a coopted function. Our findings highlight a new function for the MreB cytoskeleton and suggest that G-protein-cytoskeleton interactions are a universally conserved feature. © 2015 Treuner-Lange et al.

The small G-protein MglA connects to the MreB actin cytoskeleton at bacterial focal adhesions

PubMed Central

Treuner-Lange, Anke; Macia, Eric; Guzzo, Mathilde; Hot, Edina; Faure, Laura M.; Jakobczak, Beata; Espinosa, Leon; Alcor, Damien; Ducret, Adrien; Keilberg, Daniela; Castaing, Jean Philippe; Lacas Gervais, Sandra; Franco, Michel

2015-01-01

In Myxococcus xanthus the gliding motility machinery is assembled at the leading cell pole to form focal adhesions, translocated rearward to propel the cell, and disassembled at the lagging pole. We show that MglA, a Ras-like small G-protein, is an integral part of this machinery. In this function, MglA stimulates the assembly of the motility complex by directly connecting it to the MreB actin cytoskeleton. Because the nucleotide state of MglA is regulated spatially and MglA only binds MreB in the guanosine triphosphate–bound form, the motility complexes are assembled at the leading pole and dispersed at the lagging pole where the guanosine triphosphatase activating protein MglB disrupts the MglA–MreB interaction. Thus, MglA acts as a nucleotide-dependent molecular switch to regulate the motility machinery spatially. The function of MreB in motility is independent of its function in peptidoglycan synthesis, representing a coopted function. Our findings highlight a new function for the MreB cytoskeleton and suggest that G-protein–cytoskeleton interactions are a universally conserved feature. PMID:26169353

International travel and acquisition of multidrug-resistant Enterobacteriaceae: a systematic review.

PubMed

Hassing, Robert Jan; Alsma, Jelmer; Arcilla, Maris S; van Genderen, Perry J; Stricker, Bruno H; Verbon, Annelies

2015-01-01

International travel is considered to be an important risk factor for acquisition of multidrug-resistant Enterobacteriaceae (MRE). The aim of this systematic review was to determine the effect of international travel on the risk of post-travel faecal carriage of MRE. Secondary outcomes were risk factors for acquisition of MRE. A systematic search for relevant literature in seven international databases was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Articles needed to report on (i) foreign travel, (ii) screening of asymptomatic participants, (iii) antimicrobial susceptibility data and (iv) faecal Enterobacteriaceae carriage. Two researchers independently screened the abstracts, assessed the full article texts for eligibility and selected or rejected them for inclusion in the systematic review. In case of disagreement, a third researcher decided on inclusion. Eleven studies were identified. In all studies, a high prevalence (>20%) of carriage of MRE after international travel was found. The highest prevalence was observed in travellers returning from southern Asia. Foreign travel was associated with an increased risk of carriage of MRE. Further research is needed to assess if this leads to an increase in the number of infections with MRE. Systematic review registration number: PROSPERO CRD42015024973.

Sample interval modulation for the simultaneous acquisition of displacement vector data in magnetic resonance elastography: theory and application

NASA Astrophysics Data System (ADS)

Klatt, Dieter; Yasar, Temel K.; Royston, Thomas J.; Magin, Richard L.

2013-12-01

SampLe Interval Modulation-magnetic resonance elastography (SLIM-MRE) is introduced for simultaneously encoding all three displacement projections of a monofrequency vibration into the MR signal phase. In SLIM-MRE, the individual displacement components are observed using different sample intervals. In doing so, the components are modulated with different apparent frequencies in the MR signal phase expressed as a harmonic function of the start time of the motion encoding gradients and can thus be decomposed by applying a Fourier transform to the sampled multidirectional MR phases. In this work, the theoretical foundations of SLIM-MRE are presented and the new idea is implemented using a high field (11.7 T) vertical bore magnetic resonance imaging system on an inhomogeneous agarose gel phantom sample. The local frequency estimation-derived stiffness values were the same within the error margins for both the new SLIM-MRE method and for conventional MRE, while the number of temporally-resolved MRE experiments needed for each study was reduced from three to one. In this work, we present for the first time, monofrequency displacement data along three sensitization directions that were acquired simultaneously and stored in the same k-space.

Sample interval modulation for the simultaneous acquisition of displacement vector data in magnetic resonance elastography: theory and application.

PubMed

Klatt, Dieter; Yasar, Temel K; Royston, Thomas J; Magin, Richard L

2013-12-21

SampLe Interval Modulation-magnetic resonance elastography (SLIM-MRE) is introduced for simultaneously encoding all three displacement projections of a monofrequency vibration into the MR signal phase. In SLIM-MRE, the individual displacement components are observed using different sample intervals. In doing so, the components are modulated with different apparent frequencies in the MR signal phase expressed as a harmonic function of the start time of the motion encoding gradients and can thus be decomposed by applying a Fourier transform to the sampled multidirectional MR phases. In this work, the theoretical foundations of SLIM-MRE are presented and the new idea is implemented using a high field (11.7 T) vertical bore magnetic resonance imaging system on an inhomogeneous agarose gel phantom sample. The local frequency estimation-derived stiffness values were the same within the error margins for both the new SLIM-MRE method and for conventional MRE, while the number of temporally-resolved MRE experiments needed for each study was reduced from three to one. In this work, we present for the first time, monofrequency displacement data along three sensitization directions that were acquired simultaneously and stored in the same k-space.

Multiple kernel SVR based on the MRE for remote sensing water depth fusion detection

NASA Astrophysics Data System (ADS)

Wang, Jinjin; Ma, Yi; Zhang, Jingyu

2018-03-01

Remote sensing has an important means of water depth detection in coastal shallow waters and reefs. Support vector regression (SVR) is a machine learning method which is widely used in data regression. In this paper, SVR is used to remote sensing multispectral bathymetry. Aiming at the problem that the single-kernel SVR method has a large error in shallow water depth inversion, the mean relative error (MRE) of different water depth is retrieved as a decision fusion factor with single kernel SVR method, a multi kernel SVR fusion method based on the MRE is put forward. And taking the North Island of the Xisha Islands in China as an experimentation area, the comparison experiments with the single kernel SVR method and the traditional multi-bands bathymetric method are carried out. The results show that: 1) In range of 0 to 25 meters, the mean absolute error(MAE)of the multi kernel SVR fusion method is 1.5m,the MRE is 13.2%; 2) Compared to the 4 single kernel SVR method, the MRE of the fusion method reduced 1.2% (1.9%) 3.4% (1.8%), and compared to traditional multi-bands method, the MRE reduced 1.9%; 3) In 0-5m depth section, compared to the single kernel method and the multi-bands method, the MRE of fusion method reduced 13.5% to 44.4%, and the distribution of points is more concentrated relative to y=x.

Digestive tract colonization by multidrug-resistant Enterobacteriaceae in travellers: An update.

PubMed

Ruppé, Etienne; Andremont, Antoine; Armand-Lefèvre, Laurence

Enterobacteriaceae have become increasingly resistant, especially due to the acquisition and spread of extended-spectrum beta-lactamases (ESBLs), which confer resistance to the majority of beta-lactams. Multi-resistant Enterobacteriaceae (MRE) were first isolated in hospitals, but now they are disseminating in the community setting, mostly in low and middle income countries. Consequently, the increasing number of international travels leads to the importation of MRE from high-prevalence to low-prevalence countries. The Pubmed database was used to conduct research from 1980 to 2016 by combining the following key words: travel, antibiotic resistance, ESBL, Enterobacteriaceae, genomic, metagenomic, urinary tract infection, infection. The research found that the MRE acquisition rates in healthy travellers from low-prevalence countries ranged from 21% to 51% depending on the study design and the visited geographic regions. After a trip to Asia and especially to South Asia, the acquisition rate could reach 85%. A trip to Africa or to the Middle East was associated with lower rates but still worrisome (13-44%). Digestive disorder, diarrhoea and antibiotics used during travel are major risks factors associated with the acquisition of MRE. Travel to endemic areas has also been identified as a risk factor for MRE infection, including urinary tract infections. Travellers are at high risk of MRE acquisition and consequently of MRE infection. This risk should not be ignored by general practitioners. To reduce the risk of acquisition and subsequent transmission to relatives, travellers should be given recommendations prior to their travel. Copyright © 2017. Published by Elsevier Ltd.

Rad50S alleles of the Mre11 complex: questions answered and questions raised.

PubMed

Usui, Takehiko; Petrini, John H J; Morales, Monica

2006-08-15

We find that Rad50S mutations in yeast and mammals exhibit constitutive PIKK (PI3-kinase like kinase)-dependent signaling [T. Usui, H. Ogawa, J.H. Petrini, A DNA damage response pathway controlled by Tel1 and the Mre11 complex. Mol. Cell 7 (2001) 1255-1266.; M. Morales, J.W. Theunissen, C.F. Kim, R. Kitagawa, M.B. Kastan, J.H. Petrini, The Rad50S allele promotes ATM-dependent DNA damage responses and suppresses ATM deficiency: implications for the Mre11 complex as a DNA damage sensor. Genes Dev. 19 (2005) 3043-4354.]. The signaling depends on Mre11 complex functions, consistent with its role as a DNA damage sensor. Rad50S is distinct from hypomorphic mutations of Mre11 and Nbs1 in mammals [M. Morales, J.W. Theunissen, C.F. Kim, R. Kitagawa, M.B. Kastan, J.H. Petrini, The Rad50S allele promotes ATM-dependent DNA damage responses and suppresses ATM deficiency: implications for the Mre11 complex as a DNA damage sensor. Genes Dev. 19 (2005) 3043-3054.; J.P. Carney, R.S. Maser, H. Olivares, E.M. Davis, Le M. Beau, J.R. Yates, III, L. Hays, W.F. Morgan, J.H. Petrini, The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response. Cell 93 (1998) 477-486.; G.S. Stewart, R.S. Maser, T. Stankovic, D.A. Bressan, M.I. Kaplan, N.G. Jaspers, A. Raams, P.J. Byrd, J.H. Petrini, A.M. Taylor, The DNA double-strand break repair gene hMRE11 is mutated in individuals with an ataxia-telangiectasia-like disorder. Cell 99 (1999) 577-587.; B.R. Williams, O.K. Mirzoeva, W.F. Morgan, J. Lin, W. Dunnick, J.H. Petrini, A murine model of nijmegen breakage syndrome. Curr. Biol. 12 (2002) 648-653.; J.W. Theunissen, M.I. Kaplan, P.A. Hunt, B.R. Williams, D.O. Ferguson, F.W. Alt, J.H. Petrini, Checkpoint failure and chromosomal instability without lymphomagenesis in Mre11(ATLD1/ATLD1) mice. Mol. Cell 12 (2003) 1511-1523.] and the Mre11 complex deficiency in yeast [T. Usui, H. Ogawa, J.H. Petrini, A DNA damage response pathway controlled by Tel1 and the Mre11 complex. Mol. Cell 7 (2001) 1255-1266.; D'D. Amours, S.P. Jackson, The yeast Xrs2 complex functions in S phase checkpoint regulation. Genes Dev. 15 (2001) 2238-49. ; M. Grenon, C. Gilbert, N.F. Lowndes, Checkpoint activation in response to double-strand breaks requires the Mre11/Rad50/Xrs2 complex. Nat. Cell Biol. 3 (2001) 844-847. ] where the signaling is compromised. Herein, we describe evidence for chronic signaling by Rad50S and discuss possible mechanisms.

Direct interaction of FtsZ and MreB is required for septum synthesis and cell division in Escherichia coli.

PubMed

Fenton, Andrew K; Gerdes, Kenn

2013-07-03

How bacteria coordinate cell growth with division is not well understood. Bacterial cell elongation is controlled by actin-MreB while cell division is governed by tubulin-FtsZ. A ring-like structure containing FtsZ (the Z ring) at mid-cell attracts other cell division proteins to form the divisome, an essential protein assembly required for septum synthesis and cell separation. The Z ring exists at mid-cell during a major part of the cell cycle without contracting. Here, we show that MreB and FtsZ of Escherichia coli interact directly and that this interaction is required for Z ring contraction. We further show that the MreB-FtsZ interaction is required for transfer of cell-wall biosynthetic enzymes from the lateral to the mature divisome, allowing cells to synthesise the septum. Our observations show that bacterial cell division is coupled to cell elongation via a direct and essential interaction between FtsZ and MreB.

Bacterial actin MreB assembles in complex with cell shape protein RodZ.

PubMed

van den Ent, Fusinita; Johnson, Christopher M; Persons, Logan; de Boer, Piet; Löwe, Jan

2010-03-17

Bacterial actin homologue MreB is required for cell shape maintenance in most non-spherical bacteria, where it assembles into helical structures just underneath the cytoplasmic membrane. Proper assembly of the actin cytoskeleton requires RodZ, a conserved, bitopic membrane protein that colocalises to MreB and is essential for cell shape determination. Here, we present the first crystal structure of bacterial actin engaged with a natural partner and provide a clear functional significance of the interaction. We show that the cytoplasmic helix-turn-helix motif of Thermotoga maritima RodZ directly interacts with monomeric as well as filamentous MreB and present the crystal structure of the complex. In vitro and in vivo analyses of mutant T. maritima and Escherichia coli RodZ validate the structure and reveal the importance of the MreB-RodZ interaction in the ability of cells to propagate as rods. Furthermore, the results elucidate how the bacterial actin cytoskeleton might be anchored to the membrane to help constrain peptidoglycan synthesis in the periplasm.

Direct interaction of FtsZ and MreB is required for septum synthesis and cell division in Escherichia coli

PubMed Central

Fenton, Andrew K; Gerdes, Kenn

2013-01-01

How bacteria coordinate cell growth with division is not well understood. Bacterial cell elongation is controlled by actin–MreB while cell division is governed by tubulin–FtsZ. A ring-like structure containing FtsZ (the Z ring) at mid-cell attracts other cell division proteins to form the divisome, an essential protein assembly required for septum synthesis and cell separation. The Z ring exists at mid-cell during a major part of the cell cycle without contracting. Here, we show that MreB and FtsZ of Escherichia coli interact directly and that this interaction is required for Z ring contraction. We further show that the MreB–FtsZ interaction is required for transfer of cell-wall biosynthetic enzymes from the lateral to the mature divisome, allowing cells to synthesise the septum. Our observations show that bacterial cell division is coupled to cell elongation via a direct and essential interaction between FtsZ and MreB. PMID:23756461

Design and verification of a hybrid nonlinear MRE vibration absorber for controllable broadband performance

NASA Astrophysics Data System (ADS)

Sun, S. S.; Yildirim, T.; Wu, Jichu; Yang, J.; Du, H.; Zhang, S. W.; Li, W. H.

2017-09-01

In this work, a hybrid nonlinear magnetorheological elastomer (MRE) vibration absorber has been designed, theoretically investigated and experimentally verified. The proposed nonlinear MRE absorber has the dual advantages of a nonlinear force-displacement relationship and variable stiffness technology; the purpose for coupling these two technologies is to achieve a large broadband vibration absorber with controllable capability. To achieve a nonlinear stiffness in the device, two pairs of magnets move at a rotary angle against each other, and the theoretical nonlinear force-displacement relationship has been theoretically calculated. For the experimental investigation, the effects of base excitation, variable currents applied to the device (i.e. variable stiffness of the MRE) and semi-active control have been conducted to determine the enhanced broadband performance of the designed device. It was observed the device was able to change resonance frequency with the applied current; moreover, the hybrid nonlinear MRE absorber displayed a softening-type nonlinear response with clear discontinuous bifurcations observed. Furthermore, the performance of the device under a semi-active control algorithm displayed the optimal performance in attenuating the vibration from a primary system to the absorber over a large frequency bandwidth from 4 to 12 Hz. By coupling nonlinear stiffness attributes with variable stiffness MRE technology, the performance of a vibration absorber is substantially improved.

Filament formation of the Escherichia coli actin-related protein, MreB, in fission yeast.

PubMed

Srinivasan, Ramanujam; Mishra, Mithilesh; Murata-Hori, Maki; Balasubramanian, Mohan K

2007-02-06

Proteins structurally related to eukaryotic actins have recently been identified in several prokaryotic organisms. These actin-like proteins (MreB and ParM) and the deviant Walker A ATPase (SopA) play a key role in DNA segregation and assemble into polymers in vitro and in vivo. MreB also plays a role in cellular morphogenesis. Whereas the dynamic properties of eukaryotic actins have been extensively characterized, those of bacterial actins are only beginning to emerge. We have established the fission yeast Schizosaccharomyces pombe as a cellular model for the functional analysis of the Escherichia coli actin-related protein MreB. We show that MreB organizes into linear bundles that grow in a symmetrically bidirectional manner at 0.46 +/- 0.03 microm/min, with new monomers and/or oligomers being added along the entire length of the bundle. Organization of linear arrays was dependent on the ATPase activity of MreB, and their alignment along the cellular long axis was achieved by sliding along the cortex of the cylindrical part of the cell. The cell ends appeared to provide a physical barrier for bundle elongation. These experiments provide new insights into the mechanism of assembly and organization of the bacterial actin cytoskeleton.

Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA.

PubMed

Mauriello, Emilia M F; Mouhamar, Fabrice; Nan, Beiyan; Ducret, Adrien; Dai, David; Zusman, David R; Mignot, Tâm

2010-01-20

Gliding motility in the bacterium Myxococcus xanthus uses two motility engines: S-motility powered by type-IV pili and A-motility powered by uncharacterized motor proteins and focal adhesion complexes. In this paper, we identified MreB, an actin-like protein, and MglA, a small GTPase of the Ras superfamily, as essential for both motility systems. A22, an inhibitor of MreB cytoskeleton assembly, reversibly inhibited S- and A-motility, causing rapid dispersal of S- and A-motility protein clusters, FrzS and AglZ. This suggests that the MreB cytoskeleton is involved in directing the positioning of these proteins. We also found that a DeltamglA motility mutant showed defective localization of AglZ and FrzS clusters. Interestingly, MglA-YFP localization mimicked both FrzS and AglZ patterns and was perturbed by A22 treatment, consistent with results indicating that both MglA and MreB bind to motility complexes. We propose that MglA and the MreB cytoskeleton act together in a pathway to localize motility proteins such as AglZ and FrzS to assemble the A-motility machineries. Interestingly, M. xanthus motility systems, like eukaryotic systems, use an actin-like protein and a small GTPase spatial regulator.

Smarcal1-Mediated Fork Reversal Triggers Mre11-Dependent Degradation of Nascent DNA in the Absence of Brca2 and Stable Rad51 Nucleofilaments.

PubMed

Kolinjivadi, Arun Mouli; Sannino, Vincenzo; De Antoni, Anna; Zadorozhny, Karina; Kilkenny, Mairi; Técher, Hervé; Baldi, Giorgio; Shen, Rong; Ciccia, Alberto; Pellegrini, Luca; Krejci, Lumir; Costanzo, Vincenzo

2017-09-07

Brca2 deficiency causes Mre11-dependent degradation of nascent DNA at stalled forks, leading to cell lethality. To understand the molecular mechanisms underlying this process, we isolated Xenopus laevis Brca2. We demonstrated that Brca2 protein prevents single-stranded DNA gap accumulation at replication fork junctions and behind them by promoting Rad51 binding to replicating DNA. Without Brca2, forks with persistent gaps are converted by Smarcal1 into reversed forks, triggering extensive Mre11-dependent nascent DNA degradation. Stable Rad51 nucleofilaments, but not RPA or Rad51 T131P mutant proteins, directly prevent Mre11-dependent DNA degradation. Mre11 inhibition instead promotes reversed fork accumulation in the absence of Brca2. Rad51 directly interacts with the Pol α N-terminal domain, promoting Pol α and δ binding to stalled replication forks. This interaction likely promotes replication fork restart and gap avoidance. These results indicate that Brca2 and Rad51 prevent formation of abnormal DNA replication intermediates, whose processing by Smarcal1 and Mre11 predisposes to genome instability. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Controlling cell volume for efficient PHB production by Halomonas.

PubMed

Jiang, Xiao-Ran; Yao, Zhi-Hao; Chen, Guo-Qiang

2017-11-01

Bacterial morphology is decided by cytoskeleton protein MreB and cell division protein FtsZ encoded by essential genes mreB and ftsZ, respectively. Inactivating mreB and ftsZ lead to increasing cell sizes and cell lengths, respectively, yet seriously reduce cell growth ability. Here we develop a temperature-responsible plasmid expression system for compensated expression of relevant gene(s) in mreB or ftsZ disrupted recombinants H. campaniensis LS21, allowing mreB or ftsZ disrupted recombinants to grow normally at 30°C in a bioreactor for 12h so that a certain cell density can be reached, followed by 36h cell size expansions or cell shape elongations at elevated 37°C at which the mreB and ftsZ encoded plasmid pTKmf failed to replicate in the recombinants and thus lost themselves. Finally, 80% PHB yield increase was achieved via controllable morphology manipulated H. campaniensis LS21. It is concluded that controllable expanding cell volumes (widths or lengths) provides more spaces for accumulating more inclusion body polyhydroxybutyrate (PHB) and the resulting cell gravity precipitation benefits the final separation of cells and product during downstream. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA

PubMed Central

Mauriello, Emilia M F; Mouhamar, Fabrice; Nan, Beiyan; Ducret, Adrien; Dai, David; Zusman, David R; Mignot, Tâm

2010-01-01

Gliding motility in the bacterium Myxococcus xanthus uses two motility engines: S-motility powered by type-IV pili and A-motility powered by uncharacterized motor proteins and focal adhesion complexes. In this paper, we identified MreB, an actin-like protein, and MglA, a small GTPase of the Ras superfamily, as essential for both motility systems. A22, an inhibitor of MreB cytoskeleton assembly, reversibly inhibited S- and A-motility, causing rapid dispersal of S- and A-motility protein clusters, FrzS and AglZ. This suggests that the MreB cytoskeleton is involved in directing the positioning of these proteins. We also found that a ΔmglA motility mutant showed defective localization of AglZ and FrzS clusters. Interestingly, MglA–YFP localization mimicked both FrzS and AglZ patterns and was perturbed by A22 treatment, consistent with results indicating that both MglA and MreB bind to motility complexes. We propose that MglA and the MreB cytoskeleton act together in a pathway to localize motility proteins such as AglZ and FrzS to assemble the A-motility machineries. Interestingly, M. xanthus motility systems, like eukaryotic systems, use an actin-like protein and a small GTPase spatial regulator. PMID:19959988

Compression-sensitive magnetic resonance elastography

NASA Astrophysics Data System (ADS)

Hirsch, Sebastian; Beyer, Frauke; Guo, Jing; Papazoglou, Sebastian; Tzschaetzsch, Heiko; Braun, Juergen; Sack, Ingolf

2013-08-01

Magnetic resonance elastography (MRE) quantifies the shear modulus of biological tissue to detect disease. Complementary to the shear elastic properties of tissue, the compression modulus may be a clinically useful biomarker because it is sensitive to tissue pressure and poromechanical interactions. In this work, we analyze the capability of MRE to measure volumetric strain and the dynamic bulk modulus (P-wave modulus) at a harmonic drive frequency commonly used in shear-wave-based MRE. Gel phantoms with various densities were created by introducing CO2-filled cavities to establish a compressible effective medium. The dependence of the effective medium's bulk modulus on phantom density was investigated via static compression tests, which confirmed theoretical predictions. The P-wave modulus of three compressible phantoms was calculated from volumetric strain measured by 3D wave-field MRE at 50 Hz drive frequency. The results demonstrate the MRE-derived volumetric strain and P-wave modulus to be sensitive to the compression properties of effective media. Since the reconstruction of the P-wave modulus requires third-order derivatives, noise remains critical, and P-wave moduli are systematically underestimated. Focusing on relative changes in the effective bulk modulus of tissue, compression-sensitive MRE may be useful for the noninvasive detection of diseases involving pathological pressure alterations such as hepatic hypertension or hydrocephalus.

Magnetic resonance elastography (MRE) of the human brain: technique, findings and clinical applications

NASA Astrophysics Data System (ADS)

Hiscox, Lucy V.; Johnson, Curtis L.; Barnhill, Eric; McGarry, Matt D. J.; Huston 3rd, John; van Beek, Edwin J. R.; Starr, John M.; Roberts, Neil

2016-12-01

Neurological disorders are one of the most important public health concerns in developed countries. Established brain imaging techniques such as magnetic resonance imaging (MRI) and x-ray computerised tomography (CT) have been essential in the identification and diagnosis of a wide range of disorders, although usually are insufficient in sensitivity for detecting subtle pathological alterations to the brain prior to the onset of clinical symptoms—at a time when prognosis for treatment is more favourable. The mechanical properties of biological tissue provide information related to the strength and integrity of the cellular microstructure. In recent years, mechanical properties of the brain have been visualised and measured non-invasively with magnetic resonance elastography (MRE), a particularly sensitive medical imaging technique that may increase the potential for early diagnosis. This review begins with an introduction to the various methods used for the acquisition and analysis of MRE data. A systematic literature search is then conducted to identify studies that have specifically utilised MRE to investigate the human brain. Through the conversion of MRE-derived measurements to shear stiffness (kPa) and, where possible, the loss tangent (rad), a summary of results for global brain tissue and grey and white matter across studies is provided for healthy participants, as potential baseline values to be used in future clinical investigations. In addition, the extent to which MRE has revealed significant alterations to the brain in patients with neurological disorders is assessed and discussed in terms of known pathophysiology. The review concludes by predicting the trends for future MRE research and applications in neuroscience.

Scattering and Diffraction of Elastodynamic Waves in a Concentric Cylindrical Phantom for MR Elastography

PubMed Central

Schwartz, Benjamin L.; Yin, Ziying; Yaşar, Temel K.; Liu, Yifei; Khan, Altaf A.; Ye, Allen Q.; Royston, Thomas J.; Magin, Richard L.

2016-01-01

Aim The focus of this paper is to report on the design and construction of a multiply connected phantom for use in magnetic resonance elasography (MRE)–an imaging technique that allows for the non-invasive visualization of the displacement field throughout an object from externally driven harmonic motion–as well as its inverse modeling with a closed-form analytic solution which is derived herein from first principles. Methods Mathematically, the phantom is described as two infinite concentric circular cylinders with unequal complex shear moduli, harmonically vibrated at the exterior surface in a direction along their common axis. Each concentric cylinder is made of a hydrocolloid with its own specific solute concentration. They are assembled in a multi-step process for which custom scaffolding was designed and built. A customized spin-echo based MR elastography sequence with a sinusoidal motion-sensitizing gradient was used for data acquisition on a 9.4 T Agilent small-animal MR scanner. Complex moduli obtained from the inverse model are used to solve the forward problem with a finite element method. Results Both complex shear moduli show a significant frequency dependence (p < 0.001) in keeping with previous work. Conclusion The novel multiply connected phantom and mathematical model are validated as a viable tool for MRE studies. Significance On a small enough scale much of physiology can be mathematically modeled with basic geometric shapes, e.g. a cylinder representing a blood vessel. This work demonstrates the possibility of elegant mathematical analysis of phantoms specifically designed and carefully constructed for biomedical MRE studies. PMID:26886963

Magnetic Resonance Enterography to Assess Multifocal and Multicentric Bowel Endometriosis.

PubMed

Nyangoh Timoh, Krystel; Stewart, Zelda; Benjoar, Mikhael; Beldjord, Selma; Ballester, Marcos; Bazot, Marc; Thomassin-Naggara, Isabelle; Darai, Emile

To prospectively determine the accuracy of magnetic resonance enterography (MRE) compared with conventional magnetic resonance imaging (MRI) for multifocal (i.e., multiple lesions affecting the same digestive segment) and multicentric (i.e., multiple lesions affecting several digestive segments) bowel endometriosis. A prospective study (Canadian Task Force classification II-2). Tenon University Hospital, Paris, France. Patients with MRI-suspected colorectal endometriosis scheduled for colorectal resection from April 2014 to February 2016 were included. Patients underwent both 1.5-Tesla MRI and MRE as well as laparoscopically assisted and open colorectal resections. The diagnostic performance of MRI and MRE was evaluated for sensitivity, specificity, positive and negative predictive values, accuracy, and positive and negative likelihood ratios (LRs). The interobserver variability of the experienced and junior radiologists was quantified using weighted statistics. Forty-seven patients were included. Twenty-two (46.8%) patients had unifocal lesions, 14 (30%) had multifocal lesions, and 11 (23.4%) had multicentric lesions. The sensitivity, specificity, positive LR, and negative LR for the diagnosis of multifocal lesions were 0.29 (6/21), 1.00 (23/24), 15.36, and 0.71 for MRI and 0.57 (12/21), 0.89 (23/25), 4.95, and 0.58 for MRE. The sensitivity, specificity, positive LR, and negative LR for the diagnosis of multicentric lesions were 0.18 (1/11), 1.00 (1/1), 15, and 0.80 for MRI and 0.46 (5/11), 0.92 (33/36), 5.45, and 0.60 for MRE. Lower accuracies for MRI compared with MRE to diagnose multicentric (p = .01) and multifocal lesions (p = .004) were noted. The interobserver agreement for MRE was good for both multifocality (κ = 0.80) and multicentricity (κ = 0.61). MRE has better accuracy for diagnosing multifocal and multicentric bowel endometriosis than conventional MRI. Copyright © 2018. Published by Elsevier Inc.

The Bacterial Cytoskeleton Modulates Motility, Type 3 Secretion, and Colonization in Salmonella

PubMed Central

Bulmer, David M.; Kharraz, Lubna; Grant, Andrew J.; Dean, Paul; Morgan, Fiona J. E.; Karavolos, Michail H.; Doble, Anne C.; McGhie, Emma J.; Koronakis, Vassilis; Daniel, Richard A.; Mastroeni, Pietro; Anjam Khan, C. M.

2012-01-01

Although there have been great advances in our understanding of the bacterial cytoskeleton, major gaps remain in our knowledge of its importance to virulence. In this study we have explored the contribution of the bacterial cytoskeleton to the ability of Salmonella to express and assemble virulence factors and cause disease. The bacterial actin-like protein MreB polymerises into helical filaments and interacts with other cytoskeletal elements including MreC to control cell-shape. As mreB appears to be an essential gene, we have constructed a viable ΔmreC depletion mutant in Salmonella. Using a broad range of independent biochemical, fluorescence and phenotypic screens we provide evidence that the Salmonella pathogenicity island-1 type three secretion system (SPI1-T3SS) and flagella systems are down-regulated in the absence of MreC. In contrast the SPI-2 T3SS appears to remain functional. The phenotypes have been further validated using a chemical genetic approach to disrupt the functionality of MreB. Although the fitness of ΔmreC is reduced in vivo, we observed that this defect does not completely abrogate the ability of Salmonella to cause disease systemically. By forcing on expression of flagella and SPI-1 T3SS in trans with the master regulators FlhDC and HilA, it is clear that the cytoskeleton is dispensable for the assembly of these structures but essential for their expression. As two-component systems are involved in sensing and adapting to environmental and cell surface signals, we have constructed and screened a panel of such mutants and identified the sensor kinase RcsC as a key phenotypic regulator in ΔmreC. Further genetic analysis revealed the importance of the Rcs two-component system in modulating the expression of these virulence factors. Collectively, these results suggest that expression of virulence genes might be directly coordinated with cytoskeletal integrity, and this regulation is mediated by the two-component system sensor kinase RcsC. PMID:22291596

SNMR pulse sequence phase cycling

DOEpatents

Walsh, David O; Grunewald, Elliot D

2013-11-12

Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

PubMed

Lemos, Brenda R; Kaplan, Adam C; Bae, Ji Eun; Ferrazzoli, Alexander E; Kuo, James; Anand, Ranjith P; Waterman, David P; Haber, James E

2018-02-27

Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

Fecal Calprotectin in Ileal Crohn's Disease: Relationship with Magnetic Resonance Enterography and a Pathology Score.

PubMed

Cerrillo, Elena; Beltrán, Belén; Pous, Salvador; Echarri, Ana; Gallego, Jose Carlos; Iborra, Marisa; Pamies, Jose; Nos, Pilar

2015-07-01

Magnetic resonance enterography (MRE) is an effective method of assessing small bowel Crohn's disease (CD). Fecal calprotectin (FC) correlates well with endoscopic disease activity. We aimed to evaluate the correlation between FC and disease activity according to MRE and surgical pathology in small bowel CD. One hundred twenty consecutive patients with ileal CD who underwent MRE assessment were included. Clinical data, C-reactive protein and FC, radiological and histological variables were obtained. Clinical activity was evaluated by the Harvey-Bradshaw Index and FC by enzyme-linked immunosorbent assay. MRE activity was assessed by means of the Magnetic Resonance Index of Activity score. Chiorean's score was used to grade pathological inflammation in surgical specimens. Seventy-five patients (62.5%) were in clinical remission (Harvey-Bradshaw Index < 5) and 45 (37.5%) had active disease (Harvey-Bradshaw Index ≥ 5). The Magnetic Resonance Index of Activity score was significantly associated with FC levels (P < 0.01), with a moderate overall correlation (Spearman's r = 0.56, P < 0.001). FC reflected MRE inflammatory activity with an area under the receiver operating characteristic curve of 0.914 (confidence interval, 0.849-0.958; P < 0.001). A cutoff value of 166.50 μg/g had 90% sensitivity, 74% specificity, 89% positive predictive value, and 76% negative predictive value for diagnosis of inflammation. Twenty-eight of 120 patients were operated. Surgical pathology showed a good agreement with FC for moderate (P = 0.03) and severe (P = 0.01) Chiorean's index. No relationship was detected for C-reactive protein. FC correlates with the degree of MRE inflammatory activity and with surgical pathology damage in ileal CD. Thus, FC could be a surrogate marker of disease control used to select patients for MRE assessment and therapeutic adjustment.

UV-induced replication arrest in the xeroderma pigmentosum variant leads to DNA double-strand breaks, γ-H2AX formation, and Mre11 relocalization

PubMed Central

Limoli, Charles L.; Giedzinski, Erich; Bonner, William M.; Cleaver, James E.

2002-01-01

UV-induced replication arrest in the xeroderma pigmentosum variant (XPV) but not in normal cells leads to an accumulation of the Mre11/Rad50/Nbs1 complex and phosphorylated histone H2AX (γ-H2AX) in large nuclear foci at sites of stalled replication forks. These complexes have been shown to signal the presence of DNA damage, in particular, double-strand breaks (DSBs). This finding suggests that UV damage leads to the formation of DSBs during the course of replication arrest. After UV irradiation, XPV cells showed a fluence-dependent increase in the yield of γ-H2AX foci that paralleled the production of Mre11 foci. The percentage of foci-positive cells increased rapidly (10–15%) up to fluences of 10 J⋅m−2 before saturating at higher fluences. Frequencies of γ-H2AX and Mre11 foci both reached maxima at 4 h after UV irradiation. This pattern contrasts sharply to the situation observed after x-irradiation, where peak levels of γ-H2AX foci were found to precede the formation of Mre11 foci by several hours. The nuclear distributions of γ-H2AX and Mre11 were found to colocalize spatially after UV- but not x-irradiation. UV-irradiated XPV cells showed a one-to-one correspondence between Mre11 and γ-H2AX foci-positive cells. These results show that XPV cells develop DNA DSBs during the course of UV-induced replication arrest. These UV-induced foci occur in cells that are unable to carry out efficient bypass replication of UV damage and may contribute to further genetic variation. PMID:11756691

Comparison of non-invasive assessment of liver fibrosis in patients with alpha1-antitrypsin deficiency using magnetic resonance elastography (MRE), acoustic radiation force impulse (ARFI) Quantification, and 2D-shear wave elastography (2D-SWE).

PubMed

Reiter, Rolf; Wetzel, Martin; Hamesch, Karim; Strnad, Pavel; Asbach, Patrick; Haas, Matthias; Siegmund, Britta; Trautwein, Christian; Hamm, Bernd; Klatt, Dieter; Braun, Jürgen; Sack, Ingolf; Tzschätzsch, Heiko

2018-01-01

Although it has been known for decades that patients with alpha1-antitrypsin deficiency (AATD) have an increased risk of cirrhosis and hepatocellular carcinoma, limited data exist on non-invasive imaging-based methods for assessing liver fibrosis such as magnetic resonance elastography (MRE) and acoustic radiation force impulse (ARFI) quantification, and no data exist on 2D-shear wave elastography (2D-SWE). Therefore, the purpose of this study is to evaluate and compare the applicability of different elastography methods for the assessment of AATD-related liver fibrosis. Fifteen clinically asymptomatic AATD patients (11 homozygous PiZZ, 4 heterozygous PiMZ) and 16 matched healthy volunteers were examined using MRE and ARFI quantification. Additionally, patients were examined with 2D-SWE. A high correlation is evident for the shear wave speed (SWS) determined with different elastography methods in AATD patients: 2D-SWE/MRE, ARFI quantification/2D-SWE, and ARFI quantification/MRE (R = 0.8587, 0.7425, and 0.6914, respectively; P≤0.0089). Four AATD patients with pathologically increased SWS were consistently identified with all three methods-MRE, ARFI quantification, and 2D-SWE. The high correlation and consistent identification of patients with pathologically increased SWS using MRE, ARFI quantification, and 2D-SWE suggest that elastography has the potential to become a suitable imaging tool for the assessment of AATD-related liver fibrosis. These promising results provide motivation for further investigation of non-invasive assessment of AATD-related liver fibrosis using elastography.

Developing Best Practices for Detecting Change at Marine Renewable Energy Sites

NASA Astrophysics Data System (ADS)

Linder, H. L.; Horne, J. K.

2016-02-01

In compliance with the National Environmental Policy Act (NEPA), an evaluation of environmental effects is mandatory for obtaining permits for any Marine Renewable Energy (MRE) project in the US. Evaluation includes an assessment of baseline conditions and on-going monitoring during operation to determine if biological conditions change relative to the baseline. Currently, there are no best practices for the analysis of MRE monitoring data. We have developed an approach to evaluate and recommend analytic models used to characterize and detect change in biological monitoring data. The approach includes six steps: review current MRE monitoring practices, identify candidate models to analyze data, fit models to a baseline dataset, develop simulated scenarios of change, evaluate model fit to simulated data, and produce recommendations on the choice of analytic model for monitoring data. An empirical data set from a proposed tidal turbine site at Admiralty Inlet, Puget Sound, Washington was used to conduct the model evaluation. Candidate models that were evaluated included: linear regression, time series, and nonparametric models. Model fit diagnostics Root-Mean-Square-Error and Mean-Absolute-Scaled-Error were used to measure accuracy of predicted values from each model. A power analysis was used to evaluate the ability of each model to measure and detect change from baseline conditions. As many of these models have yet to be applied in MRE monitoring studies, results of this evaluation will generate comprehensive guidelines on choice of model to detect change in environmental monitoring data from MRE sites. The creation of standardized guidelines for model selection enables accurate comparison of change between life stages of a MRE project, within life stages to meet real time regulatory requirements, and comparison of environmental changes among MRE sites.

Magnetic resonance enterography versus capsule endoscopy activity indices for quantification of small bowel inflammation in Crohn’s disease

PubMed Central

Kopylov, Uri; Klang, Eyal; Yablecovitch, Doron; Lahat, Adi; Avidan, Benjamin; Neuman, Sandra; Levhar, Nina; Greener, Tomer; Rozendorn, Noa; Beytelman, Arkadi; Yanai, Henit; Dotan, Iris; Chowers, Yehuda; Weiss, Batya; Ben-Horin, Shomron; Amitai, Marianne M.; Eliakim, Rami

2016-01-01

Background: Video capsule endoscopy (VCE) and magnetic resonance enterography (MRE) are the prime modalities for the evaluation of small bowel (SB) Crohn’s disease (CD). Mucosal inflammation on VCE is quantified using the Lewis score (LS). Diffusion-weighted (DW) magnetic resonance imaging (MRI) allows for accurate assessment of SB inflammation without administration of intravenous contrast material. The Magnetic Resonance Index of Activity (MaRiA) and the Clermont index are quantitative activity indices validated for contrast-enhanced MRE and DW-MRE, respectively. The aim of this study was to compare the quantification of distal SB inflammation by VCE and MR-related activity indices. Methods: Patients with known quiescent SB CD were prospectively recruited and underwent MRE and VCE. LS, MaRIA and Clermont scores were calculated for the distal SB. Results: Both MRI-based indices significantly correlated with the LS and the Clermont index (r = 0.50, p = 0.001 and r = 0.53, p = 0.001, respectively). Both MaRIA and Clermont scores were significantly lower in patients with mucosal healing (LS < 135). The area under the curve (AUC) with both MR scores was moderate for prediction of any mucosal inflammation (LS ⩾ 135) and excellent for prediction of moderate-to-severe inflammation (LS ⩾ 790) (0.71 and 0.74 versus 0.93 and 0.91 for MaRIA and Clermont score, respectively). Conclusions: Modest correlation between VCE- and MRE-based quantitative indices of inflammation in patients with quiescent SB CD was observed. Between-modality correlation was higher in patients with endoscopically severe disease. DW-MRE gauged by Clermont score was at least as accurate as contrast-enhanced MRE for quantification of SB inflammation. PMID:27582877

Quality Improvement of Cheese Spread

DTIC Science & Technology

2008-02-25

is a popular component used in the U.S. military feeding program in Meal , Ready to-Eat (MRE) rations. Currently, the military requires a 3-yr shelf...Rations, Cheese Spread, CORANET, Meal , Ready-to-Eat (MRE), Operational Rations, Unclassified U U U U 33 Lana Zivanovic 865-974-0844 ii Table of...program in Meal , Ready- to-Eat (MRE) rations. Currently, the military requires a 3-yr shelf life if stored at 80°F. However, due to product deployment

Simultaneous 3D MR elastography of the in vivo mouse brain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kearney, Steven P.; Majumdar, Shreyan; Royston, Thomas J.

The feasibility of sample interval modulation (SLIM) magnetic resonance elastography (MRE) for the in vivo mouse brain is assessed, and an alternative SLIM-MRE encoding method is introduced. In SLIMMRE, the phase accumulation for each motion direction is encoded simultaneously by varying either the start time of the motion encoding gradient (MEG), SLIM-phase constant (SLIM-PC), or the initial phase of the MEG, SLIM-phase varying (SLIM-PV). SLIM-PC provides gradient moment nulling, but the mutual gradient shift necessitates increased echo time (TE). SLIM-PV requires no increased TE, but exhibits nonuniform flow compensation. Comparison was to conventional MRE using six C57BL/6 mice. For SLIMPC,more » the Spearman’s rank correlation to conventional MRE for the shear storage and loss modulus images were 80% and 76%, respectively, and likewise for SLIM-PV, 73% and 69%, respectively. The results of the Wilcoxon rank sum test showed that there were no statistically significant differences between the spatially averaged shear moduli derived from conventional-MRE, SLIM-PC, and SLIM-PV acquisitions. Both SLIM approaches were comparable to conventional MRE scans with Spearman’s rank correlation of 69%-80% and with 3 times reduction in scan time. As a result, the SLIM-PC method had the best correlation, and SLIM-PV may be a useful tool in experimental conditions, where both measurement time and T2 relaxation is critical.« less

Simultaneous 3D MR elastography of the in vivo mouse brain

DOE PAGES

Kearney, Steven P.; Majumdar, Shreyan; Royston, Thomas J.; ...

2017-09-15

The feasibility of sample interval modulation (SLIM) magnetic resonance elastography (MRE) for the in vivo mouse brain is assessed, and an alternative SLIM-MRE encoding method is introduced. In SLIMMRE, the phase accumulation for each motion direction is encoded simultaneously by varying either the start time of the motion encoding gradient (MEG), SLIM-phase constant (SLIM-PC), or the initial phase of the MEG, SLIM-phase varying (SLIM-PV). SLIM-PC provides gradient moment nulling, but the mutual gradient shift necessitates increased echo time (TE). SLIM-PV requires no increased TE, but exhibits nonuniform flow compensation. Comparison was to conventional MRE using six C57BL/6 mice. For SLIMPC,more » the Spearman’s rank correlation to conventional MRE for the shear storage and loss modulus images were 80% and 76%, respectively, and likewise for SLIM-PV, 73% and 69%, respectively. The results of the Wilcoxon rank sum test showed that there were no statistically significant differences between the spatially averaged shear moduli derived from conventional-MRE, SLIM-PC, and SLIM-PV acquisitions. Both SLIM approaches were comparable to conventional MRE scans with Spearman’s rank correlation of 69%-80% and with 3 times reduction in scan time. As a result, the SLIM-PC method had the best correlation, and SLIM-PV may be a useful tool in experimental conditions, where both measurement time and T2 relaxation is critical.« less

Mre11 and Exo1 contribute to the initiation and processivity of resection at meiotic double-strand breaks made independently of Spo11.

PubMed

Hodgson, Adam; Terentyev, Yaroslav; Johnson, Rebecca A; Bishop-Bailey, Anna; Angevin, Thibaut; Croucher, Adam; Goldman, Alastair S H

2011-02-07

During meiosis DNA double-strand breaks (DSBs) are induced and repaired by homologous recombination to create gene conversion and crossover products. Mostly these DSBs are made by Spo11, which covalently binds to the DSB ends. More rarely in Saccharomyces cerevisiae, other meiotic DSBs are formed by self-homing endonucleases such as VDE, which is site specific and does not covalently bind to the DSB ends. We have used experimentally located VDE-DSB sites to analyse an intermediate step in homologous recombination, resection of the single-strand ending 5' at the DSB site. Analysis of strains with different mutant alleles of MRE11 (mre11-58S and mre11-H125N) and deleted for EXO1 indicated that these two nucleases make significant contributions to repair of VDE-DSBs. Physical analysis of single-stranded repair intermediates indicates that efficient initiation and processivity of resection at VDE-DSBs require both Mre11 and Exo1, with loss of function for either protein causing severe delay in resection. We propose that these experiments model what happens at Spo11-DSBs after removal of the covalently bound protein, and that Mre11 and Exo1 are the major nucleases involved in creating resection tracts of widely varying lengths typical of meiotic recombination. Copyright © 2010 Elsevier B.V. All rights reserved.

MRI-based staging of hepatic fibrosis: Comparison of intravoxel incoherent motion diffusion-weighted imaging with magnetic resonance elastography.

PubMed

Ichikawa, Shintaro; Motosugi, Utaroh; Morisaka, Hiroyuki; Sano, Katsuhiro; Ichikawa, Tomoaki; Enomoto, Nobuyuki; Matsuda, Masanori; Fujii, Hideki; Onishi, Hiroshi

2015-07-01

To evaluate the use of intravoxel incoherent motion (IVIM) imaging for staging hepatic fibrosis, and compare its staging ability with that of magnetic resonance elastography (MRE). This study included 129 patients with pathologically staged liver fibrosis, and 53 patients with healthy livers. All patients underwent both MRE and IVIM imaging. Four diffusivity indices were calculated with 11 b-values; slow diffusion coefficient related to molecular diffusion (D), fast diffusion coefficient related to perfusion in micro-vessels (D*), perfusion-related diffusion fraction (f), and apparent diffusion coefficient (ADC). Receiver operating characteristic curve analysis was performed to determine the accuracy of IVIM imaging and MRE for staging hepatic fibrosis. D*, f, and ADC values decreased significantly with fibrosis stage (P < 0.0124), and liver stiffness increased (P < 0.0001). The Az value of MRE was significantly higher than that of D* for all fibrosis stages (D* vs. MRE for ≥ F1, 0.851 vs. 0.992 [P < 0.0001]; ≥ F2, 0.898 vs. 0.998 [P = 0.0003]; ≥ F3, 0.904 vs. 0.995 [P = 0.0004]; F4, 0.885 vs. 0.996 [P < 0.0001]). IVIM imaging is a useful technique for evaluating hepatic fibrosis, but MRE is better able to discriminate fibrosis stages than IVIM imaging. © 2014 Wiley Periodicals, Inc.

