An extracytoplasmic function sigma factor cotranscribed with its cognate anti-sigma factor confers tolerance to NaCl, ethanol and methylene blue in Azospirillum brasilense Sp7.

PubMed

Mishra, Mukti Nath; Kumar, Santosh; Gupta, Namrata; Kaur, Simarjot; Gupta, Ankush; Tripathi, Anil K

2011-04-01

Azospirillum brasilense, a plant-growth-promoting rhizobacterium, is exposed to changes in its abiotic environment, including fluctuations in temperature, salinity, osmolarity, oxygen concentration and nutrient concentration, in the rhizosphere and in the soil. Since extra-cytoplasmic function (ECF) sigma factors play an important role in stress adaptation, we analysed the role of ECF sigma factor (also known as RpoE or σ(E)) in abiotic stress tolerance in A. brasilense. An in-frame rpoE deletion mutant of A. brasilense Sp7 was carotenoidless and slow-growing, and was sensitive to salt, ethanol and methylene blue stress. Expression of rpoE in the rpoE deletion mutant complemented the defects in growth, carotenoid biosynthesis and sensitivity to different stresses. Based on data from reverse transcriptase-PCR, a two-hybrid assay and a pull-down assay, we present evidence that rpoE is cotranscribed with chrR and the proteins synthesized from these two overlapping genes interact with each other. Identification of the transcription start site by 5' rapid amplification of cDNA ends showed that the rpoE-chrR operon was transcribed by two promoters. The proximal promoter was less active than the distal promoter, whose consensus sequence was characteristic of RpoE-dependent promoters found in alphaproteobacteria. Whereas the proximal promoter was RpoE-independent and constitutively expressed, the distal promoter was RpoE-dependent and strongly induced in response to stationary phase and elevated levels of ethanol, salt, heat and methylene blue. This study shows the involvement of RpoE in controlling carotenoid synthesis as well as in tolerance to some abiotic stresses in A. brasilense, which might be critical in the adaptation, survival and proliferation of this rhizobacterium in the soil and rhizosphere under stressful conditions.

Carotenoid Biosynthetic Pathways Are Regulated by a Network of Multiple Cascades of Alternative Sigma Factors in Azospirillum brasilense Sp7.

PubMed

Rai, Ashutosh Kumar; Dubey, Ashutosh Prakash; Kumar, Santosh; Dutta, Debashis; Mishra, Mukti Nath; Singh, Bhupendra Narain; Tripathi, Anil Kumar

2016-11-01

Carotenoids constitute an important component of the defense system against photooxidative stress in bacteria. In Azospirillum brasilense Sp7, a nonphotosynthetic rhizobacterium, carotenoid synthesis is controlled by a pair of extracytoplasmic function sigma factors (RpoEs) and their cognate zinc-binding anti-sigma factors (ChrRs). Its genome harbors two copies of the gene encoding geranylgeranyl pyrophosphate synthase (CrtE), the first critical step in the carotenoid biosynthetic pathway in bacteria. Inactivation of each of two crtE paralogs found in A. brasilense caused reduction in carotenoid content, suggesting their involvement in carotenoid synthesis. However, the effect of crtE1 deletion was more pronounced than that of crtE2 deletion. Out of the five paralogs of rpoH in A. brasilense, overexpression of rpoH1 and rpoH2 enhanced carotenoid synthesis. Promoters of crtE2 and rpoH2 were found to be dependent on RpoH2 and RpoE1, respectively. Using a two-plasmid system in Escherichia coli, we have shown that the crtE2 gene of A. brasilense Sp7 is regulated by two cascades of sigma factors: one consisting of RpoE1and RpoH2 and the other consisting of RpoE2 and RpoH1. In addition, expression of crtE1 was upregulated indirectly by RpoE1 and RpoE2. This study shows, for the first time in any carotenoid-producing bacterium, that the regulation of carotenoid biosynthetic pathway involves a network of multiple cascades of alternative sigma factors. Carotenoids play a very important role in coping with photooxidative stress in prokaryotes and eukaryotes. Although extracytoplasmic function (ECF) sigma factors are known to directly regulate the expression of carotenoid biosynthetic genes in bacteria, regulation of carotenoid biosynthesis by one or multiple cascades of sigma factors had not been reported. This study provides the first evidence of the involvement of multiple cascades of sigma factors in the regulation of carotenoid synthesis in any bacterium by showing the regulation of a gene encoding geranylgeranyl pyrophosphate synthase (crtE2) by RpoE1→RpoH2→CrtE2 and RpoE2→RpoH1→CrtE2 cascades in A. brasilense It also provides an insight into existence of an additional cascade or cascades regulating expression of another paralog of crtE. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Carotenoid Biosynthetic Pathways Are Regulated by a Network of Multiple Cascades of Alternative Sigma Factors in Azospirillum brasilense Sp7

PubMed Central

Rai, Ashutosh Kumar; Dubey, Ashutosh Prakash; Kumar, Santosh; Dutta, Debashis; Mishra, Mukti Nath; Singh, Bhupendra Narain

2016-01-01

ABSTRACT Carotenoids constitute an important component of the defense system against photooxidative stress in bacteria. In Azospirillum brasilense Sp7, a nonphotosynthetic rhizobacterium, carotenoid synthesis is controlled by a pair of extracytoplasmic function sigma factors (RpoEs) and their cognate zinc-binding anti-sigma factors (ChrRs). Its genome harbors two copies of the gene encoding geranylgeranyl pyrophosphate synthase (CrtE), the first critical step in the carotenoid biosynthetic pathway in bacteria. Inactivation of each of two crtE paralogs found in A. brasilense caused reduction in carotenoid content, suggesting their involvement in carotenoid synthesis. However, the effect of crtE1 deletion was more pronounced than that of crtE2 deletion. Out of the five paralogs of rpoH in A. brasilense, overexpression of rpoH1 and rpoH2 enhanced carotenoid synthesis. Promoters of crtE2 and rpoH2 were found to be dependent on RpoH2 and RpoE1, respectively. Using a two-plasmid system in Escherichia coli, we have shown that the crtE2 gene of A. brasilense Sp7 is regulated by two cascades of sigma factors: one consisting of RpoE1and RpoH2 and the other consisting of RpoE2 and RpoH1. In addition, expression of crtE1 was upregulated indirectly by RpoE1 and RpoE2. This study shows, for the first time in any carotenoid-producing bacterium, that the regulation of carotenoid biosynthetic pathway involves a network of multiple cascades of alternative sigma factors. IMPORTANCE Carotenoids play a very important role in coping with photooxidative stress in prokaryotes and eukaryotes. Although extracytoplasmic function (ECF) sigma factors are known to directly regulate the expression of carotenoid biosynthetic genes in bacteria, regulation of carotenoid biosynthesis by one or multiple cascades of sigma factors had not been reported. This study provides the first evidence of the involvement of multiple cascades of sigma factors in the regulation of carotenoid synthesis in any bacterium by showing the regulation of a gene encoding geranylgeranyl pyrophosphate synthase (crtE2) by RpoE1→RpoH2→CrtE2 and RpoE2→RpoH1→CrtE2 cascades in A. brasilense. It also provides an insight into existence of an additional cascade or cascades regulating expression of another paralog of crtE. PMID:27551017

Campylobacter protein oxidation influences epithelial cell invasion or intracellular survival as well as intestinal tract colonization in chickens.