Meals ready to eat: a brief history and clinical vignette with discussion on civilian applications.

PubMed

Feagans, Jacob M; Jahann, Darius A; Barkin, Jamie S

2010-03-01

Meals ready to eat (MRE) have undergone many revisions of their origins in the trench ration from World War I. The MRE was implemented in 1980. Its design allows extended storage and easy, safe meal preparation. MRE sodium content varies by meal and may range from 1.6 g/meal to 2.3 g/meal. The average MRE contains 1,200 kcal. When consumed as intended, MREs are adequate for maintaining a soldier's physical parameters without undesirable consequences. The average soldier has a healthy cardiovascular system, has the ability to excrete high sodium loads, and has high insensible losses. The American Heart Association recommends limiting sodium to 2.3 g/day for the general population. Additionally, those with heart failure should limit sodium to 2 g/day. Excess intake of calories and electrolytes may lead to adverse outcomes in certain populations. We describe a case of heart failure exacerbated by regular MRE consumption and the "perfect storm" of risk factors encountered with postdisaster distribution of MREs to a civilian population.

MreB is important for cell shape but not for chromosome segregation of the filamentous cyanobacterium Anabaena sp. PCC 7120.

PubMed

Hu, Bin; Yang, Guohua; Zhao, Weixing; Zhang, Yingjiao; Zhao, Jindong

2007-03-01

MreB is a bacterial actin that plays important roles in determination of cell shape and chromosome partitioning in Escherichia coli and Caulobacter crescentus. In this study, the mreB from the filamentous cyanobacterium Anabaena sp. PCC 7120 was inactivated. Although the mreB null mutant showed a drastic change in cell shape, its growth rate, cell division and the filament length were unaltered. Thus, MreB in Anabaena maintains cell shape but is not required for chromosome partitioning. The wild type and the mutant had eight and 10 copies of chromosomes per cell respectively. We demonstrated that DNA content in two daughter cells after cell division in both strains was not always identical. The ratios of DNA content in two daughter cells had a Gaussian distribution with a standard deviation much larger than a value expected if the DNA content in two daughter cells were identical, suggesting that chromosome partitioning is a random process. The multiple copies of chromosomes in cyanobacteria are likely required for chromosome random partitioning in cell division.

Metamorphosis of Magnetospirillum magneticum AMB-1 cells

NASA Astrophysics Data System (ADS)

Zhang, Fengli; Yu-Zhang, Kui; Zhao, Sanjun; Xiao, Tian; Denis, Michel; Wu, Longfei

2010-03-01

Magnetospirillum magneticum strain AMB-1 belongs to the family of magnetotactic bacteria. It possesses a magnetosome chain aligning, with the assistance of cytoskeleton filaments MamK, along the long axis of the spiral cells. Most fresh M. magneticum AMB-1 cells exhibit spiral morphology. In addition, other cell shapes such as curved and spherical were also observed in this organism. Interestingly, the spherical cell shape increased steadily with prolonged incubation time. As the actin-like cytoskeleton protein MreB is involved in maintenance of cell shapes in rod-shaped bacteria such as Escherichia coli and Bacillus subtilis, the correlation between MreB protein levels and cell shape was investigated in this study. Immunoblotting analysis showed that the quantity of MreB decreased when the cell shape changed along with incubation time. As an internal control, the quantity of MamA was not obviously changed under the same conditions. Cell shape directs cell-wall synthesis during growth and division. MreB is required for maintaining the cell shape. Thus, MreB might play an essential role in maintaining the spiral shape of M. magneticum AMB-1 cells.

Anti-Pseudomonas aeruginosa compound, 1,2,3,4-tetrahydro-1,3,5-triazine derivative, exerts its action by primarily targeting MreB.

PubMed

Yamachika, Shinichiro; Sugihara, Chika; Tsuji, Hayato; Muramatsu, Yasunori; Kamai, Yasuki; Yamashita, Makoto

2012-01-01

In order to find new anti-Pseudomonas agents, we carried out whole-cell based P. aeruginosa growth assay, and identified 1,2,3,4-tetrahydro-1,3,5-triazine (Compound A). This compound showed anti-Pseudomonas activity against wild as well as pumpless strain equally at a same concentration. Also, this compound was structurally very similar to A22, which is known to inhibit the bacterial actin-like protein MreB. By the analysis of resistant strains, the primary target of this compound in P. aeruginosa was definitely confirmed to be MreB. In addition, these compounds showed a bacteriostatic effect, and induced the morphology changes in P. aeruginosa from rod shape to sphere shape, which leads to be clinically favorable in terms of susceptibility to phagocytosis and release of endotoxin. These results display that Compound A is a very attractive compound which shows anti-P. aeruginosa activity based on inhibition of MreB without being affected by efflux pumps, and could provide a new step toward development of new promising anti-Pseudomonas agents, MreB inhibitors.

Contrasting mechanisms of growth in two model rod-shaped bacteria

PubMed Central

Billaudeau, Cyrille; Chastanet, Arnaud; Yao, Zhizhong; Cornilleau, Charlène; Mirouze, Nicolas; Fromion, Vincent; Carballido-López, Rut

2017-01-01

How cells control their shape and size is a long-standing question in cell biology. Many rod-shaped bacteria elongate their sidewalls by the action of cell wall synthesizing machineries that are associated to actin-like MreB cortical patches. However, little is known about how elongation is regulated to enable varied growth rates and sizes. Here we use total internal reflection fluorescence microscopy and single-particle tracking to visualize MreB isoforms, as a proxy for cell wall synthesis, in Bacillus subtilis and Escherichia coli cells growing in different media and during nutrient upshift. We find that these two model organisms appear to use orthogonal strategies to adapt to growth regime variations: B. subtilis regulates MreB patch speed, while E. coli may mainly regulate the production capacity of MreB-associated cell wall machineries. We present numerical models that link MreB-mediated sidewall synthesis and cell elongation, and argue that the distinct regulatory mechanism employed might reflect the different cell wall integrity constraints in Gram-positive and Gram-negative bacteria. PMID:28589952

A high-damping magnetorheological elastomer with bi-directional magnetic-control modulus for potential application in seismology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Miao, E-mail: yumiao@cqu.edu.cn; Qi, Song; Fu, Jie

A high-damping magnetorheological elastomer (MRE) with bi-directional magnetic-control modulus is developed. This MRE was synthesized by filling NdFeB particles into polyurethane (PU)/ epoxy (EP) interpenetrating network (IPN) structure. The anisotropic samples were prepared in a permanent magnetic field and magnetized in an electromagnetic field of 1 T. Dynamic mechanical responses of the MRE to applied magnetic fields are investigated through magneto-rheometer, and morphology of MREs is observed via scanning electron microscope (SEM). Test result indicates that when the test field orientation is parallel to that of the sample's magnetization, the shear modulus of sample increases. On the other hand, when themore » orientation is opposite to that of the sample's magnetization, shear modulus decreases. In addition, this PU/EP IPN matrix based MRE has a high-damping property, with high loss factor and can be controlled by applying magnetic field. It is expected that the high damping property and the ability of bi-directional magnetic-control modulus of this MRE offer promising advantages in seismologic application.« less

Evaluation of Meal, Ready-to-Eat 8 at Market Square 2

DTIC Science & Technology

1988-09-01

the MRE were elicited from soldiers in a questionnaire that was administered at the completion of one field study (2). Analysis of this questionnaire...of the cakes , and hot sauce is in four menus. The MRE VIII is still packaged the same way as previous versions. On the average the MRE VIII provides...included the brownie and beef stew which were the two lowest rated items and the nut cakes which got variable ratings depending on type (see Table 4

Development of the Flameless Ration Heater for the Meal, Ready-to-Eat

DTIC Science & Technology

1993-04-01

DRHD FB FED FTA FDTE FED-STD FPU FSC FY GRAS HDPE HHAR JSR JWG IDPE MANFRDTT MIL-H-44398 MILrR-44398 MORE MRE MRHD MSDS MSR...Bragg, NO Again, the CRH consisted of the ZT Energy Pad and an instruction card , with the MRE meal bag being used as the heating container...pack and assemble MRE menus with the following new items: FRH, pork chow mein, smokey links, sugar free beverage base, potato sticks, chew mein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinto, F. T.; Iglesias, G.; Santos, P. R.

Marine renewable energy (MRE) is generates from waves, currents, tides, and thermal resources in the ocean. MRE has been identified as a potential commercial-scale source of renewable energy. This special topic presents a compilation of works selected from the 3rd IAHR Europe Congress, held in Porto, Portugal, in 2014. It covers different subjects relevant to MRE, including resource assessment, marine energy sector policies, energy source comparisons based on levelized cost, proof-of-concept and new-technology development for wave and tidal energy exploitation, and assessment of possible inference between wave energy converters (WEC).

A record of large earthquakes during the past two millennia on the southern Green Valley Fault, California

USGS Publications Warehouse

Lienkaemper, James J.; Baldwin, John N.; Turner, Robert; Sickler, Robert R.; Brown, Johnathan

2013-01-01

We document evidence for surface-rupturing earthquakes (events) at two trench sites on the southern Green Valley fault, California (SGVF). The 75-80-km long dextral SGVF creeps ~1-4 mm/yr. We identify stratigraphic horizons disrupted by upward-flowering shears and in-filled fissures unlikely to have formed from creep alone. The Mason Rd site exhibits four events from ~1013 CE to the Present. The Lopes Ranch site (LR, 12 km to the south) exhibits three events from 18 BCE to Present including the most recent event (MRE), 1610 ±52 yr CE (1σ) and a two-event interval (18 BCE-238 CE) isolated by a millennium of low deposition. Using Oxcal to model the timing of the 4-event earthquake sequence from radiocarbon data and the LR MRE yields a mean recurrence interval (RI or μ) of 199 ±82 yr (1σ) and ±35 yr (standard error of the mean), the first based on geologic data. The time since the most recent earthquake (open window since MRE) is 402 yr ±52 yr, well past μ~200 yr. The shape of the probability density function (pdf) of the average RI from Oxcal resembles a Brownian Passage Time (BPT) pdf (i.e., rather than normal) that permits rarer longer ruptures potentially involving the Berryessa and Hunting Creek sections of the northernmost GVF. The model coefficient of variation (cv, σ/μ) is 0.41, but a larger value (cv ~0.6) fits better when using BPT. A BPT pdf with μ of 250 yr and cv of 0.6 yields 30-yr rupture probabilities of 20-25% versus a Poisson probability of 11-17%.

Altered Viral Replication and Cell Responses by Inserting MicroRNA Recognition Element into PB1 in Pandemic Influenza A Virus (H1N1) 2009

PubMed Central

Shen, Xiaoyue; Sun, Wenkui; Shi, Yi; Xing, Zheng; Su, Xin

2015-01-01

Objective. MicroRNAs (miRNAs) are endogenous noncoding RNAs that spatiotemporally modulate mRNAs in a posttranscriptional manner. Engineering mutant viruses by inserting cell-specific miRNA recognition element (MRE) into viral genome may alter viral infectivity and host responses in vital tissues and organs infected with pandemic influenza A virus (H1N1) 2009 (H1N1pdm). Methods. In this study, we employed reverse genetics approach to generate a recombinant H1N1pdm with a cell-specific miRNA target sequence inserted into its PB1 genomic segment to investigate whether miRNAs are able to suppress H1N1pdm replication. We inserted an MRE of microRNA-let-7b (miR-let-7b) into the open reading frame of PB1 to test the feasibility of creating a cell-restricted H1N1pdm virus since let-7b is abundant in human bronchial epithelial cells. Results. miR-let-7b is rich in human bronchial epithelial cells (HBE). Incorporation of the miR-let-7b-MRE confers upon the recombinant H1N1pdm virus susceptibility to miR-let-7b targeting, suggesting that the H1N1pdm and influenza A viruses can be engineered to exert the desired replication restrictive effect and decrease infectivity in vital tissues and organs. Conclusions. This approach provides an additional layer of biosafety and thus has great potential for the application in the rational development of safer and more effective influenza viral vaccines. PMID:25788763

High Resolution Imaging of Viscoelastic Properties of Intracranial Tumours by Multi-Frequency Magnetic Resonance Elastography.

PubMed

Reiss-Zimmermann, M; Streitberger, K-J; Sack, I; Braun, J; Arlt, F; Fritzsch, D; Hoffmann, K-T

2015-12-01

In recent years Magnetic Resonance Elastography (MRE) emerged into a clinically applicable imaging technique. It has been shown that MRE is capable of measuring global changes of the viscoelastic properties of cerebral tissue. The purpose of our study was to evaluate a spatially resolved three-dimensional multi-frequent MRE (3DMMRE) for assessment of the viscoelastic properties of intracranial tumours. A total of 27 patients (63 ± 13 years) were included. All examinations were performed on a 3.0 T scanner, using a modified phase-contrast echo planar imaging sequence. We used 7 vibration frequencies in the low acoustic range with a temporal resolution of 8 dynamics per wave cycle. Post-processing included multi-frequency dual elasto-visco (MDEV) inversion to generate high-resolution maps of the magnitude |G*| and the phase angle φ of the complex valued shear modulus. The tumour entities included in this study were: glioblastoma (n = 11), anaplastic astrocytoma (n = 3), meningioma (n = 7), cerebral metastasis (n = 5) and intracerebral abscess formation (n = 1). Primary brain tumours and cerebral metastases were not distinguishable in terms of |G*| and φ. Glioblastoma presented the largest range of |G*| values and a trend was delineable that glioblastoma were slightly softer than WHO grade III tumours. In terms of φ, meningiomas were clearly distinguishable from all other entities. In this pilot study, while analysing the viscoelastic constants of various intracranial tumour entities with an improved spatial resolution, it was possible to characterize intracranial tumours by their mechanical properties. We were able to clearly delineate meningiomas from intraaxial tumours, while for the latter group an overlap remains in viscoelastic terms.

The Worldwide Marine Radiocarbon Reservoir Effect: Definitions, Mechanisms, and Prospects

NASA Astrophysics Data System (ADS)

Alves, Eduardo Q.; Macario, Kita; Ascough, Philippa; Bronk Ramsey, Christopher

2018-03-01

When a carbon reservoir has a lower radiocarbon content than the atmosphere, this is referred to as a reservoir effect. This is expressed as an offset between the radiocarbon ages of samples from the two reservoirs at a single point in time. The marine reservoir effect (MRE) has been a major concern in the radiocarbon community, as it introduces an additional source of error that is often difficult to accurately quantify. For this reason, researchers are often reluctant to date marine material where they have another option. The influence of this phenomenon makes the study of the MRE important for a broad range of applications. The advent of Accelerator Mass Spectrometry (AMS) has reduced sample size requirements and increased measurement precision, in turn increasing the number of studies seeking to measure marine samples. These studies rely on overcoming the influence of the MRE on marine radiocarbon dates through the worldwide quantification of the local parameter ΔR, that is, the local variation from the global average MRE. Furthermore, the strong dependence on ocean dynamics makes the MRE a useful indicator for changes in oceanic circulation, carbon exchange between reservoirs, and the fate of atmospheric CO2, all of which impact Earth's climate. This article explores data from the Marine Reservoir Database and reviews the place of natural radiocarbon in oceanic records, focusing on key questions (e.g., changes in ocean dynamics) that have been answered by MRE studies and on their application to different subjects.

The Diagnostic Role of Magnetic Resonance Enterography as a Complementary Test to Colonoscopy in Active Crohn's Disease.

PubMed

Aryan, Arvin; Azizi, Zahra; Teimouri, Azam; Ebrahimi Daryani, Nasser; Aletaha, Najme; Jahanbakhsh, Ali; Nouritaromlou, Mohammad Kazem; Alborzi, Forough; Mami, Masoud; Basirat, Vahid; Javid Anbardan, Sanam

2016-04-01

BACKGROUND According to recent studies comparing magnetic resonance enterography (MRE) with ileocolonoscopy for assessing inflammation of small bowel and colonic segments in adults with active Crohn's disease (CD), we aimed to compare the accuracy of these two diagnostic methods in Iranian population. METHODS During 2013-2014 a follow-up study was done on 30 patients with active CD in a gastroenterology clinic affiliated to Tehran University of Medical Sciences. MRE and ileocolonoscopy were performed for all the patients. All statistical analyses were performed using SPSS (version 18) and p-value<0.05 was considered as statistically significant. RESULTS Of the 30 patients with active CD, 11(36.7%) were men and 19 (63.3%) were women with mean age of 37.30±13.66 years (range: 19-67 years). MRE had sensitivity and specificity of 50% and 90% with positive predictive value (PPV) and negative predictive value (NPV) of 71.43 and 78.26, respectively for localizing sigmoid lesions and ileum had sensitivity and specificity of 84.21 and 45.45 with PPV and NPV of 72.73 and 62.50, respectively. CONCLUSION While moderate sensitivity and high specificity of MRE in localizing colonic lesions makes it an appropriate confirmatory test after colonoscopy, the reported high sensitivity and moderate specificity of MRE versus colonoscopy in detecting ileal lesions makes it a suitable screening test for ileal lesions. Finally we can conclude that MRE can be an important complementary test to colonoscopy in detecting active disease.

Using magnetic resonance elastography to assess the dynamic mechanical properties of cartilage

NASA Astrophysics Data System (ADS)

Lopez, Orlando; Amrami, Kimberly; Rossman, Phillip; Ehman, Richard L.

2004-04-01

This work explored the feasibility of using Magnetic Resonance Elastography (MRE) technology to enable in vitro quantification of dynamic mechanical behavior of cartilage through its thickness. A customized system for MRE of cartilage was designed to include components for adequate generation and detection of high frequency mechanical shear waves within small and stiff materials. The system included components for mechanical excitation, motion encoding, and imaging of small samples. Limitations in sensitivity to motion encoding of high frequency propagating mechanical waves using a whole body coil (i.e. Gmax = 2.2 G/cm) required the design of a local gradient coil system to achieve a gain in gradient strength of at least 5 times. The performance of the new system was tested using various cartilage-mimicking phantom materials. MRE of a stiff 5% agar gelatin phantom demonstrated gains in sensitivity to motion encoding of high frequency mechanical waves in cartilage like materials. MRE of fetal bovine cartilage samples yielded a distribution of shear stiffness within the thickness of the cartilage similar to values found in the literature, hence, suggesting the feasibility of using MRE to non-invasively and directly assess the dynamic mechanical properties of cartilage.

YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli.

PubMed

Masuda, Hisako; Tan, Qian; Awano, Naoki; Wu, Kuen-Phon; Inouye, Masayori

2012-06-01

All free-living bacteria carry the toxin-antitoxin (TA) systems controlling cell growth and death under stress conditions. YeeU-YeeV (CbtA) is one of the Escherichia coli TA systems, and the toxin, CbtA, has been reported to inhibit the polymerization of bacterial cytoskeletal proteins, MreB and FtsZ. Here, we demonstrate that the antitoxin, YeeU, is a novel type of antitoxin (type IV TA system), which does not form a complex with CbtA but functions as an antagonist for CbtA toxicity. Specifically, YeeU was found to directly interact with MreB and FtsZ, and enhance the bundling of their filamentous polymers in vitro. Surprisingly, YeeU neutralized not only the toxicity of CbtA but also the toxicity caused by other inhibitors of MreB and FtsZ, such as A22, SulA and MinC, indicating that YeeU-induced bundling of MreB and FtsZ has an intrinsic global stabilizing effect on their homeostasis. Here we propose to rename YeeU as CbeA for cytoskeleton bundling-enhancing factor A. © 2012 Blackwell Publishing Ltd.

Differentiated roles for MreB-actin isologues and autolytic enzymes in Bacillus subtilis morphogenesis.

PubMed

Domínguez-Cuevas, Patricia; Porcelli, Ida; Daniel, Richard A; Errington, Jeff

2013-09-01

Cell morphogenesis in most bacteria is governed by spatiotemporal growth regulation of the peptidoglycan cell wall layer. Much is known about peptidoglycan synthesis but regulation of its turnover by hydrolytic enzymes is much less well understood. Bacillus subtilis has a multitude of such enzymes. Two of the best characterized are CwlO and LytE: cells lacking both enzymes have a lethal block in cell elongation. Here we show that activity of CwlO is regulated by an ABC transporter, FtsEX, which is required for cell elongation, unlike cell division as in Escherichia coli. Actin-like MreB proteins are thought to play a key role in orchestrating cell wall morphogenesis. B. subtilis has three MreB isologues with partially differentiated functions. We now show that the three MreB isologues have differential roles in regulation of the CwlO and LytE systems and that autolysins control different aspects of cell morphogenesis. The results add major autolytic activities to the growing list of functions controlled by MreB isologues in bacteria and provide new insights into the different specialized functions of essential cell wall autolysins. © 2013 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

Imaging mechanical properties of hepatic tissue by magnetic resonance elastography

NASA Astrophysics Data System (ADS)

Yin, Meng; Rouviere, Olivier; Burgart, Lawrence J.; Fidler, Jeff L.; Manduca, Armando; Ehman, Richard L.

2006-03-01

PURPOSE: To assess the feasibility of a modified phase-contrast MRI technique (MR Elastography) for quantitatively assessing the mechanical properties of hepatic tissues by imaging propagating acoustic shear waves. MATERIALS AND METHODS: Both phantom and human studies were performed to develop and optimize a practical imaging protocol by visualizing and investigating the diffraction field of shear waves generated from pneumatic longitudinal drivers. The effects of interposed ribs in a transcostal approach were also investigated. A gradient echo MRE pulse sequence was adapted for shear wave imaging in the liver during suspended respiration, and then tested to measure hepatic shear stiffness in 13 healthy volunteers and 1 patient with chronic liver disease to determine the potential of non-invasively detecting liver fibrosis. RESULTS: Phantom studies demonstrate that longitudinal waves generated by the driver are mode-converted to shear waves in a distribution governed by diffraction principles. The transcostal approach was determined to be the most effective method for generating shear waves in human studies. Hepatic stiffness measurements in the 13 normal volunteers demonstrated a mean value of 2.0+/-0.2kPa. The shear stiffness measurement in the patient was much higher at 8.5kPa. CONCLUSION: MR Elastography of the liver shows promise as a method to non-invasively detect and characterize diffuse liver disease, potentially reducing the need for biopsy to diagnose hepatic fibrosis.

Bacterial morphogenesis and the enigmatic MreB helix.

PubMed

Errington, Jeff

2015-04-01

Work over the past decade has highlighted the pivotal role of the actin-like MreB family of proteins in the determination and maintenance of rod cell shape in bacteria. Early images of MreB localization revealed long helical filaments, which were suggestive of a direct role in governing cell wall architecture. However, several more recent, higher-resolution studies have questioned the existence or importance of the helical structures. In this Opinion article, I navigate a path through these conflicting reports, revive the helix model and summarize the key questions that remain to be answered.

Field Evaluation of Improved MRE (Meal, Ready-to-Eat), MRE VII, and MRE IV

DTIC Science & Technology

1987-01-01

SLICES MEATBALLS W/RICE IN TOMATO SAUCE* TUNA W/NOODLES* CHICKEN W/ RICE* ESC. POTATOES W/HAM CHUNKS* STARCHES CRACKERS POTATOES AU GRATIN...HAM/ CHIC KEN LOAF 4.9 0.39 HAM SLICES 7.7 0.21 MEATBALLS W/BBQ SAUCE* 6.5 0.24 PORK SAUSAGE PATTIES 6.6 0.25 TURKEY W/ GRAVY* 7.6 0. 17...FRANKFURTERS HAM/CHICKEN LOAF OR CHICKEN LOAF HAM SLICES MEATBALLS W/BBQ SAUCE PORK SAUSAGE PATTIES TURKEY W/GRAVY STARCHES CRACKERS BEANS W/TOMATO

Analysis of MreB interactors in Chlamydia reveals a RodZ homolog but fails to detect an interaction with MraY.

PubMed

Ouellette, Scot P; Rueden, Kelsey J; Gauliard, Emilie; Persons, Logan; de Boer, Piet A; Ladant, Daniel

2014-01-01

Chlamydia is an obligate intracellular bacterial pathogen that has significantly reduced its genome in adapting to the intracellular environment. One class of genes for which the bacterium has few annotated examples is cell division, and Chlamydia lacks FtsZ, a central coordinator of the division apparatus. We have previously implicated MreB as a potential substitute for FtsZ in Chlamydia (Ouellette et al., 2012). Thus, to identify new chlamydial cell division components, we searched for proteins that interacted with MreB. We performed a small-scale screen using a Gateway® compatible version of the Bacterial Adenylate Cyclase Two Hybrid (BACTH) system, BACTHGW, to detect proteins interacting with chlamydial MreB and identified a RodZ (YfgA) homolog. The chlamydial RodZ aligns well with the cytoplasmic domain of E. coli RodZ but lacks the periplasmic domain that is dispensable for rod cell shape maintenance in E. coli. The expression pattern of yfgA/rodZ was similar to that of mreB and ftsI, suggesting that these genes may operate in a common functional pathway. The chlamydial RodZ correctly localized to the membrane of E. coli but was unable to complement an E. coli rodZ mutant strain, likely because of the inability of chlamydial RodZ to interact with the native E. coli MreB. Finally, we also tested whether chlamydial MreB could interact with MraY, as suggested by Gaballah et al. (2011). However, we did not detect an interaction between these proteins even when using an implementation of the BACTH system to allow native orientation of the N- and C-termini of MraY in the periplasm. Thus, further work will be needed to establish this proposed interaction. In sum, we have added to the repertoire of potential cell division proteins of Chlamydia.

Analysis of MreB interactors in Chlamydia reveals a RodZ homolog but fails to detect an interaction with MraY

PubMed Central

Ouellette, Scot P.; Rueden, Kelsey J.; Gauliard, Emilie; Persons, Logan; de Boer, Piet A.; Ladant, Daniel

2014-01-01

Chlamydia is an obligate intracellular bacterial pathogen that has significantly reduced its genome in adapting to the intracellular environment. One class of genes for which the bacterium has few annotated examples is cell division, and Chlamydia lacks FtsZ, a central coordinator of the division apparatus. We have previously implicated MreB as a potential substitute for FtsZ in Chlamydia (Ouellette et al., 2012). Thus, to identify new chlamydial cell division components, we searched for proteins that interacted with MreB. We performed a small-scale screen using a Gateway® compatible version of the Bacterial Adenylate Cyclase Two Hybrid (BACTH) system, BACTHGW, to detect proteins interacting with chlamydial MreB and identified a RodZ (YfgA) homolog. The chlamydial RodZ aligns well with the cytoplasmic domain of E. coli RodZ but lacks the periplasmic domain that is dispensable for rod cell shape maintenance in E. coli. The expression pattern of yfgA/rodZ was similar to that of mreB and ftsI, suggesting that these genes may operate in a common functional pathway. The chlamydial RodZ correctly localized to the membrane of E. coli but was unable to complement an E. coli rodZ mutant strain, likely because of the inability of chlamydial RodZ to interact with the native E. coli MreB. Finally, we also tested whether chlamydial MreB could interact with MraY, as suggested by Gaballah et al. (2011). However, we did not detect an interaction between these proteins even when using an implementation of the BACTH system to allow native orientation of the N- and C-termini of MraY in the periplasm. Thus, further work will be needed to establish this proposed interaction. In sum, we have added to the repertoire of potential cell division proteins of Chlamydia. PMID:24936201

Piezoelectric actuator design for MR elastography: implementation and vibration issues.

PubMed

Tse, Zion Tsz Ho; Chan, Yum Ji; Janssen, Henning; Hamed, Abbi; Young, Ian; Lamperth, Michael

2011-09-01

MR elastography (MRE) is an emerging technique for tumor diagnosis. MRE actuation devices require precise mechanical design and radiofrequency engineering to achieve the required mechanical vibration performance and MR compatibility. A method of designing a general-purpose, compact and inexpensive MRE actuator is presented. It comprises piezoelectric bimorphs arranged in a resonant structure designed to operate at its resonant frequency for maximum vibration amplitude. An analytical model was established to understand the device vibration characteristics. The model-predicted performance was validated in experiments, showing its accuracy in predicting the actuator resonant frequency with an error < 4%. The device MRI compatibility was shown to cause minimal interference to a 1.5 tesla MRI scanner, with maximum signal-to-noise ratio reduction of 7.8% and generated artefact of 7.9 mm in MR images. A piezoelectric MRE actuator is proposed, and its implementation, vibration issues and future work are discussed. Copyright © 2011 John Wiley & Sons, Ltd.

Note: Real time control of a tunable vibration absorber based on magnetorheological elastomer for suppressing tonal vibrations

NASA Astrophysics Data System (ADS)

Kim, Young-Keun; Bae, Hyo-In; Koo, Jeong-Hoi; Kim, Kyung-Soo; Kim, Soohyun

2012-04-01

An adaptive tunable vibration absober based on magnetorheological elastomer (MRE) is designed as an intelligent device for auto-tuning itself to the time-varying harmonic disturbance force to reduce the unwanted vibration of the primary system in the steady state. The objectives of this note are to develop and implement a continuous control method for a MRE tunable vibration absorber (TVA) and to evaluate its performance in suppressing time-varying tonal vibrations. In the proposed control, the stiffness of MREs is continuously varied based on a nonlinear tuning function that relates the response of the system to the input magnetic field density. Through experiments, it will be shown that the proposed MRE TVA reduces in real time the transmission of a time-varying excited vibration of 48-55 Hz, which shows the potential applicability of the MRE in reducing unwanted vibration to precision devices.

Development of a novel multi-layer MRE isolator for suppression of building vibrations under seismic events

NASA Astrophysics Data System (ADS)

Yang, Jian; Sun, Shuaishuai; Tian, Tongfei; Li, Weihua; Du, Haiping; Alici, Gursel; Nakano, Masami

2016-03-01

Protecting civil engineering structures from uncontrollable events such as earthquakes while maintaining their structural integrity and serviceability is very important; this paper describes the performance of a stiffness softening magnetorheological elastomer (MRE) isolator in a scaled three storey building. In order to construct a closed-loop system, a scaled three storey building was designed and built according to the scaling laws, and then four MRE isolator prototypes were fabricated and utilised to isolate the building from the motion induced by a scaled El Centro earthquake. Fuzzy logic was used to output the current signals to the isolators, based on the real-time responses of the building floors, and then a simulation was used to evaluate the feasibility of this closed loop control system before carrying out an experimental test. The simulation and experimental results showed that the stiffness softening MRE isolator controlled by fuzzy logic could suppress structural vibration well.

A New Strategy to Enhance Cavitational Tissue Erosion Using a High-Intensity, Initiating Sequence

PubMed Central

Xu, Zhen; Fowlkes, J. Brian; Cain, Charles A.

2009-01-01

Our previous studies have shown that pulsed ultrasound can physically remove soft tissue through cavitation. A new strategy to enhance the cavitation-induced erosion is proposed wherein tissue erosion is initiated by a short, high-intensity sequence of pulses and sustained by lower intensity pulses. We investigated effects of the initiating sequence on erosion and cavitation sustained by lower intensity pulses. Multiple three-cycle pulses at a pulse repetition frequency of 20 kHz delivered by a 788-kHz focused transducer were used for tissue erosion. Fixing the initiating sequence at ISPPA of 9000 W/cm2, 16 combinations of different numbers of pulses within the initiating sequence and different sustaining pulse intensities were tested. Results showed: the initiating sequence increases the probability of erosion occurrence and the erosion rate with only slight overall increases in propagated energy; the initiating sequence containing more pulses does not increase the sustained cavitation period; and if extinguished and reinitiated, the sustained cavitation period becomes shorter after each initiation, although the waiting time between adjacent cavitation periods is random. The high-intensity, initiating sequence enhances cavitational tissue erosion and enables erosion at intensities significantly lower than what is required to initiate erosion. PMID:16921893

[Imaging of breast tumors using MR elastography].

PubMed

Lorenzen, J; Sinkus, R; Schrader, D; Lorenzen, M; Leussler, C; Dargatz, M; Röschmann, P

2001-01-01

Imaging of breast tumors using MR-Elastography. Low-frequency mechanical waves are transmitted into breast-tissue by means of an oscillator. The local characteristics of the mechanical wave are determined by the elastic properties of the tissue. By means of a motion-sensitive spin-echo-sequence these waves can be displayed within the phase of the MR image. Subsequently, these images can be used to reconstruct the local distribution of elasticity. In-vivo measurements were performed in 3 female patients with malignant tumors of the breast. All patients tolerated the measurement set-up without any untoward sensation in the contact area of skin and oszillator. The waves completely penetrated the breast, encompassing the axilla and regions close to the chest wall. All tumors were localized by MRE as structures of markedly stiffer tissue when compared to the surrounding tissue. Furthermore, in one patient, a metastasis in an axillary lymph node was detected. In all patients, local regions of increased elasticity were found in the remaining parenchyma of the breast, which, however, did not reach the high levels of elasticity found in the tumors. MRE is an imaging modality enabling adjunct tissue differentiation of mammary tumors.

Interaction of MreB-derived antimicrobial peptides with membranes.

PubMed

Saikia, Karabi; Chaudhary, Nitin

2018-03-25

Antimicrobial peptides are critical components of defense systems in living forms. The activity is conferred largely by the selective membrane-permeabilizing ability. In our earlier work, we derived potent antimicrobial peptides from the 9-residue long, N-terminal amphipathic helix of E. coli MreB protein. The peptides display broad-spectrum activity, killing not only Gram-positive and Gram-negative bacteria but opportunistic fungus, Candida albicans as well. These results proved that membrane-binding stretches of bacterial proteins could turn out to be self-harming when applied from outside. Here, we studied the membrane-binding and membrane-perturbing potential of these peptides. Steady-state tryptophan fluorescence studies with tryptophan extended peptides, WMreB 1-9 and its N-terminal acetylated analog, Ac-WMreB 1-9 show preferential binding to negatively-charged liposomes. Both the peptides cause permeabilization of E. coli inner and outer-membranes. Tryptophan-lacking peptides, though permeabilize the outer-membrane efficiently, little permeabilization of the inner-membrane is observed. These data attest membrane-destabilization as the mechanism of rapid bacterial killing. This study is expected to motivate the research in identifying microbes' self-sequences to combat them. Copyright © 2018 Elsevier Inc. All rights reserved.

Superresolution Imaging of Dynamic MreB Filaments in B. subtilis—A Multiple-Motor-Driven Transport?

PubMed Central

Olshausen, Philipp v.; Defeu Soufo, Hervé Joël; Wicker, Kai; Heintzmann, Rainer; Graumann, Peter L.; Rohrbach, Alexander

2013-01-01

The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillus subtilis cells, MreB forms filamentous structures of variable lengths, typically not longer than 1 μm. These filaments move along their orientation and mainly perpendicular to the long bacterial axis, revealing a maximal velocity at an intermediate length and a decreasing velocity with increasing filament length. Filaments move along straight trajectories but can reverse or alter their direction of propagation. Based on our measurements, we provide a mechanistic model that is consistent with all observations. In this model, MreB filaments mechanically couple several motors that putatively synthesize the cell wall, whereas the filaments’ traces mirror the trajectories of the motors. On the basis of our mechanistic model, we developed a mathematical model that can explain the nonlinear velocity length dependence. We deduce that the coupling of cell wall synthesis motors determines the MreB filament transport velocity, and the filament mechanically controls a concerted synthesis of parallel peptidoglycan strands to improve cell wall stability. PMID:24010660

Processive motions of MreB micro-filaments coordinate cell wall growth

NASA Astrophysics Data System (ADS)

Garner, Ethan

2012-02-01

Rod-shaped bacteria elongate by the action of cell-wall synthesis complexes linked to underlying dynamic MreB filaments, but how these proteins function to allow continued elongation as a rod remains unknown. To understand how the movement of these filaments relates to cell wall synthesis, we characterized the dynamics of MreB and the cell wall elongation machinery using high-resolution particle tracking in Bacillus subtilis. We found that both MreB and the elongation machinery move in linear paths across the cell, moving at similar rates (˜20nm / second) and angles to the cell body, suggesting they function as single complexes. These proteins move circumferentially around the cell, principally perpendicular to its length. We find that the motions of these complexes are independent, as they can pause and reverse,and also as nearby complexes move independently in both directions across one surface of the cell. Inhibition of cell wall synthesis with antibiotics or depletions in the cell wall synthesis machinery blocked MreB movement, suggesting that the cell wall synthetic machinery is the motor in this system. We propose that bacteria elongate by the uncoordinated, circumferential movements of synthetic complexes that span the plasma membrane and insert radial hoops of new peptidoglycan during their transit.

Superresolution imaging of dynamic MreB filaments in B. subtilis--a multiple-motor-driven transport?

PubMed

Olshausen, Philipp V; Defeu Soufo, Hervé Joël; Wicker, Kai; Heintzmann, Rainer; Graumann, Peter L; Rohrbach, Alexander

2013-09-03

The cytoskeletal protein MreB is an essential component of the bacterial cell-shape generation system. Using a superresolution variant of total internal reflection microscopy with structured illumination, as well as three-dimensional stacks of deconvolved epifluorescence microscopy, we found that inside living Bacillus subtilis cells, MreB forms filamentous structures of variable lengths, typically not longer than 1 μm. These filaments move along their orientation and mainly perpendicular to the long bacterial axis, revealing a maximal velocity at an intermediate length and a decreasing velocity with increasing filament length. Filaments move along straight trajectories but can reverse or alter their direction of propagation. Based on our measurements, we provide a mechanistic model that is consistent with all observations. In this model, MreB filaments mechanically couple several motors that putatively synthesize the cell wall, whereas the filaments' traces mirror the trajectories of the motors. On the basis of our mechanistic model, we developed a mathematical model that can explain the nonlinear velocity length dependence. We deduce that the coupling of cell wall synthesis motors determines the MreB filament transport velocity, and the filament mechanically controls a concerted synthesis of parallel peptidoglycan strands to improve cell wall stability. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Surface association and the MreB cytoskeleton regulate pilus production, localization and function in Pseudomonas aeruginosa.

PubMed

Cowles, Kimberly N; Gitai, Zemer

2010-06-01

Spatial organization of bacterial proteins influences many cellular processes, including division, chromosome segregation and motility. Virulence-associated proteins also localize to specific destinations within bacterial cells. However, the functions and mechanisms of virulence factor localization remain largely unknown. In this work, we demonstrate that polar assembly of the Pseudomonas aeruginosa PAO1 type IV pilus is regulated by surface association in a manner that affects gene transcription, protein levels and protein localization. We also uncover one mechanism for this regulation that acts through the actin homologue MreB. Inactivation of MreB leads to mislocalization of the pilus retraction ATPase PilT, mislocalization of the pili themselves and a reduction in motility. Furthermore, the role of MreB in polar localization of PilT is modulated by surface association, corroborating our results that environmental factors influence the regulation of pilus production. Specifically, MreB mediates both the initiation and maintenance of PilT localization when cells are grown in suspension but only affects the initiation of localization when cells are grown on a surface. Together, these results suggest that the bacterial cytoskeleton provides a mechanism for the polar localization of P. aeruginosa pili and demonstrate that protein localization may represent an important aspect of virulence factor regulation in bacterial pathogens.

Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swulius, Matthew T.; Chen, Songye; Jane Ding, H.

2011-04-22

Highlights: {yields} No long helical filaments are seen near or along rod-shaped bacterial inner membranes by electron cryo-tomography. {yields} Electron cryo-tomography has the resolution to detect single filaments in vivo. -- Abstract: How rod-shaped bacteria form and maintain their shape is an important question in bacterial cell biology. Results from fluorescent light microscopy have led many to believe that the actin homolog MreB and a number of other proteins form long helical filaments along the inner membrane of the cell. Here we show using electron cryotomography of six different rod-shaped bacterial species, at macromolecular resolution, that no long (>80 nm)more » helical filaments exist near or along either surface of the inner membrane. We also use correlated cryo-fluorescent light microscopy (cryo-fLM) and electron cryo-tomography (ECT) to identify cytoplasmic bundles of MreB, showing that MreB filaments are detectable by ECT. In light of these results, the structure and function of MreB must be reconsidered: instead of acting as a large, rigid scaffold that localizes cell-wall synthetic machinery, moving MreB complexes may apply tension to growing peptidoglycan strands to ensure their orderly, linear insertion.« less

Adenoid Cystic Carcinoma Metastatic to the Pituitary: A Case Report and Discussion of Potential Diagnostic Value of Magnetic Resonance Elastography in Pituitary Tumors.

PubMed

D Hughes, Joshua; Retzlaff, Amber; Sims, John; O'Brien, Erin; Giannini, Caterina; Huston, John; Van Gompel, Jamie J

2016-07-01

Adenoid cystic carcinoma (ACC) is an exocrine gland tumor accounting for approximately 10%-15% of all epithelial salivary neoplasms and occurs most often in the parotid and submandibular glands. Metastatic pituitary tumors are rare, and there is only 1 previously reported case of parotid ACC metastatic to the pituitary. Magnetic resonance elastography (MRE) is a dynamic magnetic resonance imaging (MRI)-based technique that measures the propagation of mechanically induced shear waves through a particular tissue to determine stiffness and offers a method to evaluate tissue consistency. We present the case of a 72-year-old woman with a remote history of parotid gland ACC and subsequent lung metastases presented after a fall that resulted in facial trauma. A non-contrast head computed tomography scan revealed a sellar/suprasellar mass, and follow-up MRI revealed a well-defined, enhancing 3.8-cm lesion. MRE showed the tumor to be firm. The tumor was resected through a transsphenoidal approach and was consistent with the MRE findings. Pathology returned as metastatic ACC. We report the second case of ACC metastatic to pituitary and the first firm pituitary tumor found by MRE and discuss the potential diagnostic value of MRE in pituitary lesions. Copyright © 2016 Elsevier Inc. All rights reserved.

Arbitrarily accurate twin composite π -pulse sequences

NASA Astrophysics Data System (ADS)

Torosov, Boyan T.; Vitanov, Nikolay V.

2018-04-01

We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

Circular RNA expression in basal cell carcinoma.

PubMed

Sand, Michael; Bechara, Falk G; Sand, Daniel; Gambichler, Thilo; Hahn, Stephan A; Bromba, Michael; Stockfleth, Eggert; Hessam, Schapoor

2016-05-01

Circular RNAs (circRNAs), are nonprotein coding RNAs consisting of a circular loop with multiple miRNA, binding sites called miRNA response elements (MREs), functioning as miRNA sponges. This study was performed to identify differentially expressed circRNAs and their MREs in basal cell carcinoma (BCC). Microarray circRNA expression profiles were acquired from BCC and control followed by qRT-PCR validation. Bioinformatical target prediction revealed multiple MREs. Sequence analysis was performed concerning MRE interaction potential with the BCC miRNome. We identified 23 upregulated and 48 downregulated circRNAs with 354 miRNA response elements capable of sequestering miRNA target sequences of the BCC miRNome. The present study describes a variety of circRNAs that are potentially involved in the molecular pathogenesis of BCC.

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data.

PubMed

Mayne, Benjamin T; Leemaqz, Shalem Y; Buckberry, Sam; Rodriguez Lopez, Carlos M; Roberts, Claire T; Bianco-Miotto, Tina; Breen, James

2018-02-01

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package ( https://bioconductor.org/packages/release/bioc/html/msgbsR.html ).

Cerebral magnetic resonance elastography in supranuclear palsy and idiopathic Parkinson's disease.

PubMed

Lipp, Axel; Trbojevic, Radmila; Paul, Friedemann; Fehlner, Andreas; Hirsch, Sebastian; Scheel, Michael; Noack, Cornelia; Braun, Jürgen; Sack, Ingolf

2013-01-01

Detection and discrimination of neurodegenerative Parkinson syndromes are challenging clinical tasks and the use of standard T1- and T2-weighted cerebral magnetic resonance (MR) imaging is limited to exclude symptomatic Parkinsonism. We used a quantitative structural MR-based technique, MR-elastography (MRE), to assess viscoelastic properties of the brain, providing insights into altered tissue architecture in neurodegenerative diseases on a macroscopic level. We measured single-slice multifrequency MRE (MMRE) and three-dimensional MRE (3DMRE) in two neurodegenerative disorders with overlapping clinical presentation but different neuropathology - progressive supranuclear palsy (PSP: N = 16) and idiopathic Parkinson's disease (PD: N = 18) as well as in controls (N = 18). In PSP, both MMRE (Δμ = - 28.8%, Δα = - 4.9%) and 3DMRE (Δ|G*|: - 10.6%, Δφ: - 34.6%) were significantly reduced compared to controls, with a pronounced reduction within the lentiform nucleus (Δμ = - 34.6%, Δα = - 8.1%; Δ|G*|: - 7.8%, Δφ: - 44.8%). MRE in PD showed a comparable pattern, but overall reduction in brain elasticity was less severe reaching significance only in the lentiform nucleus (Δμ n.s., Δα = - 7.4%; Δ|G*|: - 6.9%, Δφ: n.s.). Beyond that, patients showed a close negative correlation between MRE constants and clinical severity. Our data indicate that brain viscoelasticity in PSP and PD is differently affected by the underlying neurodegeneration; whereas in PSP all MRE constants are reduced and changes in brain softness (reduced μ and |G*|) predominate those of viscosity (α and φ) in PD.

[Travels and spreading of multi-resistant bacteria].

PubMed

Nitsch-Osuch, Aneta

2017-05-23

The increasing number of international travel for tourism, business and for medical reasons rises the risk of spreading of multi-resistant bacteria. It has been shown that an intercontinental travel, mainly to Asia (Indian Subcontinent), promotes a colonization of the digestive tract, mainly by multi-resistant Enterobacteriaceae (MRE) and increases the risk of symptomatic infections caused by these agents. The colonization of the digestive tract by MRE is reported in 29-88% of travelers. It sustains 3 to 12 months, respectively in 10% and 2% of travelers. Risk factors for the acquisition of colonization with MRE include: travel duration and destination, treatment with betalactam antibiotics during the travel, the use of local medical services, including hospitalization, presence of gastrointestinal symptoms during the travel (mainly diarrhea), age >65 years. The need of the hospitalization during the travel increases the risk of colonization, but is not a prerequisite factor for the acquisition of the colonization, as cases of the MRE carriage are reported in patients who had never used medical services outside the country. It indicates other possible transmission routes, including food. In order to reduce the risk of MRE spreading, it is recommended to ask patients about a history of travel and treatment within the last 12 months. All patient who report such events and require hospitalization in their home countries should be microbiologically screened. Hospitalized patients colonized with multiple resistant bacteria require an isolation or cohortation. Educational activities related to the hand hygiene compliance should be performed. The risk of the home transmission of MRE is not high, it lasts for a short period (up to 3 months). Routine microbiological testing for all persons returning from an international or intercontinental travel is not recommended, neither microbiological screening among their households.

MR elastography of hydrocephalus

NASA Astrophysics Data System (ADS)

Pattison, Adam J.; Lollis, S. Scott; Perrinez, Phillip R.; Weaver, John B.; Paulsen, Keith D.

2009-02-01

Hydrocephalus occurs due to a blockage in the transmission of cerebrospinal fluid (CSF) in either the ventricles or subarachnoid space. Characteristics of this condition include increased intracranial pressure, which can result in neurologic deterioration [1]. Magnetic resonance elastography (MRE) is an imaging technique that estimates the mechanical properties of tissue in vivo. While some investigations of brain tissue have been performed using MRE [2,3,4,5], the effects due to changes in interstitial pressure and fluid content on the mechanical properties of the brain remain unknown. The purpose of this work is to assess the potential of MRE to differentiate between the reconstructed properties of normal and hydrocephalic brains. MRE data was acquired in 18 female feline subjects, 12 of which received kaolin injections resulting in an acute form of hydrocephalus. In each animal, four MRE scans were performed during the process including one pre-injection and three post-injection scans. The elastic parameters were obtained using a subzone-based reconstruction algorithm that solves Navier's equations for linearly elastic materials [6]. The remaining cats were used as controls, injected with saline instead of kaolin. To determine the state of hydrocephalus, ventricular volume was estimated from segmenting anatomical images. The mean ventricular volume of hydrocephalic cats significantly increased (P <~ 0.0001) between the first and second scans. The mean volume was not observed to increase (P >~ 0.5) for the control cats. Also, there was an observable increase in the recorded elastic shear modulus of brain tissue in the normal and hydrocephalic acquisitions. Results suggest that MRE is able to detect changes in the mechanical properties of brain tissue resulting from kaolin-induced hydrocephalus, indicating the need for further study.

MreB-Dependent Organization of the E. coli Cytoplasmic Membrane Controls Membrane Protein Diffusion.

PubMed

Oswald, Felix; Varadarajan, Aravindan; Lill, Holger; Peterman, Erwin J G; Bollen, Yves J M

2016-03-08

The functional organization of prokaryotic cell membranes, which is essential for many cellular processes, has been challenging to analyze due to the small size and nonflat geometry of bacterial cells. Here, we use single-molecule fluorescence microscopy and three-dimensional quantitative analyses in live Escherichia coli to demonstrate that its cytoplasmic membrane contains microdomains with distinct physical properties. We show that the stability of these microdomains depends on the integrity of the MreB cytoskeletal network underneath the membrane. We explore how the interplay between cytoskeleton and membrane affects trans-membrane protein (TMP) diffusion and reveal that the mobility of the TMPs tested is subdiffusive, most likely caused by confinement of TMP mobility by the submembranous MreB network. Our findings demonstrate that the dynamic architecture of prokaryotic cell membranes is controlled by the MreB cytoskeleton and regulates the mobility of TMPs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB.

PubMed

Tan, Qian; Awano, Naoki; Inouye, Masayori

2011-01-01

Toxin-antitoxin (TA) systems of free-living bacteria have recently demonstrated that these toxins inhibit cell growth by targeting essential functions of cellular metabolism. Here we show that YeeV toxin inhibits cell division, leads to a change in morphology and lysis of Escherichia coli cells. YeeV interacts with two essential cytoskeleton proteins, FtsZ and MreB. Purified YeeV inhibits both the GTPase activity and the GTP-dependent polymerization of FtsZ. YeeV also inhibits ATP-dependent polymerization of MreB. Truncated C-terminal deletions of YeeV result in elongation of cells, and a deletion of the first 15 amino acids from the N-terminus of YeeV caused lemon-shaped cell formation. The YeeV toxin is distinct from other well-studied toxins: it directs the binding of two cytoskeletal proteins and inhibits FtsZ and MreB simultaneously. © 2010 Blackwell Publishing Ltd.

How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction.

PubMed

Shi, Handuo; Bratton, Benjamin P; Gitai, Zemer; Huang, Kerwyn Casey

2018-03-08

Cell shape matters across the kingdoms of life, and cells have the remarkable capacity to define and maintain specific shapes and sizes. But how are the shapes of micron-sized cells determined from the coordinated activities of nanometer-sized proteins? Here, we review general principles that have surfaced through the study of rod-shaped bacterial growth. Imaging approaches have revealed that polymers of the actin homolog MreB play a central role. MreB both senses and changes cell shape, thereby generating a self-organizing feedback system for shape maintenance. At the molecular level, structural and computational studies indicate that MreB filaments exhibit tunable mechanical properties that explain their preference for certain geometries and orientations along the cylindrical cell body. We illustrate the regulatory landscape of rod-shape formation and the connectivity between cell shape, cell growth, and other aspects of cell physiology. These discoveries provide a framework for future investigations into the architecture and construction of microbes. Copyright © 2018 Elsevier Inc. All rights reserved.

A feasibility work on the applications of MRE to automotive components

NASA Astrophysics Data System (ADS)

Kim, S. H.; Park, Y. J.; Cha, A. R.; Kim, G. W.; Bang, J. H.; Lim, C. S.; Choi, S. B.

2018-03-01

A feasibility work on the application of magneto-rheological elastomers (MREs) to automotive components, such as engine mounts is presented. While vehicle components require the high resonance frequency in terms of ride quality and handling, it is required to have the low resonance frequency to isolate the incoming vibration. With the conventional automotive technologies, it is challenging to combine these two conflicting performance trade-offs, ride quality including handling, and NVH (noise, vibration and harshness). Over the last decades, MREs, one of the new emerging smart materials, have been widely used to resolve this technical limitation. For example, an advanced engine mount was developed by using MRE to isolate the vibration transmitting from engines. In this paper, we will focus on rear cross member bushes, which is a key component for isolating the vibration from the road, and demonstrate their improved performance by utilizing MRE. The resonance frequency shift induced by the stiffness change of MRE will be presented through the frequency response functions estimated by simulation result.

Anisotropic elastic moduli reconstruction in transversely isotropic model using MRE

NASA Astrophysics Data System (ADS)

Song, Jiah; In Kwon, Oh; Seo, Jin Keun

2012-11-01

Magnetic resonance elastography (MRE) is an elastic tissue property imaging modality in which the phase-contrast based MRI imaging technique is used to measure internal displacement induced by a harmonically oscillating mechanical vibration. MRE has made rapid technological progress in the past decade and has now reached the stage of clinical use. Most of the research outcomes are based on the assumption of isotropy. Since soft tissues like skeletal muscles show anisotropic behavior, the MRE technique should be extended to anisotropic elastic property imaging. This paper considers reconstruction in a transversely isotropic model, which is the simplest case of anisotropy, and develops a new non-iterative reconstruction method for visualizing the elastic moduli distribution. This new method is based on an explicit representation formula using the Newtonian potential of measured displacement. Hence, the proposed method does not require iterations since it directly recovers the anisotropic elastic moduli. We perform numerical simulations in order to demonstrate the feasibility of the proposed method in recovering a two-dimensional anisotropic tensor.

Pulse sequence programming in a dynamic visual environment: SequenceTree.

PubMed

Magland, Jeremy F; Li, Cheng; Langham, Michael C; Wehrli, Felix W

2016-01-01

To describe SequenceTree, an open source, integrated software environment for implementing MRI pulse sequences and, ideally, exporting them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for programmers and nonprogrammers alike. The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically, allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally, other types of scanners will be supported in the future. SequenceTree has been used for 8 years in our laboratory and elsewhere and has contributed to more than 50 peer-reviewed publications in areas such as cardiovascular imaging, solid state and nonproton NMR, MR elastography, and high-resolution structural imaging. SequenceTree is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal both for advanced users and users with limited programming experience. © 2015 Wiley Periodicals, Inc.

MR Elastography and Diffusion-Weighted Imaging of ex-vivo Prostate Cancer: quantitative comparison to histopathology

PubMed Central

Nir, Guy; Gagnon, Louis O.; Ischia, Joseph; Jones, Edward C.; Chang, Silvia; Yung, Andrew; Honarvar, Mohammad; Fazli, Ladan; Goldenberg, Larry; Rohling, Robert; Sinkus, Ralph; Kozlowski, Piotr

2017-01-01

Purpose 1) to develop a Magnetic Resonance Elastography (MRE) system for imaging of the ex-vivo human prostate, 2) to assess the diagnostic power of mono-frequency and multi-frequency MRE and diffusion weighted imaging (DWI) alone and combined as correlated with histopathology in a patient study. Materials and Methods An electromagnetic driver was designed specifically for MRE studies in small-bore MR scanners. Ex-vivo prostate specimens (post-fixation) of fourteen patients who underwent radical prostatectomy were imaged with MRE at 7 T (nine cases had DWI). In six patients, the MRE examination was performed at three frequencies (600, 800, 1000 Hz) to extract the power-law exponent Gamma. The images were registered to wholemount pathology slides marked with the Gleason score. The areas under the Receiver-Operator-Characteristic curves (AUC) were calculated. Results The methods were validated in a phantom study and demonstrated that (i) the driver does not interfere with the acquisition process, (ii) the driver can generate amplitudes greater than 100 μm for frequencies <1kHz. In the quantitative study, cancerous tissue with Gleason score at least 3+3 was distinguished from normal tissue in the peripheral zone with an average AUC of 0.75 (Gd), 0.75 (Gl), 0.70 (Gamma-Gd), 0.68 (ADC), and 0.82 (Gd+Gl+ADC). The differentiation between PZ and CG was modest for Gd (p<0.07), Gl (p<0.06) but not significant for Gamma (p<0.2). A correlation of 0.4 kPa/h was found between fixation time of the prostate specimen to the stiffness of the tissue which could affect the diagnostic power results. Conclusion DWI and MRE may provide complementary information; in fact MRE performed better than ADC in distinguishing normal from cancerous tissue in some cases. Multi-frequency (Gamma) analysis did not appear to improve the results. However, in light of effect of tissue fixation, the clinical implication of our results may be inconclusive and more experiments are needed. PMID:25382459

The Saccharomyces cerevisiae Mre11-Rad50-Xrs2 complex promotes trinucleotide repeat expansions independently of homologous recombination.

PubMed

Ye, Yanfang; Kirkham-McCarthy, Lucy; Lahue, Robert S

2016-07-01

Trinucleotide repeats (TNRs) are tandem arrays of three nucleotides that can expand in length to cause at least 17 inherited human diseases. Somatic expansions in patients can occur in differentiated tissues where DNA replication is limited and cannot be a primary source of somatic mutation. Instead, mouse models of TNR diseases have shown that both inherited and somatic expansions can be suppressed by the loss of certain DNA repair factors. It is generally believed that these repair factors cause misprocessing of TNRs, leading to expansions. Here we extend this idea to show that the Mre11-Rad50-Xrs2 (MRX) complex of Saccharomyces cerevisiae is a causative factor in expansions of short TNRs. Mutations that eliminate MRX subunits led to significant suppression of expansions whereas mutations that inactivate Rad51 had only a minor effect. Coupled with previous evidence, this suggests that MRX drives expansions of short TNRs through a process distinct from homologous recombination. The nuclease function of Mre11 was dispensable for expansions, suggesting that expansions do not occur by Mre11-dependent nucleolytic processing of the TNR. Epistasis between MRX and post-replication repair (PRR) was tested. PRR protects against expansions, so a rad5 mutant gave a high expansion rate. In contrast, the mre11 rad5 double mutant gave a suppressed expansion rate, indistinguishable from the mre11 single mutant. This suggests that MRX creates a TNR substrate for PRR. Protein acetylation was also tested as a mechanism regulating MRX activity in expansions. Six acetylation sites were identified in Rad50. Mutation of all six lysine residues to arginine gave partial bypass of a sin3 HDAC mutant, suggesting that Rad50 acetylation is functionally important for Sin3-mediated expansions. Overall we conclude that yeast MRX helps drive expansions of short TNRs by a mechanism distinct from its role in homologous recombination and independent of the nuclease function of Mre11. Copyright © 2016 Elsevier B.V. All rights reserved.

Review of MR Elastography Applications and Recent Developments

PubMed Central

Glaser, Kevin J.; Manduca, Armando; Ehman, Richard L.

2012-01-01

The technique of MR elastography (MRE) has emerged as a useful modality for quantitatively imaging the mechanical properties of soft tissues in vivo. Recently, MRE has been introduced as a clinical tool for evaluating chronic liver disease, but many other potential applications are being explored. These applications include measuring tissue changes associated with diseases of the liver, breast, brain, heart, and skeletal muscle including both focal lesions (e.g., hepatic, breast, and brain tumors) and diffuse diseases (e.g., fibrosis and multiple sclerosis). The purpose of this review article is to summarize some of the recent developments of MRE and to highlight some emerging applications. PMID:22987755

Assessing Resource Assessment for MRE (Invited)

NASA Astrophysics Data System (ADS)

Hanson, H. P.; Bozec, A.; Duerr, A. S.; Rauchenstein, L. T.

2010-12-01

The Southeast National Marine Renewable Energy Center at Florida Atlantic University is concerned with marine renewable energy (MRE) recovery from the Florida Current using marine hydrokinetic technology and, in the future, from the thermocline in the Florida Straits via ocean thermal energy conversion. Although neither concept is new, technology improvements and the evolution of policy now warrant optimism for the future of these potentially rich resources. In moving toward commercial-scale deployments of energy-generating systems, an important first step is accurate and unembellished assessment of the resource itself. In short, we must ask: how much energy might be available? The answer to this deceptively simple question depends, of course, on the technology itself - system efficiencies, for example - but it also depends on a variety of other limiting factors such as deployment strategies, environmental considerations, and the overall economics of MRE in the context of competing energy resources. While it is universally agreed that MRE development must occur within a framework of environmental stewardship, it is nonetheless inevitable that there will be trade-offs between absolute environmental protection and realizing the benefits of MRE implementation. As with solar-energy and wind-power technologies, MRE technologies interact with the environment in which they are deployed. Ecological, societal, and even physical resource concerns all require investigation and, in some cases, mitigation. Moreover, the converse - how will the environment affect the equipment? - presents technical challenges that have confounded the seagoing community forever. Biofouling, for example, will affect system efficiency and create significant maintenance and operations issues. Because this will also affect the economics of MRE, nonlinear interactions among the limiting factors complicate the overall issue of resource assessment significantly. While MRE technology development is largely an engineering task, resource assessment falls more to the oceanography community. Current and temperature structure measurements, for example, are critical for these efforts. Once again, however, the picture is complicated by the nature of the endeavor: deploying complex equipment of scales of tens of meters into a medium that is traditionally measured on scales of tens of kilometers implies a scale mismatch that must be overcome. The challenge, then, is to develop assessments of the resource on larger scales - so that the potential of the resource may be understood - while characterizing it on very small scales to be able to understand how equipment will be affected. Meeting this challenge will require both funding and time, but it will also result in new oceanographic insight and understanding.

Optimizing symmetry-based recoupling sequences in solid-state NMR by pulse-transient compensation and asynchronous implementation

NASA Astrophysics Data System (ADS)

Hellwagner, Johannes; Sharma, Kshama; Tan, Kong Ooi; Wittmann, Johannes J.; Meier, Beat H.; Madhu, P. K.; Ernst, Matthias

2017-06-01

Pulse imperfections like pulse transients and radio-frequency field maladjustment or inhomogeneity are the main sources of performance degradation and limited reproducibility in solid-state nuclear magnetic resonance experiments. We quantitatively analyze the influence of such imperfections on the performance of symmetry-based pulse sequences and describe how they can be compensated. Based on a triple-mode Floquet analysis, we develop a theoretical description of symmetry-based dipolar recoupling sequences, in particular, R2 6411, calculating first- and second-order effective Hamiltonians using real pulse shapes. We discuss the various origins of effective fields, namely, pulse transients, deviation from the ideal flip angle, and fictitious fields, and develop strategies to counteract them for the restoration of full transfer efficiency. We compare experimental applications of transient-compensated pulses and an asynchronous implementation of the sequence to a supercycle, SR26, which is known to be efficient in compensating higher-order error terms. We are able to show the superiority of R26 compared to the supercycle, SR26, given the ability to reduce experimental error on the pulse sequence by pulse-transient compensation and a complete theoretical understanding of the sequence.

Double dissociation of structure-function relationships in memory and fluid intelligence observed with magnetic resonance elastography.

PubMed

Johnson, Curtis L; Schwarb, Hillary; Horecka, Kevin M; McGarry, Matthew D J; Hillman, Charles H; Kramer, Arthur F; Cohen, Neal J; Barbey, Aron K

2018-05-01

Brain tissue mechanical properties, measured in vivo with magnetic resonance elastography (MRE), have proven to be sensitive metrics of neural tissue integrity. Recently, our group has reported on the positive relationship between viscoelasticity of the hippocampus and performance on a relational memory task in healthy young adults, which highlighted the potential of sensitive MRE measures for studying brain health and its relation to cognitive function; however, structure-function relationships outside of the hippocampus have not yet been explored. In this study, we examined the relationships between viscoelasticity of both the hippocampus and the orbitofrontal cortex and performance on behavioral assessments of relational memory and fluid intelligence. In a sample of healthy, young adults (N = 53), there was a significant, positive relationship between orbitofrontal cortex viscoelasticity and fluid intelligence performance (r = 0.42; p = .002). This finding is consistent with the previously reported relationship between hippocampal viscoelasticity and relational memory performance (r = 0.41; p = .002). Further, a significant double dissociation between the orbitofrontal-fluid intelligence relationship and the hippocampal-relational memory relationship was observed. These data support the specificity of regional brain MRE measures in support of separable cognitive functions. This report of a structure-function relationship observed with MRE beyond the hippocampus suggests a future role for MRE as a sensitive neuroimaging technique for brain mapping. Copyright © 2018 Elsevier Inc. All rights reserved.

EXO1 is critical for embryogenesis and the DNA damage response in mice with a hypomorphic Nbs1 allele

PubMed Central

Rein, Katrin; Yanez, Diana A.; Terré, Berta; Palenzuela, Lluís; Aivio, Suvi; Wei, Kaichun; Edelmann, Winfried; Stark, Jeremy M.; Stracker, Travis H.

2015-01-01

The maintenance of genome stability is critical for the suppression of diverse human pathologies that include developmental disorders, premature aging, infertility and predisposition to cancer. The DNA damage response (DDR) orchestrates the appropriate cellular responses following the detection of lesions to prevent genomic instability. The MRE11 complex is a sensor of DNA double strand breaks (DSBs) and plays key roles in multiple aspects of the DDR, including DNA end resection that is critical for signaling and DNA repair. The MRE11 complex has been shown to function both upstream and in concert with the 5′-3′ exonuclease EXO1 in DNA resection, but it remains unclear to what extent EXO1 influences DSB responses independently of the MRE11 complex. Here we examine the genetic relationship of the MRE11 complex and EXO1 during mammalian development and in response to DNA damage. Deletion of Exo1 in mice expressing a hypomorphic allele of Nbs1 leads to severe developmental impairment, embryonic death and chromosomal instability. While EXO1 plays a minimal role in normal cells, its loss strongly influences DNA replication, DNA repair, checkpoint signaling and damage sensitivity in NBS1 hypomorphic cells. Collectively, our results establish a key role for EXO1 in modulating the severity of hypomorphic MRE11 complex mutations. PMID:26160886

Alteration of gene conversion tract length and associated crossing over during plasmid gap repair in nuclease-deficient strains of Saccharomyces cerevisiae.

PubMed

Symington, L S; Kang, L E; Moreau, S

2000-12-01

A plasmid gap repair assay was used to assess the role of three known nucleases, Exo1, Mre11 and Rad1, in the processing of DNA ends and resolution of recombination intermediates during double-strand gap repair. In this assay, alterations in end processing or branch migration are reflected by the frequency of co-conversion of a chromosomal marker 200 bp from the gap. Gap repair associated with crossing over results in integration at the homologous chromosomal locus, whereas the plasmid remains episomal for non-crossover repair events. In mre11 strains, the frequency of gap repair was reduced 3- to 10-fold and conversion tracts were shorter than in the wild-type strain, consistent with a role for this nuclease in processing double-strand breaks. However, conversion tracts were longer in a strain containing the nuclease deficient allele, mre11-H125N, suggesting increased end processing by redundant nucleases. The frequency of gap repair was reduced 2-fold in rad1 mutants and crossing over was reduced, consistent with a role for Rad1 in cleaving recombination intermediates. The frequency of gap repair was increased in exo1 mutants with a significant increase in crossing over. In exo1 mre11 double mutants gap repair was reduced to below the mre11 single mutant level.

Neural-network-designed pulse sequences for robust control of singlet-triplet qubits

NASA Astrophysics Data System (ADS)

Yang, Xu-Chen; Yung, Man-Hong; Wang, Xin

2018-04-01

Composite pulses are essential for universal manipulation of singlet-triplet spin qubits. In the absence of noise, they are required to perform arbitrary single-qubit operations due to the special control constraint of a singlet-triplet qubit, while in a noisy environment, more complicated sequences have been developed to dynamically correct the error. Tailoring these sequences typically requires numerically solving a set of nonlinear equations. Here we demonstrate that these pulse sequences can be generated by a well-trained, double-layer neural network. For sequences designed for the noise-free case, the trained neural network is capable of producing almost exactly the same pulses known in the literature. For more complicated noise-correcting sequences, the neural network produces pulses with slightly different line shapes, but the robustness against noises remains comparable. These results indicate that the neural network can be a judicious and powerful alternative to existing techniques in developing pulse sequences for universal fault-tolerant quantum computation.

7 CFR 98.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.2... acceptable one meal serving, retorted pouched or 18-24 serving hermetically-sealed tray packed meat, or meal... operational food rations, and as an item of general issue by the military. Meat. This includes the edible part...

Characterizing emissions from open burning of military food waste and ration packaging compositions

EPA Science Inventory

Emissions from open burning of Meals, Ready-To-Eat (MRE) and MRE packaging were characterized in response to inhalation concerns at military forward operating bases. Emissions from four compositions of MREs and four types of packaging were compared to assess contributions of ind...

7 CFR 98.1 - General.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false General. 98.1 Section 98.1 Agriculture Regulations of..., READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.1 General. Analytical services of meat and meat food products are performed for fat, moisture, salt, protein...

7 CFR 98.1 - General.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false General. 98.1 Section 98.1 Agriculture Regulations of..., READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.1 General. Analytical services of meat and meat food products are performed for fat, moisture, salt, protein...

7 CFR 98.1 - General.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false General. 98.1 Section 98.1 Agriculture Regulations of..., READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.1 General. Analytical services of meat and meat food products are performed for fat, moisture, salt, protein...

7 CFR 98.1 - General.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false General. 98.1 Section 98.1 Agriculture Regulations of..., READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.1 General. Analytical services of meat and meat food products are performed for fat, moisture, salt, protein...

Correlation of hepatic fractional extracellular space using gadolinium enhanced MRI with liver stiffness using magnetic resonance elastography.

PubMed

Wells, Michael L; Moynagh, Michael R; Carter, Rickey E; Childs, Robert A; Leitch, Cameron E; Fletcher, Joel G; Yeh, Benjamin M; Venkatesh, Sudhakar K

2017-01-01

To compare MR hepatic fractional extracellular space (fECS) to liver stiffness (LS) with magnetic resonance elastography (MRE) for evaluation of liver fibrosis. 71 consecutive patients with suspected chronic liver disease underwent standard liver MRI with MR elastography and additional delayed Gd-DTPA-enhanced sequences at 5 and 10 min in order to calculate hepatic fECS (%) and LS (kilopascals, kPa). Two radiologists blinded to clinical history examined MR images and calculated fECS and LS in identical locations for every patient. Interobserver agreement was calculated using the intraclass correlation coefficient. Pearson's correlation was calculated for LS and fECS measures, as was the area under the receiver operatic curve (AUROC), sensitivity and specificity of fECS to predict liver stiffness ≥2.93 and ≥5 kPa. The sensitivity of fECS for detecting fibrosis was separately analyzed in the subgroup of patients without anatomic findings of cirrhosis. Substantial to excellent interobserver agreement for both LS and fECS measurements was seen with intraclass correlation of 0.88 (95% CI 0.81-0.92) for LS, 0.77 (95% CI 0.66-0.85) for fECS 5 and 0.76 (95% CI 0.64-0.84) for fECS 10 . A significant correlation was found between MRE and fECS 5 (r = 0.47, p < 0.0001) and fECS 10 (r = 0.44, p < 0.0001). The performance of fECS improved for detection of advanced fibrosis (≥5 kPa) with AUROC, sensitivity and specificity of 0.72, 38%, and 94% for fECS 5 and 0.72, 67%, and 66% for fECS 10 . fECS correlates modestly with MRE-determined LS. fECS at MRI is a simple calculation to perform and may represent a practical way to suggest the presence of fibrosis during routine liver evaluation.

Experiences of Latino Couples in Relationship Education: A Critical Analysis

ERIC Educational Resources Information Center

Perez, Carlos; Brown, Matthew D.; Whiting, Jason B.; Harris, Steven M.

2013-01-01

There exists a need to better understand the applicability of Marriage and Relationship Education (MRE) initiatives with diverse populations. This study presents findings from focus groups with Latino men and women (N = 16) who participated in MRE classes. A critical theory approach guided the researchers who used grounded theory methodology to…

7 CFR 98.5 - Fees and charges.

Code of Federal Regulations, 2011 CFR

2011-01-01

... MEALS, READY-TO-EAT (MRE's), MEATS, AND MEAT PRODUCTS MRE's, Meats, and Related Meat Food Products § 98.5 Fees and charges. (a) The fee charged for any single laboratory analysis of meat, meat food... schedules of charges in paragraph (a) of § 91.37 of this subchapter. (b) The laboratory analyses of meat...

MreB and MurG as scaffolds for the cytoplasmic steps of peptidoglycan biosynthesis.

PubMed

Favini-Stabile, Sandy; Contreras-Martel, Carlos; Thielens, Nicole; Dessen, Andréa

2013-12-01

Peptidoglycan is a major determinant of cell shape in bacteria, and its biosynthesis involves the concerted action of cytoplasmic, membrane-associated and periplasmic enzymes. Within the cytoplasm, Mur enzymes catalyse the first steps leading to peptidoglycan precursor biosynthesis, and have been suggested as being part of a multicomponent complex that could also involve the transglycosylase MurG and the cytoskeletal protein MreB. In order to initialize the characterization of a potential Mur interaction network, we purified MurD, MurE, MurF, MurG and MreB from Thermotoga maritima and characterized their interactions using membrane blotting and surface plasmon resonance. MurD, MurE and MurF all recognize MurG and MreB, but not each other, while the two latter proteins interact. In addition, we solved the crystal structures of MurD, MurE and MurF, which indicate that their C-termini display high conformational flexibilities. The differences in Mur conformations could be important parameters for the stability of an intracytoplasmic murein biosynthesis complex. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

An octahedral shear strain-based measure of SNR for 3D MR elastography

NASA Astrophysics Data System (ADS)

McGarry, M. D. J.; Van Houten, E. E. W.; Perriñez, P. R.; Pattison, A. J.; Weaver, J. B.; Paulsen, K. D.

2011-07-01

A signal-to-noise ratio (SNR) measure based on the octahedral shear strain (the maximum shear strain in any plane for a 3D state of strain) is presented for magnetic resonance elastography (MRE), where motion-based SNR measures are commonly used. The shear strain, γ, is directly related to the shear modulus, μ, through the definition of shear stress, τ = μγ. Therefore, noise in the strain is the important factor in determining the quality of motion data, rather than the noise in the motion. Motion and strain SNR measures were found to be correlated for MRE of gelatin phantoms and the human breast. Analysis of the stiffness distributions of phantoms reconstructed from the measured motion data revealed a threshold for both strain and motion SNR where MRE stiffness estimates match independent mechanical testing. MRE of the feline brain showed significantly less correlation between the two SNR measures. The strain SNR measure had a threshold above which the reconstructed stiffness values were consistent between cases, whereas the motion SNR measure did not provide a useful threshold, primarily due to rigid body motion effects.

Prediction of heat transfer coefficients for forced convective boiling of N2-hydrocarbon mixtures at cryogenic conditions using artificial neural networks

NASA Astrophysics Data System (ADS)

Barroso-Maldonado, J. M.; Belman-Flores, J. M.; Ledesma, S.; Aceves, S. M.

2018-06-01

A key problem faced in the design of heat exchangers, especially for cryogenic applications, is the determination of convective heat transfer coefficients in two-phase flow such as condensation and boiling of non-azeotropic refrigerant mixtures. This paper proposes and evaluates three models for estimating the convective coefficient during boiling. These models are developed using computational intelligence techniques. The performance of the proposed models is evaluated using the mean relative error (mre), and compared to two existing models: the modified Granryd's correlation and the Silver-Bell-Ghaly method. The three proposed models are distinguished by their architecture. The first is based on directly measured parameters (DMP-ANN), the second is based on equivalent Reynolds and Prandtl numbers (eq-ANN), and the third on effective Reynolds and Prandtl numbers (eff-ANN). The results demonstrate that the proposed artificial neural network (ANN)-based approaches greatly outperform available methodologies. While Granryd's correlation predicts experimental data within a mean relative error mre = 44% and the S-B-G method produces mre = 42%, DMP-ANN has mre = 7.4% and eff-ANN has mre = 3.9%. Considering that eff-ANN has the lowest mean relative error (one tenth of previously available methodologies) and the broadest range of applicability, it is recommended for future calculations. Implementation is straightforward within a variety of platforms and the matrices with the ANN weights are given in the appendix for efficient programming.

Reconstruction of mreB Expression in Staphylococcus aureus via a Collection of New Integrative Plasmids

PubMed Central

Yepes, Ana; Koch, Gudrun; Waldvogel, Andrea; Garcia-Betancur, Juan-Carlos

2014-01-01

Protein localization has been traditionally explored in unicellular organisms, whose ease of genetic manipulation facilitates molecular characterization. The two rod-shaped bacterial models Escherichia coli and Bacillus subtilis have been prominently used for this purpose and have displaced other bacteria whose challenges for genetic manipulation have complicated any study of cell biology. Among these bacteria is the spherical pathogenic bacterium Staphylococcus aureus. In this report, we present a new molecular toolbox that facilitates gene deletion in staphylococci in a 1-step recombination process and additional vectors that facilitate the insertion of diverse reporter fusions into newly identified neutral loci of the S. aureus chromosome. Insertion of the reporters does not add any antibiotic resistance genes to the chromosomes of the resultant strains, thereby making them amenable for further genetic manipulations. We used this toolbox to reconstitute the expression of mreB in S. aureus, a gene that encodes an actin-like cytoskeletal protein which is absent in coccal cells and is presumably lost during the course of speciation. We observed that in S. aureus, MreB is organized in discrete structures in association with the membrane, leading to an unusual redistribution of the cell wall material. The production of MreB also caused cell enlargement, but it did not revert staphylococcal shape. We present interactions of MreB with key staphylococcal cell wall-related proteins. This work facilitates the use S. aureus as a model system in exploring diverse aspects of cellular microbiology. PMID:24747904

Modeling and semi-active fuzzy control of magnetorheological elastomer-based isolator for seismic response reduction

NASA Astrophysics Data System (ADS)

Nguyen, Xuan Bao; Komatsuzaki, Toshihiko; Iwata, Yoshio; Asanuma, Haruhiko

2018-02-01

In this paper, a magnetorheological elastomer (MRE) based isolator was investigated to mitigate excessive vibrations in structures during seismic events. The primary objectives of this research are to propose a numerical model that expresses viscoelastic behaviors of the MRE and predict operation process of the MRE-based isolator for future design of isolator systems for various technical applications. Despite the simplicity in parameter definition in comparison to the conventional models, the proposed model works efficiently in a wide range of frequencies and amplitudes. The model consists of the following components: viscoelasticity of host MRE, magnetic field-induced property, nominal viscosity as well as high stiffness in low excitation frequency that are modeled in analogy with a standard linear solid model (Zener model), a stiffness variable spring, and a smooth Coulomb friction, respectively. Furthermore, a semi-active fuzzy controller was designed to enhance the performance of the isolator in suppressing structural vibrations. The control strategy was built to determine the command applied current. The controller is completely adequate for handling the nonlinearity of the isolator and works independently with the building structure. The efficiency of the MRE-based isolator was evaluated by the responses of the scaled building under seismic excitation. Numerical and experimental results show that the isolator accompanied with a fuzzy controller remarkably reduces the relative displacement and absolute acceleration of the scaled building compared to passive-off and passive-on cases.

EXO1 is critical for embryogenesis and the DNA damage response in mice with a hypomorphic Nbs1 allele.

PubMed

Rein, Katrin; Yanez, Diana A; Terré, Berta; Palenzuela, Lluís; Aivio, Suvi; Wei, Kaichun; Edelmann, Winfried; Stark, Jeremy M; Stracker, Travis H

2015-09-03

The maintenance of genome stability is critical for the suppression of diverse human pathologies that include developmental disorders, premature aging, infertility and predisposition to cancer. The DNA damage response (DDR) orchestrates the appropriate cellular responses following the detection of lesions to prevent genomic instability. The MRE11 complex is a sensor of DNA double strand breaks (DSBs) and plays key roles in multiple aspects of the DDR, including DNA end resection that is critical for signaling and DNA repair. The MRE11 complex has been shown to function both upstream and in concert with the 5'-3' exonuclease EXO1 in DNA resection, but it remains unclear to what extent EXO1 influences DSB responses independently of the MRE11 complex. Here we examine the genetic relationship of the MRE11 complex and EXO1 during mammalian development and in response to DNA damage. Deletion of Exo1 in mice expressing a hypomorphic allele of Nbs1 leads to severe developmental impairment, embryonic death and chromosomal instability. While EXO1 plays a minimal role in normal cells, its loss strongly influences DNA replication, DNA repair, checkpoint signaling and damage sensitivity in NBS1 hypomorphic cells. Collectively, our results establish a key role for EXO1 in modulating the severity of hypomorphic MRE11 complex mutations. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Development of Vibration System for Applying Magnetic Resonance Elastography (MRE) to the Supraspinatus Muscle.

PubMed

Ito, Daiki; Numano, Tomokazu; Mizuhara, Kazuyuki; Takamoto, Kouichi; Onishi, Takaaki; Nishijo, Hisao

2016-01-01

Palpation is a standard clinical tool to diagnose abnormal stiffness changes in soft tissues. However, it is difficult to palpate the supraspinatus muscle because it locates under the trapezius muscle. The magnetic resonance elastography (MRE) uses harmonic mechanical excitation to quantitatively measure the stiffness (shear modulus) of both the superficial and deep tissues. The purpose of this study was to build a vibration system for applying the MRE to the supraspinatus muscle. In this study, a power amplifier and a pneumatic pressure generator were used to supply vibrations to a vibration pad. Six healthy volunteers underwent MRE. We investigated the effects of position (the head of the humerus and the trapezius muscle) of the vibration pad on the patterns of wave propagation (wave image). When the vibration pad was placed in the trapezius muscle, the wave images represented clear wave propagation. On the other hand, when the vibration pad was placed in the head of the humerus, the wave images represented unclear wave propagation. This result might be caused by wave interferences resulting from the vibrations from bones and an intramuscular tendon of the supraspinatus muscle. The mean shear modulus also was 8.12 ± 1.83 (mean ± SD) kPa, when the vibration pad was placed in the trapezius muscle. Our results demonstrated that the vibration pad should be placed in the trapezius muscle in the MRE of the supraspinatus muscle.

The Fisheries and Marine Renewable Energy Working Group: creating an agenda for improved co-existence.

NASA Astrophysics Data System (ADS)

Campbell, M. S.; De Groot, J.; Ashley, M.; Rodwell, L.

2014-12-01

As an emerging industry, Marine Renewable Energy (MRE) is expected to play a major contributory role if the UK is to successfully reach its desired target of renewable energy production by 2020. However, due to the competing objectives and priorities of MRE and other industries, for example fisheries, and in the delivering of conservation measures, the demand for space within our marine landscape is increasing, and interactions are inevitable. In order to promote better understanding of the challenges in resolving interactions between these industries, a Fisheries and Marine Renewable Energy Working Group was set up under the Natural Environment Research Council Marine Renewable Energy Knowledge Exchange Programme (NERC MREKEP). The Working Group carried out an initial scoping survey in order to summarise recent and current research activities and identify key issues and topics in the fields of fisheries and MRE interactions. Mixed stakeholder groups discussed four primary topics: priority issues; barriers to progress; problem mitigation; and thoughts on the consultation process. Points of discussion were categorized into themes to aid analysis and protocol development. These themes were: culture, community and economy; legislation and rights; data and information; and collaboration and communication. Subsequent invited stakeholder and expert panel workshops were held to facilitate knowledge exchange between fisheries and development of MRE in order to identify priority research issues, knowledge gaps and collaboration needs. Four group sessions identified: practical steps to aid interaction between industries; barriers, opportunities and solutions; an agenda for action, timescales and partners; and action points carried forward by each stakeholder group. This Working Group, guided under the MREKEP banner, is the first of its kind in the UK, bringing together individuals from a nationally diverse group of academics, regulators, policy makers and representatives from fisheries, MRE sectors and conservation bodies. Therefore, it has the potential, for the first time, to develop effective guidelines and protocols for both mitigation and assessment of displacement of fishing effort, for the entire life cycle of MRE projects.

Prospective cohort study of ultrasound-ultrasound and ultrasound-MR enterography agreement in the evaluation of pediatric small bowel Crohn disease.

PubMed

Dillman, Jonathan R; Smith, Ethan A; Sanchez, Ramon; DiPietro, Michael A; Dehkordy, Soudabeh Fazeli; Adler, Jeremy; DeMatos-Maillard, Vera; Khalatbari, Shokoufeh; Davenport, Matthew S

2016-04-01

There is a paucity of published literature describing ultrasound (US)-US and US-MR enterography (MRE) inter-radiologist agreement in pediatric small bowel Crohn disease. To prospectively assess US-US and US-MRE inter-radiologist agreement in pediatric small bowel Crohn disease. Institutional Review Board approval and informed consent/assent were obtained for this HIPAA-compliant prospective cohort study of children with newly diagnosed distal small bowel Crohn disease (July 2012 to December 2014). Enrolled subjects (n = 29) underwent two small bowel US examinations performed by blinded independent radiologists both before and at multiple time points after initiation of medical therapy (231 unique US examinations, in total); 134 US examinations were associated with concurrent MRE. The MRE examination was interpreted by a third blinded radiologist. The following was documented on each examination: involved length of ileum (cm); maximum bowel wall thickness (mm); amount of bowel wall and mesenteric Doppler signal, and presence of stricture, penetrating disease and/or abscess. Inter-radiologist agreement was assessed with single-measure, three-way, mixed-model intra-class correlation coefficients (ICC) and prevalence-adjusted, bias-adjusted kappa statistics (κ). Numbers in brackets are 95% confidence intervals. Ultrasound-US agreement was moderate for involved length (ICC: 0.41 [0.35-0.49]); substantial for maximum bowel wall thickness (ICC: 0.67 [0.64-0.70]); moderate for bowel wall Doppler signal (ICC: 0.53 [0.48-0.59]); slight for mesenteric Doppler signal (ICC: 0.25 [0.18-0.42]), and moderate to almost perfect for stricture (κ: 0.54), penetrating disease (κ: 0.80), and abscess (κ: 0.96). US-MRE agreement was moderate for involved length (ICC: 0.42 [0.37-0.49]); substantial for maximum bowel wall thickness (ICC: 0.66 [0.65-0.69]), and substantial to almost perfect for stricture (κ: 0.61), penetrating disease (κ: 0.72) and abscess (κ: 0.88). Ultrasound-US agreement was similar to US-MRE agreement for assessing pediatric small bowel Crohn disease. Discrepancies in US-US and US-MRE reporting question the utility of US as an accurate, reproducible radiologic biomarker for assessing response to medical therapy and disease-related complications.

MR elastography and diffusion-weighted imaging of ex vivo prostate cancer: quantitative comparison to histopathology.

PubMed

Sahebjavaher, Ramin S; Nir, Guy; Gagnon, Louis O; Ischia, Joseph; Jones, Edward C; Chang, Silvia D; Yung, Andrew; Honarvar, Mohammad; Fazli, Ladan; Goldenberg, S Larry; Rohling, Robert; Sinkus, Ralph; Kozlowski, Piotr; Salcudean, Septimiu E

2015-01-01

The purpose of this work was (1) to develop a magnetic resonance elastography (MRE) system for imaging of the ex vivo human prostate and (2) to assess the diagnostic power of mono-frequency and multi-frequency MRE and diffusion weighted imaging (DWI) alone and combined as correlated with histopathology in a patient study. An electromagnetic driver was designed specifically for MRE studies in small-bore MR scanners. Ex vivo prostate specimens (post-fixation) of 14 patients who underwent radical prostatectomy were imaged with MRE at 7 T (nine cases had DWI). In six patients, the MRE examination was performed at three frequencies (600, 800, 1000 Hz) to extract the power-law exponent Gamma. The images were registered to wholemount pathology slides marked with the Gleason score. The areas under the receiver-operator-characteristic curves (AUC) were calculated. The methods were validated in a phantom study and it was demonstrated that (i) the driver does not interfere with the acquisition process and (ii) the driver can generate amplitudes greater than 100 µm for frequencies less than 1 kHz. In the quantitative study, cancerous tissue with Gleason score at least 3 + 3 was distinguished from normal tissue in the peripheral zone (PZ) with an average AUC of 0.75 (Gd ), 0.75 (Gl ), 0.70 (Gamma-Gd ), 0.68 (apparent diffusion coefficient, ADC), and 0.82 (Gd  + Gl  + ADC). The differentiation between PZ and central gland was modest for Gd (p < 0.07), Gl (p < 0.06) but not significant for Gamma (p < 0.2). A correlation of 0.4 kPa/h was found between the fixation time of the prostate specimen and the stiffness of the tissue, which could affect the diagnostic power results. DWI and MRE may provide complementary information; in fact MRE performed better than ADC in distinguishing normal from cancerous tissue in some cases. Multi-frequency (Gamma) analysis did not appear to improve the results. However, in light of the effect of tissue fixation, the clinical implication of our results may be inconclusive and more experiments are needed. Copyright © 2014 John Wiley & Sons, Ltd.

Quasi-steady-state air plasma channel produced by a femtosecond laser pulse sequence

PubMed Central

Lu, Xin; Chen, Shi-You; Ma, Jing-Long; Hou, Lei; Liao, Guo-Qian; Wang, Jin-Guang; Han, Yu-Jing; Liu, Xiao-Long; Teng, Hao; Han, Hai-Nian; Li, Yu-Tong; Chen, Li-Ming; Wei, Zhi-Yi; Zhang, Jie

2015-01-01

A long air plasma channel can be formed by filamentation of intense femtosecond laser pulses. However, the lifetime of the plasma channel produced by a single femtosecond laser pulse is too short (only a few nanoseconds) for many potential applications based on the conductivity of the plasma channel. Therefore, prolonging the lifetime of the plasma channel is one of the key challenges in the research of femtosecond laser filamentation. In this study, a unique femtosecond laser source was developed to produce a high-quality femtosecond laser pulse sequence with an interval of 2.9 ns and a uniformly distributed single-pulse energy. The metre scale quasi-steady-state plasma channel with a 60–80 ns lifetime was formed by such pulse sequences in air. The simulation study for filamentation of dual femtosecond pulses indicated that the plasma channel left by the previous pulse was weakly affected the filamentation of the next pulse in sequence under our experimental conditions. PMID:26493279

Coherent control of acoustic vibrations in metal nanoparticles and thin films with sequences of femtosecond pulses: Harmonic-oscillator model

NASA Astrophysics Data System (ADS)

Zheltikov, A. M.

2002-08-01

A harmonic oscillator model is used to demonstrate the possibility of coherent control of acoustic vibrations of metal nanoparticles and thin films with sequences of femtosecond laser pulses. When the interval between the pulses in such a sequence is chosen equal to the oscillation period of the expansion mode of a nanoscale system, the relevant acoustic vibrations can be excited in a resonant and selective way. Sequences of femtosecond pulses with picosecond time intervals between the pulses are shown to be ideally suited for a resonant excitation and coherent control of acoustic modes of silver nanoparticles.

Value of a single-shot turbo spin-echo pulse sequence for assessing the architecture of the subarachnoid space and the constitutive nature of cerebrospinal fluid.

PubMed

Pease, Anthony; Sullivan, Stacey; Olby, Natasha; Galano, Heather; Cerda-Gonzalez, Sophia; Robertson, Ian D; Gavin, Patrick; Thrall, Donald

2006-01-01

Three case history reports are presented to illustrate the value of the single-shot turbo spin-echo pulse sequence for assessment of the subarachnoid space. The use of the single-shot turbo spin-echo pulse sequence, which is a heavily T2-weighted sequence, allows for a rapid, noninvasive evaluation of the subarachnoid space by using the high signal from cerebrospinal fluid. This sequence can be completed in seconds rather than the several minutes required for a T2-fast spin-echo sequence. Unlike the standard T2-fast spin-echo sequence, a single-shot turbo spin-echo pulse sequence also provides qualitative information about the protein and the cellular content of the cerebrospinal fluid, such as in patients with inflammatory debris or hemorrhage in the cerebrospinal fluid. Although the resolution of the single-shot turbo spin-echo pulse sequence images is relatively poor compared with more conventional sequences, the qualitative information about the subarachnoid space and cerebrospinal fluid and the rapid acquisition time, make it a useful sequence to include in standard protocols of spinal magnetic resonance imaging.

Pulse Sequence Programming in a Dynamic Visual Environment: SequenceTree

PubMed Central

Magland, Jeremy F.; Li, Cheng; Langham, Michael C.; Wehrli, Felix W.

2015-01-01

Purpose To describe SequenceTree (ST), an open source. integrated software environment for implementing MRI pulse sequences, and ideally exported them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for non-programmers and programmers alike. Methods The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally other types of scanners will be supported in the future. Results The software has been used for eight years in the authors’ laboratory and elsewhere and has been utilized in more than fifty peer-reviewed publications in areas such as cardiovascular imaging, solid state and non-proton NMR, MR elastography, and high resolution structural imaging. Conclusion ST is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal for both advanced users and those with limited programming experience. PMID:25754837

A powerful graphical pulse sequence programming tool for magnetic resonance imaging.

PubMed

Jie, Shen; Ying, Liu; Jianqi, Li; Gengying, Li

2005-12-01

A powerful graphical pulse sequence programming tool has been designed for creating magnetic resonance imaging (MRI) applications. It allows rapid development of pulse sequences in graphical mode (allowing for the visualization of sequences), and consists of three modules which include a graphical sequence editor, a parameter management module and a sequence compiler. Its key features are ease to use, flexibility and hardware independence. When graphic elements are combined with a certain text expressions, the graphical pulse sequence programming is as flexible as text-based programming tool. In addition, a hardware-independent design is implemented by using the strategy of two step compilations. To demonstrate the flexibility and the capability of this graphical sequence programming tool, a multi-slice fast spin echo experiment is performed on our home-made 0.3 T permanent magnet MRI system.

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1996-04-23

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. 7 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1996-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence.

47 CFR 2.201 - Emission, modulation, and transmission characteristics.

Code of Federal Regulations, 2014 CFR

2014-10-01

... carrier is amplitude-modulated (including cases where sub-carriers are angle-modulated): —Double-sideband... is amplitude and angle-modulated either simultaneously or in a pre-established sequence D (5) Emission of pulses: 1 —Sequence of unmodulated pulses P —A sequence of pulses: —Modulated in amplitude K...