PubMed

Lasica, A M; Wyszynska, A; Szymanek, K; Majewski, P; Jagusztyn-Krynicka, E K

2010-01-01

The Dsb family of redox proteins catalyzes disulfide bond formation and isomerization. Since mutations in dsb genes change the conformation and stability of many extracytoplasmic proteins, and since many virulence factors of pathogenic bacteria are extracytoplasmic, inactivation of dsb genes often results in pathogen attenuation. This study investigated the role of 2 membrane-bound oxidoreductases, DsbB and DsbI, in the Campylobacter jejuni oxidative Dsb pathway. Campylobacter mutants, lacking DsbB or DsbI or both, were constructed by allelic replacement and used in the human intestinal epithelial T84 cell line for the gentamicin protection assay (invasion assay) and chicken colonization experiments. In C. coli strain 23/1, the inactivation of the dsbB or dsbI gene separately did not significantly affect the colonization process. However, simultaneous disruption of both membrane-bound oxidoreductase genes significantly decreased the strain’s ability to colonize chicken intestines. Moreover, C. jejuni strain 81-176 with mutated dsbB or dsbI genes showed reduced invasion/intracellular survival abilities. No cells of the double mutants (dsbB⁻ dsbI⁻) of C. jejuni 81-176 were recovered from human cells after 3 h of invasion.

Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ-factor activity by proteolysis

PubMed Central

Jaiswal, Ravi K.; Prabha, Tangirala Surya; Manjeera, Gowravaram; Gopal, Balasubramanian

2013-01-01

The relative levels of different σ factors dictate the expression profile of a bacterium. Extracytoplasmic function σ factors synchronize the transcriptional profile with environmental conditions. The cellular concentration of free extracytoplasmic function σ factors is regulated by the localization of this protein in a σ/anti-σ complex. Anti-σ factors are multi-domain proteins with a receptor to sense environmental stimuli and a conserved anti-σ domain (ASD) that binds a σ factor. Here we describe the structure of Mycobacterium tuberculosis anti-σD (RsdA) in complex with the -35 promoter binding domain of σD (σD4). We note distinct conformational features that enable the release of σD by the selective proteolysis of the ASD in RsdA. The structural and biochemical features of the σD/RsdA complex provide a basis to reconcile diverse regulatory mechanisms that govern σ/anti-σ interactions despite high overall structural similarity. Multiple regulatory mechanisms embedded in an ASD scaffold thus provide an elegant route to rapidly re-engineer the expression profile of a bacterium in response to an environmental stimulus. PMID:23314154

The Ca2+ induced two-component system, CvsSR regulates the Type III secretion system and the extracytoplasmic function sigma-factor AlgU in Pseudomonas syringae pv. tomato DC3000

USDA-ARS?s Scientific Manuscript database

Two-component systems (TCSs) of bacteria regulate many different aspects of the bacterial life cycle including pathogenesis. Most TCSs remain uncharacterized with no information about the signal(s) or regulatory targets and/or role in bacterial pathogenesis. Here, we characterize a TCS in the plant-...

Identification of Disulphide Stress-responsive Extracytoplasmic Function Sigma Factors in Rothia mucilaginosa

DTIC Science & Technology

2013-01-01

GC) content of deoxyribonucleic acid (DNA).1 This organism belongs to the actinobacteria , which includes the genera Actinomyces, Corynebacterium...however, it still remains unclear how Rothia species respond to environmental stress. The responsiveness and adaptation of a few actinobacteria to various... actinobacteria , the number of sigma factors in R. mucilaginosa is relatively small (microbial signal transduction (MiST2) database, http://mistdb.com/); however

Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain

PubMed Central

Wecke, Tina; Halang, Petra; Staroń, Anna; Dufour, Yann S; Donohue, Timothy J; Mascher, Thorsten

2012-01-01

Bacteria need signal transducing systems to respond to environmental changes. Next to one- and two-component systems, alternative σ factors of the extra-cytoplasmic function (ECF) protein family represent the third fundamental mechanism of bacterial signal transduction. A comprehensive classification of these proteins identified more than 40 phylogenetically distinct groups, most of which are not experimentally investigated. Here, we present the characterization of such a group with unique features, termed ECF41. Among analyzed bacterial genomes, ECF41 σ factors are widely distributed with about 400 proteins from 10 different phyla. They lack obvious anti-σ factors that typically control activity of other ECF σ factors, but their structural genes are often predicted to be cotranscribed with carboxymuconolactone decarboxylases, oxidoreductases, or epimerases based on genomic context conservation. We demonstrate for Bacillus licheniformis and Rhodobacter sphaeroides that the corresponding genes are preceded by a highly conserved promoter motif and are the only detectable targets of ECF41-dependent gene regulation. In contrast to other ECF σ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for σ factor activity. Our data demonstrate that ECF41 σ factors are regulated by a novel mechanism based on the presence of a fused regulatory domain. PMID:22950025