47 CFR 2.201 - Emission, modulation, and transmission characteristics.

Code of Federal Regulations, 2013 CFR

2013-10-01

... carrier is amplitude-modulated (including cases where sub-carriers are angle-modulated): —Double-sideband... is amplitude and angle-modulated either simultaneously or in a pre-established sequence D (5) Emission of pulses: 1 —Sequence of unmodulated pulses P —A sequence of pulses: —Modulated in amplitude K...

47 CFR 2.201 - Emission, modulation, and transmission characteristics.

Code of Federal Regulations, 2012 CFR

2012-10-01

... carrier is amplitude-modulated (including cases where sub-carriers are angle-modulated): —Double-sideband... is amplitude and angle-modulated either simultaneously or in a pre-established sequence D (5) Emission of pulses: 1 —Sequence of unmodulated pulses P —A sequence of pulses: —Modulated in amplitude K...

Investigation of the effect of finite pulse errors on the BABA pulse sequence using the Floquet-Magnus expansion approach

NASA Astrophysics Data System (ADS)

Mananga, Eugene S.; Reid, Alicia E.

2013-01-01

This paper presents a study of finite pulse widths for the BABA pulse sequence using the Floquet-Magnus expansion (FME) approach. In the FME scheme, the first order ? is identical to its counterparts in average Hamiltonian theory (AHT) and Floquet theory (FT). However, the timing part in the FME approach is introduced via the ? function not present in other schemes. This function provides an easy way for evaluating the spin evolution during the time in between' through the Magnus expansion of the operator connected to the timing part of the evolution. The evaluation of ? is particularly useful for the analysis of the non-stroboscopic evolution. Here, the importance of the boundary conditions, which provide a natural choice of ? , is ignored. This work uses the ? function to compare the efficiency of the BABA pulse sequence with ? and the BABA pulse sequence with finite pulses. Calculations of ? and ? are presented.

Quantitative MRI of kidneys in renal disease.

PubMed

Kline, Timothy L; Edwards, Marie E; Garg, Ishan; Irazabal, Maria V; Korfiatis, Panagiotis; Harris, Peter C; King, Bernard F; Torres, Vicente E; Venkatesh, Sudhakar K; Erickson, Bradley J

2018-03-01

To evaluate the reproducibility and utility of quantitative magnetic resonance imaging (MRI) sequences for the assessment of kidneys in young adults with normal renal function (eGFR ranged from 90 to 130 mL/min/1.73 m 2 ) and patients with early renal disease (autosomal dominant polycystic kidney disease). This prospective case-control study was performed on ten normal young adults (18-30 years old) and ten age- and sex-matched patients with early renal parenchymal disease (autosomal dominant polycystic kidney disease). All subjects underwent a comprehensive kidney MRI protocol, including qualitative imaging: T1w, T2w, FIESTA, and quantitative imaging: 2D cine phase contrast of the renal arteries, and parenchymal diffusion weighted imaging (DWI), magnetization transfer imaging (MTI), blood oxygen level dependent (BOLD) imaging, and magnetic resonance elastography (MRE). The normal controls were imaged on two separate occasions ≥24 h apart (range 24-210 h) to assess reproducibility of the measurements. Quantitative MR imaging sequences were found to be reproducible. The mean ± SD absolute percent difference between quantitative parameters measured ≥24 h apart were: MTI-derived ratio = 4.5 ± 3.6%, DWI-derived apparent diffusion coefficient (ADC) = 6.5 ± 3.4%, BOLD-derived R2* = 7.4 ± 5.9%, and MRE-derived tissue stiffness = 7.6 ± 3.3%. Compared with controls, the ADPKD patient's non-cystic renal parenchyma (NCRP) had statistically significant differences with regard to quantitative parenchymal measures: lower MTI percent ratios (16.3 ± 4.4 vs. 23.8 ± 1.2, p < 0.05), higher ADCs (2.46 ± 0.20 vs. 2.18 ± 0.10 × 10 -3  mm 2 /s, p < 0.05), lower R2*s (14.9 ± 1.7 vs. 18.1 ± 1.6 s -1 , p < 0.05), and lower tissue stiffness (3.2 ± 0.3 vs. 3.8 ± 0.5 kPa, p < 0.05). Excellent reproducibility of the quantitative measurements was obtained in all cases. Significantly different quantitative MR parenchymal measurement parameters between ADPKD patients and normal controls were obtained by MT, DWI, BOLD, and MRE indicating the potential for detecting and following renal disease at an earlier stage than the conventional qualitative imaging techniques.

Effect of TiC addition on microstructure and magnetic properties for MRE{sub 2}(Fe,Co){sub 14}B melt-spun ribbons (MRE=Nd+Y+Dy)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, W.; Wu, Y. Q.; Dennis, K. W.

2006-04-15

Effects of a TiC addition on microstructure and magnetic properties in [MRE{sub 2.2}Fe{sub 14}B]{sub (100-2x)/17.2}+Ti{sub x}C{sub x}(MRE=Nd+Y+Dy,x=1-5) ribbons, melt spun at a wheel speed of 16 m/s, were systematically studied. X-ray diffraction and differential thermal analysis data revealed that the addition of TiC improves the glass formability in the mixed rare earth alloys without Co, resulting in partially amorphous alloys. TEM observations showed that the average grain size in the as spun samples decreases from 200 to 20 nm with increasing x from 1 to 5, confirming that the addition of TiC can significantly improve microstructure. For an optimized [MRE{submore » 2}(Fe,Co){sub 14}B]{sub (100-2x)/17.2}+Ti{sub x}C{sub x} sample with x=2, spun at 25 m/s and annealed at 750 deg. C for 15 min, the room-temperature magnetic properties of H{sub cj}=11.8 kOe, M{sub r}=7.2 kGs, and (BH){sub max}=11.3 MGOe were obtained. Temperature coefficients for M{sub r} and H{sub cj} of -0.06 and -0.37%/ deg. C, respectively, also were measured in the temperature range of 27-100 deg. C. The new magnet alloy exhibits more uniform magnetic properties and a usable energy product to nearly 300 deg. C.« less

Reconstruction of mreB expression in Staphylococcus aureus via a collection of new integrative plasmids.

PubMed

Yepes, Ana; Koch, Gudrun; Waldvogel, Andrea; Garcia-Betancur, Juan-Carlos; Lopez, Daniel

2014-07-01

Protein localization has been traditionally explored in unicellular organisms, whose ease of genetic manipulation facilitates molecular characterization. The two rod-shaped bacterial models Escherichia coli and Bacillus subtilis have been prominently used for this purpose and have displaced other bacteria whose challenges for genetic manipulation have complicated any study of cell biology. Among these bacteria is the spherical pathogenic bacterium Staphylococcus aureus. In this report, we present a new molecular toolbox that facilitates gene deletion in staphylococci in a 1-step recombination process and additional vectors that facilitate the insertion of diverse reporter fusions into newly identified neutral loci of the S. aureus chromosome. Insertion of the reporters does not add any antibiotic resistance genes to the chromosomes of the resultant strains, thereby making them amenable for further genetic manipulations. We used this toolbox to reconstitute the expression of mreB in S. aureus, a gene that encodes an actin-like cytoskeletal protein which is absent in coccal cells and is presumably lost during the course of speciation. We observed that in S. aureus, MreB is organized in discrete structures in association with the membrane, leading to an unusual redistribution of the cell wall material. The production of MreB also caused cell enlargement, but it did not revert staphylococcal shape. We present interactions of MreB with key staphylococcal cell wall-related proteins. This work facilitates the use S. aureus as a model system in exploring diverse aspects of cellular microbiology. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

On the relative contributions of multisensory integration and crossmodal exogenous spatial attention to multisensory response enhancement.

PubMed

Van der Stoep, N; Spence, C; Nijboer, T C W; Van der Stigchel, S

2015-11-01

Two processes that can give rise to multisensory response enhancement (MRE) are multisensory integration (MSI) and crossmodal exogenous spatial attention. It is, however, currently unclear what the relative contribution of each of these is to MRE. We investigated this issue using two tasks that are generally assumed to measure MSI (a redundant target effect task) and crossmodal exogenous spatial attention (a spatial cueing task). One block of trials consisted of unimodal auditory and visual targets designed to provide a unimodal baseline. In two other blocks of trials, the participants were presented with spatially and temporally aligned and misaligned audiovisual (AV) targets (0, 50, 100, and 200ms SOA). In the integration block, the participants were instructed to respond to the onset of the first target stimulus that they detected (A or V). The instruction for the cueing block was to respond only to the onset of the visual targets. The targets could appear at one of three locations: left, center, and right. The participants were instructed to respond only to lateral targets. The results indicated that MRE was caused by MSI at 0ms SOA. At 50ms SOA, both crossmodal exogenous spatial attention and MSI contributed to the observed MRE, whereas the MRE observed at the 100 and 200ms SOAs was attributable to crossmodal exogenous spatial attention, alerting, and temporal preparation. These results therefore suggest that there may be a temporal window in which both MSI and exogenous crossmodal spatial attention can contribute to multisensory response enhancement. Copyright © 2015 Elsevier B.V. All rights reserved.

Measuring shear-wave speed with point shear-wave elastography and MR elastography: a phantom study

PubMed Central

Kishimoto, Riwa; Suga, Mikio; Koyama, Atsuhisa; Omatsu, Tokuhiko; Tachibana, Yasuhiko; Ebner, Daniel K; Obata, Takayuki

2017-01-01

Objectives To compare shear-wave speed (SWS) measured by ultrasound-based point shear-wave elastography (pSWE) and MR elastography (MRE) on phantoms with a known shear modulus, and to assess method validity and variability. Methods 5 homogeneous phantoms of different stiffnesses were made. Shear modulus was measured by a rheometer, and this value was used as the standard. 10 SWS measurements were obtained at 4 different depths with 1.0–4.5 MHz convex (4C1) and 4.0–9.0 MHz linear (9L4) transducers using pSWE. MRE was carried out once per phantom, and SWSs at 5 different depths were obtained. These SWSs were then compared with those from a rheometer using linear regression analyses. Results SWSs obtained with both pSWE as well as MRE had a strong correlation with those obtained by a rheometer (R2>0.97). The relative difference in SWS between the procedures was from −25.2% to 25.6% for all phantoms, and from −8.1% to 6.9% when the softest and hardest phantoms were excluded. Depth dependency was noted in the 9L4 transducer of pSWE and MRE. Conclusions SWSs from pSWE and MRE showed a good correlation with a rheometer-determined SWS. Although based on phantom studies, SWSs obtained with these methods are not always equivalent, the measurement can be thought of as reliable and these SWSs were reasonably close to each other for the middle range of stiffness within the measurable range. PMID:28057657

A versatile pulse programmer for pulsed nuclear magnetic resonance spectroscopy.

NASA Technical Reports Server (NTRS)

Tarr, C. E.; Nickerson, M. A.

1972-01-01

A digital pulse programmer producing the standard pulse sequences required for pulsed nuclear magnetic resonance spectroscopy is described. In addition, a 'saturation burst' sequence, useful in the measurement of long relaxation times in solids, is provided. Both positive and negative 4 V trigger pulses are produced that are fully synchronous with a crystal-controlled time base, and the pulse programmer may be phase-locked with a maximum pulse jitter of 3 ns to the oscillator of a coherent pulse spectrometer. Medium speed TTL integrated circuits are used throughout.

Study on a new self-sensing magnetorheological elastomer bearing

NASA Astrophysics Data System (ADS)

Li, Rui; Zhou, Mengjiao; Wang, Minglian; Yang, Ping-an

2018-06-01

The complexity of a semi-active vibration isolation system results in the difficulty of realizing its role on impact load effectively. Thus, a new self-sensing bearing based on modified anisotropic magnetorheological elastomer (MRE) is proposed in this study. This self-sensing bearing was fabricated by dispersed multi-walled carbon nanotubes and carbonyl iron particles into polydimethylsiloxane matrix under a magnetic field. The working conditions of the bearing were analyzed and decoupled. An optimal structure size of the bearing was selected and used for setting up the experiment test system. The self-sensing characteristic of the MRE bearing under the multi-field coupling of load and magnetic fields was then investigated by this test system. Results showed that the resistance of the modified MRE, in which a preload was applied by the bearing, could change approximately 28%-56% under extrusion force, mechanical force, and external magnetic field. The vibration isolation performance was tested based on the self-sensing characteristic. The bearing had excellent mechanical properties, which could reduce at least 30% of vibration. Thus, the modified MRE of the magnetorheological elastomer bearing could be simultaneously used as an actuator and a sensor.

Modeling of Soft Poroelastic Tissue in Time-Harmonic MR Elastography

PubMed Central

Perriñez, Phillip R.; Kennedy, Francis E.; Van Houten, Elijah E. W.; Weaver, John B.; Paulsen, Keith D.

2010-01-01

Elastography is an emerging imaging technique that focuses on assessing the resistance to deformation of soft biological tissues in vivo. Magnetic resonance elastography (MRE) uses measured displacement fields resulting from low-amplitude, low-frequency (10 Hz–1 kHz) time-harmonic vibration to recover images of the elastic property distribution of tissues including breast, liver, muscle, prostate, and brain. While many soft tissues display complex time-dependent behavior not described by linear elasticity, the models most commonly employed in MRE parameter reconstructions are based on elastic assumptions. Further, elasticity models fail to include the interstitial fluid phase present in vivo. Alternative continuum models, such as consolidation theory, are able to represent tissue and other materials comprising two distinct phases, generally consisting of a porous elastic solid and penetrating fluid. MRE reconstructions of simulated elastic and poroelastic phantoms were performed to investigate the limitations of current-elasticity-based methods in producing accurate elastic parameter estimates in poroelastic media. The results indicate that linearly elastic reconstructions of fluid-saturated porous media at amplitudes and frequencies relevant to steady-state MRE can yield misleading effective property distributions resulting from the complex interaction between their solid and fluid phases. PMID:19272864

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

PubMed

Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

Improving the time efficiency of the Fourier synthesis method for slice selection in magnetic resonance imaging.

PubMed

Tahayori, B; Khaneja, N; Johnston, L A; Farrell, P M; Mareels, I M Y

2016-01-01

The design of slice selective pulses for magnetic resonance imaging can be cast as an optimal control problem. The Fourier synthesis method is an existing approach to solve these optimal control problems. In this method the gradient field as well as the excitation field are switched rapidly and their amplitudes are calculated based on a Fourier series expansion. Here, we provide a novel insight into the Fourier synthesis method via representing the Bloch equation in spherical coordinates. Based on the spherical Bloch equation, we propose an alternative sequence of pulses that can be used for slice selection which is more time efficient compared to the original method. Simulation results demonstrate that while the performance of both methods is approximately the same, the required time for the proposed sequence of pulses is half of the original sequence of pulses. Furthermore, the slice selectivity of both sequences of pulses changes with radio frequency field inhomogeneities in a similar way. We also introduce a measure, referred to as gradient complexity, to compare the performance of both sequences of pulses. This measure indicates that for a desired level of uniformity in the excited slice, the gradient complexity for the proposed sequence of pulses is less than the original sequence. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Properties of the unusually short pulse sequences occurring prior to the first strokes of negative cloud-to-ground lightning flashes

NASA Astrophysics Data System (ADS)

Kolmasova, Ivana; Santolik, Ondrej; Farges, Thomas; Rison, William; Lan, Radek; Uhlir, Ludek

2014-05-01

We analyze pulse sequences occurring prior to first return strokes of negative cloud-to-ground lightning flashes. The magnetic-field waveforms are measured close to the thunderstorm using a broad-band analyzer with a sampling interval of 12.5 ns. The electric-field waveforms are measured at the distance of ~ 400 km using an analyzer with a sampling interval of 80 ns. The sequence is usually composed of three parts. It begins with a larger pulse train which is believed to be connected with initial breakdown processes. The train of preliminary breakdown pulses ("B" part) is followed by a relatively low and irregular pulse activity ("I" part), which is sometimes missing. The sequence ends with a pulse train attributed to the stepped leader ("L" part). We recognize two different patterns ("B-I-L" and "B-L" types) in recorded waveforms. For the first time, we analyze the time evolution of the pulse amplitudes in the "B" part of "B-I-L" type sequences. The pulse amplitude is decreasing on average by 34% of the maximum value within a given train. We observe an unusually short duration of sequences. This is probably linked to a low height of the thundercloud. Another possible explanation may be based on an untypical precipitation mix resulting in faster steeped leaders.

A partial least squares based spectrum normalization method for uncertainty reduction for laser-induced breakdown spectroscopy measurements

NASA Astrophysics Data System (ADS)

Li, Xiongwei; Wang, Zhe; Lui, Siu-Lung; Fu, Yangting; Li, Zheng; Liu, Jianming; Ni, Weidou

2013-10-01

A bottleneck of the wide commercial application of laser-induced breakdown spectroscopy (LIBS) technology is its relatively high measurement uncertainty. A partial least squares (PLS) based normalization method was proposed to improve pulse-to-pulse measurement precision for LIBS based on our previous spectrum standardization method. The proposed model utilized multi-line spectral information of the measured element and characterized the signal fluctuations due to the variation of plasma characteristic parameters (plasma temperature, electron number density, and total number density) for signal uncertainty reduction. The model was validated by the application of copper concentration prediction in 29 brass alloy samples. The results demonstrated an improvement on both measurement precision and accuracy over the generally applied normalization as well as our previously proposed simplified spectrum standardization method. The average relative standard deviation (RSD), average of the standard error (error bar), the coefficient of determination (R2), the root-mean-square error of prediction (RMSEP), and average value of the maximum relative error (MRE) were 1.80%, 0.23%, 0.992, 1.30%, and 5.23%, respectively, while those for the generally applied spectral area normalization were 3.72%, 0.71%, 0.973, 1.98%, and 14.92%, respectively.

Purification and characterization of Escherichia coli MreB protein.

PubMed

Nurse, Pearl; Marians, Kenneth J

2013-02-01

The actin homolog MreB is required in rod-shaped bacteria for maintenance of cell shape and is intimately connected to the holoenzyme that synthesizes the peptidoglycan layer. The protein has been reported variously to exist in helical loops under the cell surface, to rotate, and to move in patches in both directions around the cell surface. Studies of the Escherichia coli protein in vitro have been hampered by its tendency to aggregate. Here we report the purification and characterization of native E. coli MreB. The protein requires ATP hydrolysis for polymerization, forms bundles with a left-hand twist that can be as long as 4 μm, forms sheets in the presence of calcium, and has a critical concentration for polymerization of 1.5 μM.

Purification and Characterization of Escherichia coli MreB Protein*

PubMed Central

Nurse, Pearl; Marians, Kenneth J.

2013-01-01

The actin homolog MreB is required in rod-shaped bacteria for maintenance of cell shape and is intimately connected to the holoenzyme that synthesizes the peptidoglycan layer. The protein has been reported variously to exist in helical loops under the cell surface, to rotate, and to move in patches in both directions around the cell surface. Studies of the Escherichia coli protein in vitro have been hampered by its tendency to aggregate. Here we report the purification and characterization of native E. coli MreB. The protein requires ATP hydrolysis for polymerization, forms bundles with a left-hand twist that can be as long as 4 μm, forms sheets in the presence of calcium, and has a critical concentration for polymerization of 1.5 μm. PMID:23235161

Characterization of scatter in digital mammography from physical measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leon, Stephanie M., E-mail: Stephanie.Leon@uth.tmc.edu; Wagner, Louis K.; Brateman, Libby F.

2014-06-15

Purpose: That scattered radiation negatively impacts the quality of medical radiographic imaging is well known. In mammography, even slight amounts of scatter reduce the high contrast required for subtle soft-tissue imaging. In current clinical mammography, image contrast is partially improved by use of an antiscatter grid. This form of scatter rejection comes with a sizeable dose penalty related to the concomitant elimination of valuable primary radiation. Digital mammography allows the use of image processing as a method of scatter correction that might avoid effects that negatively impact primary radiation, while potentially providing more contrast improvement than is currently possible withmore » a grid. For this approach to be feasible, a detailed characterization of the scatter is needed. Previous research has modeled scatter as a constant background that serves as a DC bias across the imaging surface. The goal of this study was to provide a more substantive data set for characterizing the spatially-variant features of scatter radiation at the image detector of modern mammography units. Methods: This data set was acquired from a model of the radiation beam as a matrix of very narrow rays or pencil beams. As each pencil beam penetrates tissue, the pencil widens in a predictable manner due to the production of scatter. The resultant spreading of the pencil beam at the detector surface can be characterized by two parameters: mean radial extent (MRE) and scatter fraction (SF). The SF and MRE were calculated from measurements obtained using the beam stop method. Two digital mammography units were utilized, and the SF and MRE were found as functions of target, filter, tube potential, phantom thickness, and presence or absence of a grid. These values were then used to generate general equations allowing the SF and MRE to be calculated for any combination of the above parameters. Results: With a grid, the SF ranged from a minimum of about 0.05 to a maximum of about 0.16, and the MRE ranged from about 3 to 13 mm. Without a grid, the SF ranged from a minimum of 0.25 to a maximum of 0.52, and the MRE ranged from about 20 to 45 mm. The SF with a grid demonstrated a mild dependence on target/filter combination and kV, whereas the SF without a grid was independent of these factors. The MRE demonstrated a complex relationship as a function of kV, with notable difference among target/filter combinations. The primary source of change in both the SF and MRE was phantom thickness. Conclusions: Because breast tissue varies spatially in physical density and elemental content, the effective thickness of breast tissue varies spatially across the imaging field, resulting in a spatially-variant scatter distribution in the imaging field. The data generated in this study can be used to characterize the scatter contribution on a point-by-point basis, for a variety of different techniques.« less

Highly potent antimicrobial peptides from N-terminal membrane-binding region of E. coli MreB.

PubMed

Saikia, Karabi; Sravani, Yalavarthi Durga; Ramakrishnan, Vibin; Chaudhary, Nitin

2017-02-23

Microbial pathogenesis is a serious health concern. The threat escalates as the existing conventional antimicrobials are losing their efficacy against the evolving pathogens. Peptides hold promise to be developed into next-generation antibiotics. Antimicrobial peptides adopt amphipathic structures that could selectively bind to and disrupt the microbial membranes. Interaction of proteins with membranes is central to all living systems and we reasoned that the membrane-binding domains in microbial proteins could be developed into efficient antimicrobials. This is an interesting approach as self-like sequences could elude the microbial strategies of degrading the antimicrobial peptides, one of the mechanisms of showing resistance to antimicrobials. We selected the 9-residue-long membrane-binding region of E. coli MreB protein. The 9-residue peptide (C-terminal amide) and its N-terminal acetylated analog displayed broad-spectrum activity, killing Gram-negative bacteria, Gram-positive bacteria, and fungi. Extension with a tryptophan residue at the N-terminus drastically improved the activity of the peptides with lethal concentrations ≤10 μM against all the organisms tested. The tryptophan-extended peptides caused complete killing of C. albicans as well as gentamicin and methicillin resistant S. aureus at 5 μM concentration. Lipid-binding studies and electron microscopic analyses of the peptide-treated microbes suggest membrane disruption as the mechanism of killing.

MR Enterography of the Ileoanal Pouch: Descriptive Radiologic Analysis With Endoscopic and Pathologic Correlation.

PubMed

Sahi, Kamaldeep Singh; Lee, Karen S; Moss, Alan; Yee, Eric; Allard, Felicia; Brook, Alexander; Mortele, Koenraad J

2015-11-01

The purpose of this study was to describe the MR enterography (MRE) appearance of inflammation of the ileoanal pouch after ileal pouch-anal anastomosis (IPAA) surgery and to correlate it with pouch endoscopic and histopathologic findings. All MRE studies performed between October 1, 2007, and September 30, 2013, for patients who had previously undergone IPAA (n = 54) were retrieved. After review of medical records, the patients who underwent MRE, pouch endoscopy, and biopsy within 90 days (14 men, 14 women; mean age, 42.2 years; range, 24-67 years) were selected for inclusion in the study. Two blinded MRI radiologists in consensus retrospectively evaluated MRE studies for multiple MRI features. Two MRI scores were then calculated: an active and a composite inflammation score. A gastroenterologist retrospectively reviewed the pouch endoscopic images, and a pathologist reviewed the slides; both of these investigators were blinded. Both MRI scores were correlated with the pouch endoscopic and histopathologic findings. The composite MRI score had strong positive correlation with the endoscopic score (r = 0.61; p = 0.0005) but weak positive correlation with the histopathologic score (r = 0.31; p = 0.10, not statistically significant). The active inflammation MRI score had moderate positive correlation with the endoscopic score (r = 0.57; p = 0.0017) and weak positive correlation with the histopathologic score (r = 0.20; p = 0.31, not statistically significant). An MRI score ≥ 4 indicated the best results, with sensitivity of 86%, specificity of 79%, positive predictive value of 80%, negative predictive value of 85%, and accuracy of 82% for pouch inflammation. A positive likelihood ratio of 4.00 and negative likelihood ratio of 0.18 were obtained. In patients who have undergone IPAA surgery, the MRE findings strongly correlate with the pouch endoscopic findings with high sensitivity and positive predictive value for pouch inflammation. Therefore, MRE is a useful noninvasive test performed without ionizing radiation that can be used to evaluate patients with clinical symptoms and possibly alleviate the need for endoscopy in a select patient population.

In vivo Proton Electron Double Resonance Imaging of Mice with Fast Spin Echo Pulse Sequence

PubMed Central

Sun, Ziqi; Li, Haihong; Petryakov, Sergey; Samouilov, Alex; Zweier, Jay L.

2011-01-01

Purpose To develop and evaluate a 2D fast spin echo (FSE) pulse sequence for enhancing temporal resolution and reducing tissue heating for in vivo proton electron double resonance imaging (PEDRI) of mice. Materials and Methods A four-compartment phantom containing 2 mM TEMPONE was imaged at 20.1 mT using 2D FSE-PEDRI and regular gradient echo (GRE)-PEDRI pulse sequences. Control mice were infused with TEMPONE over ∼1 min followed by time-course imaging using the 2D FSE-PEDRI sequence at intervals of 10 – 30 s between image acquisitions. The average signal intensity from the time-course images was analyzed using a first-order kinetics model. Results Phantom experiments demonstrated that EPR power deposition can be greatly reduced using the FSE-PEDRI pulse sequence compared to the conventional gradient echo pulse sequence. High temporal resolution was achieved at ∼4 s per image acquisition using the FSE-PEDRI sequence with a good image SNR in the range of 233-266 in the phantom study. The TEMPONE half-life measured in vivo was ∼72 s. Conclusion Thus, the FSE-PEDRI pulse sequence enables fast in vivo functional imaging of free radical probes in small animals greatly reducing EPR irradiation time with decreased power deposition and provides increased temporal resolution. PMID:22147559

Investigation of the Effect of Finite Pulse Errors on BABA Pulse Sequence Using Floquet-Magnus Expansion Approach.

PubMed

Mananga, Eugene S; Reid, Alicia E

This paper presents the study of finite pulse widths for the BABA pulse sequence using the Floquet-Magnus expansion (FME) approach. In the FME scheme, the first order F 1 is identical to its counterparts in average Hamiltonian theory (AHT) and Floquet theory (FT). However, the timing part in the FME approach is introduced via the Λ 1 ( t ) function not present in other schemes. This function provides an easy way for evaluating the spin evolution during "the time in between" through the Magnus expansion of the operator connected to the timing part of the evolution. The evaluation of Λ 1 ( t ) is useful especially for the analysis of the non-stroboscopic evolution. Here, the importance of the boundary conditions, which provides a natural choice of Λ 1 (0) is ignored. This work uses the Λ 1 ( t ) function to compare the efficiency of the BABA pulse sequence with δ - pulses and the BABA pulse sequence with finite pulses. Calculations of Λ 1 ( t ) and F 1 are presented.

Investigation of the Effect of Finite Pulse Errors on BABA Pulse Sequence Using Floquet-Magnus Expansion Approach

PubMed Central

Mananga, Eugene S.; Reid, Alicia E.

2013-01-01

This paper presents the study of finite pulse widths for the BABA pulse sequence using the Floquet-Magnus expansion (FME) approach. In the FME scheme, the first order F1 is identical to its counterparts in average Hamiltonian theory (AHT) and Floquet theory (FT). However, the timing part in the FME approach is introduced via the Λ1 (t) function not present in other schemes. This function provides an easy way for evaluating the spin evolution during “the time in between” through the Magnus expansion of the operator connected to the timing part of the evolution. The evaluation of Λ1 (t) is useful especially for the analysis of the non-stroboscopic evolution. Here, the importance of the boundary conditions, which provides a natural choice of Λ1 (0) is ignored. This work uses the Λ1 (t) function to compare the efficiency of the BABA pulse sequence with δ – pulses and the BABA pulse sequence with finite pulses. Calculations of Λ1 (t) and F1 are presented. PMID:25792763

Transient effects in π-pulse sequences in MAS solid-state NMR

NASA Astrophysics Data System (ADS)

Hellwagner, Johannes; Wili, Nino; Ibáñez, Luis Fábregas; Wittmann, Johannes J.; Meier, Beat H.; Ernst, Matthias

2018-02-01

Dipolar recoupling techniques that use isolated rotor-synchronized π pulses are commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological molecules. These sequences excel through their simplicity, stability towards radio-frequency (rf) inhomogeneity, and low rf requirements. For a theoretical understanding of such sequences, we present a Floquet treatment based on an interaction-frame transformation including the chemical-shift offset dependence. This approach is applied to the homonuclear dipolar-recoupling sequence Radio-Frequency Driven Recoupling (RFDR) and the heteronuclear recoupling sequence Rotational Echo Double Resonance (REDOR). Based on the Floquet approach, we show the influence of effective fields caused by pulse transients and discuss the advantages of pulse-transient compensation. We demonstrate experimentally that the transfer efficiency for homonuclear recoupling can be doubled in some cases in model compounds as well as in simple peptides if pulse-transient compensation is applied to the π pulses. Additionally, we discuss the influence of various phase cycles on the recoupling efficiency in order to reduce the magnitude of effective fields. Based on the findings from RFDR, we are able to explain why the REDOR sequence does not suffer in the recoupling efficiency despite the presence of effective fields.

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1997-08-26

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation. 8 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1997-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation.

MR elastography of the liver at 3.0 T in diagnosing liver fibrosis grades; preliminary clinical experience.

PubMed

Yoshimitsu, Kengo; Mitsufuji, Toshimichi; Shinagawa, Yoshinobu; Fujimitsu, Ritsuko; Morita, Ayako; Urakawa, Hiroshi; Hayashi, Hiroyuki; Takano, Koichi

2016-03-01

To clarify the usefulness of 3.0-T MR elastography (MRE) in diagnosing the histological grades of liver fibrosis using preliminary clinical data. Between November 2012 and March 2014, MRE was applied to all patients who underwent liver MR study at a 3.0-T clinical unit. Among them, those who had pathological evaluation of liver tissue within 3 months from MR examinations were retrospectively recruited, and the liver stiffness measured by MRE was correlated with histological results. Institutional review board approved this study, waiving informed consent. There were 70 patients who met the inclusion criteria. Liver stiffness showed significant correlation with the pathological grades of liver fibrosis (rho = 0.89, p < 0.0001, Spearman's rank correlation). Areas under the receiver operating characteristic curve were 0.93, 0.95, 0.99 and 0.95 for fibrosis score greater than or equal to F1, F2, F3 and F4, with cut-off values of 3.13, 3.85, 4.28 and 5.38 kPa, respectively. Multivariate analysis suggested that grades of necroinflammation also affected liver stiffness, but to a significantly lesser degree as compared to fibrosis. 3.0-T clinical MRE was suggested to be sufficiently useful in assessing the grades of liver fibrosis. MR elastography may help clinicians assess patients with chronic liver diseases. Usefulness of 3.0-T MR elastography has rarely been reported. Measured liver stiffness correlated well with the histological grades of liver fibrosis. Measured liver stiffness was also affected by necroinflammation, but to a lesser degree. 3.0-T MRE could be a non-invasive alternative to liver biopsy.

CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB.

PubMed

Heller, Danielle M; Tavag, Mrinalini; Hochschild, Ann

2017-09-01

The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation. However, whether or not the toxic effects of CbtA are due to direct interactions with these predicted targets is not known. Here, we genetically separate the effects of CbtA on cell elongation and cell division, showing that CbtA interacts directly and independently with FtsZ and MreB. Using complementary genetic approaches, we identify the functionally relevant target surfaces on FtsZ and MreB, revealing that in both cases, CbtA binds to surfaces involved in essential cytoskeletal filament architecture. We show further that each interaction contributes independently to CbtA-mediated toxicity and that disruption of both interactions is required to alleviate the observed toxicity. Although several other protein modulators are known to target FtsZ, the CbtA-interacting surface we identify represents a novel inhibitory target. Our findings establish CbtA as a dual function toxin that inhibits both cell division and cell elongation via direct and independent interactions with FtsZ and MreB.

PrkC-mediated phosphorylation of overexpressed YvcK protein regulates PBP1 protein localization in Bacillus subtilis mreB mutant cells.

PubMed

Foulquier, Elodie; Pompeo, Frédérique; Freton, Céline; Cordier, Baptiste; Grangeasse, Christophe; Galinier, Anne

2014-08-22

The YvcK protein has been shown to be necessary for growth under gluconeogenic conditions in Bacillus subtilis. Amazingly, its overproduction rescues growth and morphology defects of the actin-like protein MreB deletion mutant by restoration of PBP1 localization. In this work, we observed that YvcK was phosphorylated at Thr-304 by the protein kinase PrkC and that phosphorylated YvcK was dephosphorylated by the cognate phosphatase PrpC. We show that neither substitution of this threonine with a constitutively phosphorylated mimicking glutamic acid residue or a phosphorylation-dead mimicking alanine residue nor deletion of prkC or prpC altered the ability of B. subtilis to grow under gluconeogenic conditions. However, we observed that a prpC mutant and a yvcK mutant were more sensitive to bacitracin compared with the WT strain. In addition, the bacitracin sensitivity of strains in which YvcK Thr-304 was replaced with either an alanine or a glutamic acid residue was also affected. We also analyzed rescue of the mreB mutant strain by overproduction of YvcK in which the phosphorylation site was substituted. We show that YvcK T304A overproduction did not rescue the mreB mutant aberrant morphology due to PBP1 mislocalization. The same observation was made in an mreB prkC double mutant overproducing YvcK. Altogether, these data show that YvcK may have two distinct functions: 1) in carbon source utilization independent of its phosphorylation level and 2) in cell wall biosynthesis and morphogenesis through its phosphorylation state. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

[E75, R78 and D82 of Escherichia coli FtsZ are key residues for FtsZ cellular self-assembly and FtsZ-MreB interaction].

PubMed

Huo, Yujia; Lu, Qiaonan; Zheng, Xiaowei; Ma, Yuanfang; Lu, Feng

2016-02-04

To explore effects of FtsZ mutants FtsZ(E75A), FtsZ(R78G) and FtsZ(D82A) on FtsZ self-assembly and interaction of FtsZ with MreB in Escherichia coli strains. METHODS) We constructed FtsZ and its mutant's plasmids by molecular clone and site-directed mutagenesis methods, and purified targeted proteins by affinity chromatography. QN6(ftsZ::yfp-cat), QN7(tsZ::yfp-cat), QN8(ftsZ(R78G)::yfp-cat) and QN9 (ftsZ(D82A):.:yfp-cat) strains were constructed by linear DNA homologous recombination. We observed cellular localization pattern of FtsZ and its mutants in E. coli by living cell imaging experiments, examined interaction of FtsZ/FtsZ*-FtsZ* and FtsZ/FtsZ*-MreB by Coimmunoprecipitation and bacteria two hybrid, and analyzed assembly characteristics of FtsZ mutants by Light scattering. RESULTS) The Yfp-labeled FtsZ(E75A), FtsZ(R78G) and FtsZ(D82A) mutant proteins failed to assemble into functional Z-ring structure and localize correctly in E. coli strains. Interaction of FtsZ with its mutants, or FtsZ*-FtsZ* and FtsZ*-MreB interaction were weakened or completely disappeared. In addition, in vitro experiments show that E75A, R78G and D82A mutations decreased the polymerization efficiency of FtsZ monomer. FtsZ E75, R78 and D82 are critical amino acids in the assembly, function of FtsZ protein and FtsZ-MreB interaction in E. coli strains.

CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB

PubMed Central

Heller, Danielle M.; Tavag, Mrinalini

2017-01-01

The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation. However, whether or not the toxic effects of CbtA are due to direct interactions with these predicted targets is not known. Here, we genetically separate the effects of CbtA on cell elongation and cell division, showing that CbtA interacts directly and independently with FtsZ and MreB. Using complementary genetic approaches, we identify the functionally relevant target surfaces on FtsZ and MreB, revealing that in both cases, CbtA binds to surfaces involved in essential cytoskeletal filament architecture. We show further that each interaction contributes independently to CbtA-mediated toxicity and that disruption of both interactions is required to alleviate the observed toxicity. Although several other protein modulators are known to target FtsZ, the CbtA-interacting surface we identify represents a novel inhibitory target. Our findings establish CbtA as a dual function toxin that inhibits both cell division and cell elongation via direct and independent interactions with FtsZ and MreB. PMID:28931012

Dry Extract of Matricaria recutita L. (Chamomile) Prevents Ligature-Induced Alveolar Bone Resorption in Rats via Inhibition of Tumor Necrosis Factor-α and Interleukin-1β.

PubMed

Guimarães, Mariana Vasconcelos; Melo, Iracema Matos; Adriano Araújo, Vilana Maria; Tenazoa Wong, Deizy Viviana; Roriz Fonteles, Cristiane Sá; Moreira Leal, Luzia Kalyne Almeida; Ribeiro, Ronaldo Albuquerque; Lima, Vilma

2016-06-01

Matricaria recutita L. (chamomile) has demonstrated anti-inflammatory activity. Accordingly, the ability of the Matricaria recutita extract (MRE) to inhibit proinflammatory cytokines and its influence on alveolar bone resorption (ABR) in rats. Wistar rats were subjected to ABR by ligature with nylon thread in the second upper-left molar, with contralateral hemiarcade as control. Rats received polysorbate TW80 (vehicle) or MRE (10, 30, and 90 mg/kg) 1 hour before ligature and daily until day 11. The periodontium was analyzed by macroscopy, histometry, histopathology, and immunohistochemistry for the receptor activator of nuclear factor-kappa B ligand (RANKL), osteoprotegerin (OPG), and tartrate-resistant acid phosphatase (TRAP). The gingival tissue was used to quantify the myeloperoxidase (MPO) activity and tumor necrosis factor (TNF)-α and interleukin (IL)-1β levels by enzyme-linked immunosorbent assay. Blood samples were collected to evaluate bone-specific alkaline phosphatase (BALP), leukogram, and dosages of aspartate and alanine transaminases, urea, and creatinine. Aspects of liver, kidneys, spleen, and body mass variations were also evaluated. The 11 days of ligature induced bone resorption, low levels of BALP, leukocyte infiltration; increase of MPO, TNF-α, and IL-1β; immunostaining increase for RANKL and TRAP; reduction of OPG and leukocytosis, which were significantly prevented by MRE, except for the low levels of BALP and the leukocytosis. Additionally, MRE did not alter organs or body weights of rats. MRE prevented the inflammation and ABR by reducing TNF-α and IL-1β, preventing the osteoclast activation via the RANKL-OPG axis, without interfering with bone anabolism.

Bacterial Actins.

PubMed

Izoré, Thierry; van den Ent, Fusinita

2017-01-01

A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell. FtsA is widespread across bacteria and it is one of the earliest components of the divisome to arrive at midcell, where it anchors the cell division machinery to the membrane. FtsA binds directly to FtsZ filaments and to the membrane through its C-terminus. FtsA shows altered domain architecture when compared to the canonical actin fold. FtsA's subdomain 1C replaces subdomain 1B of other members of the actin family and is located on the opposite side of the molecule. Nevertheless, when FtsA assembles into protofilaments, the protofilament structure is preserved, as subdomain 1C replaces subdomain IB of the following subunit in a canonical actin filament. MreB has an essential role in shape-maintenance of most rod-shaped bacteria. Unusually, MreB filaments assemble from two protofilaments in a flat and antiparallel arrangement. This non-polar architecture implies that both MreB filament ends are structurally identical. MreB filaments bind directly to membranes where they interact with both cytosolic and membrane proteins, thereby forming a key component of the elongasome. MreB filaments in cells are short and dynamic, moving around the long axis of rod-shaped cells, sensing curvature of the membrane and being implicated in peptidoglycan synthesis.

Bean Metal-Responsive Element-Binding Transcription Factor Confers Cadmium Resistance in Tobacco1

PubMed Central

Sun, Na; Liu, Meng; Zhang, Wentao; Yang, Wanning; Bei, Xiujuan; Ma, Hui; Qiao, Fan; Qi, Xiaoting

2015-01-01

Cadmium (Cd) is highly toxic to plants. Modulation of Cd-responsive transcription is an important way for Cd detoxification in plants. Metal-responsive element (MRE) is originally described in animal metallothionein genes. Although functional MREs also exist in Cd-regulated plant genes, specific transcription factors that bind MRE to regulate Cd tolerance have not been identified. Previously, we showed that Cd-inducible bean (Phaseolus vulgaris) stress-related gene2 (PvSR2) produces a short (S) PvSR2 transcript (S-PvSR2) driven by an intronic promoter. Here, we demonstrate that S-PvSR2 encodes a bean MRE-binding transcription factor1 (PvMTF-1) that confers Cd tolerance in tobacco (Nicotiana tabacum). PvMTF-1 expression was up-regulated by Cd at the levels of RNA and protein. Importantly, expression of PvMTF-1 in tobacco enhanced Cd tolerance, indicating its role in regulating Cd resistance in planta. This was achieved through direct regulation of a feedback-insensitive Anthranilate Synthase α-2 chain gene (ASA2), which catalyzes the first step for tryptophan biosynthesis. In vitro and in vivo DNA-protein interaction studies further revealed that PvMTF-1 directly binds to the MRE in the ASA2 promoter, and this binding depends on the zinc finger-like motif of PvMTF-1. Through modulating ASA2 up-regulation by Cd, PvMTF-1 increased free tryptophan level and subsequently reduced Cd accumulation, thereby enhancing Cd tolerance of transgenic tobacco plants. Consistent with this observation, tobacco transiently overexpressing ASA2 also exhibited increased tolerance to Cd. We conclude that PvMTF-1 is a zinc finger-like transcription factor that links MRE to Cd resistance in transgenic tobacco through activation of tryptophan biosynthesis. PMID:25624396

Evaluating Effects of Marine Energy Devices on the Marine Environment - A Risk-Based and In-Water Testing Approach

NASA Astrophysics Data System (ADS)

Harker-Klimes, G.; Copping, A. E.

2016-02-01

The portfolio of emerging renewables includes generating power from offshore winds, tides, waves, and ocean currents, as well as seawater temperature and salinity differentials. These new systems are collectively known as marine renewable energy (MRE). MRE development worldwide is in the early stages of design, deployment, and commercialization. A major barrier to bringing these systems into commercial use is the need to overcome uncertainties in environmental effects that slow siting and permitting of devices. Using a risk-based approach, this paper will discuss pathways for evaluating potential effects of tidal turbines and wave energy converters (WECs) on marine animals, habitats, and ecosystem processes. Using basic biological principles and knowledge of specific MRE technologies, the Environmental Risk Evaluation System has been used to narrow pertinent risks from devices, enabling laboratory and field studies to focus on the most important interactions. These interactions, include: potential collisions and behavioral disturbances of marine mammals, fish and other organisms; effects of underwater sound on animal communication and navigation; changes in sediment transport, benthic habitats, and water quality constituents; and effects of electromagnetic fields on animals. It is then necessary to apply these findings to the projects themselves. Another uncertainty is how to measure these key interactions in high-energy locations where MRE deployment is desirable. Consequently, new systems are being developed: instrumentation, innovative platforms for deployment, and new management strategies for collecting and analyzing very large data streams. Inherent in this development pathway is the need to test, deploy, and calibrate these monitoring systems. The Triton initiative is designed to enable this development, and has initiated testing of devices in Washington State to move the MRE industry forward while protecting marine animals, habitats and processes.

Effects of a mini-trampoline rebounding exercise program on functional parameters, body composition and quality of life in overweight women.

PubMed

Cugusi, Lucia; Manca, Andrea; Serpe, Roberto; Romita, Giovanni; Bergamin, Marco; Cadeddu, Christian; Solla, Paolo; Mercuro, Giuseppe

2018-03-01

Mini-trampoline rebounding exercise (MRE) is becoming a very popular form of fitness training. Despite awareness of this activity worldwide, a limited number of studies have systematically investigated the health effects correlated with MRE training. The aim of our study was to evaluate manifold health outcomes after 12 weeks of an MRE program in a group of overweight Italian women. Eighteen overweight women (age 38.05±10.5 years, BMI: 27.6±2.1 kg/m2) were enrolled in this study. Functional profile, strength, body composition, quality of life and pain intensity were assessed at baseline and after 12 weeks of MRE. Significant improvements were observed in the measurements of anthropometric profile and body composition (circumferences, fat mass, lean and muscular mass). Both a significant decrease in systolic and diastolic blood pressure values (from 128/80.5 to 123/71 mmHg, P<0.05) and an improvement in lipid and glucose profiles were observed. At maximal exercise testing, an increase in work capacity (from 104 to 123 watts, P=0.003) and VO2max (from 15.4 to 16.9 mL/kg/min, P=0.04) was found. SF-36 showed positive changes in four of the eight items as well as in the Mental Component Summary. With regard to the Brief Pain Inventory-SF, a decrease in both pain severity and the pain interference score was detected. MRE appears feasible to ensure positive effects on overall health and can be proposed to populations that could greatly benefit from training programs, such as overweight women.

Tickling the retina: integration of subthreshold electrical pulses can activate retinal neurons

NASA Astrophysics Data System (ADS)

Sekhar, S.; Jalligampala, A.; Zrenner, E.; Rathbun, D. L.

2016-08-01

Objective. The field of retinal prosthetics has made major progress over the last decade, restoring visual percepts to people suffering from retinitis pigmentosa. The stimulation pulses used by present implants are suprathreshold, meaning individual pulses are designed to activate the retina. In this paper we explore subthreshold pulse sequences as an alternate stimulation paradigm. Subthreshold pulses have the potential to address important open problems such as fading of visual percepts when patients are stimulated at moderate pulse repetition rates and the difficulty in preferentially stimulating different retinal pathways. Approach. As a first step in addressing these issues we used Gaussian white noise electrical stimulation combined with spike-triggered averaging to interrogate whether a subthreshold sequence of pulses can be used to activate the mouse retina. Main results. We demonstrate that the retinal network can integrate multiple subthreshold electrical stimuli under an experimental paradigm immediately relevant to retinal prostheses. Furthermore, these characteristic stimulus sequences varied in their shape and integration window length across the population of retinal ganglion cells. Significance. Because the subthreshold sequences activate the retina at stimulation rates that would typically induce strong fading (25 Hz), such retinal ‘tickling’ has the potential to minimize the fading problem. Furthermore, the diversity found across the cell population in characteristic pulse sequences suggests that these sequences could be used to selectively address the different retinal pathways (e.g. ON versus OFF). Both of these outcomes may significantly improve visual perception in retinal implant patients.

A multi-purpose electromagnetic actuator for magnetic resonance elastography.