The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response

PubMed Central

Butcher, Bronwyn G.; Bao, Zhongmeng; Wilson, Janet; Swingle, Bryan; Filiatrault, Melanie; Schneider, David; Cartinhour, Samuel

2017-01-01

The bacterial plant pathogen Pseudomonas syringae adapts to changes in the environment by modifying its gene expression profile. In many cases, the response is mediated by the activation of extracytoplasmic function (ECF) sigma factors that direct RNA polymerase to transcribe specific sets of genes. In this study we focus on PSPTO_1043, one of ten ECF sigma factors in P. syringae pv. tomato DC3000 (DC3000). PSPTO_1043, together with PSPTO_1042, encode an RpoERsp/ChrR-like sigma/anti-sigma factor pair. Although this gene pair is unique to the P. syringae group among the pseudomonads, homologous genes can be found in photosynthetic genera such as Rhodospirillum, Thalassospira, Phaeospirillum and Parvibaculum. Using ChIP-Seq, we detected 137 putative PSPTO_1043 binding sites and identified a likely promoter motif. We characterized 13 promoter candidates, six of which regulate genes that appear to be found only in P. syringae. PSPTO_1043 responds to the presence of singlet oxygen (1O2) and tert-butyl hydroperoxide (tBOOH) and several of the genes regulated by PSPTO_1043 appear to be involved in response to oxidative stress. PMID:28700608

The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response.

PubMed

Butcher, Bronwyn G; Bao, Zhongmeng; Wilson, Janet; Stodghill, Paul; Swingle, Bryan; Filiatrault, Melanie; Schneider, David; Cartinhour, Samuel

2017-01-01

The bacterial plant pathogen Pseudomonas syringae adapts to changes in the environment by modifying its gene expression profile. In many cases, the response is mediated by the activation of extracytoplasmic function (ECF) sigma factors that direct RNA polymerase to transcribe specific sets of genes. In this study we focus on PSPTO_1043, one of ten ECF sigma factors in P. syringae pv. tomato DC3000 (DC3000). PSPTO_1043, together with PSPTO_1042, encode an RpoERsp/ChrR-like sigma/anti-sigma factor pair. Although this gene pair is unique to the P. syringae group among the pseudomonads, homologous genes can be found in photosynthetic genera such as Rhodospirillum, Thalassospira, Phaeospirillum and Parvibaculum. Using ChIP-Seq, we detected 137 putative PSPTO_1043 binding sites and identified a likely promoter motif. We characterized 13 promoter candidates, six of which regulate genes that appear to be found only in P. syringae. PSPTO_1043 responds to the presence of singlet oxygen (1O2) and tert-butyl hydroperoxide (tBOOH) and several of the genes regulated by PSPTO_1043 appear to be involved in response to oxidative stress.

The cell envelope stress response of Bacillus subtilis: from static signaling devices to dynamic regulatory network.

PubMed

Radeck, Jara; Fritz, Georg; Mascher, Thorsten

2017-02-01

The cell envelope stress response (CESR) encompasses all regulatory events that enable a cell to protect the integrity of its envelope, an essential structure of any bacterial cell. The underlying signaling network is particularly well understood in the Gram-positive model organism Bacillus subtilis. It consists of a number of two-component systems (2CS) and extracytoplasmic function σ factors that together regulate the production of both specific resistance determinants and general mechanisms to protect the envelope against antimicrobial peptides targeting the biogenesis of the cell wall. Here, we summarize the current picture of the B. subtilis CESR network, from the initial identification of the corresponding signaling devices to unraveling their interdependence and the underlying regulatory hierarchy within the network. In the course of detailed mechanistic studies, a number of novel signaling features could be described for the 2CSs involved in mediating CESR. This includes a novel class of so-called intramembrane-sensing histidine kinases (IM-HKs), which-instead of acting as stress sensors themselves-are activated via interprotein signal transfer. Some of these IM-HKs are involved in sensing the flux of antibiotic resistance transporters, a unique mechanism of responding to extracellular antibiotic challenge.

Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA.

PubMed

Lee, Eun-Jin; Groisman, Eduardo A

2012-06-13

The facultative intracellular pathogen Salmonella enterica resides within a membrane-bound compartment inside macrophages. This compartment must be acidified for Salmonella to survive within macrophages, possibly because acidic pH promotes expression of Salmonella virulence proteins. We reasoned that Salmonella might sense its surroundings have turned acidic not only upon protonation of the extracytoplasmic domain of a protein sensor but also by an increase in cytosolic ATP levels, because conditions that enhance the proton gradient across the bacterial inner membrane stimulate ATP synthesis. Here we report that an increase in cytosolic ATP promotes transcription of the coding region for the virulence gene mgtC, which is the most highly induced horizontally acquired gene when Salmonella is inside macrophages. This transcript is induced both upon media acidification and by physiological conditions that increase ATP levels independently of acidification. ATP is sensed by the coupling/uncoupling of transcription of the unusually long mgtC leader messenger RNA and translation of a short open reading frame located in this region. A mutation in the mgtC leader messenger RNA that eliminates the response to ATP hinders mgtC expression inside macrophages and attenuates Salmonella virulence in mice. Our results define a singular example of an ATP-sensing leader messenger RNA. Moreover, they indicate that pathogens can interpret extracellular cues by the impact they have on cellular metabolites.

Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs

PubMed Central

Guzina, Jelena

2016-01-01

ABSTRACT Extracytoplasmic function (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both −35 and −10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended −10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ2, which is responsible for the interaction with the identified extension of the −10 element. Interestingly, a similar protein motif is found C-terminal of domain σ2 in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the −10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable −35 element and σ4 domain, which we identify in a homologous phage, 7-11, indicating that the extended −10 element can compensate for the lack of −35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested. IMPORTANCE ECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors. PMID:27137497

The extracytoplasmic function sigma factor SigY is important for efficient maintenance of the Spβ prophage that encodes sublancin in Bacillus subtilis.

PubMed

Mendez, Rebecca; Gutierrez, Alba; Reyes, Jasmin; Márquez-Magaña, Leticia

2012-06-01

Many strains of the soil bacterium Bacillus subtilis are capable of producing and being resistant to the antibiotic sublancin because they harbor the Spβ prophage. This 135 kb viral genome is integrated into the circular DNA chromosome of B. subtilis, and contains genes for the production of and resistance to sublancin. We investigated the role of SigY in sublancin production and resistance, finding that it is important for efficient maintenance of the Spβ prophage. We were unable to detect the prophage in mutants lacking SigY. Additionally, these mutants were no longer able to produce sublancin, were sensitive to killing by this factor, and displayed a delay in sporulation. Wild-type cells with normal SigY activity were found to partially lose the Spβ prophage during growth and early sporulation, suggesting a mechanism for the bistable outcome of sibling cells capable of killing and of being killed. The appropriate regulation of SigY appears to be essential for growth as evidenced by the inability to disrupt the gene for its putative antisigma. Our results confirm a role for SigY in antibiotic production and resistance, as has been found for other members of the extracytoplasmic function sigma factor family in B. subtilis, and shows that this role is achieved by affecting maintenance of the Spβ prophage.

Direct cell-cell contact activates SigM to express the ESX-4 secretion system in Mycobacterium smegmatis.