PubMed

Feng, Yuan; Zhu, Mo; Qiu, Suhao; Shen, Ping; Ma, Shengyuan; Zhao, Xuefeng; Hu, Chun-Hong; Guo, Liang

2018-04-19

An electromagnetic actuator was designed for magnetic resonance elastography (MRE). The actuator is unique in that it is simple, portable, and capable of brain, abdomen, and phantom imagings. A custom-built control unit was used for controlling the vibration frequency and synchronizing the trigger signals. An actuation unit was built and mounted on the specifically designed clamp and holders for different imaging applications. MRE experiments with respect to gel phantoms, brain, and liver showed that the actuator could produce stable and consistent mechanical waves. Estimated shear modulus using local frequency estimate method demonstrated that the measurement results were in line with that from MRE studies using different actuation systems. The relatively easy setup procedure and simple design indicated that the actuator system had the potential to be applied in many different clinical studies. Copyright © 2018 Elsevier Inc. All rights reserved.

Wideband Arrhythmia-Insensitive-Rapid (AIR) Pulse Sequence for Cardiac T1 mapping without Image Artifacts induced by ICD

PubMed Central

Hong, KyungPyo; Jeong, Eun-Kee; Wall, T. Scott; Drakos, Stavros G.; Kim, Daniel

2015-01-01

Purpose To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). Methods We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz), in order to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and “wideband” AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5T. Results In 5 phantoms representing native myocardium and blood and post-contrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error >29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error <5%). Similarly, in 11 human subjects, compared with the control T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error >10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error <2.0%). Conclusion This study demonstrates the feasibility of a wideband pulse sequence for cardiac T1 mapping without significant image artifacts induced by ICD. PMID:25975192

Bacterial Actins? An Evolutionary Perspective

NASA Technical Reports Server (NTRS)

Doolittle, Russell F.; York, Amanda L.

2003-01-01

According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

Applicability of the "Frame of Reference" approach for environmental monitoring of offshore renewable energy projects.

PubMed

Garel, Erwan; Rey, Cibran Camba; Ferreira, Oscar; van Koningsveld, Mark

2014-08-01

This paper assesses the applicability of the Frame of Reference (FoR) approach for the environmental monitoring of large-scale offshore Marine Renewable Energy (MRE) projects. The focus is on projects harvesting energy from winds, waves and currents. Environmental concerns induced by MRE projects are reported based on a classification scheme identifying stressors, receptors, effects and impacts. Although the potential effects of stressors on most receptors are identified, there are large knowledge gaps regarding the corresponding (positive and negative) impacts. In that context, the development of offshore MRE requires the implementation of fit-for-purpose monitoring activities aimed at environmental protection and knowledge development. Taking European legislation as an example, it is suggested to adopt standardized monitoring protocols for the enhanced usage and utility of environmental indicators. Towards this objective, the use of the FoR approach is advocated since it provides guidance for the definition and use of coherent set of environmental state indicators. After a description of this framework, various examples of applications are provided considering a virtual MRE project located in European waters. Finally, some conclusions and recommendations are provided for the successful implementation of the FoR approach and for future studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Deficient Repair of Particulate Hexavalent chromium-Induced DNA Double Strand Breaks Leads To Neoplastic Transformation

PubMed Central

Xie, Hong; Wise, Sandra S.; Wise, John. P.

2008-01-01

Hexavalent chromium (Cr(VI)) is a potent respiratory toxicant and carcinogen. The most carcinogenic forms of Cr(VI) are the particulate salts such as lead chromate, which deposit and persist in the respiratory tract after inhalation. We demonstrate here that particulate chromate induces DNA double strand breaks in human lung cells with 0.1, 0.5, and 1 ug/cm2 lead chromate inducing 1.5, 2 and 5 relative increases in the percent of DNA in the comet tail, respectively. These lesions are repaired within 24 h and require Mre11 expression for their repair. Particulate chromate also caused Mre11 to co-localize with gamma-H2A.X and ATM. Failure to repair these breaks with Mre11 induced neoplastic transformation including loss of cell contact inhibition and anchorage independent growth. A 5-day exposure to lead chromate induced loss of cell contact inhibition in a concentration-dependent manner with 0, 0.1, 0.5 and 1 ug/cm2 lead chromate inducing 1, 78 and 103 foci in 20 dishes, respectively. These data indicate that Mre11 is critical to repairing particulate Cr(VI)-induced double strand breaks and preventing Cr(VI)-induced neoplastic transformation. PMID:18023605

A Caulobacter MreB mutant with irregular cell shape exhibits compensatory widening to maintain a preferred surface area to volume ratio

PubMed Central

Harris, Leigh K.; Dye, Natalie A.; Theriot, Julie A.

2014-01-01

Summary Rod-shaped bacteria typically elongate at a uniform width. To investigate the genetic and physiological determinants involved in this process, we studied a mutation in the morphogenetic protein MreB in Caulobacter crescentus that gives rise to cells with a variable-width phenotype, where cells have regions that are both thinner and wider than wild-type. During growth, individual cells develop a balance of wide and thin regions, and mutant MreB dynamically localizes to poles and thin regions. Surprisingly, the surface area to volume ratio of these irregularly-shaped cells is, on average, very similar to wild-type. We propose that, while mutant MreB localizes to thin regions and promotes rod-like growth there, wide regions develop as a compensatory mechanism, allowing cells to maintain a wild-type-like surface area to volume ratio. To support this model, we have shown that cell widening is abrogated in growth conditions that promote higher surface area to volume ratios, and we have observed individual cells with high ratios return to wild-type levels over several hours by developing wide regions, suggesting that compensation can take place at the level of individual cells. PMID:25266768

A novel high amplitude piezoceramic actuator for applications in magnetic resonance elastography: a compliant mechanical amplifier approach

NASA Astrophysics Data System (ADS)

Arani, Arvin; Eskandari, Amiraslan; Ouyang, Puren; Chopra, Rajiv

2017-08-01

Piezoceramic actuators are capable of precise positioning with high force, but suffer from limited displacement range, which has hindered their application in the field of magnetic resonance elastography (MRE). The objective of this study was to investigate the feasibility of using a mechanical amplifier in combination with a piezoceramic actuator for the application of endorectal prostate MRE. A five-bar symmetric structure was designed in ANSYS® and manufactured out of brass. Laser vibrometer measurements were used to characterize the amplitude of the CMA actuator while attached to masses in the 0-325 g range and over operating frequencies of 90-500 Hz. The response of the CMA was investigated while mechanically coupled to a balloon type endorectal coil. The resonant frequency of the prototype CMA actuator was predicted within 10% error using ANSYS simulations. The amplification ratio of the CMA actuator was measured to be 10 with the laser vibrometer and 7.6 ± 1.7 (max: 9.2, min: 6.5) using MRE, at a vibration frequency of 200 Hz. Laser vibrometer data also showed that the CMA actuator’s performance did not change whether it was connected to an empty or inflated endorectal. The feasibility of performing endorectal prostate MRE with a CMA actuator was successfully demonstrated in a human volunteer.

Facilitated Nurse Medication-Related Event Reporting to Improve Medication Management Quality and Safety in Intensive Care Units.

PubMed

Xu, Jie; Reale, Carrie; Slagle, Jason M; Anders, Shilo; Shotwell, Matthew S; Dresselhaus, Timothy; Weinger, Matthew B

Medication safety presents an ongoing challenge for nurses working in complex, fast-paced, intensive care unit (ICU) environments. Studying ICU nurse's medication management-especially medication-related events (MREs)-provides an approach to analyze and improve medication safety and quality. The goal of this study was to explore the utility of facilitated MRE reporting in identifying system deficiencies and the relationship between MREs and nurses' work in the ICUs. We conducted 124 structured 4-hour observations of nurses in three different ICUs. Each observation included measurement of nurse's moment-to-moment activity and self-reports of workload and negative mood. The observer then obtained MRE reports from the nurse using a structured tool. The MREs were analyzed by three experts. MREs were reported in 35% of observations. The 60 total MREs included four medication errors and seven adverse drug events. Of the 49 remaining MREs, 65% were associated with negative patient impact. Task/process deficiencies were the most common contributory factor for MREs. MRE occurrence was correlated with increased total task volume. MREs also correlated with increased workload, especially during night shifts. Most of these MREs would not be captured by traditional event reporting systems. Facilitated MRE reporting provides a robust information source about potential breakdowns in medication management safety and opportunities for system improvement.

The Relationship of Three-Dimensional Human Skull Motion to Brain Tissue Deformation in Magnetic Resonance Elastography Studies

PubMed Central

Badachhape, Andrew A.; Okamoto, Ruth J.; Durham, Ramona S.; Efron, Brent D.; Nadell, Sam J.; Johnson, Curtis L.; Bayly, Philip V.

2017-01-01

In traumatic brain injury (TBI), membranes such as the dura mater, arachnoid mater, and pia mater play a vital role in transmitting motion from the skull to brain tissue. Magnetic resonance elastography (MRE) is an imaging technique developed for noninvasive estimation of soft tissue material parameters. In MRE, dynamic deformation of brain tissue is induced by skull vibrations during magnetic resonance imaging (MRI); however, skull motion and its mode of transmission to the brain remain largely uncharacterized. In this study, displacements of points in the skull, reconstructed using data from an array of MRI-safe accelerometers, were compared to displacements of neighboring material points in brain tissue, estimated from MRE measurements. Comparison of the relative amplitudes, directions, and temporal phases of harmonic motion in the skulls and brains of six human subjects shows that the skull–brain interface significantly attenuates and delays transmission of motion from skull to brain. In contrast, in a cylindrical gelatin “phantom,” displacements of the rigid case (reconstructed from accelerometer data) were transmitted to the gelatin inside (estimated from MRE data) with little attenuation or phase lag. This quantitative characterization of the skull–brain interface will be valuable in the parameterization and validation of computer models of TBI. PMID:28267188

The Relationship of Three-Dimensional Human Skull Motion to Brain Tissue Deformation in Magnetic Resonance Elastography Studies.

PubMed

Badachhape, Andrew A; Okamoto, Ruth J; Durham, Ramona S; Efron, Brent D; Nadell, Sam J; Johnson, Curtis L; Bayly, Philip V

2017-05-01

In traumatic brain injury (TBI), membranes such as the dura mater, arachnoid mater, and pia mater play a vital role in transmitting motion from the skull to brain tissue. Magnetic resonance elastography (MRE) is an imaging technique developed for noninvasive estimation of soft tissue material parameters. In MRE, dynamic deformation of brain tissue is induced by skull vibrations during magnetic resonance imaging (MRI); however, skull motion and its mode of transmission to the brain remain largely uncharacterized. In this study, displacements of points in the skull, reconstructed using data from an array of MRI-safe accelerometers, were compared to displacements of neighboring material points in brain tissue, estimated from MRE measurements. Comparison of the relative amplitudes, directions, and temporal phases of harmonic motion in the skulls and brains of six human subjects shows that the skull-brain interface significantly attenuates and delays transmission of motion from skull to brain. In contrast, in a cylindrical gelatin "phantom," displacements of the rigid case (reconstructed from accelerometer data) were transmitted to the gelatin inside (estimated from MRE data) with little attenuation or phase lag. This quantitative characterization of the skull-brain interface will be valuable in the parameterization and validation of computer models of TBI.

Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations.

PubMed

Li, Wei-Kang; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-01-01

TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1.

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.

PubMed

Shave, Steven; Mann, Stefan; Koszela, Joanna; Kerr, Alastair; Auer, Manfred

2018-01-01

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.

Investigation of timing effects in modified composite quadrupolar echo pulse sequences by mean of average Hamiltonian theory

NASA Astrophysics Data System (ADS)

Mananga, Eugene Stephane

2018-01-01

The utility of the average Hamiltonian theory and its antecedent the Magnus expansion is presented. We assessed the concept of convergence of the Magnus expansion in quadrupolar spectroscopy of spin-1 via the square of the magnitude of the average Hamiltonian. We investigated this approach for two specific modified composite pulse sequences: COM-Im and COM-IVm. It is demonstrated that the size of the square of the magnitude of zero order average Hamiltonian obtained on the appropriated basis is a viable approach to study the convergence of the Magnus expansion. The approach turns to be efficient in studying pulse sequences in general and can be very useful to investigate coherent averaging in the development of high resolution NMR technique in solids. This approach allows comparing theoretically the two modified composite pulse sequences COM-Im and COM-IVm. We also compare theoretically the current modified composite sequences (COM-Im and COM-IVm) to the recently published modified composite pulse sequences (MCOM-I, MCOM-IV, MCOM-I_d, MCOM-IV_d).

Time-optimal excitation of maximum quantum coherence: Physical limits and pulse sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Köcher, S. S.; Institute of Energy and Climate Research; Heydenreich, T.

Here we study the optimum efficiency of the excitation of maximum quantum (MaxQ) coherence using analytical and numerical methods based on optimal control theory. The theoretical limit of the achievable MaxQ amplitude and the minimum time to achieve this limit are explored for a set of model systems consisting of up to five coupled spins. In addition to arbitrary pulse shapes, two simple pulse sequence families of practical interest are considered in the optimizations. Compared to conventional approaches, substantial gains were found both in terms of the achieved MaxQ amplitude and in pulse sequence durations. For a model system, theoreticallymore » predicted gains of a factor of three compared to the conventional pulse sequence were experimentally demonstrated. Motivated by the numerical results, also two novel analytical transfer schemes were found: Compared to conventional approaches based on non-selective pulses and delays, double-quantum coherence in two-spin systems can be created twice as fast using isotropic mixing and hard spin-selective pulses. Also it is proved that in a chain of three weakly coupled spins with the same coupling constants, triple-quantum coherence can be created in a time-optimal fashion using so-called geodesic pulses.« less

Three-dimensional T1rho-weighted MRI at 1.5 Tesla.

PubMed

Borthakur, Arijitt; Wheaton, Andrew; Charagundla, Sridhar R; Shapiro, Erik M; Regatte, Ravinder R; Akella, Sarma V S; Kneeland, J Bruce; Reddy, Ravinder

2003-06-01

To design and implement a magnetic resonance imaging (MRI) pulse sequence capable of performing three-dimensional T(1rho)-weighted MRI on a 1.5-T clinical scanner, and determine the optimal sequence parameters, both theoretically and experimentally, so that the energy deposition by the radiofrequency pulses in the sequence, measured as the specific absorption rate (SAR), does not exceed safety guidelines for imaging human subjects. A three-pulse cluster was pre-encoded to a three-dimensional gradient-echo imaging sequence to create a three-dimensional, T(1rho)-weighted MRI pulse sequence. Imaging experiments were performed on a GE clinical scanner with a custom-built knee-coil. We validated the performance of this sequence by imaging articular cartilage of a bovine patella and comparing T(1rho) values measured by this sequence to those obtained with a previously tested two-dimensional imaging sequence. Using a previously developed model for SAR calculation, the imaging parameters were adjusted such that the energy deposition by the radiofrequency pulses in the sequence did not exceed safety guidelines for imaging human subjects. The actual temperature increase due to the sequence was measured in a phantom by a MRI-based temperature mapping technique. Following these experiments, the performance of this sequence was demonstrated in vivo by obtaining T(1rho)-weighted images of the knee joint of a healthy individual. Calculated T(1rho) of articular cartilage in the specimen was similar for both and three-dimensional and two-dimensional methods (84 +/- 2 msec and 80 +/- 3 msec, respectively). The temperature increase in the phantom resulting from the sequence was 0.015 degrees C, which is well below the established safety guidelines. Images of the human knee joint in vivo demonstrate a clear delineation of cartilage from surrounding tissues. We developed and implemented a three-dimensional T(1rho)-weighted pulse sequence on a 1.5-T clinical scanner. Copyright 2003 Wiley-Liss, Inc.

MRI diffusion-weighted imaging (DWI) in pediatric small bowel Crohn disease: correlation with MRI findings of active bowel wall inflammation.

PubMed

Ream, Justin M; Dillman, Jonathan R; Adler, Jeremy; Khalatbari, Shokoufeh; McHugh, Jonathan B; Strouse, Peter J; Dhanani, Muhammad; Shpeen, Benjamin; Al-Hawary, Mahmoud M

2013-09-01

Restricted diffusion on diffusion-weighted imaging (DWI) sequences during magnetic resonance enterography (MRE) has been shown in segments of bowel affected by Crohn disease. However, the exact meaning of this finding, particularly within the pediatric Crohn disease population, is poorly understood. The purpose of this study was to determine the significance of bowel wall restricted diffusion in children with small bowel Crohn disease by correlating apparent diffusion coefficient (ADC) values with other MRI markers of disease activity. A retrospective review of pediatric patients (≤ 18 years of age) with Crohn disease terminal ileitis who underwent MRE with DWI at our institution between May 1, 2009 and May 31, 2011 was undertaken. All of the children had either biopsy-proven Crohn disease terminal ileitis or clinically diagnosed Crohn disease, including terminal ileal involvement by imaging. The mean minimum ADC value within the wall of the terminal ileum was determined for each examination. ADC values were tested for correlation/association with other MRI findings to determine whether a relationship exists between bowel wall restricted diffusion and disease activity. Forty-six MRE examinations with DWI in children with terminal ileitis were identified (23 girls and 23 boys; mean age, 14.3 years). There was significant negative correlation or association between bowel wall minimum ADC value and established MRI markers of disease activity, including degree of bowel wall thickening (R = (-)0.43; P = 0.003), striated pattern of arterial enhancement (P = 0.01), degree of arterial enhancement (P = 0.01), degree of delayed enhancement (P = 0.045), amount of mesenteric inflammatory changes (P < 0.0001) and presence of a stricture (P = 0.02). ADC values were not significantly associated with bowel wall T2-weighted signal intensity, length of disease involvement or mesenteric fibrofatty proliferation. Increasing bowel wall restricted diffusion (lower ADC values) is associated with multiple MRI findings that are traditionally associated with active inflammation in pediatric small bowel Crohn disease.

Department of Defense Food Procurement: Background and Status

DTIC Science & Technology

2008-08-28

and guidelines for the acquisition of subsistence items. The solicitation is prepared based on what represents the best value to the federal government...www.natick.army.mil/soldier/media/fact/food/mre.htm]. One MRE provides an average of 1,250 calories composed of 13% protein , 36% fat, and 51...for the military, the military services also consider the special dietary needs of the soldiers (including vegetarian and kosher needs). The Produce

Role of Magnetic Resonance Elastography as a Noninvasive Measurement Tool of Fibrosis in a Renal Allograft: A Case Report.

PubMed

Kim, J K; Yuen, D A; Leung, G; Jothy, S; Zaltzman, J; Ramesh Prasad, G V; Prabhudesai, V; Mnatzakanian, G; Kirpalani, A

2017-09-01

A major reason for poor long-term kidney transplant outcomes is the development of chronic allograft injury, characterized by interstitial fibrosis and tubular atrophy. Currently, an invasive biopsy that samples only <1% of the kidney is the gold standard for detecting kidney allograft fibrosis. We report the use of magnetic resonance elastography (MRE) to quantify tissue stiffness as a noninvasive and whole-kidney measurement tool of allograft fibrosis in a kidney transplant patient at 2 time points. The MRE whole-kidney stiffness values reflected the changes in fibrosis of the kidney allograft as assessed by histologic examination. To our knowledge, this technique is the first observation of change over time in MRE-derived whole-kidney stiffness in an allograft that is consistent with changes in histology-derived fibrosis scores in a single patient. Copyright © 2017 Elsevier Inc. All rights reserved.

Real-time evaluation and visualization of learner performance in a mixed-reality environment for clinical breast examination.

PubMed

Kotranza, Aaron; Lind, D Scott; Lok, Benjamin

2012-07-01

We investigate the efficacy of incorporating real-time feedback of user performance within mixed-reality environments (MREs) for training real-world tasks with tightly coupled cognitive and psychomotor components. This paper presents an approach to providing real-time evaluation and visual feedback of learner performance in an MRE for training clinical breast examination (CBE). In a user study of experienced and novice CBE practitioners (n = 69), novices receiving real-time feedback performed equivalently or better than more experienced practitioners in the completeness and correctness of the exam. A second user study (n = 8) followed novices through repeated practice of CBE in the MRE. Results indicate that skills improvement in the MRE transfers to the real-world task of CBE of human patients. This initial case study demonstrates the efficacy of MREs incorporating real-time feedback for training real-world cognitive-psychomotor tasks.

Efficient and precise calculation of the b-matrix elements in diffusion-weighted imaging pulse sequences.

PubMed

Zubkov, Mikhail; Stait-Gardner, Timothy; Price, William S

2014-06-01

Precise NMR diffusion measurements require detailed knowledge of the cumulative dephasing effect caused by the numerous gradient pulses present in most NMR pulse sequences. This effect, which ultimately manifests itself as the diffusion-related NMR signal attenuation, is usually described by the b-value or the b-matrix in the case of multidirectional diffusion weighting, the latter being common in diffusion-weighted NMR imaging. Neglecting some of the gradient pulses introduces an error in the calculated diffusion coefficient reaching in some cases 100% of the expected value. Therefore, ensuring the b-matrix calculation includes all the known gradient pulses leads to significant error reduction. Calculation of the b-matrix for simple gradient waveforms is rather straightforward, yet it grows cumbersome when complexly shaped and/or numerous gradient pulses are introduced. Making three broad assumptions about the gradient pulse arrangement in a sequence results in an efficient framework for calculation of b-matrices as well providing some insight into optimal gradient pulse placement. The framework allows accounting for the diffusion-sensitising effect of complexly shaped gradient waveforms with modest computational time and power. This is achieved by using the b-matrix elements of the simple unmodified pulse sequence and minimising the integration of the complexly shaped gradient waveform in the modified sequence. Such re-evaluation of the b-matrix elements retains all the analytical relevance of the straightforward approach, yet at least halves the amount of symbolic integration required. The application of the framework is demonstrated with the evaluation of the expression describing the diffusion-sensitizing effect, caused by different bipolar gradient pulse modules. Copyright © 2014 Elsevier Inc. All rights reserved.

A modularized pulse programmer for NMR spectroscopy

NASA Astrophysics Data System (ADS)

Mao, Wenping; Bao, Qingjia; Yang, Liang; Chen, Yiqun; Liu, Chaoyang; Qiu, Jianqing; Ye, Chaohui

2011-02-01

A modularized pulse programmer for a NMR spectrometer is described. It consists of a networked PCI-104 single-board computer and a field programmable gate array (FPGA). The PCI-104 is dedicated to translate the pulse sequence elements from the host computer into 48-bit binary words and download these words to the FPGA, while the FPGA functions as a sequencer to execute these binary words. High-resolution NMR spectra obtained on a home-built spectrometer with four pulse programmers working concurrently demonstrate the effectiveness of the pulse programmer. Advantages of the module include (1) once designed it can be duplicated and used to construct a scalable NMR/MRI system with multiple transmitter and receiver channels, (2) it is a totally programmable system in which all specific applications are determined by software, and (3) it provides enough reserve for possible new pulse sequences.

Validation of FRET Assay for the Screening of Growth Inhibitors of Escherichia coli Reveals Elongasome Assembly Dynamics

PubMed Central

van der Ploeg, René; Goudelis, Spyridon Theodoros; den Blaauwen, Tanneke

2015-01-01

The increase in antibiotic resistant bacteria demands the development of new antibiotics against preferably new targets. The common approach is to test compounds for their ability to kill bacteria or to design molecules that inhibit essential protein activities in vitro. In the first case, the mode of action of the drug is unknown and in the second case, it is not known whether the compound will pass the impermeable barrier of the bacterial envelope. We developed an assay that detects the target of a compound, as well as its ability to pass the membrane(s) simultaneously. The Escherichia coli cytoskeletal protein MreB recruits protein complexes (elongasomes) that are essential for cell envelope growth. An in cell Förster Resonance Energy Transfer (FRET) assay was developed to detect the interaction between MreB molecules and between MreB and the elongasome proteins RodZ, RodA and PBP2. Inhibition of the polymerization of MreB by S-(3,4-dichlorobenzyl) isothiourea (A22) or of the activity of PBP2 by mecilinam resulted in loss or reduction of all measured interactions. This suggests that the interactions between the elongasome proteins are governed by a combination of weak affinities and substrate availability. This validated in cell FRET assay can be used to screen for cell envelope growth inhibitors. PMID:26263980

Magnetic resonance elastography can monitor changes in medullary stiffness in response to treatment in the swine ischemic kidney

PubMed Central

Zhang, Xin; Zhu, Xiangyang; Ferguson, Christopher M.; Jiang, Kai; Burningham, Tyson; Lerman, Amir; Lerman, Lilach O.

2018-01-01

Object Low-energy shockwave (SW) therapy attenuates damage in the stenotic kidney (STK) caused by atherosclerotic renal artery stenosis (ARAS). We hypothesized that magnetic resonance elastography (MRE) would detect attenuation of fibrosis following SW in unilateral ARAS kidneys. Materials and Methods Domestic pigs were randomized to control, unilateral ARAS, and ARAS treated with 6 sessions of SW over 3 consecutive weeks (n=7 each) starting after 3 weeks of ARAS or sham. Four weeks after SW treatment, renal fibrosis was evaluated with MRE in-vivo or trichrome staining ex-vivo. Blood pressure, single-kidney renal-blood-flow (RBF) and glomerular-filtration-rate (GFR) were assessed. Results MRE detected increased stiffness in the STK medulla (15.3±2.1 vs. 10.1±0.8 kPa, p<0.05) that moderately correlated with severity of fibrosis (R2=0.501, p<0.01), but did not identify mild STK cortical or contralateral kidney fibrosis. Trichrome staining showed that medullary fibrosis was increased in ARAS and alleviated by SW (10.4±1.8% vs. 2.9±0.2%, p<0.01). SW slightly decreased blood pressure and normalized STK RBF and GFR in ARAS. In the contralateral kidney, SW reversed the increase in RBF and GFR. Conclusion MRE might be a tool for noninvasive monitoring of medullary fibrosis in response to treatment in kidney disease. PMID:29289980

Future role of MR elastography in tissue engineering and regenerative medicine.

PubMed

Othman, Shadi F; Xu, Huihui; Mao, Jeremy J

2015-05-01

Tissue engineering (TE) has been introduced for more than 25 years without a boom in clinical trials. More than 70 TE-related start-up companies spent more than $600 million/year, with only two FDA-approved tissue-engineered products. Given the modest performance in clinically approved organs, TE is a tenaciously promising field. The TE community is advocating the application of clinically driven methodologies in large animal models enabling clinical translation. This challenge is hindered by the scarcity of tissue biopsies and the absence of standardized evaluation tools, but can be negated through non-invasive assessment of growth and integration, with reduced sample size and low cost. Solving this issue will speed the transition to cost-efficient clinical studies. In this paper we: (a) introduce magnetic resonance elastography to the tissue-engineering and regenerative medicine (TERM) community; (b) review recent MRE applications in TERM; and (c) discuss future directions of MRE in TERM. We have used MRE to study engineered tissues both in vitro and in vivo, where the mechanical properties of mesenchymally derived constructs were progressively monitored before and after tissues were implanted in mouse models. This study represents a stepping stone toward the applications of MRE in directing clinical trials with low cost and likely expediting the translation to more relevantly large animal models and clinical trials. Copyright © 2013 John Wiley & Sons, Ltd.

PULSE SORTER

DOEpatents

Wade, E.J.

1958-07-29

An apparatus is described for counting and recording the number of electrical pulses occurring in each of a timed sequence of groups of pulses. The particular feature of the invention resides in a novel timing circuit of the univibrator type which provides very accurately timed pulses for opening each of a series of coincidence channels in sequence. The univibrator is shown incorporated in a pulse analyzing system wherein a series of pulse counting channels are periodically opened in order, one at a time, for a predetermtned open time interval, so that only one channel will be open at the time of occurrence of any of the electrical pulses to be sorted.

Chirped pulse digital holography for measuring the sequence of ultrafast optical wavefronts

NASA Astrophysics Data System (ADS)

Karasawa, Naoki

2018-04-01

Optical setups for measuring the sequence of ultrafast optical wavefronts using a chirped pulse as a reference wave in digital holography are proposed and analyzed. In this method, multiple ultrafast object pulses are used to probe the temporal evolution of ultrafast phenomena and they are interfered with a chirped reference wave to record a digital hologram. Wavefronts at different times can be reconstructed separately from the recorded hologram when the reference pulse can be treated as a quasi-monochromatic wave during the pulse width of each object pulse. The feasibility of this method is demonstrated by numerical simulation.

Temporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth

PubMed Central

Carabetta, Valerie J.; Greco, Todd M.; Tanner, Andrew W.

2016-01-01

ABSTRACT Nε-Lysine acetylation has been recognized as a ubiquitous regulatory posttranslational modification that influences a variety of important biological processes in eukaryotic cells. Recently, it has been realized that acetylation is also prevalent in bacteria. Bacteria contain hundreds of acetylated proteins, with functions affecting diverse cellular pathways. Still, little is known about the regulation or biological relevance of nearly all of these modifications. Here we characterize the cellular growth-associated regulation of the Bacillus subtilis acetylome. Using acetylation enrichment and quantitative mass spectrometry, we investigate the logarithmic and stationary growth phases, identifying over 2,300 unique acetylation sites on proteins that function in essential cellular pathways. We determine an acetylation motif, EK(ac)(D/Y/E), which resembles the eukaryotic mitochondrial acetylation signature, and a distinct stationary-phase-enriched motif. By comparing the changes in acetylation with protein abundances, we discover a subset of critical acetylation events that are temporally regulated during cell growth. We functionally characterize the stationary-phase-enriched acetylation on the essential shape-determining protein MreB. Using bioinformatics, mutational analysis, and fluorescence microscopy, we define a potential role for the temporal acetylation of MreB in restricting cell wall growth and cell diameter. IMPORTANCE The past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis. To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth. PMID:27376153

Temporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth.

PubMed

Carabetta, Valerie J; Greco, Todd M; Tanner, Andrew W; Cristea, Ileana M; Dubnau, David

2016-05-01

N ε -Lysine acetylation has been recognized as a ubiquitous regulatory posttranslational modification that influences a variety of important biological processes in eukaryotic cells. Recently, it has been realized that acetylation is also prevalent in bacteria. Bacteria contain hundreds of acetylated proteins, with functions affecting diverse cellular pathways. Still, little is known about the regulation or biological relevance of nearly all of these modifications. Here we characterize the cellular growth-associated regulation of the Bacillus subtilis acetylome. Using acetylation enrichment and quantitative mass spectrometry, we investigate the logarithmic and stationary growth phases, identifying over 2,300 unique acetylation sites on proteins that function in essential cellular pathways. We determine an acetylation motif, EK(ac)(D/Y/E), which resembles the eukaryotic mitochondrial acetylation signature, and a distinct stationary-phase-enriched motif. By comparing the changes in acetylation with protein abundances, we discover a subset of critical acetylation events that are temporally regulated during cell growth. We functionally characterize the stationary-phase-enriched acetylation on the essential shape-determining protein MreB. Using bioinformatics, mutational analysis, and fluorescence microscopy, we define a potential role for the temporal acetylation of MreB in restricting cell wall growth and cell diameter. The past decade highlighted N ε -lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis . To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth.

Development of magnetorheological elastomers based on Deproteinised natural rubber as smart damping materials

NASA Astrophysics Data System (ADS)

Ismail, Nik Intan Nik; Kamaruddin, Shamsul

2017-12-01

Magnetorheological elastomers (MREs) are composite materials consist of micron-sized magnetizable particles carbonyl iron particles [CIPs]) embedded in a soft elastomer matrix. MRE technology offers variable stiffness and damping properties under the influence of a magnetic field. Herein, the feasibility of incorporating a new generation specialty rubber, Pureprena as a matrix for MREs was investigated. Pureprena or Deproteinised Natural Rubber (DPNR) is a specialty natural rubber that has good dynamic properties, particularly with respect to damping parameters. DPNR was compounded with 60 wt% of CIPs to fabricate MREs. The performance of the DPNR-based MRE was measured in terms of tensile strength, dynamic properties, and magnetorheological (MR) effect and compared with polyisoprene (IR)-based MRE with the same amount of CIPs. Dynamic Mechanical Analyzer (DMA) showed that the loss factor in the glass transition region of the DPNR-based MRE was higher than that of the IR-based MRE, indicating better damping properties. Further investigation was undertaken using a servo-hydraulic testing machine to characterise the effect of strain amplitude and frequency on the dynamic properties (e.g. damping coefficient) of MREs at zero magnetic fields. The results demonstrate that DPNR-based MREs possess a comparable damping coefficient to that of IR-based MREs. In addition, MR effect, which relates to the ratio between elastic modulus with applied magnetic field (on-state) to the same modulus without applied fields (off-state), was measured using a parallel plate rheometer. As a result, DPNR-based MREs have improved MR effect than that of IR-based MREs. Moreover, variable stiffness is obtained when the magnetic field was increased to 0.8T. Loss factor or tan δ of MREs was found to vary against different magnetic fields. Finally, MREs with varied stiffness and damping were found to have potential as active control devices for smart damping materials.

Compact field programmable gate array-based pulse-sequencer and radio-frequency generator for experiments with trapped atoms.

PubMed

Pruttivarasin, Thaned; Katori, Hidetoshi

2015-11-01

We present a compact field-programmable gate array (FPGA) based pulse sequencer and radio-frequency (RF) generator suitable for experiments with cold trapped ions and atoms. The unit is capable of outputting a pulse sequence with at least 32 transistor-transistor logic (TTL) channels with a timing resolution of 40 ns and contains a built-in 100 MHz frequency counter for counting electrical pulses from a photo-multiplier tube. There are 16 independent direct-digital-synthesizers RF sources with fast (rise-time of ∼60 ns) amplitude switching and sub-mHz frequency tuning from 0 to 800 MHz.

Compact field programmable gate array-based pulse-sequencer and radio-frequency generator for experiments with trapped atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruttivarasin, Thaned, E-mail: thaned.pruttivarasin@riken.jp; Katori, Hidetoshi; Innovative Space-Time Project, ERATO, JST, Bunkyo-ku, Tokyo 113-8656

We present a compact field-programmable gate array (FPGA) based pulse sequencer and radio-frequency (RF) generator suitable for experiments with cold trapped ions and atoms. The unit is capable of outputting a pulse sequence with at least 32 transistor-transistor logic (TTL) channels with a timing resolution of 40 ns and contains a built-in 100 MHz frequency counter for counting electrical pulses from a photo-multiplier tube. There are 16 independent direct-digital-synthesizers RF sources with fast (rise-time of ∼60 ns) amplitude switching and sub-mHz frequency tuning from 0 to 800 MHz.

Optimized, unequal pulse spacing in multiple echo sequences improves refocusing in magnetic resonance.

PubMed

Jenista, Elizabeth R; Stokes, Ashley M; Branca, Rosa Tamara; Warren, Warren S

2009-11-28

A recent quantum computing paper (G. S. Uhrig, Phys. Rev. Lett. 98, 100504 (2007)) analytically derived optimal pulse spacings for a multiple spin echo sequence designed to remove decoherence in a two-level system coupled to a bath. The spacings in what has been called a "Uhrig dynamic decoupling (UDD) sequence" differ dramatically from the conventional, equal pulse spacing of a Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo sequence. The UDD sequence was derived for a model that is unrelated to magnetic resonance, but was recently shown theoretically to be more general. Here we show that the UDD sequence has theoretical advantages for magnetic resonance imaging of structured materials such as tissue, where diffusion in compartmentalized and microstructured environments leads to fluctuating fields on a range of different time scales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T(2)-weighted contrast than do CPMG sequences with the same number of pulses and total delay, with substantial enhancements in most regions. This permits improved characterization of low-frequency spectral density functions in a wide range of applications.

Direct DNA binding by Brca1.

PubMed

Paull, T T; Cortez, D; Bowers, B; Elledge, S J; Gellert, M

2001-05-22

The tumor suppressor Brca1 plays an important role in protecting mammalian cells against genomic instability, but little is known about its modes of action. In this work we demonstrate that recombinant human Brca1 protein binds strongly to DNA, an activity conferred by a domain in the center of the Brca1 polypeptide. As a result of this binding, Brca1 inhibits the nucleolytic activities of the Mre11/Rad50/Nbs1 complex, an enzyme implicated in numerous aspects of double-strand break repair. Brca1 displays a preference for branched DNA structures and forms protein-DNA complexes cooperatively between multiple DNA strands, but without DNA sequence specificity. This fundamental property of Brca1 may be an important part of its role in DNA repair and transcription.

Robustness of composite pulse sequences to time-dependent noise

NASA Astrophysics Data System (ADS)

Kabytayev, Chingiz; Green, Todd J.; Khodjasteh, Kaveh; Viola, Lorenza; Biercuk, Michael J.; Brown, Kenneth R.

2014-03-01

Quantum control protocols can minimize the effect of noise sources that reduce the quality of quantum operations. Originally developed for NMR, composite pulse sequences correct for unknown static control errors . We study these compensating pulses in the general case of time-varying Gaussian control noise using a filter-function approach and detailed numerics. Three different noise models were considered in this work: amplitude noise, detuning noise and simultaneous presence of both noises. Pulse sequences are shown to be robust to noise up to frequencies as high as ~10% of the Rabi frequency. Robustness of pulses designed for amplitude noise is explained using a geometric picture that naturally follows from filter function. We also discuss future directions including new pulses correcting for noise of certain frequency. True J. Merrill and Kenneth R. Brown. arXiv:1203.6392v1. In press Adv. Chem. Phys. (2013)

A DS-UWB Cognitive Radio System Based on Bridge Function Smart Codes

NASA Astrophysics Data System (ADS)

Xu, Yafei; Hong, Sheng; Zhao, Guodong; Zhang, Fengyuan; di, Jinshan; Zhang, Qishan

This paper proposes a direct-sequence UWB Gaussian pulse of cognitive radio systems based on bridge function smart sequence matrix and the Gaussian pulse. As the system uses the spreading sequence code, that is the bridge function smart code sequence, the zero correlation zones (ZCZs) which the bridge function sequences' auto-correlation functions had, could reduce multipath fading of the pulse interference. The Modulated channel signal was sent into the IEEE 802.15.3a UWB channel. We analysis the ZCZs's inhibition to the interference multipath interference (MPI), as one of the main system sources interferences. The simulation in SIMULINK/MATLAB is described in detail. The result shows the system has better performance by comparison with that employing Walsh sequence square matrix, and it was verified by the formula in principle.

Study of the Use of Oxygen-Absorbing Packaging Material to Prolong Shelf-Life of Rations

DTIC Science & Technology

2010-05-28

technology can be used for retortable items (MRE 28 “Italian” entrée, chicken pesto with noodles ) since it maintained the 4 product shelf-life and...packages that have head spacing issues (e.g., retort item or those containing olive oil). Products included chicken pest with noodles (retorted entrée...of the MRE applesauce, they did not prevent the darkening problem. It is suspected that the retort processing step for applesauce manufacture may

Acousto-optic replication of ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Yushkov, Konstantin B.; Molchanov, Vladimir Ya.; Ovchinnikov, Andrey V.; Chefonov, Oleg V.

2017-10-01

Precisely controlled sequences of ultrashort laser pulses are required in various scientific and engineering applications. We developed a phase-only acousto-optic pulse shaping method for replication of ultrashort laser pulses in a TW laser system. A sequence of several Fourier-transform-limited pulses is generated from a single femtosecond laser pulse by means of applying a piecewise linear phase modulation over the whole emission spectrum. Analysis demonstrates that the main factor which limits maximum delay between the pulse replicas is spectral resolution of the acousto-optic dispersive delay line used for pulse shaping. In experiments with a Cr:forsterite laser system, we obtained delays from 0.3 to 3.5 ps between two replicas of 190 fs transform-limited pulses at the central wavelength of laser emission, 1230 nm.

Principles of Quantitative MR Imaging with Illustrated Review of Applicable Modular Pulse Diagrams.

PubMed

Mills, Andrew F; Sakai, Osamu; Anderson, Stephan W; Jara, Hernan

2017-01-01

Continued improvements in diagnostic accuracy using magnetic resonance (MR) imaging will require development of methods for tissue analysis that complement traditional qualitative MR imaging studies. Quantitative MR imaging is based on measurement and interpretation of tissue-specific parameters independent of experimental design, compared with qualitative MR imaging, which relies on interpretation of tissue contrast that results from experimental pulse sequence parameters. Quantitative MR imaging represents a natural next step in the evolution of MR imaging practice, since quantitative MR imaging data can be acquired using currently available qualitative imaging pulse sequences without modifications to imaging equipment. The article presents a review of the basic physical concepts used in MR imaging and how quantitative MR imaging is distinct from qualitative MR imaging. Subsequently, the article reviews the hierarchical organization of major applicable pulse sequences used in this article, with the sequences organized into conventional, hybrid, and multispectral sequences capable of calculating the main tissue parameters of T1, T2, and proton density. While this new concept offers the potential for improved diagnostic accuracy and workflow, awareness of this extension to qualitative imaging is generally low. This article reviews the basic physical concepts in MR imaging, describes commonly measured tissue parameters in quantitative MR imaging, and presents the major available pulse sequences used for quantitative MR imaging, with a focus on the hierarchical organization of these sequences. © RSNA, 2017.

Towards answering the "so what" question in marine renewables environmental impact assessment.

NASA Astrophysics Data System (ADS)

Degraer, Steven; Birchenough, Silvana N. R.; Braeckman, Ulrike; Coolen, Joop W. P.; Dannheim, Jennifer; De Mesel, Ilse; Grégoire, Marilaure; Kerckhof, Francis; Lacroix, Geneviève; Lindeboom, Han; Moens, Tom; Soetaert, Karline; Vanaverbeke, Jan; Van Hoey, Gert

2016-04-01

Marine renewable energy (MRE) projects are increasingly occupying the European North-Atlantic coasts and this is clearly observed in the North Sea. Given the expected impacts on the marine environment, each individual project is accompanied by a legally mandatory, environmental monitoring programme. These programmes are focused on the resultant effects on ecosystem component structure (e.g. species composition, numbers and densities) of single industrial projects. To date, there is a tendency to further narrow down to only a selection of ecosystem components (e.g. marine mammals and birds). While a wide knowledge-based understanding of structural impacts on (a selection of) ecosystem components exists, this evidence is largely lacking when undertaking impact assessments at the ecosystem functioning level (e.g. trophic interactions, dispersal and nutrient cycling). This critical knowledge gap compromises a scientifically-underpinned answer to the "so what" question of environmental impacts, i.e. whether the observed impacts are considered to be good or bad, or acceptable or unacceptable. The importance of ecosystem functioning is further acknowledged in the descriptors 4 and 6 of the Marine Strategy Framework Directive (EU MSFD) and is at the heart of a sustainable use and management of our marine resources. There hence is a fundamental need to focus on ecosystem functioning at the spatial scales at which marine ecosystems function when assessing MRE impacts. Here, we make a plea for an increased investment in a large (spatial) scale impact assessment of MRE projects focused on ecosystem functioning. This presentation will cover a selection of examples from North Sea MRE monitoring programmes, where the current knowledge has limited conclusions on the "so what" question. We will demonstrate how an ecosystem functioning-focused approach at an appropriate spatial scale could advance our current understanding, whilst assessing these issues. These examples will cover biogeochemical cycling, food webs and connectivity in a cumulative MRE impact assessment context. This presentation will highlight both the available knowledge base and further elaborate on the knowledge gaps. We will offer guidance on how these knowledge gaps could be further investigated, based on examples taken from the recently started projects FaCE-It, Functional biodiversity in a changing sedimentary environment: implications for biogeochemistry and food webs in a managerial setting (financed by the Belgian Science Policy) and UNDINE, Understanding the influence of man-made structures on the ecosystem functions of the North Sea (financed by INSITE). This presentation will set the scene and offer further thinking on the current issues associated to MRE monitoring, particularly beyond the level of ecological structure and individual industrial projects. The overall message will aid advancing and strengthening a collaborative MRE monitoring, helping scientists, managers and regulators to answer the much needed "so what" question to support environmental assessments. Keywords: offshore wind farms, cumulative effects, spatial upscaling, ecosystem functioning, biogeochemical cycling, food webs Contact author: Steven Degraer, steven.degraer@naturalsciences.be

A simple method for MR elastography: a gradient-echo type multi-echo sequence.

PubMed

Numano, Tomokazu; Mizuhara, Kazuyuki; Hata, Junichi; Washio, Toshikatsu; Homma, Kazuhiro

2015-01-01

To demonstrate the feasibility of a novel MR elastography (MRE) technique based on a conventional gradient-echo type multi-echo MR sequence which does not need additional bipolar magnetic field gradients (motion encoding gradient: MEG), yet is sensitive to vibration. In a gradient-echo type multi-echo MR sequence, several images are produced from each echo of the train with different echo times (TEs). If these echoes are synchronized with the vibration, each readout's gradient lobes achieve a MEG-like effect, and the later generated echo causes a greater MEG-like effect. The sequence was tested for the tissue-mimicking agarose gel phantoms and the psoas major muscles of healthy volunteers. It was confirmed that the readout gradient lobes caused an MEG-like effect and the later TE images had higher sensitivity to vibrations. The magnitude image of later generated echo suffered the T2 decay and the susceptibility artifacts, but the wave image and elastogram of later generated echo were unaffected by these effects. In in vivo experiments, this method was able to measure the mean shear modulus of the psoas major muscle. From the results of phantom experiments and volunteer studies, it was shown that this method has clinical application potential. Copyright © 2014 Elsevier Inc. All rights reserved.

Pulse sequences for efficient multi-cycle terahertz generation in periodically poled lithium niobate.

PubMed

Ravi, Koustuban; Schimpf, Damian N; Kärtner, Franz X

2016-10-31

The use of laser pulse sequences to drive the cascaded difference frequency generation of high energy, high peak-power and multi-cycle terahertz pulses in cryogenically cooled (100 K) periodically poled Lithium Niobate is proposed and studied. Detailed simulations considering the coupled nonlinear interaction of terahertz and optical waves (or pump depletion), show that unprecedented optical-to-terahertz energy conversion efficiencies > 5%, peak electric fields of hundred(s) of mega volts/meter at terahertz pulse durations of hundred(s) of picoseconds can be achieved. The proposed methods are shown to circumvent laser induced damage limitations at Joule-level pumping by 1µm lasers to enable multi-cycle terahertz sources with pulse energies > 10 milli-joules. Various pulse sequence formats are proposed and analyzed. Numerical calculations for periodically poled structures accounting for cascaded difference frequency generation, self-phase-modulation, cascaded second harmonic generation and laser induced damage are introduced. The physics governing terahertz generation using pulse sequences in this high conversion efficiency regime, limitations and practical considerations are discussed. It is shown that varying the poling period along the crystal length and further reduction of absorption can lead to even higher energy conversion efficiencies >10%. In addition to numerical calculations, an analytic formulation valid for arbitrary pulse formats and closed-form expressions for important cases are presented. Parameters optimizing conversion efficiency in the 0.1-1 THz range, the corresponding peak electric fields, crystal lengths and terahertz pulse properties are furnished.

Pulse sequences for uniform perfluorocarbon droplet vaporization and ultrasound imaging.

PubMed

Puett, C; Sheeran, P S; Rojas, J D; Dayton, P A

2014-09-01

Phase-change contrast agents (PCCAs) consist of liquid perfluorocarbon droplets that can be vaporized into gas-filled microbubbles by pulsed ultrasound waves at diagnostic pressures and frequencies. These activatable contrast agents provide benefits of longer circulating times and smaller sizes relative to conventional microbubble contrast agents. However, optimizing ultrasound-induced activation of these agents requires coordinated pulse sequences not found on current clinical systems, in order to both initiate droplet vaporization and image the resulting microbubble population. Specifically, the activation process must provide a spatially uniform distribution of microbubbles and needs to occur quickly enough to image the vaporized agents before they migrate out of the imaging field of view. The development and evaluation of protocols for PCCA-enhanced ultrasound imaging using a commercial array transducer are described. The developed pulse sequences consist of three states: (1) initial imaging at sub-activation pressures, (2) activating droplets within a selected region of interest, and (3) imaging the resulting microbubbles. Bubble clouds produced by the vaporization of decafluorobutane and octafluoropropane droplets were characterized as a function of focused pulse parameters and acoustic field location. Pulse sequences were designed to manipulate the geometries of discrete microbubble clouds using electronic steering, and cloud spacing was tailored to build a uniform vaporization field. The complete pulse sequence was demonstrated in the water bath and then in vivo in a rodent kidney. The resulting contrast provided a significant increase (>15 dB) in signal intensity. Copyright © 2014 Elsevier B.V. All rights reserved.

In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against the Pesticide Fipronil and Sensitive Detection in River Water

PubMed Central

Sooter, Letha J.

2017-01-01

Fipronil is a commonly used insecticide that has been shown to have environmental and human health risks. The current standard methods of detection for fipronil and its metabolites, such as GC-MS, are time consuming and labor intensive. In this study, a variant of systematic evolution of ligands by exponential enrichment (SELEX), was utilized to identify the first single-stranded DNA (ssDNA) molecular recognition element (MRE) that binds to fipronil with high affinity (Kd = 48 ± 8 nM). The selected MRE displayed low cross binding activity on various environmentally relevant, structurally unrelated herbicides and pesticides, in addition to broad-spectrum binding activity on major metabolites of fipronil and a structurally similar pesticide in prepared river samples. Additionally, a proof-of-principle fluorescent detection assay was developed by using the selected ssDNA MRE as a signal-reporting element, with a limit of detection of 105 nM in a prepared river water sample. PMID:29283416

Interdependence of the rad50 hook and globular domain functions.

PubMed

Hohl, Marcel; Kochańczyk, Tomasz; Tous, Cristina; Aguilera, Andrés; Krężel, Artur; Petrini, John H J

2015-02-05

Rad50 contains a conserved Zn(2+) coordination domain (the Rad50 hook) that functions as a homodimerization interface. Hook ablation phenocopies Rad50 deficiency in all respects. Here, we focused on rad50 mutations flanking the Zn(2+)-coordinating hook cysteines. These mutants impaired hook-mediated dimerization, but recombination between sister chromatids was largely unaffected. This may reflect that cohesin-mediated sister chromatid interactions are sufficient for double-strand break repair. However, Mre11 complex functions specified by the globular domain, including Tel1 (ATM) activation, nonhomologous end joining, and DNA double-strand break end resection were affected, suggesting that dimerization exerts a broad influence on Mre11 complex function. These phenotypes were suppressed by mutations within the coiled-coil and globular ATPase domains, suggesting a model in which conformational changes in the hook and globular domains are transmitted via the extended coils of Rad50. We propose that transmission of spatial information in this manner underlies the regulation of Mre11 complex functions. Copyright © 2015 Elsevier Inc. All rights reserved.

Alternative surgical approaches in epilepsy.

PubMed

Gigante, Paul R; Goodman, Robert R

2011-08-01

The mainstay of epilepsy surgery is the resection of a presumed seizure focus or disruption of seizure propagation pathways. These approaches cannot be applied to all patients with medically refractory epilepsy (MRE). Since 1997, vagus nerve stimulation has been a palliative adjunct to the care of MRE patients. Deep brain stimulation (DBS) in select locations has been reported to reduce seizure frequency in small studies over the past three decades. Recently published results from the SANTE (Stimulation of the Anterior Nuclei of Thalamus for Epilepsy) trial-the first large-scale, randomized, double-blind trial of bilateral anterior thalamus DBS for MRE-demonstrate a significant reduction in seizure frequency with programmed stimulation. Another surgical alternative is the RNS™ System (NeuroPace, Mountain View, CA), which uses a closed-loop system termed responsive neurostimulation to both detect apparent seizure onsets and deliver stimulation. Recently presented results from the RNS™ pivotal trial demonstrate a sustained reduction in seizure frequency with stimulation, although comprehensive trial results are pending.

Development of high repetition rate nitric oxide planar laser induced fluorescence imaging

NASA Astrophysics Data System (ADS)

Jiang, Naibo

This thesis has documented the development of a MHz repitition rate pulse burst laser system. Second harmonic and third harmonic efficiencies are improved by adding a Phase Conjugate Mirror to the system. Some high energy fundamental, second harmonic, and third harmonic burst sequences consisting of 1--12 pulses separated in time by between 4 and 12 microseconds are now routinely obtained. The reported burst envelopes are quite uniform. We have also demonstrated the ability to generate ultra-high frequency sequences of broadly wavelength tunable, high intensity laser pulses using a home built injection seeded Optical Parametric Oscillator (OPO), pumped by the second and third harmonic output of the pulse burst laser. Typical OPO output burst sequences consist of 6--10 pulses, separated in time by between 6 and 10 microseconds. With third harmonic pumping of the OPO system, we studied four conditions, two-crystal Singly Resonant OPO (SRO) cavity, three-crystal OPO cavity, single pass two-crystal Doubly Resonant OPO (DRO) cavity and double pass two-crystal OPO cavity. The double pass two-crystal OPO cavity gives the best operation in burst mode. For single pass OPO, the average total OPO conversion efficiency is approximately 25%. For double pass OPO, the average total OPO conversion efficiency is approximately 35%. As a preliminary work, we studied 532nm pumping of a single crystal OPO cavity. With single pulse pumping, the conversion efficiency can reach 30%. For both 355nm and 532nm pumping OPO, we have demonstrated injection seeding. The OPO output light linewidth is significantly narrowed. Some preliminary etalon traces are also reported. By mixing the OPO signal output at 622nm with residual third harmonic at 355nm, we obtained 226nm burst sequences with average pulse energy of ˜0.2 mJ. Injection seeding of the OPO increases the energy achieved by a factor of ˜2. 226nm burst sequences with reasonably uniform burst envelopes are reported. Using the system we have obtained, for the first time by any known optical method, Planar Laser Induced Fluorescence (PLIF) image sequences at ultrahigh (≥100kHz) frame rates, in particular NO PLIF image sequences, have been obtained in a Mach 2 jet. We also studied the possibility of utilizing a 250 kHz pulsed Nd:YVO 4 laser as the master oscillator. 10-pulse-10-mus spacing burst sequences with reasonably uniform burst envelope have been obtained. The total energy of the burst sequence is ˜2.5J.

A spin echo sequence with a single-sided bipolar diffusion gradient pulse to obtain snapshot diffusion weighted images in moving media

NASA Astrophysics Data System (ADS)

Freidlin, R. Z.; Kakareka, J. W.; Pohida, T. J.; Komlosh, M. E.; Basser, P. J.

2012-08-01

In vivo MRI data can be corrupted by motion. Motion artifacts are particularly troublesome in Diffusion Weighted MRI (DWI), since the MR signal attenuation due to Brownian motion can be much less than the signal loss due to dephasing from other types of complex tissue motion, which can significantly degrade the estimation of self-diffusion coefficients, diffusion tensors, etc. This paper describes a snapshot DWI sequence, which utilizes a novel single-sided bipolar diffusion sensitizing gradient pulse within a spin echo sequence. The proposed method shortens the diffusion time by applying a single refocused bipolar diffusion gradient on one side of a refocusing RF pulse, instead of a set of diffusion sensitizing gradients, separated by a refocusing RF pulse, while reducing the impact of magnetic field inhomogeneity by using a spin echo sequence. A novel MRI phantom that can exhibit a range of complex motions was designed to demonstrate the robustness of the proposed DWI sequence.

Molecular breeding of the Mureka-non-forming sake koji mold from Aspergillus oryzae by the disruption of the mreA gene.

PubMed

Kubodera, Takafumi; Yamashita, Nobuo; Nishimura, Akira

2003-01-01

Mureka-non-forming sake koji molds were constructed from an Aspergillus oryzae industrial strain by the disruption of the mreA gene using a host-vector system with the ptrA gene as a dominant selectable marker. All of the mreA gene disruptants obtained retained the advantages of the host strain in terms of the brewing characteristics, while their isoamyl alcohol oxidase (IAAOD) activities were significantly lower than that of the host strain. Sake brewing was successfully carried out using the koji prepared with the disruptants, followed by storage of the resultant non-pasteurized sake (nama-shu). The isovaleraldehyde (i-Val) concentration in the sake brewed the host strain increased rapidly and reached the threshold values for mureka, 1.8 ppm and 2.6 ppm after storage at 20 degrees C for 42 d and 63 d, respectively, while those of the disruptants were less than 0.5 ppm even after storage at 20 degrees C or 30 degrees C for 63 d. In the sensory evaluation of the sake stored at 20 degrees C or 30 degrees C for 63 d, all members of the panel recognized the strong mureka flavor of the sake brewed with the host strain, while they did not detect this flavor in the sake brewed with the disruptants. Thus, we concluded that the mreA gene disruptants can be used for the production of sake in which mureka is not formed.

Escherichia coli DnaA forms helical structures along the longitudinal cell axis distinct from MreB filaments.

PubMed

Boeneman, Kelly; Fossum, Solveig; Yang, Yanhua; Fingland, Nicholas; Skarstad, Kirsten; Crooke, Elliott

2009-05-01

DnaA initiates chromosomal replication in Escherichia coli at a well-regulated time in the cell cycle. To determine how the spatial distribution of DnaA is related to the location of chromosomal replication and other cell cycle events, the localization of DnaA in living cells was visualized by confocal fluorescence microscopy. The gfp gene was randomly inserted into a dnaA-bearing plasmid via in vitro transposition to create a library that included internally GFP-tagged DnaA proteins. The library was screened for the ability to rescue dnaA(ts) mutants, and a candidate gfp-dnaA was used to replace the dnaA gene of wild-type cells. The resulting cells produce close to physiological levels of GFP-DnaA from the endogenous promoter as their only source of DnaA and somewhat under-initiate replication with moderate asynchrony. Visualization of GFP-tagged DnaA in living cells revealed that DnaA adopts a helical pattern that spirals along the long axis of the cell, a pattern also seen in wild-type cells by immunofluorescence with affinity purified anti-DnaA antibody. Although the DnaA helices closely resemble the helices of the actin analogue MreB, co-visualization of GFP-tagged DnaA and RFP-tagged MreB demonstrates that DnaA and MreB adopt discrete helical structures along the length of the longitudinal cell axis.

Mechanical Characterization of Tissue-Engineered Cartilage Using Microscopic Magnetic Resonance Elastography

PubMed Central

Yin, Ziying; Schmid, Thomas M.; Yasar, Temel K.; Liu, Yifei; Royston, Thomas J.

2014-01-01

Knowledge of mechanical properties of tissue-engineered cartilage is essential for the optimization of cartilage tissue engineering strategies. Microscopic magnetic resonance elastography (μMRE) is a recently developed MR-based technique that can nondestructively visualize shear wave motion. From the observed wave pattern in MR phase images the tissue mechanical properties (e.g., shear modulus or stiffness) can be extracted. For quantification of the dynamic shear properties of small and stiff tissue-engineered cartilage, μMRE needs to be performed at frequencies in the kilohertz range. However, at frequencies greater than 1 kHz shear waves are rapidly attenuated in soft tissues. In this study μMRE, with geometric focusing, was used to overcome the rapid wave attenuation at high frequencies, enabling the measurement of the shear modulus of tissue-engineered cartilage. This methodology was first tested at a frequency of 5 kHz using a model system composed of alginate beads embedded in agarose, and then applied to evaluate extracellular matrix development in a chondrocyte pellet over a 3-week culture period. The shear stiffness in the pellet was found to increase over time (from 6.4 to 16.4 kPa), and the increase was correlated with both the proteoglycan content and the collagen content of the chondrocyte pellets (R2=0.776 and 0.724, respectively). Our study demonstrates that μMRE when performed with geometric focusing can be used to calculate and map the shear properties within tissue-engineered cartilage during its development. PMID:24266395

Two alleles of the AtCesA3 gene in Arabidopsis thaliana display intragenic complementation.

PubMed

Pysh, Leonard D

2015-09-01

Cellulose is the most abundant biomolecule on the planet, yet the mechanism by which it is synthesized by higher plants remains largely unknown. In Arabidopsis thaliana (L.) Heynh, synthesis of cellulose in the primary cell wall requires three different cellulose synthase genes (AtCesA1, AtCesA3, and AtCesA6-related genes [AtCesA2, AtCesA5, and AtCesA6]). The multiple response expansion1 (mre1) mutant contains a hypomorphic AtCesA3 allele that results in significantly shorter, expanded roots. Crosses between mre1 and another allele of AtCesA3 (constitutive expression of VSP1, cev1) yielded an F1 with roots considerably longer and thinner than either parent, suggesting intragenic complementation. The F2 generation resulting from self-crossing these F1 showed three different root phenotypes: roots like mre1, roots like cev1, and roots like the F1. The segregation patterns of the three root phenotypes in multiple F2 and F3 generations were determined. Multiple characteristics of the roots and shoots were analyzed both qualitatively and quantitatively at different developmental stages, both on plates and on soil. The trans-heterozygous plants differed significantly from the parental mre1 and cev1 lines. The two alleles display intragenic complementation. A classic genetic interpretation of these results would suggest that cellulose synthesis requires homo-multimerization of cellulose synthase monomers. © 2015 Botanical Society of America.

Magnetic resonance elastography can monitor changes in medullary stiffness in response to treatment in the swine ischemic kidney.

PubMed

Zhang, Xin; Zhu, Xiangyang; Ferguson, Christopher Martyn; Jiang, Kai; Burningham, Tyson; Lerman, Amir; Lerman, Lilach Orly

2018-06-01

Low-energy shockwave (SW) therapy attenuates damage in the stenotic kidney (STK) caused by atherosclerotic renal artery stenosis (ARAS). We hypothesized that magnetic resonance elastography (MRE) would detect attenuation of fibrosis following SW in unilateral ARAS kidneys. Domestic pigs were randomized to control, unilateral ARAS, and ARAS treated with 6 sessions of SW over 3 consecutive weeks (n = 7 each) starting after 3 weeks of ARAS or sham. Four weeks after SW treatment, renal fibrosis was evaluated with MRE in vivo or trichrome staining ex vivo. Blood pressure, single-kidney renal-blood-flow (RBF) and glomerular-filtration-rate (GFR) were assessed. MRE detected increased stiffness in the STK medulla (15.3 ± 2.1 vs. 10.1 ± 0.8 kPa, p < 0.05) that moderately correlated with severity of fibrosis (R 2  = 0.501, p < 0.01), but did not identify mild STK cortical or contralateral kidney fibrosis. Trichrome staining showed that medullary fibrosis was increased in ARAS and alleviated by SW (10.4 ± 1.8% vs. 2.9 ± 0.2%, p < 0.01). SW slightly decreased blood pressure and normalized STK RBF and GFR in ARAS. In the contralateral kidney, SW reversed the increase in RBF and GFR. MRE might be a tool for noninvasive monitoring of medullary fibrosis in response to treatment in kidney disease.

Characterization of a hyper-viscoelastic phantom mimicking biological soft tissue using an abdominal pneumatic driver with Magnetic Resonance Elastography (MRE)

PubMed Central

Leclerc, Gwladys E.; Debernard, Laetitia; Foucart, Félix; Robert, Ludovic; Pelletier, Kay M.; Charleux, Fabrice; Ehman, Richard; Tho, Marie-Christine Ho Ba; Bensamoun, Sabine F.

2012-01-01

The purpose of this study was to create a polymer phantom mimicking the mechanical properties of soft tissues using experimental tests and rheological models. Multifrequency Magnetic Resonance Elastography (MMRE) tests were performed on the present phantom with a pneumatic driver to characterize the viscoelastic (μ, η) properties using Voigt, Maxwell, Zener and Springpot models. To optimize the MMRE protocol, the driver behavior was analyzed with a vibrometer. Moreover, the hyperelastic properties of the phantom were determined using compressive tests and Mooney-Rivlin model. The range of frequency to be used with the round driver was found between 60 Hz and 100 Hz as it exhibits one type of vibration mode for the membrane. MRE analysis revealed an increase in the shear modulus with frequency reflecting the viscoelastic properties of the phantom showing similar characteristic of soft tissues. Rheological results demonstrated that Springpot model better revealed the viscoelastic properties (μ = 3.45 kPa, η = 6.17 Pa.s) of the phantom and the Mooney-Rivlin coefficients were C10 = 1.09.10-2 MPa and C01 = −8.96.10-3 MPa corresponding to μ = 3.95 kPa. These studies suggest that the phantom, mimicking soft tissue, could be used for preliminary MRE tests to identify the optimal parameters necessary for in vivo investigations. Further developments of the phantom may allow clinicians to more accurately mimic healthy and pathological soft tissues using MRE. PMID:22284992

Characterization of a hyper-viscoelastic phantom mimicking biological soft tissue using an abdominal pneumatic driver with magnetic resonance elastography (MRE).

PubMed

Leclerc, Gwladys E; Debernard, Laëtitia; Foucart, Félix; Robert, Ludovic; Pelletier, Kay M; Charleux, Fabrice; Ehman, Richard; Ho Ba Tho, Marie-Christine; Bensamoun, Sabine F

2012-04-05

The purpose of this study was to create a polymer phantom mimicking the mechanical properties of soft tissues using experimental tests and rheological models. Multifrequency Magnetic Resonance Elastography (MMRE) tests were performed on the present phantom with a pneumatic driver to characterize the viscoelastic (μ, η) properties using Voigt, Maxwell, Zener and Springpot models. To optimize the MMRE protocol, the driver behavior was analyzed with a vibrometer. Moreover, the hyperelastic properties of the phantom were determined using compressive tests and Mooney-Rivlin model. The range of frequency to be used with the round driver was found between 60 Hz and 100 Hz as it exhibits one type of vibration mode for the membrane. MRE analysis revealed an increase in the shear modulus with frequency reflecting the viscoelastic properties of the phantom showing similar characteristic of soft tissues. Rheological results demonstrated that Springpot model better revealed the viscoelastic properties (μ=3.45 kPa, η=6.17 Pas) of the phantom and the Mooney-Rivlin coefficients were C(10)=1.09.10(-2) MPa and C(01)=-8.96.10(-3) MPa corresponding to μ=3.95 kPa. These studies suggest that the phantom, mimicking soft tissue, could be used for preliminary MRE tests to identify the optimal parameters necessary for in vivo investigations. Further developments of the phantom may allow clinicians to more accurately mimic healthy and pathological soft tissues using MRE. Copyright © 2012 Elsevier Ltd. All rights reserved.

Acceleration of Magnetospheric Relativistic Electrons by Ultra-Low Frequency Waves: A Comparison between Two Cases Observed by Cluster and LANL Satellites

NASA Technical Reports Server (NTRS)

Shao, X.; Fung, S. F.; Tan, L. C.; Sharma, A. S.

2010-01-01

Understanding the origin and acceleration of magnetospheric relativistic electrons (MREs) in the Earth's radiation belt during geomagnetic storms is an important subject and yet one of outstanding questions in space physics. It has been statistically suggested that during geomagnetic storms, ultra-low-frequency (ULF) Pc-5 wave activities in the magnetosphere are correlated with order of magnitude increase of MRE fluxes in the outer radiation belt. Yet, physical and observational understandings of resonant interactions between ULF waves and MREs remain minimum. In this paper, we show two events during storms on September 25, 2001 and November 25, 2001, the solar wind speeds in both cases were > 500 km/s while Cluster observations indicate presence of strong ULF waves in the magnetosphere at noon and dusk, respectively, during a approx. 3-hour period. MRE observations by the Los Alamos (LANL) spacecraft show a quadrupling of 1.1-1.5 MeV electron fluxes in the September 25, 2001 event, but only a negligible increase in the November 2.5, 2001 event. We present a detailed comparison between these two events. Our results suggest that the effectiveness of MRE acceleration during the September 25, 2001 event can be attributed to the compressional wave mode with strong ULF wave activities and the physical origin of MRE acceleration depends more on the distribution of toroidal and poloidal ULF waves in the outer radiation belt.

On-Chip AC self-test controller

DOEpatents

Flanagan, John D [Rhinebeck, NY; Herring, Jay R [Poughkeepsie, NY; Lo, Tin-Chee [Fishkill, NY

2009-09-29

A system for performing AC self-test on an integrated circuit that includes a system clock for normal operation is provided. The system includes the system clock, self-test circuitry, a first and second test register to capture and launch test data in response to a sequence of data pulses, and a logic circuit to be tested. The self-test circuitry includes an AC self-test controller and a clock splitter. The clock splitter generates the sequence of data pulses including a long data capture pulse followed by an at speed data launch pulse and an at speed data capture pulse followed by a long data launch pulse. The at speed data launch pulse and the at speed data capture pulse are generated for a common cycle of the system clock.

Formation of laser-induced periodic surface structures on fused silica upon two-color double-pulse irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Höhm, S.; Herzlieb, M.; Rosenfeld, A.

2013-12-16

The formation of laser-induced periodic surface structures (LIPSS) upon irradiation of fused silica with multiple irradiation sequences consisting of laser pulse pairs (50 fs single-pulse duration) of two different wavelengths (400 and 800 nm) is studied experimentally. Parallel polarized double-pulse sequences with a variable delay Δt between −10 and +10 ps and between the individual fs-laser pulses were used to investigate the LIPSS periods versus Δt. These two-color experiments reveal the importance of the ultrafast energy deposition to the silica surface by the first laser pulse for LIPSS formation. The second laser pulse subsequently reinforces the previously seeded spatial LIPSSmore » frequencies.« less

Trace level detection of compounds related to the chemical weapons convention by 1H-detected 13C NMR spectroscopy executed with a sensitivity-enhanced, cryogenic probehead.

PubMed

Cullinan, David B; Hondrogiannis, George; Henderson, Terry J

2008-04-15

Two-dimensional 1H-13C HSQC (heteronuclear single quantum correlation) and fast-HMQC (heteronuclear multiple quantum correlation) pulse sequences were implemented using a sensitivity-enhanced, cryogenic probehead for detecting compounds relevant to the Chemical Weapons Convention present in complex mixtures. The resulting methods demonstrated exceptional sensitivity for detecting the analytes at trace level concentrations. 1H-13C correlations of target analytes at < or = 25 microg/mL were easily detected in a sample where the 1H solvent signal was approximately 58,000-fold more intense than the analyte 1H signals. The problem of overlapping signals typically observed in conventional 1H spectroscopy was essentially eliminated, while 1H and 13C chemical shift information could be derived quickly and simultaneously from the resulting spectra. The fast-HMQC pulse sequences generated magnitude mode spectra suitable for detailed analysis in approximately 4.5 h and can be used in experiments to efficiently screen a large number of samples. The HSQC pulse sequences, on the other hand, required roughly twice the data acquisition time to produce suitable spectra. These spectra, however, were phase-sensitive, contained considerably more resolution in both dimensions, and proved to be superior for detecting analyte 1H-13C correlations. Furthermore, a HSQC spectrum collected with a multiplicity-edited pulse sequence provided additional structural information valuable for identifying target analytes. The HSQC pulse sequences are ideal for collecting high-quality data sets with overnight acquisitions and logically follow the use of fast-HMQC pulse sequences to rapidly screen samples for potential target analytes. Use of the pulse sequences considerably improves the performance of NMR spectroscopy as a complimentary technique for the screening, identification, and validation of chemical warfare agents and other small-molecule analytes present in complex mixtures and environmental samples.

TOPPE: A framework for rapid prototyping of MR pulse sequences.

PubMed

Nielsen, Jon-Fredrik; Noll, Douglas C

2018-06-01

To introduce a framework for rapid prototyping of MR pulse sequences. We propose a simple file format, called "TOPPE", for specifying all details of an MR imaging experiment, such as gradient and radiofrequency waveforms and the complete scan loop. In addition, we provide a TOPPE file "interpreter" for GE scanners, which is a binary executable that loads TOPPE files and executes the sequence on the scanner. We also provide MATLAB scripts for reading and writing TOPPE files and previewing the sequence prior to hardware execution. With this setup, the task of the pulse sequence programmer is reduced to creating TOPPE files, eliminating the need for hardware-specific programming. No sequence-specific compilation is necessary; the interpreter only needs to be compiled once (for every scanner software upgrade). We demonstrate TOPPE in three different applications: k-space mapping, non-Cartesian PRESTO whole-brain dynamic imaging, and myelin mapping in the brain using inhomogeneous magnetization transfer. We successfully implemented and executed the three example sequences. By simply changing the various TOPPE sequence files, a single binary executable (interpreter) was used to execute several different sequences. The TOPPE file format is a complete specification of an MR imaging experiment, based on arbitrary sequences of a (typically small) number of unique modules. Along with the GE interpreter, TOPPE comprises a modular and flexible platform for rapid prototyping of new pulse sequences. Magn Reson Med 79:3128-3134, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Second-order shaped pulsed for solid-state quantum computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, Pinaki

2008-01-01

We present the construction and detailed analysis of highly optimized self-refocusing pulse shapes for several rotation angles. We characterize the constructed pulses by the coefficients appearing in the Magnus expansion up to second order. This allows a semianalytical analysis of the performance of the constructed shapes in sequences and composite pulses by computing the corresponding leading-order error operators. Higher orders can be analyzed with the numerical technique suggested by us previously. We illustrate the technique by analyzing several composite pulses designed to protect against pulse amplitude errors, and on decoupling sequences for potentially long chains of qubits with on-site andmore » nearest-neighbor couplings.« less

Nutritional and Hedonic Consequences of Consuming the Meal, Ready-to-Eat (MRE) VIII or the Soldier Enhancement Program (SEP) MRE

DTIC Science & Technology

1993-01-01

Larry I.. 1edxrh, MUM&i WnoIUn, WU: D6101QOOO DiET. B. RVW1I, SLMa I. DaWy, Jdim II. ibid II, HUT Ow-ia Thau **, ion~ i)1ldc 7. PERFORMING ORGANIZATION...existing chains of command make the present assignment strategy the clear method of choice under the conditions imposed by military structure and field...Bread (White) Caramels Potato Sticks Orange Beverage Base** Cheese Spread Menu 9 Cheese Pizza Lemon Pound Cake Peaches/Pears (Dehydrated) Strawberry

A peripheral component interconnect express-based scalable and highly integrated pulsed spectrometer for solution state dynamic nuclear polarization.

PubMed

He, Yugui; Feng, Jiwen; Zhang, Zhi; Wang, Chao; Wang, Dong; Chen, Fang; Liu, Maili; Liu, Chaoyang

2015-08-01

High sensitivity, high data rates, fast pulses, and accurate synchronization all represent challenges for modern nuclear magnetic resonance spectrometers, which make any expansion or adaptation of these devices to new techniques and experiments difficult. Here, we present a Peripheral Component Interconnect Express (PCIe)-based highly integrated distributed digital architecture pulsed spectrometer that is implemented with electron and nucleus double resonances and is scalable specifically for broad dynamic nuclear polarization (DNP) enhancement applications, including DNP-magnetic resonance spectroscopy/imaging (DNP-MRS/MRI). The distributed modularized architecture can implement more transceiver channels flexibly to meet a variety of MRS/MRI instrumentation needs. The proposed PCIe bus with high data rates can significantly improve data transmission efficiency and communication reliability and allow precise control of pulse sequences. An external high speed double data rate memory chip is used to store acquired data and pulse sequence elements, which greatly accelerates the execution of the pulse sequence, reduces the TR (time of repetition) interval, and improves the accuracy of TR in imaging sequences. Using clock phase-shift technology, we can produce digital pulses accurately with high timing resolution of 1 ns and narrow widths of 4 ns to control the microwave pulses required by pulsed DNP and ensure overall system synchronization. The proposed spectrometer is proved to be both feasible and reliable by observation of a maximum signal enhancement factor of approximately -170 for (1)H, and a high quality water image was successfully obtained by DNP-enhanced spin-echo (1)H MRI at 0.35 T.

A peripheral component interconnect express-based scalable and highly integrated pulsed spectrometer for solution state dynamic nuclear polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Yugui; Liu, Chaoyang, E-mail: chyliu@wipm.ac.cn; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071

2015-08-15

High sensitivity, high data rates, fast pulses, and accurate synchronization all represent challenges for modern nuclear magnetic resonance spectrometers, which make any expansion or adaptation of these devices to new techniques and experiments difficult. Here, we present a Peripheral Component Interconnect Express (PCIe)-based highly integrated distributed digital architecture pulsed spectrometer that is implemented with electron and nucleus double resonances and is scalable specifically for broad dynamic nuclear polarization (DNP) enhancement applications, including DNP-magnetic resonance spectroscopy/imaging (DNP-MRS/MRI). The distributed modularized architecture can implement more transceiver channels flexibly to meet a variety of MRS/MRI instrumentation needs. The proposed PCIe bus with highmore » data rates can significantly improve data transmission efficiency and communication reliability and allow precise control of pulse sequences. An external high speed double data rate memory chip is used to store acquired data and pulse sequence elements, which greatly accelerates the execution of the pulse sequence, reduces the TR (time of repetition) interval, and improves the accuracy of TR in imaging sequences. Using clock phase-shift technology, we can produce digital pulses accurately with high timing resolution of 1 ns and narrow widths of 4 ns to control the microwave pulses required by pulsed DNP and ensure overall system synchronization. The proposed spectrometer is proved to be both feasible and reliable by observation of a maximum signal enhancement factor of approximately −170 for {sup 1}H, and a high quality water image was successfully obtained by DNP-enhanced spin-echo {sup 1}H MRI at 0.35 T.« less

Light beam range finder

DOEpatents

McEwan, Thomas E.

1998-01-01

A "laser tape measure" for measuring distance which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%.

Light beam range finder

DOEpatents

McEwan, T.E.

1998-06-16

A ``laser tape measure`` for measuring distance is disclosed which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%. 7 figs.

Phase incremented echo train acquisition applied to magnetic resonance pore imaging

NASA Astrophysics Data System (ADS)

Hertel, S. A.; Galvosas, P.

2017-02-01

Efficient phase cycling schemes remain a challenge for NMR techniques if the pulse sequences involve a large number of rf-pulses. Especially complex is the Carr Purcell Meiboom Gill (CPMG) pulse sequence where the number of rf-pulses can range from hundreds to several thousands. Our recent implementation of Magnetic Resonance Pore Imaging (MRPI) is based on a CPMG rf-pulse sequence in order to refocus the effect of internal gradients inherent in porous media. While the spin dynamics for spin- 1 / 2 systems in CPMG like experiments are well understood it is still not straight forward to separate the desired pathway from the spectrum of unwanted coherence pathways. In this contribution we apply Phase Incremented Echo Train Acquisition (PIETA) to MRPI. We show how PIETA offers a convenient way to implement a working phase cycling scheme and how it allows one to gain deeper insights into the amplitudes of undesired pathways.

Characterization of scatter in digital mammography from use of Monte Carlo simulations and comparison to physical measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leon, Stephanie M., E-mail: Stephanie.Leon@uth.tmc.edu; Wagner, Louis K.; Brateman, Libby F.

2014-11-01

Purpose: Monte Carlo simulations were performed with the goal of verifying previously published physical measurements characterizing scatter as a function of apparent thickness. A secondary goal was to provide a way of determining what effect tissue glandularity might have on the scatter characteristics of breast tissue. The overall reason for characterizing mammography scatter in this research is the application of these data to an image processing-based scatter-correction program. Methods: MCNPX was used to simulate scatter from an infinitesimal pencil beam using typical mammography geometries and techniques. The spreading of the pencil beam was characterized by two parameters: mean radial extentmore » (MRE) and scatter fraction (SF). The SF and MRE were found as functions of target, filter, tube potential, phantom thickness, and the presence or absence of a grid. The SF was determined by separating scatter and primary by the angle of incidence on the detector, then finding the ratio of the measured scatter to the total number of detected events. The accuracy of the MRE was determined by placing ring-shaped tallies around the impulse and fitting those data to the point-spread function (PSF) equation using the value for MRE derived from the physical measurements. The goodness-of-fit was determined for each data set as a means of assessing the accuracy of the physical MRE data. The effect of breast glandularity on the SF, MRE, and apparent tissue thickness was also considered for a limited number of techniques. Results: The agreement between the physical measurements and the results of the Monte Carlo simulations was assessed. With a grid, the SFs ranged from 0.065 to 0.089, with absolute differences between the measured and simulated SFs averaging 0.02. Without a grid, the range was 0.28–0.51, with absolute differences averaging −0.01. The goodness-of-fit values comparing the Monte Carlo data to the PSF from the physical measurements ranged from 0.96 to 1.00 with a grid and 0.65 to 0.86 without a grid. Analysis of the data suggested that the nongrid data could be better described by a biexponential function than the single exponential used here. The simulations assessing the effect of breast composition on SF and MRE showed only a slight impact on these quantities. When compared to a mix of 50% glandular/50% adipose tissue, the impact of substituting adipose or glandular breast compositions on the apparent thickness of the tissue was about 5%. Conclusions: The findings show agreement between the physical measurements published previously and the Monte Carlo simulations presented here; the resulting data can therefore be used more confidently for an application such as image processing-based scatter correction. The findings also suggest that breast composition does not have a major impact on the scatter characteristics of breast tissue. Application of the scatter data to the development of a scatter-correction software program can be simplified by ignoring the variations in density among breast tissues.« less

Composite pulses robust against charge noise and magnetic field noise for universal control of a singlet-triplet qubit

NASA Astrophysics Data System (ADS)

Wang, Xin; Barnes, Edwin; Kestner, Jason P.; Bishop, Lev S.; Das Sarma, Sankar

2013-03-01

We generalize our SUPCODE pulse sequences for singlet-triplet qubits to correct errors from imperfect control. This yields gates that are simultaneously corrected for both charge noise and magnetic field gradient fluctuations, addressing the two dominant T2* processes. By using this more efficient version of SUPCODE, we are able to introduce this capability while also substantially reducing the overall pulse time compared to the previous sequence. We show that our sequence remains realistic under experimental constraints such as finite bandwidth. This work is supported by LPS-NSA-CMTC, IARPA-MQCO and CNAM.

Short-Term Repeatability of Magnetic Resonance Elastography at 3.0T: Effects of Motion-Encoding Gradient Direction, Slice Position, and Meal Ingestion.

PubMed

Zhang, Jiming; Arena, Claudio; Pednekar, Amol; Lambert, Brenda; Dees, Debra; Lee, Vei Vei; Muthupillai, Raja

2016-03-01

Magnetic resonance elastography (MRE) can estimate liver stiffness (LS) noninvasively. We prospectively assessed whether motion-encoding gradient (MEG) direction, slice position, or high-caloric food intake affects the repeatability of MRE measurements of LS. Twenty healthy volunteers (8 women, 12 men; age, 48 ± 12 years) were imaged in a 3.0T scanner at four timepoints: twice after overnight fasting (B1 , B2 ) and twice after consuming a 1050-calorie standardized meal (A1 , A2 ; after 30 and 60 min, respectively). Each session comprised sequential MRE acquisitions in which MEG was applied in three orthogonal directions with three slices positioned over the liver for each. Between sessions, the participants were repositioned to assess test-retest reproducibility. The LS measurements before/after food intake were 3.36 ± 1.31 kPa/3.22 ± 1.03 kPa, 2.04 ± 0.33 kPa/2.27 ± 0.38 kPa, and 2.47 ± 0.50 kPa/2.64 ± 0.76 kPa for MEG superimposed along the anterior-posterior (AP), foot-head (FH), and right-left (RL) directions, respectively. Before and after food intake, LS estimates were lower and more reproducible (<10% coefficient of variation) when the MEG was in the FH direction, not the AP or RL direction. Liver stiffness estimates were significantly elevated after meal consumption when the MEG was in the FH direction (P < 0.05 for B1 vs. A1 , B1 vs. A2 , B2 vs. A1 , and B2 vs. A2 ). MRE estimates of LS were highly reproducible, particularly when MEG was applied in the FH direction, suggesting that this method could be used for long-term monitoring of antifibrotic therapy without repeated biopsies. High-caloric food intake resulted in slightly elevated LS on MRE. © 2015 Wiley Periodicals, Inc.

Magnetic resonance elastography of the pancreas: Measurement reproducibility and relationship with age.

PubMed

Kolipaka, Arunark; Schroeder, Samuel; Mo, Xiaokui; Shah, Zarine; Hart, Phil A; Conwell, Darwin L

2017-10-01

To determine magnetic resonance elastography (MRE)-derived stiffness of pancreas in healthy volunteers with emphasis on: 1) short term and midterm repeatability; and 2) variance as a function of age. Pancreatic MRE was performed on 22 healthy volunteers (age range:20-64years) in a 3T-scanner. For evaluation of reproducibility of stiffness estimates, the scans were repeated per volunteer on the same day (short term) and one month apart (midterm). MRE wave images were analyzed using 3D inversion to estimate the stiffness of overall pancreas and different anatomic regions (i.e., head, neck, body, and tail). Concordance and Spearman correlation tests were performed to determine reproducibility of stiffness measurements and relationship to age. A strong concordance correlation (ρ c =0.99; p-value<0.001) was found between short term and midterm repeatability pancreatic stiffness measurements. Additionally, the pancreatic stiffness significantly increased with age with good Spearman correlation coefficient (all ρ>0.81; p<0.001). The older age group (>45yrs) had significantly higher stiffness compared to the younger group (≤45yrs) (p<0.001). No significant difference (p>0.05) in stiffness measurements was observed between different anatomical regions of pancreas, except neck stiffness was slightly lower (p<0.012) compared to head and overall pancreas at month 1. MRE-derived pancreatic stiffness measurements are highly reproducible in the short and midterm and increase linearly with age in healthy volunteers. Further studies are needed to examine these effects in patients with various pancreatic diseases to understand potential clinical applications. Copyright © 2017 Elsevier Inc. All rights reserved.

In vivo time-harmonic multifrequency elastography of the human liver

NASA Astrophysics Data System (ADS)

Tzschätzsch, Heiko; Ipek-Ugay, Selcan; Guo, Jing; Streitberger, Kaspar-Josche; Gentz, Enno; Fischer, Thomas; Klaua, Robert; Schultz, Michael; Braun, Jürgen; Sack, Ingolf

2014-04-01

Elastography is capable of noninvasively detecting hepatic fibrosis by imposing mechanical stress and measuring the viscoelastic response in the liver. Magnetic resonance elastography (MRE) relies on time-harmonic vibrations, while most dynamic ultrasound elastography methods employ transient stimulation methods. This study attempts to benefit from the advantages of time-harmonic tissue stimulation, i.e. relative insensitivity to obesity and ascites and mechanical approachability of the entire liver, and the advantages of ultrasound, i.e. time efficiency, low costs, and wide availability, by introducing in vivo time-harmonic elastography (THE) of the human liver using ultrasound and a broad range of harmonic stimulation frequencies. THE employs continuous harmonic shear vibrations at 7 frequencies from 30 to 60 Hz in a single examination and determines the elasticity and the viscosity of the liver from the dispersion of the shear wave speed within the applied frequency range. The feasibility of the method is demonstrated in the livers of eight healthy volunteers and a patient with cirrhosis. Multifrequency MRE at the same drive frequencies was used as elastographic reference method. Similar values of shear modulus and shear viscosity according the Kelvin-Voigt model were obtained by MRE and THE, indicating that the new method is suitable for in vivo quantification of the shear viscoelastic properties of the liver, however, in real-time and at a fraction of the costs of MRE. In conclusion, THE may provide a useful tool for fast assessment of the viscoelastic properties of the liver at low costs and without limitations in obesity, ascites or hemochromatosis.

Effects of frequency- and direction-dependent elastic materials on linearly elastic MRE image reconstructions

NASA Astrophysics Data System (ADS)

Perreard, I. M.; Pattison, A. J.; Doyley, M.; McGarry, M. D. J.; Barani, Z.; Van Houten, E. E.; Weaver, J. B.; Paulsen, K. D.

2010-11-01

The mechanical model commonly used in magnetic resonance elastography (MRE) is linear elasticity. However, soft tissue may exhibit frequency- and direction-dependent (FDD) shear moduli in response to an induced excitation causing a purely linear elastic model to provide an inaccurate image reconstruction of its mechanical properties. The goal of this study was to characterize the effects of reconstructing FDD data using a linear elastic inversion (LEI) algorithm. Linear and FDD phantoms were manufactured and LEI images were obtained from time-harmonic MRE acquisitions with variations in frequency and driving signal amplitude. LEI responses to artificially imposed uniform phase shifts in the displacement data from both purely linear elastic and FDD phantoms were also evaluated. Of the variety of FDD phantoms considered, LEI appeared to tolerate viscoelastic data-model mismatch better than deviations caused by poroelastic and anisotropic mechanical properties in terms of visual image contrast. However, the estimated shear modulus values were substantially incorrect relative to independent mechanical measurements even in the successful viscoelastic cases and the variations in mean values with changes in experimental conditions associated with uniform phase shifts, driving signal frequency and amplitude were unpredictable. Overall, use of LEI to reconstruct data acquired in phantoms with FDD material properties provided biased results under the best conditions and significant artifacts in the worst cases. These findings suggest that the success with which LEI is applied to MRE data in tissue will depend on the underlying mechanical characteristics of the tissues and/or organs systems of clinical interest.

Effects of frequency- and direction-dependent elastic materials on linearly elastic MRE image reconstructions.

PubMed

Perreard, I M; Pattison, A J; Doyley, M; McGarry, M D J; Barani, Z; Van Houten, E E; Weaver, J B; Paulsen, K D

2010-11-21

The mechanical model commonly used in magnetic resonance elastography (MRE) is linear elasticity. However, soft tissue may exhibit frequency- and direction-dependent (FDD) shear moduli in response to an induced excitation causing a purely linear elastic model to provide an inaccurate image reconstruction of its mechanical properties. The goal of this study was to characterize the effects of reconstructing FDD data using a linear elastic inversion (LEI) algorithm. Linear and FDD phantoms were manufactured and LEI images were obtained from time-harmonic MRE acquisitions with variations in frequency and driving signal amplitude. LEI responses to artificially imposed uniform phase shifts in the displacement data from both purely linear elastic and FDD phantoms were also evaluated. Of the variety of FDD phantoms considered, LEI appeared to tolerate viscoelastic data-model mismatch better than deviations caused by poroelastic and anisotropic mechanical properties in terms of visual image contrast. However, the estimated shear modulus values were substantially incorrect relative to independent mechanical measurements even in the successful viscoelastic cases and the variations in mean values with changes in experimental conditions associated with uniform phase shifts, driving signal frequency and amplitude were unpredictable. Overall, use of LEI to reconstruct data acquired in phantoms with FDD material properties provided biased results under the best conditions and significant artifacts in the worst cases. These findings suggest that the success with which LEI is applied to MRE data in tissue will depend on the underlying mechanical characteristics of the tissues and/or organs systems of clinical interest.

DBIO Best Thesis Award: Mechanics, Dynamics, and Organization of the Bacterial Cytoskeleton and Cell Wall

NASA Astrophysics Data System (ADS)

Wang, Siyuan

2012-02-01

Bacteria come in a variety of shapes. While the peptidoglycan (PG) cell wall serves as an exoskeleton that defines the static cell shape, the internal bacterial cytoskeleton mediates cell shape by recruiting PG synthesis machinery and thus defining the pattern of cell-wall synthesis. While much is known about the chemistry and biology of the cytoskeleton and cell wall, much of their biophysics, including essential aspects of the functionality, dynamics, and organization, remain unknown. This dissertation aims to elucidate the detailed biophysical mechanisms of cytoskeleton guided wall synthesis. First, I find that the bacterial cytoskeleton MreB contributes nearly as much to the rigidity of an Escherichia coli cell as the cell wall. This conclusion implies that the cytoskeletal polymer MreB applies meaningful force to the cell wall, an idea favored by theoretical modeling of wall growth, and suggests an evolutionary origin of cytoskeleton-governed cell rigidity. Second, I observe that MreB rotates around the long axis of E. coli, and the motion depends on wall synthesis. This is the first discovery of a cell-wall assembly driven molecular motor in bacteria. Third, I prove that both cell-wall synthesis and the PG network have chiral ordering, which is established by the spatial pattern of MreB. This work links the molecular structure of the cytoskeleton and of the cell wall with organismal-scale behavior. Finally, I develop a mathematical model of cytoskeleton-cell membrane interactions, which explains the preferential orientation of different cytoskeleton components in bacteria.

Changes in nucleoid morphology and origin localization upon inhibition or alteration of the actin homolog, MreB, of Vibrio cholerae.

PubMed

Srivastava, Preeti; Demarre, Gäelle; Karpova, Tatiana S; McNally, James; Chattoraj, Dhruba K

2007-10-01

MreB is an actin homolog required for the morphogenesis of most rod-shaped bacteria and for other functions, including chromosome segregation. In Caulobacter crescentus and Escherichia coli, the protein seems to play a role in the segregation of sister origins, but its role in Bacillus subtilis chromosome segregation is less clear. To help clarify its role in segregation, we have here studied the protein in Vibrio cholerae, whose chromosome I segregates like the one in C. crescentus and whose chromosome II like the one in E. coli or B. subtilis. The properties of Vibrio MreB were similar to those of its homologs in other bacteria in that it formed dynamic helical filaments, was essential for viability, and was inhibited by the drug A22. Wild-type (WT) cells exposed to A22 became spherical and larger. The nucleoids enlarged correspondingly, and the origin positions for both the chromosomes no longer followed any fixed pattern. However, the sister origins separated, unlike the situation in other bacteria. In mutants isolated as A22 resistant, the nucleoids in some cases appeared compacted even when the cell shape was nearly normal. In these cells, the origins of chromosome I were at the distal edges of the nucleoid but not all the way to the poles where they normally reside. The sister origins of chromosome II also separated less. Thus, it appears that the inhibition or alteration of Vibrio MreB can affect both the nucleoid morphology and origin localization.

"FLIPSY"—A New Solvent-Suppression Sequence for Nonexchanging Solutes Offering Improved Integral Accuracy Relative to 1D NOESY

NASA Astrophysics Data System (ADS)

Neuhaus, David; Ismail, Ismail M.; Chung, Chun-Wa

A new method of solvent suppression is described, based on presaturation in combination with volume selection; the name "FLIPSY" is proposed for this sequence. A low-flip-angle pulse is used for excitation, immediately followed by two 180° pulses, each of which is independently phase cycled through Exorcycle. The phase-cycled inversion pulses achieve volume selection in a way similar to the widely used 1D NOESY sequence, thereby largely eliminating any residual "hump" signal from the solvent. The two 180° pulses combine to produce a net 360° rotation for zmagnetization and either a 180° or a 360° rotation for transverse magnetization, depending on the step in the phase cycle. This allows the overall flip angle of the sequence to be controlled by adjusting the length of the initial excitation pulse. It is demonstrated that this property allows one to choose freely a suitable compromise between signal strength and integral accuracy when using FLIPSY, just as when using single-pulse excitation. Such a choice cannot be made when using 1D NOESY, since the effective flip angle in that experiment is always 90°. The application of FLIPSY to recording LC-NMR spectra is demonstrated.

Optimization of identity operation in NMR spectroscopy via genetic algorithm: Application to the TEDOR experiment

NASA Astrophysics Data System (ADS)

Manu, V. S.; Veglia, Gianluigi

2016-12-01

Identity operation in the form of π pulses is widely used in NMR spectroscopy. For an isolated single spin system, a sequence of even number of π pulses performs an identity operation, leaving the spin state essentially unaltered. For multi-spin systems, trains of π pulses with appropriate phases and time delays modulate the spin Hamiltonian to perform operations such as decoupling and recoupling. However, experimental imperfections often jeopardize the outcome, leading to severe losses in sensitivity. Here, we demonstrate that a newly designed Genetic Algorithm (GA) is able to optimize a train of π pulses, resulting in a robust identity operation. As proof-of-concept, we optimized the recoupling sequence in the transferred-echo double-resonance (TEDOR) pulse sequence, a key experiment in biological magic angle spinning (MAS) solid-state NMR for measuring multiple carbon-nitrogen distances. The GA modified TEDOR (GMO-TEDOR) experiment with improved recoupling efficiency results in a net gain of sensitivity up to 28% as tested on a uniformly 13C, 15N labeled microcrystalline ubiquitin sample. The robust identity operation achieved via GA paves the way for the optimization of several other pulse sequences used for both solid- and liquid-state NMR used for decoupling, recoupling, and relaxation experiments.

Operation and beam profiling of an up to 200 kHz pulse-burst laser for Thomson scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, W. C., E-mail: wcyoung2@wisc.edu; Den Hartog, D. J.; Center for Magnetic Self-Organization in Laboratory and Astrophysical Plasmas, University of Wisconsin-Madison, Madison, Wisconsin 53706

2014-11-15

A new, high-repetition rate laser is in development for use on the Thomson scattering diagnostic on the Madison Symmetric Torus. The laser has been tested at a rate of 200 kHz in a pulse-burst operation, producing bursts of 5 pulses above 1.5 J each, while capable of bursts of 17 pulses at 100 kHz. A master oscillator-power amplifier architecture is used with a Nd:YVO{sub 4} oscillator, four Nd:YAG amplifiers, and a Nd:glass amplifier. A radial profile over the pulse sequence is measured by using a set of graphite apertures and an energy meter, showing a change in beam quality overmore » a pulsing sequence.« less

Theoretical investigations of quantum correlations in NMR multiple-pulse spin-locking experiments

NASA Astrophysics Data System (ADS)

Gerasev, S. A.; Fedorova, A. V.; Fel'dman, E. B.; Kuznetsova, E. I.

2018-04-01

Quantum correlations are investigated theoretically in a two-spin system with the dipole-dipole interactions in the NMR multiple-pulse spin-locking experiments. We consider two schemes of the multiple-pulse spin-locking. The first scheme consists of π /2-pulses only and the delays between the pulses can differ. The second scheme contains φ-pulses (0<φ <π ) and has equal delays between them. We calculate entanglement for both schemes for an initial separable state. We show that entanglement is absent for the first scheme at equal delays between π /2-pulses at arbitrary temperatures. Entanglement emerges after several periods of the pulse sequence in the second scheme at φ =π /4 at milliKelvin temperatures. The necessary number of the periods increases with increasing temperature. We demonstrate the dependence of entanglement on the number of the periods of the multiple-pulse sequence. Quantum discord is obtained for the first scheme of the multiple-pulse spin-locking experiment at different temperatures.

Multishot versus Single-Shot Pulse Sequences in Very High Field fMRI: A Comparison Using Retinotopic Mapping

PubMed Central

Gatenby, J. Christopher; Gore, John C.; Tong, Frank

2012-01-01

High-resolution functional MRI is a leading application for very high field (7 Tesla) human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR) and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm) using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR) than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI. PMID:22514646

Multishot versus single-shot pulse sequences in very high field fMRI: a comparison using retinotopic mapping.

PubMed

Swisher, Jascha D; Sexton, John A; Gatenby, J Christopher; Gore, John C; Tong, Frank

2012-01-01

High-resolution functional MRI is a leading application for very high field (7 Tesla) human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR) and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm) using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR) than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.

In vitro selection of single-stranded DNA molecular recognition elements against S. aureus alpha toxin and sensitive detection in human serum.

PubMed

Hong, Ka L; Battistella, Luisa; Salva, Alysia D; Williams, Ryan M; Sooter, Letha J

2015-01-27

Alpha toxin is one of the major virulence factors secreted by Staphylococcus aureus, a bacterium that is responsible for a wide variety of infections in both community and hospital settings. Due to the prevalence of S. aureus related infections and the emergence of methicillin-resistant S. aureus, rapid and accurate diagnosis of S. aureus infections is crucial in benefiting patient health outcomes. In this study, a rigorous Systematic Evolution of Ligands by Exponential Enrichment (SELEX) variant previously developed by our laboratory was utilized to select a single-stranded DNA molecular recognition element (MRE) targeting alpha toxin with high affinity and specificity. At the end of the 12-round selection, the selected MRE had an equilibrium dissociation constant (Kd) of 93.7 ± 7.0 nM. Additionally, a modified sandwich enzyme-linked immunosorbent assay (ELISA) was developed by using the selected ssDNA MRE as the toxin-capturing element and a sensitive detection of 200 nM alpha toxin in undiluted human serum samples was achieved.

A forward chemical genetic screen reveals an inhibitor of the Mre11–Rad50–Nbs1 complex

PubMed Central

Dupré, Aude; Boyer-Chatenet, Louise; Sattler, Rose M; Modi, Ami P; Lee, Ji-Hoon; Nicolette, Matthew L; Kopelovich, Levy; Jasin, Maria; Baer, Richard; Paull, Tanya T; Gautier, Jean

2009-01-01

The MRN (Mre11-Rad50-Nbs1)-ATM (ataxia-telangiectasia mutated) pathway is essential for sensing and signaling from DNA double-strand breaks. The MRN complex acts as a DNA damage sensor, maintains genome stability during DNA replication, promotes homology-dependent DNA repair and activates ATM. MRN is essential for cell viability, which has limited functional studies of the complex. Small-molecule inhibitors of MRN could circumvent this experimental limitation and could also be used as cellular radio- and chemosensitization compounds. Using cell-free systems that recapitulate faithfully the MRN-ATM signaling pathway, we designed a forward chemical genetic screen to identify inhibitors of the pathway, and we isolated Z-5-(4-hydroxybenzylidene)-2-imino-1,3-thiazolidin-4-one (mirin, 1) as an inhibitor of MRN. Mirin prevents MRN-dependent activation of ATM without affecting ATM protein kinase activity, and it inhibits Mre11-associated exonuclease activity. Consistent with its ability to target the MRN complex, mirin abolishes the G2/M checkpoint and homology-dependent repair in mammalian cells. PMID:18176557

Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles

NASA Astrophysics Data System (ADS)

Shih, Yu-Ling; Le, Trung; Rothfield, Lawrence

2003-06-01

The MinCDE proteins of Escherichia coli are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the E. coli MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in Bacillus subtilis. The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in E. coli and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.

A Parametric Sizing Model for Molten Regolith Electrolysis Reactors to Produce Oxygen from Lunar Regolith

NASA Technical Reports Server (NTRS)

Schreiner, Samuel S.; Dominguez, Jesus A.; Sibille, Laurent; Hoffman, Jeffrey A.

2015-01-01

We present a parametric sizing model for a Molten Electrolysis Reactor that produces oxygen and molten metals from lunar regolith. The model has a foundation of regolith material properties validated using data from Apollo samples and simulants. A multiphysics simulation of an MRE reactor is developed and leveraged to generate a vast database of reactor performance and design trends. A novel design methodology is created which utilizes this database to parametrically design an MRE reactor that 1) can sustain the required mass of molten regolith, current, and operating temperature to meet the desired oxygen production level, 2) can operate for long durations via joule heated, cold wall operation in which molten regolith does not touch the reactor side walls, 3) can support a range of electrode separations to enable operational flexibility. Mass, power, and performance estimates for an MRE reactor are presented for a range of oxygen production levels. The effects of several design variables are explored, including operating temperature, regolith type/composition, batch time, and the degree of operational flexibility.

Methods for magnetic resonance analysis using magic angle technique

DOEpatents

Hu, Jian Zhi [Richland, WA; Wind, Robert A [Kennewick, WA; Minard, Kevin R [Kennewick, WA; Majors, Paul D [Kennewick, WA

2011-11-22

Methods of performing a magnetic resonance analysis of a biological object are disclosed that include placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. In particular embodiments the method includes pulsing the radio frequency to provide at least two of a spatially selective read pulse, a spatially selective phase pulse, and a spatially selective storage pulse. Further disclosed methods provide pulse sequences that provide extended imaging capabilities, such as chemical shift imaging or multiple-voxel data acquisition.

Relaxation time estimation in surface NMR

DOEpatents

Grunewald, Elliot D.; Walsh, David O.

2017-03-21

NMR relaxation time estimation methods and corresponding apparatus generate two or more alternating current transmit pulses with arbitrary amplitudes, time delays, and relative phases; apply a surface NMR acquisition scheme in which initial preparatory pulses, the properties of which may be fixed across a set of multiple acquisition sequence, are transmitted at the start of each acquisition sequence and are followed by one or more depth sensitive pulses, the pulse moments of which are varied across the set of multiple acquisition sequences; and apply processing techniques in which recorded NMR response data are used to estimate NMR properties and the relaxation times T.sub.1 and T.sub.2* as a function of position as well as one-dimensional and two-dimension distributions of T.sub.1 versus T.sub.2* as a function of subsurface position.

Current density imaging sequence for monitoring current distribution during delivery of electric pulses in irreversible electroporation.

PubMed

Serša, Igor; Kranjc, Matej; Miklavčič, Damijan

2015-01-01

Electroporation is gaining its importance in everyday clinical practice of cancer treatment. For its success it is extremely important that coverage of the target tissue, i.e. treated tumor, with electric field is within the specified range. Therefore, an efficient tool for the electric field monitoring in the tumor during delivery of electroporation pulses is needed. The electric field can be reconstructed by the magnetic resonance electric impedance tomography method from current density distribution data. In this study, the use of current density imaging with MRI for monitoring current density distribution during delivery of irreversible electroporation pulses was demonstrated. Using a modified single-shot RARE sequence, where four 3000 V and 100 μs long pulses were included at the start, current distribution between a pair of electrodes inserted in a liver tissue sample was imaged. Two repetitions of the sequence with phases of refocusing radiofrequency pulses 90° apart were needed to acquire one current density image. For each sample in total 45 current density images were acquired to follow a standard protocol for irreversible electroporation where 90 electric pulses are delivered at 1 Hz. Acquired current density images showed that the current density in the middle of the sample increased from first to last electric pulses by 60%, i.e. from 8 kA/m2 to 13 kA/m2 and that direction of the current path did not change with repeated electric pulses significantly. The presented single-shot RARE-based current density imaging sequence was used successfully to image current distribution during delivery of short high-voltage electric pulses. The method has a potential to enable monitoring of tumor coverage by electric field during irreversible electroporation tissue ablation.

Comparison of pulse sequences for R1-based electron paramagnetic resonance oxygen imaging.

PubMed

Epel, Boris; Halpern, Howard J

2015-05-01

Electron paramagnetic resonance (EPR) spin-lattice relaxation (SLR) oxygen imaging has proven to be an indispensable tool for assessing oxygen partial pressure in live animals. EPR oxygen images show remarkable oxygen accuracy when combined with high precision and spatial resolution. Developing more effective means for obtaining SLR rates is of great practical, biological and medical importance. In this work we compared different pulse EPR imaging protocols and pulse sequences to establish advantages and areas of applicability for each method. Tests were performed using phantoms containing spin probes with oxygen concentrations relevant to in vivo oxymetry. We have found that for small animal size objects the inversion recovery sequence combined with the filtered backprojection reconstruction method delivers the best accuracy and precision. For large animals, in which large radio frequency energy deposition might be critical, free induction decay and three pulse stimulated echo sequences might find better practical usage. Copyright © 2015 Elsevier Inc. All rights reserved.

20-Hz pulses and other vocalizations of fin whales, Balaenoptera physalus, in the Gulf of California, Mexico.

PubMed

Thompson, P O; Findley, L T; Vidal, O

1992-12-01

Low-frequency vocalizations were recorded from fin whales, Balaenoptera physalus, in the Gulf of California, Mexico, during three cruises. In March 1985, recorded 20-Hz pulses were in sequences of regular 9-s interpulse intervals. In August 1987, nearly all were in sequences of doublets with alternating 5- and 18-s interpulse intervals. No 20-Hz pulse sequences of any kind were detected in February 1987. The typical pulse modulated from 42 to 20 Hz and its median duration was 0.7 s (1985 data). Most other fin whale sounds were also short tonal pulses averaging 82, 56, and 68 Hz, respectively, for the three cruises; 89% were modulated in frequency, mostly downward. Compared to Atlantic and Pacific Ocean regions, Gulf of California 20-Hz pulses were unique in terms of frequency modulation, interpulse sound levels, and temporal patterns. Fin whales in the Gulf may represent a regional stock revealed by their sound characteristics, a phenomenon previously shown for humpback whales, birds, and fish. Regional differences in fin whale sounds were found in comparisons of Atlantic and Pacific locations.

The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

PubMed Central

Li, Shihong; Chang, Eric Y.; Bae, Won C.; Chung, Christine B.; Hua, Yanqing; Zhou, Yi; Du, Jiang

2014-01-01

Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal models were utilized to calculate the T2*s and/or relative fractions of short and long T2*s. Results: For all bone samples UTE T2* signal decay showed bicomponent behavior. A higher short T2* fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2* fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2* fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2* components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2*s and relative fractions can be assessed using UTE bicomponent analysis. Long T2* components are affected more by long T2 saturation and IR pulses, and short T2* components are affected more by fat saturation pulses. PMID:24506644

The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shihong; Department of Radiology, Hua Dong Hospital, Fudan University, Shanghai 200040; Yancheng Medical College, Jiangsu

Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal modelsmore » were utilized to calculate the T2{sup *}s and/or relative fractions of short and long T2{sup *}s. Results: For all bone samples UTE T2{sup *} signal decay showed bicomponent behavior. A higher short T2{sup *} fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2{sup *} fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2{sup *} fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2{sup *} components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2{sup *}s and relative fractions can be assessed using UTE bicomponent analysis. Long T2{sup *} components are affected more by long T2 saturation and IR pulses, and short T2{sup *} components are affected more by fat saturation pulses.« less

Superconductivity achieved at over liquid nitrogen temperature by (mixed rare earths)-Ba-Cu oxides

NASA Astrophysics Data System (ADS)

Kishio, Kohji; Kuwahara, Kazuyuki; Kitazawa, Koichi; Fueki, Kazuo; Nakamura, Osamu

1987-05-01

Superconducting oxides were fabricated by reaction of powders of BaCO3, CuO and mixed rare earth (RE) carbonates at compositions expressed as (RE)1Ba2Cu3O(9-y). Two types of incompletely separated raw materials of mixed rare earths, namely, heavy rare earths (HRE) and medium rare earths (MRE), were examined. The zero-resistivity critical temperatures were observed at 92.5 K for the (HRE)-Ba-Cu-O and 85.0 K for the (MRE)-Ba-Cu-O systems, respectively, both of which were well above the boiling point of liquid nitrogen.

A method to synchronize signals from multiple patient monitoring devices through a single input channel for inclusion in list-mode acquisitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

O’Connor, J. Michael; Pretorius, P. Hendrik; Johnson, Karen

2013-12-15

Purpose: This technical note documents a method that the authors developed for combining a signal to synchronize a patient-monitoring device with a second physiological signal for inclusion into list-mode acquisition. Our specific application requires synchronizing an external patient motion-tracking system with a medical imaging system by multiplexing the tracking input with the ECG input. The authors believe that their methodology can be adapted for use in a variety of medical imaging modalities including single photon emission computed tomography (SPECT) and positron emission tomography (PET). Methods: The authors insert a unique pulse sequence into a single physiological input channel. This sequencemore » is then recorded in the list-mode acquisition along with the R-wave pulse used for ECG gating. The specific form of our pulse sequence allows for recognition of the time point being synchronized even when portions of the pulse sequence are lost due to collisions with R-wave pulses. This was achieved by altering our software used in binning the list-mode data to recognize even a portion of our pulse sequence. Limitations on heart rates at which our pulse sequence could be reliably detected were investigated by simulating the mixing of the two signals as a function of heart rate and time point during the cardiac cycle at which our pulse sequence is mixed with the cardiac signal. Results: The authors have successfully achieved accurate temporal synchronization of our motion-tracking system with acquisition of SPECT projections used in 17 recent clinical research cases. In our simulation analysis the authors determined that synchronization to enable compensation for body and respiratory motion could be achieved for heart rates up to 125 beats-per-minute (bpm). Conclusions: Synchronization of list-mode acquisition with external patient monitoring devices such as those employed in motion-tracking can reliably be achieved using a simple method that can be implemented using minimal external hardware and software modification through a single input channel, while still recording cardiac gating signals.« less

Cardiovascular magnetic resonance physics for clinicians: part II

PubMed Central

2012-01-01

This is the second of two reviews that is intended to cover the essential aspects of cardiovascular magnetic resonance (CMR) physics in a way that is understandable and relevant to clinicians using CMR in their daily practice. Starting with the basic pulse sequences and contrast mechanisms described in part I, it briefly discusses further approaches to accelerate image acquisition. It then continues by showing in detail how the contrast behaviour of black blood fast spin echo and bright blood cine gradient echo techniques can be modified by adding rf preparation pulses to derive a number of more specialised pulse sequences. The simplest examples described include T2-weighted oedema imaging, fat suppression and myocardial tagging cine pulse sequences. Two further important derivatives of the gradient echo pulse sequence, obtained by adding preparation pulses, are used in combination with the administration of a gadolinium-based contrast agent for myocardial perfusion imaging and the assessment of myocardial tissue viability using a late gadolinium enhancement (LGE) technique. These two imaging techniques are discussed in more detail, outlining the basic principles of each pulse sequence, the practical steps required to achieve the best results in a clinical setting and, in the case of perfusion, explaining some of the factors that influence current approaches to perfusion image analysis. The key principles of contrast-enhanced magnetic resonance angiography (CE-MRA) are also explained in detail, especially focusing on timing of the acquisition following contrast agent bolus administration, and current approaches to achieving time resolved MRA. Alternative MRA techniques that do not require the use of an endogenous contrast agent are summarised, and the specialised pulse sequence used to image the coronary arteries, using respiratory navigator gating, is described in detail. The article concludes by explaining the principle behind phase contrast imaging techniques which create images that represent the phase of the MR signal rather than the magnitude. It is shown how this principle can be used to generate velocity maps by designing gradient waveforms that give rise to a relative phase change that is proportional to velocity. Choice of velocity encoding range and key pitfalls in the use of this technique are discussed. PMID:22995744

Romanian MRE Rocket Engines Program - An Early Endeavor

NASA Astrophysics Data System (ADS)

Rugescu, R. E.

2002-01-01

(MRE) was initiated in the years '60 of the past century at the Chair of Aerospace Sciences "Elie Carafoli" from the "Politehnica" University in Bucharest (PUB). Consisting of theoretical and experimental investigations in the form of computational methods and technological solutions for small size MRE-s and the concept of the test stand for these engines, the program ended in the construction of the first Romanian liquid rocket motors. Hermann Oberth and Dorin Pavel, were known from 1923, no experimental practice was yet tempted, at the time level of 1960. It was the intention of the developers at PUB to cover this gap and initiate a feasible, low-cost, demonstrative program of designing and testing experimental models of MRE. The research program was oriented towards future development of small size space carrier vehicles for scientific applications only, as an independent program with no connection to other defense programs imagined by the authorities in Bucharest, at that time. Consequently the entire financial support was assured by "Politehnica" university. computerized methods in the thermochemistry of heterogeneous combustion, for both steady and unsteady flows with chemical reactions and two phase flows. The research was gradually extended to the production of a professional CAD program for steady-state heat transfer simulations and the loading capacity analyses of the double wall, cooled thrust chamber. The resulting computer codes were run on a 360-30 IMB machine, beginning in 1968. Some of the computational methods were first exposed at the 9th International Conference on Applied Mechanics, held in Bucharest between June 23-27, 1969. hot testing of a series of storable propellant, variable thrust, variable geometry, liquid rocket motors, with a maximal thrust of 200N. A remotely controlled, portable test bad, actuated either automatically or manually and consisting of a 6-modules construction was built for this motor series, with a simple 8 analog-channel and 5 digital-channel data measuring and recording system. The first hot test firing of the MRE-1B motor took place successfully on April 9th, 1969 in Bucharest, at the "Elie Carafoli" Chair of UPB. The research program continued with the development of a series of solid, double base propellant rocket and ram-rocket motors, with emphasize on the optimization of the gasdynamic contour of the engine, in order to increase the flight performances. Increments of up to 8% in specific thrust were measured on the test stand, with mass savings and no extra costs. The test firing of the first Romanian, air-breathing ram-rocket engine took place successfully in august 1987 at the Chemical Works in Fagaras, Romania. Astronautics", founded in Bucharest. The principles and history of the "MRE" research program are presented in the proposed paper.

B1 gradient coherence selection using a tapered stripline.

PubMed

van Meerten, S G J; Tijssen, K C H; van Bentum, P J M; Kentgens, A P M

2018-01-01

Pulsed-field gradients are common in modern liquid state NMR pulse sequences. They are often used instead of phase cycles for the selection of coherence pathways, thereby decreasing the time required for the NMR experiment. Soft off-resonance pulses with a B 1 gradient result in a spatial encoding similar to that created by pulsed-field (B 0 ) gradients. In this manuscript we show that pulse sequences with pulsed-field gradients can easily be converted to one which uses off-resonance B 1 field gradient (OFFBEAT) pulses. The advantage of B 1 gradient pulses for coherence selection is that the chemical shift evolution during the pulses is (partially) suppressed. Therefore no refocusing echos are required to correct for evolution during the gradient pulses. A tapered stripline is shown to be a convenient tool for creating a well-defined gradient in the B 1 field strength. B 1 gradient coherence selection using a tapered stripline is a simple and cheap alternative to B 0 pulsed-field gradients. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Method and apparatus for characterizing reflected ultrasonic pulses

NASA Technical Reports Server (NTRS)

Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor)

1991-01-01

The invention is a method of and apparatus for characterizing the amplitudes of a sequence of reflected pulses R1, R2, and R3 by converting them into corresponding electric signals E1, E2, and E3 to substantially the same value during each sequence thereby restoring the reflected pulses R1, R2, and R3 to their initial reflection values by timing means, an exponential generator, and a time gain compensator. Envelope and baseline reject circuits permit the display and accurate location of the time spaced sequence of electric signals having substantially the same amplitude on a measurement scale on a suitable video display or oscilloscope.

Femtosecond laser-induced periodic surface structures on silicon upon polarization controlled two-color double-pulse irradiation.

PubMed

Höhm, Sandra; Herzlieb, Marcel; Rosenfeld, Arkadi; Krüger, Jörg; Bonse, Jörn

2015-01-12

Two-color double-fs-pulse experiments were performed on silicon wafers to study the temporally distributed energy deposition in the formation of laser-induced periodic surface structures (LIPSS). A Mach-Zehnder interferometer generated parallel or cross-polarized double-pulse sequences at 400 and 800 nm wavelength, with inter-pulse delays up to a few picoseconds between the sub-ablation 50-fs-pulses. Multiple two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample. The resulting LIPSS characteristics (periods, areas) were analyzed by scanning electron microscopy. A wavelength-dependent plasmonic mechanism is proposed to explain the delay-dependence of the LIPSS. These two-color experiments extend previous single-color studies and prove the importance of the ultrafast energy deposition for LIPSS formation.

Programmable Pulse Generator

NASA Technical Reports Server (NTRS)

Rhim, W. K.; Dart, J. A.

1982-01-01

New pulse generator programmed to produce pulses from several ports at different pulse lengths and intervals and virtually any combination and sequence. Unit contains a 256-word-by-16-bit memory loaded with instructions either manually or by computer. Once loaded, unit operates independently of computer.

Passive and active pulse stacking scheme for pulse shaping

DOEpatents

Harney, Robert C.; Schipper, John F.

1977-01-01

Apparatus and method for producing a sequence of radiation pulses with a pulse envelope of time variation which is controllable by an external electromagnetic signal applied to an active medium or by a sectored reflector, through which the radiation passes.

The set of triple-resonance sequences with a multiple quantum coherence evolution period

NASA Astrophysics Data System (ADS)

Koźmiński, Wiktor; Zhukov, Igor

2004-12-01

The new pulse sequence building block that relies on evolution of heteronuclear multiple quantum coherences is proposed. The particular chemical shifts are obtained in multiple quadrature, using linear combinations of frequencies taken from spectra measured at different quantum levels. The pulse sequences designed in this way consist of small number of RF-pulses, are as short as possible, and could be applied for determination of coupling constants. The examples presented involve 2D correlations H NCO, H NCA, H N(CO) CA, and H(N) COCA via heteronuclear zero and double coherences, as well as 2D H NCOCA technique with simultaneous evolution of triple and three distinct single quantum coherences. Applications of the new sequences are presented for 13C, 15N-labeled ubiquitin.

Magnetic resonance assessment of parenchymal elasticity in normal and edematous, ventilator-injured lung.

PubMed

McGee, Kiaran P; Mariappan, Yogesh K; Hubmayr, Rolf D; Carter, Rickey E; Bao, Zhonghao; Levin, David L; Manduca, Armando; Ehman, Richard L

2012-08-15

Magnetic resonance elastography (MRE) is a MR imaging method capable of spatially resolving the intrinsic mechanical properties of normal lung parenchyma. We tested the hypothesis that the mechanical properties of edematous lung exhibit local properties similar to those of a fluid-filled lung at transpulmonary pressures (P(tp)) up to 25 cm H(2)O. Pulmonary edema was induced in anesthetized female adult Sprague-Dawley rats by mechanical ventilation to a pressure of 40 cm H(2)O for ≈ 30 min. Prior to imaging the wet weight of each ex vivo lung set was measured. MRE, high-resolution T(1)-weighted spin echo and T(2)* gradient echo data were acquired at each P(tp) for both normal and injured ex vivo lungs. At P(tp)s of 6 cm H(2)O and greater, the shear stiffness of normal lungs was greater than injured lungs (P ≤ 0.0003). For P(tp)s up to 12 cm H(2)O, shear stiffness was equal to 1.00, 1.07, 1.16, and 1.26 kPa for the injured and 1.31, 1.89, 2.41, and 2.93 kPa for normal lungs at 3, 6, 9, and 12 cm H(2)O, respectively. For injured lungs MRE magnitude signal and shear stiffness within regions of differing degrees of alveolar flooding were calculated as a function of P(tp). Differences in shear stiffness were statistically significant between groups (P < 0.001) with regions of lower magnitude signal being stiffer than those of higher signal. These data demonstrate that when the alveolar space filling material is fluid, MRE-derived parenchymal shear stiffness of the lung decreases, and the lung becomes inherently softer compared with normal lung.

Prediction of major complications after hepatectomy using liver stiffness values determined by magnetic resonance elastography.

PubMed

Sato, N; Kenjo, A; Kimura, T; Okada, R; Ishigame, T; Kofunato, Y; Shimura, T; Abe, K; Ohira, H; Marubashi, S

2018-04-23

Liver fibrosis is a risk factor for hepatectomy but cannot be determined accurately before hepatectomy because diagnostic procedures are too invasive. Magnetic resonance elastography (MRE) can determine liver stiffness (LS), a surrogate marker for assessing liver fibrosis, non-invasively. The aim of this study was to investigate whether the LS value determined by MRE is predictive of major complications after hepatectomy. This prospective study enrolled consecutive patients who underwent hepatic resection between April 2013 and August 2016. LS values were measured by imaging shear waves by MRE in the liver before hepatectomy. The primary endpoint was major complications, defined as Clavien-Dindo grade IIIa or above. Logistic regression analysis identified independent predictive factors, from which a logistic model to estimate the probability of major complications was constructed. A total of 96 patients were included in the study. Major complications were observed in 15 patients (16 per cent). Multivariable logistic analysis confirmed that higher LS value (P = 0·021) and serum albumin level (P = 0·009) were independent predictive factors for major complications after hepatectomy. Receiver operating characteristic (ROC) analysis showed that the best LS cut-off value was 4·3 kPa for detecting major complications, comparable to liver fibrosis grade F4, with a sensitivity of 80 per cent and specificity of 82 per cent. A logistic model using the LS value and serum albumin level to estimate the probability of major complications was constructed; the area under the ROC curve for predicting major complications was 0·84. The LS value determined by MRE in patients undergoing hepatectomy was an independent predictive factor for major complications. © 2018 BJS Society Ltd Published by John Wiley & Sons Ltd.

Assessment of Activity of Crohn Disease by Diffusion-Weighted Magnetic Resonance Imaging

PubMed Central

Li, Xue-hua; Sun, Can-hui; Mao, Ren; Zhang, Zhong-wei; Jiang, Xiao-song; Pui, Margaret H.; Chen, Min-hu; Li, Zi-ping

2015-01-01

Abstract To assess the diagnostic efficacy of diffusion-weighted MR imaging (DWI) for evaluating inflammatory activity in patients with Crohn's disease (CD). A total of 47 CD patients underwent MR enterography (MRE) and DWI using 3 b values of 50, 400, and 800 s/mm.2 Apparent diffusion coefficients (ADCs) of inflamed and normal bowel wall were calculated. The conventional MRE findings and DWI signal intensities were qualitatively scored from 0 to 3. The correlation between Crohn disease activity index (CDAI) and both ADCs and magnetic resonance imaging scores was analyzed. Receiver-operating characteristic curve analysis was used to determine the diagnostic accuracy of CD activity. Of the 47 patients, 25 were active CD (CDAI≥150) and 22 were inactive (CDAI<150). Diffusion-weighted MR imaging and MRE + DWI scores of active CD were significantly higher than that of inactive CD (both P < 0.001). Apparent diffusion coefficients in inflamed segments of active CD were lower than that of inactive CD (P < 0.001). The DWI scores (r = 0.74, P < 0.001), ADCs (r = −0.71, P < 0.001), MRE scores (r = 0.54, P < 0.001), and MRE + DWI scores (r = 0.66, P < 0.001) were all correlated with CDAI. The areas under the receiver-operating characteristics curves for ADCs, DWI scores, MRE scores, and MRE + DWI scores ranged from 0.83 to 0.98. The threshold ADC value of 1.17 × 10−3 mm2/s allowed differentiation of active from inactive CD with 100% sensitivity and 88% specificity. Diffusion-weighted MR imaging and ADC correlated with CD activity, and had excellent diagnostic accuracy for differentiating active from inactive CD. PMID:26512584

Increased Prevalence of Luminal Narrowing and Stricturing Identified by Enterography in Pediatric Crohn Disease Patients with Elevated Granulocyte-Macrophage Colony Stimulating Factor Auto-antibodies

PubMed Central

Dykes, Dana M.H.; Towbin, Alexander J.; Bonkowski, Erin; Chalk, Claudia; Bezold, Ramona; Lake, Kathleen; Kim, Mi-Ok; Heubi, James E.; Trapnell, Bruce C.; Podberesky, Daniel J.; Denson, Lee A.

2013-01-01

Background Crohn disease (CD) patients with elevated Granulocyte-Macrophage Colony-Stimulating Factor auto-antibodies (GM-CSF Ab) are more likely to develop stricturing behavior requiring surgery. Computed Tomography or Magnetic Resonance Enterography (CTE or MRE) may detect luminal narrowing (LN) prior to stricture development. Objective To determine whether CD patients with elevated GM-CSF Ab (≥ 1.6 mcg/mL) have a higher prevalence of LN and stricturing on CTE or MRE. Methods A single center, cross-sectional study of 153 pediatric CD patients and controls undergoing CTE or MRE. A novel scoring system evaluated for disease activity, presence of LN, stricture, intra-abdominal abscess, or fistulae Ouutcomes were compared with respect to antibody status using Fisher's exact test, logistic regression, and the unpaired t-test. Results GM-CSF Ab were elevated in CD patients (n=114) with a median (IQR) GM-CSF Ab level of 2.3 mcg/mL (0.5, 6.6) compared with healthy and disease controls, p=0.001. Ileal disease location was more common in CD patients with high GM-CSF Ab, p<0.001. Luminal narrowing increased from 39% in CD patients with low GM-CSF Ab to 71% in those with high levels (p=0.004). High GM-CSF Ab remained significantly associated with LN in a multivariate logistic model. Stricturing increased from 4% in CD patients with low GM-CSF Ab to 19% in those with high GM-CSF Ab (p=0.03). Conclusions Pediatric CD patients with high GM-CSF Ab levels have a higher prevalence of LN on CTE or MRE. Further study will be needed to determine whether medical therapy will reduce progression to stricturing behavior in these patients. PMID:23893081

Molecular Basis for Glucocorticoid Induction of the Krüppel-Like Factor 9 Gene in Hippocampal Neurons

PubMed Central

Bagamasbad, Pia; Ziera, Tim; Borden, Steffen A.; Bonett, Ronald M.; Rozeboom, Aaron M.; Seasholtz, Audrey

2012-01-01

Stress has complex effects on hippocampal structure and function, which consequently affects learning and memory. These effects are mediated in part by circulating glucocorticoids (GC) acting via the intracellular GC receptor (GR) and mineralocorticoid receptor (MR). Here, we investigated GC regulation of Krüppel-like factor 9 (KLF9), a transcription factor implicated in neuronal development and plasticity. Injection of corticosterone (CORT) in postnatal d 6 and 30 mice increased Klf9 mRNA and heteronuclear RNA by 1 h in the hippocampal region. Treatment of the mouse hippocampal cell line HT-22 with CORT caused a time- and dose-dependent increase in Klf9 mRNA. The CORT induction of Klf9 was resistant to protein synthesis inhibition, suggesting that Klf9 is a direct CORT-response gene. In support of this hypothesis, we identified two GR/MR response elements (GRE/MRE) located −6.1 and −5.3 kb relative to the transcription start site, and we verified their functionality by enhancer-reporter, gel shift, and chromatin immunoprecipitation assays. The −5.3-kb GRE/MRE is largely conserved across tetrapods, but conserved orthologs of the −6.1-kb GRE/MRE were only detected in therian mammals. GC treatment caused recruitment of the GR, histone hyperacetylation, and nucleosome removal at Klf9 upstream regions. Our findings support a predominant role for GR, with a minor contribution of MR, in the direct regulation of Klf9 acting via two GRE/MRE located in the 5′-flanking region of the gene. KLF9 may play a key role in GC actions on hippocampal development and plasticity. PMID:22962255

Comparison of 3% sorbitol vs psyllium fibre as oral contrast agents in MR enterography.

PubMed

Saini, Sidharth; Colak, Errol; Anthwal, Shalini; Vlachou, Paraskevi A; Raikhlin, Antony; Kirpalani, Anish

2014-10-01

To compare the degree of small bowel distension achieved by 3% sorbitol, a high osmolarity solution, and a psyllium-based bulk fibre as oral contrast agents (OCAs) in MR enterography (MRE). This retrospective study was approved by our institutional review board. A total of 45 consecutive normal MRE examinations (sorbitol, n = 20; psyllium, n = 25) were reviewed. The patients received either 1.5 l of 3% sorbitol or 2 l of 1.6 g kg(-1) psyllium prior to imaging. Quantitative small bowel distension measurements were taken in five segments: proximal jejunum, distal jejunum, proximal ileum, distal ileum and terminal ileum by two independent radiologists. Distension in these five segments was also qualitatively graded from 0 (very poor) to 4 (excellent) by two additional independent radiologists. Statistical analysis comparing the groups and assessing agreement included intraclass coefficients, Student's t-test and Mann-Whitney U-test. Small bowel distension was not significantly different in any of the five small bowel segments between the use of sorbitol and psyllium as OCAs in both the qualitative (p = 0.338-0.908) and quantitative assessments (p = 0.083-0.856). The mean bowel distension achieved was 20.1 ± 2.2 mm for sorbitol and 19.8 ± 2.5 mm for psyllium (p = 0.722). Visualization of the ileum was good or excellent in 65% of the examinations in both groups. Sorbitol and psyllium are not significantly different at distending the small bowel and both may be used as OCAs for MRE studies. This is the first study to directly compare the degree of distension in MRE between these two common, readily available and inexpensive OCAs.

Adeno-associated virus inverted terminal repeats stimulate gene editing.

PubMed

Hirsch, M L

2015-02-01

Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repeat (ITR) into the egfp gene. Compared with a non-structured DNA control sequence, the ITR induced DNA damage as evidenced by increased gamma-H2AX and Mre11 foci formation. As local DNA damage stimulates HR, ITR-mediated gene editing was investigated using DNA oligonucleotides as repair substrates. The AAV ITR stimulated gene editing >1000-fold in a replication-independent manner and was not biased by the polarity of the repair oligonucleotide. Analysis of additional human DNA sequences demonstrated stimulation of gene editing to varying degrees. In particular, inverted yet not direct, Alu repeats induced gene editing, suggesting a role for DNA structure in the repair event. Collectively, the results demonstrate that inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences.

Compressed Sensing SEMAC: 8-fold Accelerated High Resolution Metal Artifact Reduction MRI of Cobalt-Chromium Knee Arthroplasty Implants.

PubMed

Fritz, Jan; Ahlawat, Shivani; Demehri, Shadpour; Thawait, Gaurav K; Raithel, Esther; Gilson, Wesley D; Nittka, Mathias

2016-10-01

The aim of this study was to prospectively test the hypothesis that a compressed sensing-based slice encoding for metal artifact correction (SEMAC) turbo spin echo (TSE) pulse sequence prototype facilitates high-resolution metal artifact reduction magnetic resonance imaging (MRI) of cobalt-chromium knee arthroplasty implants within acquisition times of less than 5 minutes, thereby yielding better image quality than high-bandwidth (BW) TSE of similar length and similar image quality than lengthier SEMAC standard of reference pulse sequences. This prospective study was approved by our institutional review board. Twenty asymptomatic subjects (12 men, 8 women; mean age, 56 years; age range, 44-82 years) with total knee arthroplasty implants underwent MRI of the knee using a commercially available, clinical 1.5 T MRI system. Two compressed sensing-accelerated SEMAC prototype pulse sequences with 8-fold undersampling and acquisition times of approximately 5 minutes each were compared with commercially available high-BW and SEMAC pulse sequences with acquisition times of approximately 5 minutes and 11 minutes, respectively. For each pulse sequence type, sagittal intermediate-weighted (TR, 3750-4120 milliseconds; TE, 26-28 milliseconds; voxel size, 0.5 × 0.5 × 3 mm) and short tau inversion recovery (TR, 4010 milliseconds; TE, 5.2-7.5 milliseconds; voxel size, 0.8 × 0.8 × 4 mm) were acquired. Outcome variables included image quality, display of the bone-implant interfaces and pertinent knee structures, artifact size, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). Statistical analysis included Friedman, repeated measures analysis of variances, and Cohen weighted k tests. Bonferroni-corrected P values of 0.005 and less were considered statistically significant. Image quality, bone-implant interfaces, anatomic structures, artifact size, SNR, and CNR parameters were statistically similar between the compressed sensing-accelerated SEMAC prototype and SEMAC commercial pulse sequences. There was mild blur on images of both SEMAC sequences when compared with high-BW images (P < 0.001), which however did not impair the assessment of knee structures. Metal artifact reduction and visibility of central knee structures and bone-implant interfaces were good to very good and significantly better on both types of SEMAC than on high-BW images (P < 0.004). All 3 pulse sequences showed peripheral structures similarly well. The implant artifact size was 46% to 51% larger on high-BW images when compared with both types of SEMAC images (P < 0.0001). Signal-to-noise ratios and CNRs of fat tissue, tendon tissue, muscle tissue, and fluid were statistically similar on intermediate-weighted MR images of all 3 pulse sequence types. On short tau inversion recovery images, the SNRs of tendon tissue and the CNRs of fat and fluid, fluid and muscle, as well as fluid and tendon were significantly higher on SEMAC and compressed sensing SEMAC images (P < 0.005, respectively). We accept the hypothesis that prospective compressed sensing acceleration of SEMAC is feasible for high-quality metal artifact reduction MRI of cobalt-chromium knee arthroplasty implants in less than 5 minutes and yields better quality than high-BW TSE and similarly high quality than lengthier SEMAC pulse sequences.

Phase coded, micro-power impulse radar motion sensor

DOEpatents

McEwan, Thomas E.

1996-01-01

A motion sensing, micro-power impulse radar MIR impresses on the transmitted signal, or the received pulse timing signal, one or more frequencies lower than the pulse repetition frequency, that become intermediate frequencies in a "IF homodyne" receiver. Thus, many advantages of classical RF receivers can be thereby be realized with ultra-wide band radar. The sensor includes a transmitter which transmits a sequence of electromagnetic pulses in response to a transmit timing signal at a nominal pulse repetition frequency. A receiver samples echoes of the sequence of electromagnetic pulses from objects within the field with controlled timing, in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The relative timing of the transmit timing signal and the receive timing signal is modulated between a first relative delay and a second relative delay at an intermediate frequency, causing the receiver to sample the echoes such that the time between transmissions of pulses in the sequence and samples by the receiver is modulated at the intermediate frequency. Modulation may be executed by modulating the pulse repetition frequency which drives the transmitter, by modulating the delay circuitry which controls the relative timing of the sample strobe, or by modulating amplitude of the transmitted pulses. The electromagnetic pulses will have a nominal center frequency related to pulse width, and the first relative delay and the second relative delay between which the timing signals are modulated, differ by less than the nominal pulse width, and preferably by about one-quarter wavelength at the nominal center frequency of the transmitted pulses.

Phase coded, micro-power impulse radar motion sensor

DOEpatents

McEwan, T.E.

1996-05-21

A motion sensing, micro-power impulse radar MIR impresses on the transmitted signal, or the received pulse timing signal, one or more frequencies lower than the pulse repetition frequency, that become intermediate frequencies in a ``IF homodyne`` receiver. Thus, many advantages of classical RF receivers can be thereby be realized with ultra-wide band radar. The sensor includes a transmitter which transmits a sequence of electromagnetic pulses in response to a transmit timing signal at a nominal pulse repetition frequency. A receiver samples echoes of the sequence of electromagnetic pulses from objects within the field with controlled timing, in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The relative timing of the transmit timing signal and the receive timing signal is modulated between a first relative delay and a second relative delay at an intermediate frequency, causing the receiver to sample the echoes such that the time between transmissions of pulses in the sequence and samples by the receiver is modulated at the intermediate frequency. Modulation may be executed by modulating the pulse repetition frequency which drives the transmitter, by modulating the delay circuitry which controls the relative timing of the sample strobe, or by modulating amplitude of the transmitted pulses. The electromagnetic pulses will have a nominal center frequency related to pulse width, and the first relative delay and the second relative delay between which the timing signals are modulated, differ by less than the nominal pulse width, and preferably by about one-quarter wavelength at the nominal center frequency of the transmitted pulses. 5 figs.

Genetic algorithm optimized triply compensated pulses in NMR spectroscopy

NASA Astrophysics Data System (ADS)

Manu, V. S.; Veglia, Gianluigi

2015-11-01

Sensitivity and resolution in NMR experiments are affected by magnetic field inhomogeneities (of both external and RF), errors in pulse calibration, and offset effects due to finite length of RF pulses. To remedy these problems, built-in compensation mechanisms for these experimental imperfections are often necessary. Here, we propose a new family of phase-modulated constant-amplitude broadband pulses with high compensation for RF inhomogeneity and heteronuclear coupling evolution. These pulses were optimized using a genetic algorithm (GA), which consists in a global optimization method inspired by Nature's evolutionary processes. The newly designed π and π / 2 pulses belong to the 'type A' (or general rotors) symmetric composite pulses. These GA-optimized pulses are relatively short compared to other general rotors and can be used for excitation and inversion, as well as refocusing pulses in spin-echo experiments. The performance of the GA-optimized pulses was assessed in Magic Angle Spinning (MAS) solid-state NMR experiments using a crystalline U-13C, 15N NAVL peptide as well as U-13C, 15N microcrystalline ubiquitin. GA optimization of NMR pulse sequences opens a window for improving current experiments and designing new robust pulse sequences.

Enhanced diffusion weighting generated by selective adiabatic pulse trains

NASA Astrophysics Data System (ADS)

Sun, Ziqi; Bartha, Robert

2007-09-01

A theoretical description and experimental validation of the enhanced diffusion weighting generated by selective adiabatic full passage (AFP) pulse trains is provided. Six phantoms (Ph-1-Ph-6) were studied on a 4 T Varian/Siemens whole body MRI system. Phantoms consisted of 2.8 cm diameter plastic tubes containing a mixture of 10 μm ORGASOL polymer beads and 2 mM Gd-DTPA dissolved in 5% agar (Ph-1) or nickel(II) ammonium sulphate hexahydrate doped (56.3-0.8 mM) water solutions (Ph-2-Ph-6). A customized localization by adiabatic selective refocusing (LASER) sequence containing slice selective AFP pulse trains and pulsed diffusion gradients applied in the phase encoding direction was used to measure 1H 2O diffusion. The b-value associated with the LASER sequence was derived using the Bloch-Torrey equation. The apparent diffusion coefficients measured by LASER were comparable to those measured by a conventional pulsed gradient spin-echo (PGSE) sequence for all phantoms. Image signal intensity increased in Ph-1 and decreased in Ph-2-Ph-6 as AFP pulse train length increased while maintaining a constant echo-time. These experimental results suggest that such AFP pulse trains can enhance contrast between regions containing microscopic magnetic susceptibility variations and homogeneous regions in which dynamic dephasing relaxation mechanisms are dominant.

ADJUSTABLE DOUBLE PULSE GENERATOR

DOEpatents

Gratian, J.W.; Gratian, A.C.

1961-08-01

>A modulator pulse source having adjustable pulse width and adjustable pulse spacing is described. The generator consists of a cross coupled multivibrator having adjustable time constant circuitry in each leg, an adjustable differentiating circuit in the output of each leg, a mixing and rectifying circuit for combining the differentiated pulses and generating in its output a resultant sequence of negative pulses, and a final amplifying circuit for inverting and square-topping the pulses. (AEC)

Simulation of the excitation of quasi-plane wake waves in a plasma by a resonant sequence of laser pulses with a variable envelope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalinnikova, E. I.; Levchenko, V. D.

2008-04-15

Results are presented from full-scale numerical simulations of the excitation of wake waves by a sequence of weakly relativistic laser pulses in a subcritical plasma. Computations were carried out with a 2D3V version of the SUR-CA code that is based on the local-recursive nonlocal-asynchronous algorithm of the particle-in-cell method. The parameters of a train of laser pulses were chosen to correspond to the resonant excitation of the wake field. The curvature of the envelope of the pulses was chosen to depend on the number of the pulse in the train. Numerical simulations showed that there are plane waves during themore » first period of the plasma wave behind the pulse train.« less

A Selective-Echo Method for Chemical-Shift Imaging of Two-Component Systems

NASA Astrophysics Data System (ADS)

Gerald, Rex E., II; Krasavin, Anatoly O.; Botto, Robert E.

A simple and effective method for selectively imaging either one of two chemical species in a two-component system is presented and demonstrated experimentally. The pulse sequence employed, selective- echo chemical- shift imaging (SECSI), is a hybrid (frequency-selective/ T1-contrast) technique that is executed in a short period of time, utilizes the full Boltzmann magnetization of each chemical species to form the corresponding image, and requires only hard pulses of quadrature phase. This approach provides a direct and unambiguous representation of the spatial distribution of the two chemical species. In addition, the performance characteristics and the advantages of the SECSI sequence are compared on a common basis to those of other pulse sequences.

Homonuclear Hartmann-Hahn transfer with reduced relaxation losses by use of the MOCCA-XY16 multiple pulse sequence

NASA Astrophysics Data System (ADS)

Furrer, Julien; Kramer, Frank; Marino, John P.; Glaser, Steffen J.; Luy, Burkhard

2004-01-01

Homonuclear Hartmann-Hahn transfer is one of the most important building blocks in modern high-resolution NMR. It constitutes a very efficient transfer element for the assignment of proteins, nucleic acids, and oligosaccharides. Nevertheless, in macromolecules exceeding ˜10 kDa TOCSY-experiments can show decreasing sensitivity due to fast transverse relaxation processes that are active during the mixing periods. In this article we propose the MOCCA-XY16 multiple pulse sequence, originally developed for efficient TOCSY transfer through residual dipolar couplings, as a homonuclear Hartmann-Hahn sequence with improved relaxation properties. A theoretical analysis of the coherence transfer via scalar couplings and its relaxation behavior as well as experimental transfer curves for MOCCA-XY16 relative to the well-characterized DIPSI-2 multiple pulse sequence are given.

Homonuclear Hartmann-Hahn transfer with reduced relaxation losses by use of the MOCCA-XY16 multiple pulse sequence.

PubMed

Furrer, Julien; Kramer, Frank; Marino, John P; Glaser, Steffen J; Luy, Burkhard

2004-01-01

Homonuclear Hartmann-Hahn transfer is one of the most important building blocks in modern high-resolution NMR. It constitutes a very efficient transfer element for the assignment of proteins, nucleic acids, and oligosaccharides. Nevertheless, in macromolecules exceeding approximately 10 kDa TOCSY-experiments can show decreasing sensitivity due to fast transverse relaxation processes that are active during the mixing periods. In this article we propose the MOCCA-XY16 multiple pulse sequence, originally developed for efficient TOCSY transfer through residual dipolar couplings, as a homonuclear Hartmann-Hahn sequence with improved relaxation properties. A theoretical analysis of the coherence transfer via scalar couplings and its relaxation behavior as well as experimental transfer curves for MOCCA-XY16 relative to the well-characterized DIPSI-2 multiple pulse sequence are given.

Powerful timing generator using mono-chip timers: An application to pulsed nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Saint-Jalmes, Hervé; Barjhoux, Yves

1982-01-01

We present a 10 line-7 MHz timing generator built on a single board around two LSI timer chips interfaced to a 16-bit microcomputer. Once programmed from the host computer, this device is able to generate elaborate logic sequences on its 10 output lines without further interventions from the CPU. Powerful architecture introduces new possibilities over conventional memory-based timing simulators and word generators. Loop control on a given sequence of events, loop nesting, and various logic combinations can easily be implemented through a software interface, using a symbolic command language. Typical applications of such a device range from development, emulation, and test of integrated circuits, circuit boards, and communication systems to pulse-controlled instrumentation (radar, ultrasonic systems). A particular application to a pulsed Nuclear Magnetic Resonance (NMR) spectrometer is presented, along with customization of the device for generating four-channel radio-frequency pulses and the necessary sequence for subsequent data acquisition.

Optimization of Pulse Sequences in MRI Scheme

NASA Astrophysics Data System (ADS)

Roy, Subhankar; Hu, Jianping; Ummal Momeen, M.

2018-04-01

Magnetic resonance imaging (MRI) has a wide range of applications towards imaging the human body. In this work we have solved the Bloch equations for different magnetic field gradients along the transverse direction. We have modified the magnetic field components based on the relaxation terms and solved the field gradient as well as the field components for both off –pulse and on -pulse configurations. In particular we focus on different pulse sequences and optimize them to realize the best possible output. We have analyzed the field components along transverse direction because the rotation of the object to form the image by emitting signal is along the xy plane.

Magnetorheological elastomer vibration isolation of tunable three-dimensional locally resonant acoustic metamaterial

NASA Astrophysics Data System (ADS)

Xu, Zhenlong; Tong, Jie; Wu, Fugen

2018-03-01

Magnetorheological elastomers (MREs) are used as cladding in three-dimensional locally resonant acoustic metamaterial (LRAM) cores. The metamaterial units are combined into a vibration isolator. Two types of LRAMs, namely, cubic and spherical kernels, are constructed. The finite element method is used to analyze the elastic band structures, transmittances, and vibration modes of the incident elastic waves. Results show that the central position and width of the LRAM elastic bandgap can be controlled by the application of an external magnetic field; furthermore, they can be adjusted by changing the MRE cladding thickness. These methods contribute to the design of metamaterial MRE vibration isolators.

An Optimum Specimen Geometry for Equibiaxial Experimental Tests of Reinforced Magnetorheological Elastomers with Iron Micro- and Nanoparticles

PubMed Central

Perales-Martínez, Imperio Anel; Moreno-Guerra, Mario Regino; Elías-Zúñiga, Alex

2017-01-01

The aim of this paper focused on obtaining the optimum cruciform geometry of reinforced magnetorheological elastomers (MRE) to perform homogeneous equibiaxial deformation tests, by using optimization algorithms and Finite Element Method (FEM) simulations. To validate the proposed specimen geometry, a digital image correlation (DIC) system was used to compare experimental result measurements with respect to those of FEM simulations. Moreover, and based on the optimum cruciform geometry, specimens produced from MRE reinforced with carbonyl-iron microparticles or iron nanoparticles were subjected to equibiaxial loading and unloading cycles to examine their Mullin’s effect and their residual strain deformations. PMID:28869523

An Optimum Specimen Geometry for Equibiaxial Experimental Tests of Reinforced Magnetorheological Elastomers with Iron Micro- and Nanoparticles.

PubMed

Palacios-Pineda, Luis Manuel; Perales-Martínez, Imperio Anel; Moreno-Guerra, Mario Regino; Elías-Zúñiga, Alex

2017-09-03

The aim of this paper focused on obtaining the optimum cruciform geometry of reinforced magnetorheological elastomers (MRE) to perform homogeneous equibiaxial deformation tests, by using optimization algorithms and Finite Element Method (FEM) simulations. To validate the proposed specimen geometry, a digital image correlation (DIC) system was used to compare experimental result measurements with respect to those of FEM simulations. Moreover, and based on the optimum cruciform geometry, specimens produced from MRE reinforced with carbonyl-iron microparticles or iron nanoparticles were subjected to equibiaxial loading and unloading cycles to examine their Mullin's effect and their residual strain deformations.

Characterization of glioblastoma in an orthotopic mouse model with magnetic resonance elastography.

PubMed

Schregel, Katharina; Nazari, Navid; Nowicki, Michal O; Palotai, Miklos; Lawler, Sean E; Sinkus, Ralph; Barbone, Paul E; Patz, Samuel

2017-11-29

Glioblastoma (GBM) is the most common primary brain tumor. It is highly malignant and has a correspondingly poor prognosis. Diagnosis and monitoring are mainly accomplished with MRI, but remain challenging in some cases. Therefore, complementary methods for tumor detection and characterization would be beneficial. Using magnetic resonance elastography (MRE), we performed a longitudinal study of the biomechanical properties of intracranially implanted GBM in mice and compared the results to histopathology. The biomechanical parameters of viscoelastic modulus, shear wave speed and phase angle were significantly lower in tumors compared with healthy brain tissue and decreased over time with tumor progression. Moreover, some MRE parameters revealed sub-regions at later tumor stages, which were not easily detectable on anatomical MRI images. Comparison with histopathology showed that softer tumor regions contained necrosis and patches of viable tumor cells. In contrast, areas of densely packed tumor cells and blood vessels identified with histology coincided with higher values of viscoelastic modulus and shear wave speed. Interestingly, the phase angle was independent from these anatomical variations. In summary, MRE depicted longitudinal and morphological changes in GBM and may prove valuable for tumor characterization in patients. Copyright © 2017 John Wiley & Sons, Ltd.

Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division

PubMed Central

Packiam, Mathanraj; Hsu, Yen-Pang; Tekkam, Srinivas; Hall, Edward; Rittichier, Jonathan T.; VanNieuwenhze, Michael; Brun, Yves V.; Maurelli, Anthony T.

2016-01-01

The peptidoglycan (PG) cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure. Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wall component in Chlamydia trachomatis. In this study, we utilize bio-orthogonal D-amino acid dipeptide probes combined with super-resolution microscopy to demonstrate that four pathogenic Chlamydiae species each possess a ≤ 140 nm wide PG ring limited to the division plane during the replicative phase of their developmental cycles. Assembly of this PG ring is rapid, processive, and linked to the bacterial actin-like protein, MreB. Both MreB polymerization and PG biosynthesis occur only in the intracellular form of pathogenic Chlamydia and are required for cell enlargement, division, and transition between the microbe’s developmental forms. Our kinetic, molecular, and biochemical analyses suggest that the development of this limited, transient, PG ring structure is the result of pathoadaptation by Chlamydia to an intracellular niche within its vertebrate host. PMID:27144308

Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division.

PubMed

Liechti, George; Kuru, Erkin; Packiam, Mathanraj; Hsu, Yen-Pang; Tekkam, Srinivas; Hall, Edward; Rittichier, Jonathan T; VanNieuwenhze, Michael; Brun, Yves V; Maurelli, Anthony T

2016-05-01

The peptidoglycan (PG) cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure. Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wall component in Chlamydia trachomatis. In this study, we utilize bio-orthogonal D-amino acid dipeptide probes combined with super-resolution microscopy to demonstrate that four pathogenic Chlamydiae species each possess a ≤ 140 nm wide PG ring limited to the division plane during the replicative phase of their developmental cycles. Assembly of this PG ring is rapid, processive, and linked to the bacterial actin-like protein, MreB. Both MreB polymerization and PG biosynthesis occur only in the intracellular form of pathogenic Chlamydia and are required for cell enlargement, division, and transition between the microbe's developmental forms. Our kinetic, molecular, and biochemical analyses suggest that the development of this limited, transient, PG ring structure is the result of pathoadaptation by Chlamydia to an intracellular niche within its vertebrate host.

Mechanical properties of porcine brain tissue in vivo and ex vivo estimated by MR elastography.

PubMed

Guertler, Charlotte A; Okamoto, Ruth J; Schmidt, John L; Badachhape, Andrew A; Johnson, Curtis L; Bayly, Philip V

2018-03-01

The mechanical properties of brain tissue in vivo determine the response of the brain to rapid skull acceleration. These properties are thus of great interest to the developers of mathematical models of traumatic brain injury (TBI) or neurosurgical simulations. Animal models provide valuable insight that can improve TBI modeling. In this study we compare estimates of mechanical properties of the Yucatan mini-pig brain in vivo and ex vivo using magnetic resonance elastography (MRE) at multiple frequencies. MRE allows estimations of properties in soft tissue, either in vivo or ex vivo, by imaging harmonic shear wave propagation. Most direct measurements of brain mechanical properties have been performed using samples of brain tissue ex vivo. It has been observed that direct estimates of brain mechanical properties depend on the frequency and amplitude of loading, as well as the time post-mortem and condition of the sample. Using MRE in the same animals at overlapping frequencies, we observe that porcine brain tissue in vivo appears stiffer than porcine brain tissue samples ex vivo at frequencies of 100 Hz and 125 Hz, but measurements show closer agreement at lower frequencies. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Main regulatory element (MRE) of the Danio rerio α/β-globin gene domain exerts enhancer activity toward the promoters of the embryonic-larval and adult globin genes].

PubMed

Kovina, A P; Petrova, N V; Razin, S V; Yarovaia, O V

2016-01-01

In warm-blooded vertebrates, the α- and β-globin genes are organized in domains of different types and are regulated in different fashion. In cold-blooded vertebrates and, in particular, the tropical fish Danio rerio, the α- and β-globin genes form two gene clusters. A major D. rerio globin gene cluster is in chromosome 3 and includes the α- and β-globin genes of embryonic-larval and adult types. The region upstream of the cluster contains c16orf35, harbors the main regulatory element (MRE) of the α-globin gene domain in warm-blooded vertebrates. In this study, transient transfection of erythroid cells with genetic constructs containing a reporter gene under the control of potential regulatory elements of the domain was performed to characterize the promoters of the embryonic-larval and adult α- and β-globin genes of the major cluster. Also, in the 5th intron of c16orf35 in Danio reriowas detected a functional analog of the warm-blooded vertebrate MRE. This enhancer stimulated activity of the promoters of both adult and embryonic-larval α- and β-globin genes.

Acute pressure changes in the brain are correlated with MR elastography stiffness measurements: initial feasibility in an in vivo large animal model.

PubMed

Arani, Arvin; Min, Hoon-Ki; Fattahi, Nikoo; Wetjen, Nicholas M; Trzasko, Joshua D; Manduca, Armando; Jack, Clifford R; Lee, Kendall H; Ehman, Richard L; Huston, John

2018-02-01

The homeostasis of intracranial pressure (ICP) is of paramount importance for maintaining normal brain function. A noninvasive technique capable of making direct measurements of ICP currently does not exist. MR elastography (MRE) is capable of noninvasively measuring brain tissue stiffness in vivo, and may act as a surrogate to measure ICP. The objective of this study was to investigate the impact of changing ICP on brain stiffness using MRE in a swine model. Baseline MRE measurements were obtained, and then catheters were surgically placed into the left and right lateral ventricles of three animals. ICP was systematically increased over the range of 0 to 55 millimeters mercury (mmHg), and stiffness measurements were made using brain MRE at vibration frequencies of 60 hertz (Hz), 90 Hz, 120 Hz, and 150 Hz. A significant linear correlation between stiffness and ICP in the cross-subject comparison was observed for all tested vibrational frequencies (P ≤ 0.01). The 120 Hz (0.030 ± 0.004 kilopascal (kPa)/mmHg, P < 0.0001) and 150 Hz (0.031 ± 0.008 kPa/mmHg, P = 0.01) vibrational frequencies had nearly identical slopes, which were approximately two- to three-fold higher than the 90 Hz (0.017 ± 0.002 kPa/mmHg, P < 0.0001) and 60 Hz (0.009 ± 0.002 kPa/mmHg, P = 0.001) slopes, respectively. In this study, MRE demonstrated the potential for noninvasive measurement of changes in ICP. Magn Reson Med 79:1043-1051, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

An improved pulse sequence and inversion algorithm of T2 spectrum

NASA Astrophysics Data System (ADS)

Ge, Xinmin; Chen, Hua; Fan, Yiren; Liu, Juntao; Cai, Jianchao; Liu, Jianyu

2017-03-01

The nuclear magnetic resonance transversal relaxation time is widely applied in geological prospecting, both in laboratory and downhole environments. However, current methods used for data acquisition and inversion should be reformed to characterize geological samples with complicated relaxation components and pore size distributions, such as samples of tight oil, gas shale, and carbonate. We present an improved pulse sequence to collect transversal relaxation signals based on the CPMG (Carr, Purcell, Meiboom, and Gill) pulse sequence. The echo spacing is not constant but varies in different windows, depending on prior knowledge or customer requirements. We use the entropy based truncated singular value decomposition (TSVD) to compress the ill-posed matrix and discard small singular values which cause the inversion instability. A hybrid algorithm combining the iterative TSVD and a simultaneous iterative reconstruction technique is implemented to reach the global convergence and stability of the inversion. Numerical simulations indicate that the improved pulse sequence leads to the same result as CPMG, but with lower echo numbers and computational time. The proposed method is a promising technique for geophysical prospecting and other related fields in future.

Adjustable shunt valve-induced magnetic resonance imaging artifact: a comparative study.

PubMed

Toma, Ahmed K; Tarnaris, Andrew; Grieve, Joan P; Watkins, Laurence D; Kitchen, Neil D

2010-07-01

In this paper, the authors' goal was to compare the artifact induced by implanted (in vivo) adjustable shunt valves in spin echo, diffusion weighted (DW), and gradient echo MR imaging pulse sequences. The MR images obtained in 8 patients with proGAV and 6 patients with Strata II adjustable shunt valves were assessed for artifact areas in different planes as well as the total volume for different pulse sequences. Artifacts induced by the Strata II valve were significantly larger than those induced by proGAV valve in spin echo MR imaging pulse sequence (29,761 vs 2450 mm(3) on T2-weighted fast spin echo, p = 0.003) and DW images (100,138 vs 38,955 mm(3), p = 0.025). Artifacts were more marked on DW MR images than on spin echo pulse sequence for both valve types. Adjustable valve-induced artifacts can conceal brain pathology on MR images. This should influence the choice of valve implantation site and the type of valve used. The effect of artifacts on DW images should be highlighted pending the development of less MR imaging artifact-inducing adjustable shunt valves.

Method and apparatus for pulse stacking

DOEpatents

Harney, Robert C.

1977-01-01

An active pulse stacking system including an etalon and an electro-optical modulator apparatus combined with a pulse-forming network capable of forming and summing a sequence of time-delayed optical waveforms arising from, for example, a single laser pulse. The Pockels cell pulse stacker may attain an efficiency of about 2.6% while providing a controllable faster-than-exponential time rise in transmitted pulse intensity.

SU-E-T-558: An Exploratory RF Pulse Sequence Technique Used to Induce Differential Heating in Tissues Containing Iron Oxide Nanoparticles for a Possible Hyperthermic Adjuvant Effect to Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yee, S; Ionascu, D; Wilson, G

2014-06-01

Purpose: In pre-clinical trials of cancer thermotherapy, hyperthermia can be induced by exposing localized super-paramagnetic iron oxide nanoparticles (SPION) to external alternating magnetic fields generated by a solenoid electrical circuit (Zhao et al., Theranostics 2012). Alternatively, an RF pulse technique implemented in a regular MRI system is explored as a possible hyperthermia induction technique . Methods: A new thermal RF pulse sequence was developed using the Philips pulse programming tool for the 3T Ingenia MRI system to provide a sinusoidal magnetic field alternating at the frequency of 1.43 kHz (multiples of sine waves of 0.7 ms period) before each excitationmore » RF pulse for imaging. The duration of each thermal RF pulse routine was approximately 3 min, and the thermal pulse was applied multiple times to a phantom that contains different concentrations (high, medium and low) of SPION samples. After applying the thermal pulse each time, the temperature change was estimated by measuring the phase changes in the T1-weighted inversion-prepared multi-shot turbo field echo (TFE) sequence (TR=5.5 ms, TE=2.7 ms, inversion time=200 ms). Results: The phase values and relative differences among them changed as the number of applied thermal RF pulses increased. After the 5th application of the thermal RF pulse, the relative phase differences increased significantly, suggesting the thermal activation of the SPION. The increase of the phase difference was approximately linear with the SPION concentration. Conclusion: A sinusoidal RF pulse from the MRI system may be utilized to selectively thermally activate tissues containing super-paramagnetic iron oxide nanoparticles.« less

Magnetic flux density measurement with balanced steady state free precession pulse sequence for MREIT: a simulation study.

PubMed

Minhas, Atul S; Woo, Eung Je; Lee, Soo Yeol

2009-01-01

Magnetic Resonance Electrical Impedance Tomography (MREIT) utilizes the magnetic flux density B(z), generated due to current injection, to find conductivity distribution inside an object. This B(z) can be measured from MR phase images using spin echo pulse sequence. The SNR of B(z) and the sensitivity of phase produced by B(z) in MR phase image are critical in deciding the resolution of MREIT conductivity images. The conventional spin echo based data acquisition has poor phase sensitivity to current injection. Longer scan time is needed to acquire data with higher SNR. We propose a balanced steady state free precession (b-SSFP) based pulse sequence which is highly sensitive to small off-resonance phase changes. A procedure to reconstruct B(z) from MR signal obtained with b-SSFP sequence is described. Phases for b-SSFP signals for two conductivity phantoms of TX 151 and Gelatin are simulated from the mathematical models of b-SSFP signal. It was observed that the phase changes obtained from b-SSFP pulse sequence are highly sensitive to current injection and hence would produce higher magnetic flux density. However, the b-SSFP signal is dependent on magnetic field inhomogeneity and the signal deteriorated highly for small offset from resonance frequency. The simulation results show that the b-SSFP sequence can be utilized for conductivity imaging of a local region where magnetic field inhomogeneity is small. A proper shimming of magnet is recommended before using the b-SSFP sequence.

A multislice gradient echo pulse sequence for CEST imaging.

PubMed

Dixon, W Thomas; Hancu, Ileana; Ratnakar, S James; Sherry, A Dean; Lenkinski, Robert E; Alsop, David C

2010-01-01

Chemical exchange-dependent saturation transfer and paramagnetic chemical exchange-dependent saturation transfer are agent-mediated contrast mechanisms that depend on saturating spins at the resonant frequency of the exchangeable protons on the agent, thereby indirectly saturating the bulk water. In general, longer saturating pulses produce stronger chemical and paramagnetic exchange-dependent saturation transfer effects, with returns diminishing for pulses longer than T1. This could make imaging slow, so one approach to chemical exchange-dependent saturation transfer imaging has been to follow a long, frequency-selective saturation period by a fast imaging method. A new approach is to insert a short frequency-selective saturation pulse before each spatially selective observation pulse in a standard, two-dimensional, gradient-echo pulse sequence. Being much less than T1 apart, the saturation pulses have a cumulative effect. Interleaved, multislice imaging is straightforward. Observation pulses directed at one slice did not produce observable, unintended chemical exchange-dependent saturation transfer effects in another slice. Pulse repetition time and signal-to noise ratio increase in the normal way as more slices are imaged simultaneously. Copyright (c) 2009 Wiley-Liss, Inc.

SU-F-J-112: Clinical Feasibility Test of An RF Pulse-Based MRI Method for the Quantitative Fat-Water Segmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yee, S; Wloch, J; Pirkola, M

Purpose: Quantitative fat-water segmentation is important not only because of the clinical utility of fat-suppressed MRI images in better detecting lesions of clinical significance (in the midst of bright fat signal) but also because of the possible physical need, in which CT-like images based on the materials’ photon attenuation properties may have to be generated from MR images; particularly, as in the case of MR-only radiation oncology environment to obtain radiation dose calculation or as in the case of hybrid PET/MR modality to obtain attenuation correction map for the quantitative PET reconstruction. The majority of such fat-water quantitative segmentations havemore » been performed by utilizing the Dixon’s method and its variations, which have to enforce the proper settings (often predefined) of echo time (TE) in the pulse sequences. Therefore, such methods have been unable to be directly combined with those ultrashort TE (UTE) sequences that, taking the advantage of very low TE values (∼ 10’s microsecond), might be beneficial to directly detect bones. Recently, an RF pulse-based method (http://dx.doi.org/10.1016/j.mri.2015.11.006), termed as PROD pulse method, was introduced as a method of quantitative fat-water segmentation that does not have to depend on predefined TE settings. Here, the clinical feasibility of this method is verified in brain tumor patients by combining the PROD pulse with several sequences. Methods: In a clinical 3T MRI, the PROD pulse was combined with turbo spin echo (e.g. TR=1500, TE=16 or 60, ETL=15) or turbo field echo (e.g. TR=5.6, TE=2.8, ETL=12) sequences without specifying TE values. Results: The fat-water segmentation was possible without having to set specific TE values. Conclusion: The PROD pulse method is clinically feasible. Although not yet combined with UTE sequences in our laboratory, the method is potentially compatible with UTE sequences, and thus, might be useful to directly segment fat, water, bone and air.« less

Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition.

PubMed

Cannon, Jonathan; Kopell, Nancy; Gardner, Timothy; Markowitz, Jeffrey

2015-11-01

Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement. One of the most prominent theoretical models of neural sequence generation is the synfire chain, in which pulses of synchronized spiking activity propagate robustly along a chain of cells connected by highly redundant feedforward excitation. But recent experimental observations in the avian song production pathway during song generation have shown excitatory activity interacting strongly with the firing patterns of inhibitory neurons, suggesting a process of sequence generation more complex than feedforward excitation. Here we propose a model of sequence generation inspired by these observations in which a pulse travels along a spatially recurrent excitatory chain, passing repeatedly through zones of local feedback inhibition. In this model, synchrony and robust timing are maintained not through redundant excitatory connections, but rather through the interaction between the pulse and the spatiotemporal pattern of inhibition that it creates as it circulates the network. These results suggest that spatially and temporally structured inhibition may play a key role in sequence generation.

Non-Cartesian Balanced SSFP Pulse Sequences for Real-Time Cardiac MRI

PubMed Central

Feng, Xue; Salerno, Michael; Kramer, Christopher M.; Meyer, Craig H.

2015-01-01

Purpose To develop a new spiral-in/out balanced steady-state free precession (bSSFP) pulse sequence for real-time cardiac MRI and compare it with radial and spiral-out techniques. Methods Non-Cartesian sampling strategies are efficient and robust to motion and thus have important advantages for real-time bSSFP cine imaging. This study describes a new symmetric spiral-in/out sequence with intrinsic gradient moment compensation and SSFP refocusing at TE=TR/2. In-vivo real-time cardiac imaging studies were performed to compare radial, spiral-out, and spiral-in/out bSSFP pulse sequences. Furthermore, phase-based fat-water separation taking advantage of the refocusing mechanism of the spiral-in/out bSSFP sequence was also studied. Results The image quality of the spiral-out and spiral-in/out bSSFP sequences was improved with off-resonance and k-space trajectory correction. The spiral-in/out bSSFP sequence had the highest SNR, CNR, and image quality ratings, with spiral-out bSSFP sequence second in each category and the radial bSSFP sequence third. The spiral-in/out bSSFP sequence provides separated fat and water images with no additional scan time. Conclusions In this work a new spiral-in/out bSSFP sequence was developed and tested. The superiority of spiral bSSFP sequences over the radial bSSFP sequence in terms of SNR and reduced artifacts was demonstrated in real-time MRI of cardiac function without image acceleration. PMID:25960254

Multi-mJ energy extraction using Yb-fiber based coherent pulse stacking amplification of fs pulses (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ruppe, John M.; Pei, Hanzhang; Chen, Siyun; Sheikhsofla, Morteza; Wilcox, Russell B.; Nees, John A.; Galvanauskas, Almantas

2017-03-01

We report multi-mJ energy (>5mJ) extraction from femtosecond-pulse Yb-doped fiber CPA using coherent pulse stacking amplification (CPSA) technique. This high energy extraction has been enabled by amplifying 10's of nanosecond long pulse sequence, and by using 85-µm core Yb-doped CCC fiber based power amplification stage. The CPSA system consists of 1-GHz repetition rate mode-locked fiber oscillator, followed by a pair of fast phase and amplitude electro-optic modulators, a diffraction-grating based pulse stretcher, a fiber amplifier chain, a GTI-cavity based pulse stacker, and a diffraction grating pulse compressor. Electro-optic modulators are used to carve out from the 1-GHz mode-locked pulse train an amplitude and phase modulated pulse burst, which after stretching and amplification, becomes equal-amplitude pulse burst consisting of 27 stretched pulses, each approximately 1-ns long. Initial pulse-burst shaping accounts for the strong amplifier saturation effects, so that it is compensated at the power amplifier output. This 27-pulse burst is then coherently stacked into a single pulse using a multiplexed sequence of 5 GTI cavities. The compact-footprint 4+1 multiplexed pulse stacker consists of 4 cavities having rountrip of 1 ns, and one Herriott-cell folded cavity - with 9ns roundtrip. After stacking, stretched pulses are compressed down to the bandwidth-limited 300 fs duration using a standard diffraction-grating pulse compressor.

Efficient theory of dipolar recoupling in solid-state nuclear magnetic resonance of rotating solids using Floquet-Magnus expansion: application on BABA and C7 radiofrequency pulse sequences.

PubMed

Mananga, Eugene S; Reid, Alicia E; Charpentier, Thibault

2012-02-01

This article describes the use of an alternative expansion scheme called Floquet-Magnus expansion (FME) to study the dynamics of spin system in solid-state NMR. The main tool used to describe the effect of time-dependent interactions in NMR is the average Hamiltonian theory (AHT). However, some NMR experiments, such as sample rotation and pulse crafting, seem to be more conveniently described using the Floquet theory (FT). Here, we present the first report highlighting the basics of the Floquet-Magnus expansion (FME) scheme and hint at its application on recoupling sequences that excite more efficiently double-quantum coherences, namely BABA and C7 radiofrequency pulse sequences. The use of Λ(n)(t) functions available only in the FME scheme, allows the comparison of the efficiency of BABA and C7 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

Efficient theory of dipolar recoupling in–solid state nuclear magnetic resonance of rotating solids using Floquet-Magnus expansion: Application on BABA and C7 radiofrequency pulse sequences

PubMed Central

Reid, Alicia E.; Charpentier, Thibault

2013-01-01

This article describes the use of an alternative expansion scheme called Floquet-Magnus expansion (FME) to study the dynamics of spin system in solid-state NMR. The main tool used to describe the effect of time-dependent interactions in NMR is the average Hamiltonian theory (AHT). However, some NMR experiments, such as sample rotation and pulse crafting, seem to be more conveniently described using the Floquet theory (FT). Here, we present the first report highlighting the basics of the Floquet-Magnus expansion (FME) scheme and hint at its application on recoupling sequences that excite more efficiently double-quantum coherences, namely BABA and C7 radiofrequency pulse sequences. The use of Λn(t) functions available only in the FME scheme, allows the comparison of the efficiency of BABA and C7 sequences. PMID:22197191

Limiting vibration in systems with constant amplitude actuators through command preshaping. M.S Thesis - MIT

NASA Technical Reports Server (NTRS)

Rogers, Keith Eric

1994-01-01

The basic concepts of command preshaping were taken and adapted to the framework of systems with constant amplitude (on-off) actuators. In this context, pulse sequences were developed which help to attenuate vibration in flexible systems with high robustness to errors in frequency identification. Sequences containing impulses of different magnitudes were approximated by sequences containing pulses of different durations. The effects of variation in pulse width on this approximation were examined. Sequences capable of minimizing loads induced in flexible systems during execution of commands were also investigated. The usefulness of these techniques in real-world situations was verified by application to a high fidelity simulation of the space shuttle. Results showed that constant amplitude preshaping techniques offer a substantial improvement in vibration reduction over both the standard and upgraded shuttle control methods and may be mission enabling for use of the shuttle with extremely massive payloads.

Jump-and-return sandwiches: A new family of binomial-like selective inversion sequences with improved performance

NASA Astrophysics Data System (ADS)

Brenner, Tom; Chen, Johnny; Stait-Gardner, Tim; Zheng, Gang; Matsukawa, Shingo; Price, William S.

2018-03-01

A new family of binomial-like inversion sequences, named jump-and-return sandwiches (JRS), has been developed by inserting a binomial-like sequence into a standard jump-and-return sequence, discovered through use of a stochastic Genetic Algorithm optimisation. Compared to currently used binomial-like inversion sequences (e.g., 3-9-19 and W5), the new sequences afford wider inversion bands and narrower non-inversion bands with an equal number of pulses. As an example, two jump-and-return sandwich 10-pulse sequences achieved 95% inversion at offsets corresponding to 9.4% and 10.3% of the non-inversion band spacing, compared to 14.7% for the binomial-like W5 inversion sequence, i.e., they afforded non-inversion bands about two thirds the width of the W5 non-inversion band.

Broadband excitation in nuclear magnetic resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tycko, Robert

1984-10-01

Theoretical methods for designing sequences of radio frequency (rf) radiation pulses for broadband excitation of spin systems in nuclear magnetic resonance (NMR) are described. The sequences excite spins uniformly over large ranges of resonant frequencies arising from static magnetic field inhomogeneity, chemical shift differences, or spin couplings, or over large ranges of rf field amplitudes. Specific sequences for creating a population inversion or transverse magnetization are derived and demonstrated experimentally in liquid and solid state NMR. One approach to broadband excitation is based on principles of coherent averaging theory. A general formalism for deriving pulse sequences is given, along withmore » computational methods for specific cases. This approach leads to sequences that produce strictly constant transformations of a spin system. The importance of this feature in NMR applications is discussed. A second approach to broadband excitation makes use of iterative schemes, i.e. sets of operations that are applied repetitively to a given initial pulse sequences, generating a series of increasingly complex sequences with increasingly desirable properties. A general mathematical framework for analyzing iterative schemes is developed. An iterative scheme is treated as a function that acts on a space of operators corresponding to the transformations produced by all possible pulse sequences. The fixed points of the function and the stability of the fixed points are shown to determine the essential behavior of the scheme. Iterative schemes for broadband population inversion are treated in detail. Algebraic and numerical methods for performing the mathematical analysis are presented. Two additional topics are treated. The first is the construction of sequences for uniform excitation of double-quantum coherence and for uniform polarization transfer over a range of spin couplings. Double-quantum excitation sequences are demonstrated in a liquid crystal system. The second additional topic is the construction of iterative schemes for narrowband population inversion. The use of sequences that invert spin populations only over a narrow range of rf field amplitudes to spatially localize NMR signals in an rf field gradient is discussed.« less

Anomalous Diffusion Measured by a Twice-Refocused Spin Echo Pulse Sequence: Analysis Using Fractional Order Calculus

PubMed Central

2011-01-01

Purpose To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. Materials and Methods The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2,600 s/mm2. For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β and μ values and the goodness-of-fit in three specific regions of interest (ROI) in white matter, gray matter, and cerebrospinal fluid were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. Results The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. Conclusion The diffusion-induced signal attenuation in a TRSE pulse sequence can be described by an FC diffusion model at high b-values. This model performs equally well for data acquired from the human brain tissues with a TRSE pulse sequence or a conventional Stejskal-Tanner sequence. PMID:21509877

Anomalous diffusion measured by a twice-refocused spin echo pulse sequence: analysis using fractional order calculus.

PubMed

Gao, Qing; Srinivasan, Girish; Magin, Richard L; Zhou, Xiaohong Joe

2011-05-01

To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2600 s/mm(2). For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β, and μ values and the goodness-of-fit in three specific regions of interest (ROIs) in white matter, gray matter, and cerebrospinal fluid, respectively, were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. The diffusion-induced signal attenuation in a TRSE pulse sequence can be described by an FC diffusion model at high b-values. This model performs equally well for data acquired from the human brain tissues with a TRSE pulse sequence or a conventional Stejskal-Tanner sequence. Copyright © 2011 Wiley-Liss, Inc.

Rare key functional domain missense substitutions in MRE11A, RAD50, and NBN contribute to breast cancer susceptibility: results from a Breast Cancer Family Registry case-control mutation-screening study

PubMed Central

2014-01-01

Introduction The MRE11A-RAD50-Nibrin (MRN) complex plays several critical roles related to repair of DNA double-strand breaks. Inherited mutations in the three components predispose to genetic instability disorders and the MRN genes have been implicated in breast cancer susceptibility, but the underlying data are not entirely convincing. Here, we address two related questions: (1) are some rare MRN variants intermediate-risk breast cancer susceptibility alleles, and if so (2) do the MRN genes follow a BRCA1/BRCA2 pattern wherein most susceptibility alleles are protein-truncating variants, or do they follow an ATM/CHEK2 pattern wherein half or more of the susceptibility alleles are missense substitutions? Methods Using high-resolution melt curve analysis followed by Sanger sequencing, we mutation screened the coding exons and proximal splice junction regions of the MRN genes in 1,313 early-onset breast cancer cases and 1,123 population controls. Rare variants in the three genes were pooled using bioinformatics methods similar to those previously applied to ATM, BRCA1, BRCA2, and CHEK2, and then assessed by logistic regression. Results Re-analysis of our ATM, BRCA1, and BRCA2 mutation screening data revealed that these genes do not harbor pathogenic alleles (other than modest-risk SNPs) with minor allele frequencies >0.1% in Caucasian Americans, African Americans, or East Asians. Limiting our MRN analyses to variants with allele frequencies of <0.1% and combining protein-truncating variants, likely spliceogenic variants, and key functional domain rare missense substitutions, we found significant evidence that the MRN genes are indeed intermediate-risk breast cancer susceptibility genes (odds ratio (OR) = 2.88, P = 0.0090). Key domain missense substitutions were more frequent than the truncating variants (24 versus 12 observations) and conferred a slightly higher OR (3.07 versus 2.61) with a lower P value (0.029 versus 0.14). Conclusions These data establish that MRE11A, RAD50, and NBN are intermediate-risk breast cancer susceptibility genes. Like ATM and CHEK2, their spectrum of pathogenic variants includes a relatively high proportion of missense substitutions. However, the data neither establish whether variants in each of the three genes are best evaluated under the same analysis model nor achieve clinically actionable classification of individual variants observed in this study. PMID:24894818

Random noise effects in pulse-mode digital multilayer neural networks.

PubMed

Kim, Y C; Shanblatt, M A

1995-01-01

A pulse-mode digital multilayer neural network (DMNN) based on stochastic computing techniques is implemented with simple logic gates as basic computing elements. The pulse-mode signal representation and the use of simple logic gates for neural operations lead to a massively parallel yet compact and flexible network architecture, well suited for VLSI implementation. Algebraic neural operations are replaced by stochastic processes using pseudorandom pulse sequences. The distributions of the results from the stochastic processes are approximated using the hypergeometric distribution. Synaptic weights and neuron states are represented as probabilities and estimated as average pulse occurrence rates in corresponding pulse sequences. A statistical model of the noise (error) is developed to estimate the relative accuracy associated with stochastic computing in terms of mean and variance. Computational differences are then explained by comparison to deterministic neural computations. DMNN feedforward architectures are modeled in VHDL using character recognition problems as testbeds. Computational accuracy is analyzed, and the results of the statistical model are compared with the actual simulation results. Experiments show that the calculations performed in the DMNN are more accurate than those anticipated when Bernoulli sequences are assumed, as is common in the literature. Furthermore, the statistical model successfully predicts the accuracy of the operations performed in the DMNN.

gr-MRI: A software package for magnetic resonance imaging using software defined radios

NASA Astrophysics Data System (ADS)

Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

Optical emission and nanoparticle generation in Al plasmas using ultrashort laser pulses temporally optimized by real-time spectroscopic feedback

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guillermin, M.; Colombier, J. P.; Audouard, E.

2010-07-15

With an interest in pulsed laser deposition and remote spectroscopy techniques, we explore here the potential of laser pulses temporally tailored on ultrafast time scales to control the expansion and the excitation degree of various ablation products including atomic species and nanoparticulates. Taking advantage of automated pulse-shaping techniques, an adaptive procedure based on spectroscopic feedback is applied to regulate the irradiance and enhance the optical emission of monocharged aluminum ions with respect to the neutral signal. This leads to optimized pulses usually consisting in a series of femtosecond peaks distributed on a longer picosecond sequence. The ablation features induced bymore » the optimized pulse are compared with those determined by picosecond pulses generated by imposed second-order dispersion or by double pulse sequences with adjustable picosecond separation. This allows to analyze the influence of fast- and slow-varying envelope features on the material heating and the resulting plasma excitation degree. Using various optimal pulse forms including designed asymmetric shapes, we analyze the establishment of surface pre-excitation that enables conditions of enhanced radiation coupling. Thin films elaborated by unshaped femtosecond laser pulses and by optimized, stretched, or double pulse sequences are compared, indicating that the nanoparticles generation efficiency is strongly influenced by the temporal shaping of the laser irradiation. A thermodynamic scenario involving supercritical heating is proposed to explain enhanced ionization rates and lower particulates density for optimal pulses. Numerical one-dimensional hydrodynamic simulations for the excited matter support the interpretation of the experimental results in terms of relative efficiency of various relaxation paths for excited matter above or below the thermodynamic stability limits. The calculation results underline the role of the temperature and density gradients along the ablated plasma plume which lead to the spatial distinct locations of excited species. Moreover, the nanoparticles sizes are computed based on liquid layer ejection followed by a Rayleigh and Taylor instability decomposition, in good agreement with the experimental findings.« less

Multiple-rotor-cycle 2D PASS experiments with applications to (207)Pb NMR spectroscopy.

PubMed

Vogt, F G; Gibson, J M; Aurentz, D J; Mueller, K T; Benesi, A J

2000-03-01

Thetwo-dimensional phase-adjusted spinning sidebands (2D PASS) experiment is a useful technique for simplifying magic-angle spinning (MAS) NMR spectra that contain overlapping or complicated spinning sideband manifolds. The pulse sequence separates spinning sidebands by their order in a two-dimensional experiment. The result is an isotropic/anisotropic correlation experiment, in which a sheared projection of the 2D spectrum effectively yields an isotropic spectrum with no sidebands. The original 2D PASS experiment works best at lower MAS speeds (1-5 kHz). At higher spinning speeds (8-12 kHz) the experiment requires higher RF power levels so that the pulses do not overlap. In the case of nuclei such as (207)Pb, a large chemical shift anisotropy often yields too many spinning sidebands to be handled by a reasonable 2D PASS experiment unless higher spinning speeds are used. Performing the experiment at these speeds requires fewer 2D rows and a correspondingly shorter experimental time. Therefore, we have implemented PASS pulse sequences that occupy multiple MAS rotor cycles, thereby avoiding pulse overlap. These multiple-rotor-cycle 2D PASS sequences are intended for use in high-speed MAS situations such as those required by (207)Pb. A version of the multiple-rotor-cycle 2D PASS sequence that uses composite pulses to suppress spectral artifacts is also presented. These sequences are demonstrated on (207)Pb test samples, including lead zirconate, a perovskite-phase compound that is representative of a large class of interesting materials. Copyright 2000 Academic Press.

Direct generation of all-optical random numbers from optical pulse amplitude chaos.

PubMed

Li, Pu; Wang, Yun-Cai; Wang, An-Bang; Yang, Ling-Zhen; Zhang, Ming-Jiang; Zhang, Jian-Zhong

2012-02-13

We propose and theoretically demonstrate an all-optical method for directly generating all-optical random numbers from pulse amplitude chaos produced by a mode-locked fiber ring laser. Under an appropriate pump intensity, the mode-locked laser can experience a quasi-periodic route to chaos. Such a chaos consists of a stream of pulses with a fixed repetition frequency but random intensities. In this method, we do not require sampling procedure and external triggered clocks but directly quantize the chaotic pulses stream into random number sequence via an all-optical flip-flop. Moreover, our simulation results show that the pulse amplitude chaos has no periodicity and possesses a highly symmetric distribution of amplitude. Thus, in theory, the obtained random number sequence without post-processing has a high-quality randomness verified by industry-standard statistical tests.

Collaborative development for setup, execution, sharing and analytics of complex NMR experiments.

PubMed

Irvine, Alistair G; Slynko, Vadim; Nikolaev, Yaroslav; Senthamarai, Russell R P; Pervushin, Konstantin

2014-02-01

Factory settings of NMR pulse sequences are rarely ideal for every scenario in which they are utilised. The optimisation of NMR experiments has for many years been performed locally, with implementations often specific to an individual spectrometer. Furthermore, these optimised experiments are normally retained solely for the use of an individual laboratory, spectrometer or even single user. Here we introduce a web-based service that provides a database for the deposition, annotation and optimisation of NMR experiments. The application uses a Wiki environment to enable the collaborative development of pulse sequences. It also provides a flexible mechanism to automatically generate NMR experiments from deposited sequences. Multidimensional NMR experiments of proteins and other macromolecules consume significant resources, in terms of both spectrometer time and effort required to analyse the results. Systematic analysis of simulated experiments can enable optimal allocation of NMR resources for structural analysis of proteins. Our web-based application (http://nmrplus.org) provides all the necessary information, includes the auxiliaries (waveforms, decoupling sequences etc.), for analysis of experiments by accurate numerical simulation of multidimensional NMR experiments. The online database of the NMR experiments, together with a systematic evaluation of their sensitivity, provides a framework for selection of the most efficient pulse sequences. The development of such a framework provides a basis for the collaborative optimisation of pulse sequences by the NMR community, with the benefits of this collective effort being available to the whole community. Copyright © 2013 Elsevier Inc. All rights reserved.

Laser-induced periodic surface structures on titanium upon single- and two-color femtosecond double-pulse irradiation.

PubMed

Höhm, Sandra; Rosenfeld, Arkadi; Krüger, Jörg; Bonse, Jörn

2015-10-05

Single- and two-color double-fs-pulse experiments were performed on titanium to study the dynamics of the formation of laser-induced periodic surface structures (LIPSS). A Mach-Zehnder inter-ferometer generated polarization controlled (parallel or cross-polarized) double-pulse sequences in two configurations - either at 800 nm only, or at 400 and 800 nm wavelengths. The inter-pulse delays of the individual 50-fs pulses ranged up to some tens of picoseconds. Multiple of these single- or two-color double-fs-pulse sequences were collinearly focused by a spherical mirror to the sample surface. In both experimental configurations, the peak fluence of each individual pulse was kept below its respective ablation threshold and only the joint action of both pulses lead to the formation of LIPSS. Their resulting characteristics were analyzed by scanning electron microscopy and the periods were quantified by Fourier analyses. The LIPSS periods along with the orientation allow a clear identification of the pulse which dominates the energy coupling to the material. A plasmonic model successfully explains the delay-dependence of the LIPSS on titanium and confirms the importance of the ultrafast energy deposition stage for LIPSS formation.

Enhanced photon indistinguishability in pulse-driven quantum emitters

NASA Astrophysics Data System (ADS)

Fotso, Herbert F.

2017-04-01

Photon indistinguishability is an essential ingredient for the realization of scalable quantum networks. For quantum bits in the solid state, this is hindered by spectral diffusion, the uncontrolled random drift of the emission/absorption spectrum as a result of fluctuations in the emitter's environment. We study optical properties of a quantum emitter in the solid state when it is driven by a periodic sequence of optical pulses with finite detuning with respect to the emitter. We find that a pulse sequence can effectively mitigate spectral diffusion and enhance photon indistinguishability. The bulk of the emission occurs at a set target frequency; Photon indistinguishability is enhanced and is restored to its optimal value after every even pulse. Also, for moderate values of the sequence period and of the detuning, both the emission spectrum and the absorption spectrum have lineshapes with little dependence on the detuning. We describe the solution and the evolution of the emission/absorption spectrum as a function time.

Determination of dipole coupling constants using heteronuclear multiple quantum NMR

NASA Astrophysics Data System (ADS)

Weitekamp, D. P.; Garbow, J. R.; Pines, A.

1982-09-01

The problem of extracting dipole couplings from a system of N spins I = 1/2 and one spin S by NMR techniques is analyzed. The resolution attainable using a variety of single quantum methods is reviewed. The theory of heteronuclear multiple quantum (HMQ) NMR is developed, with particular emphasis being placed on the superior resolution available in HMQ spectra. Several novel pulse sequences are introduced, including a two-step method for the excitation of HMQ coherence. Experiments on partially oriented [1-13C] benzene demonstrate the excitation of the necessary HMQ coherence and illustrate the calculation of relative line intensities. Spectra of high order HMQ coherence under several different effective Hamiltonians achievable by multiple pulse sequences are discussed. A new effective Hamiltonian, scalar heteronuclear recoupled interactions by multiple pulse (SHRIMP), achieved by the simultaneous irradiation of both spin species with the same multiple pulse sequence, is introduced. Experiments are described which allow heteronuclear couplings to be correlated with an S-spin spreading parameter in spectra free of inhomogeneous broadening.