PubMed

Clark, Ryan R; Judd, Julius; Lasek-Nesselquist, Erica; Montgomery, Sarah A; Hoffmann, Jennifer G; Derbyshire, Keith M; Gray, Todd A

2018-06-25

Conjugal cell-cell contact between strains of Mycobacterium smegmatis induces the esxUT transcript, which encodes the putative primary substrates of the ESAT-6 secretion system 4 (ESX-4) secretion system. This recipient response was required for conjugal transfer of chromosomal DNA from the donor strain. Here we show that the extracytoplasmic σ factor, SigM, is a cell contact-dependent activator of ESX-4 expression and is required for conjugal transfer of DNA in the recipient strain. The SigM regulon includes genes outside the seven-gene core esx4 locus that we show are also required for conjugation, and we show that some of these SigM-induced proteins likely function through ESX-4. A fluorescent reporter revealed that SigM is specifically activated in recipient cells in direct contact with donor cells. Coculture RNA-seq experiments indicated that SigM regulon induction occurred early and before transconjugants are detected. This work supports a model wherein donor contact with the recipient cell surface inactivates the transmembrane anti-SigM, thereby releasing SigM. Free SigM induces an extended ESX-4 secretion system, resulting in changes that facilitate chromosomal transfer. The contact-dependent inactivation of an extracytoplasmic σ-factor that tightly controls ESX-4 activity suggests a mechanism dedicated to detect, and appropriately respond to, external stimuli from mycobacteria.

Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response

DOE PAGES

Allen, Michael S.; Hurst, Gregory B.; Lu, Tse-Yuan S.; ...

2015-04-08

Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. In this paper, to begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σ RPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensusmore » sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Finally, taken together, these data suggest that ECF σ RPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.« less

Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response

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

Allen, Michael S.; Hurst, Gregory B.; Lu, Tse-Yuan S.

Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. In this paper, to begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σ RPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensusmore » sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Finally, taken together, these data suggest that ECF σ RPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.« less

Campylobacter jejuni dsb gene expression is regulated by iron in a Fur-dependent manner and by a translational coupling mechanism

PubMed Central

2011-01-01

Background Many bacterial extracytoplasmic proteins are stabilized by intramolecular disulfide bridges that are formed post-translationally between their cysteine residues. This protein modification plays an important role in bacterial pathogenesis, and is facilitated by the Dsb (disulfide bond) family of the redox proteins. These proteins function in two parallel pathways in the periplasmic space: an oxidation pathway and an isomerization pathway. The Dsb oxidative pathway in Campylobacter jejuni is more complex than the one in the laboratory E. coli K-12 strain. Results In the C. jejuni 81-176 genome, the dsb genes of the oxidative pathway are arranged in three transcriptional units: dsbA2-dsbB-astA, dsbA1 and dba-dsbI. Their transcription responds to an environmental stimulus - iron availability - and is regulated in a Fur-dependent manner. Fur involvement in dsb gene regulation was proven by a reporter gene study in a C. jejuni wild type strain and its isogenic fur mutant. An electrophoretic mobility shift assay (EMSA) confirmed that analyzed genes are members of the Fur regulon but each of them is regulated by a disparate mechanism, and both the iron-free and the iron-complexed Fur are able to bind in vitro to the C. jejuni promoter regions. This study led to identification of a new iron- and Fur-regulated promoter that drives dsbA1 gene expression in an indirect way. Moreover, the present work documents that synthesis of DsbI oxidoreductase is controlled by the mechanism of translational coupling. The importance of a secondary dba-dsbI mRNA structure for dsbI mRNA translation was verified by estimating individual dsbI gene expression from its own promoter. Conclusions The present work shows that iron concentration is a significant factor in dsb gene transcription. These results support the concept that iron concentration - also through its influence on dsb gene expression - might control the abundance of extracytoplasmic proteins during different stages of infection. Our work further shows that synthesis of the DsbI membrane oxidoreductase is controlled by a translational coupling mechanism. The dba expression is not only essential for the translation of the downstream dsbI gene, but also Dba protein that is produced might regulate the activity and/or stability of DsbI. PMID:21787430

Campylobacter jejuni dsb gene expression is regulated by iron in a Fur-dependent manner and by a translational coupling mechanism.

PubMed

Grabowska, Anna D; Wandel, Michał P; Łasica, Anna M; Nesteruk, Monika; Roszczenko, Paula; Wyszyńska, Agnieszka; Godlewska, Renata; Jagusztyn-Krynicka, Elzbieta K

2011-07-25

Many bacterial extracytoplasmic proteins are stabilized by intramolecular disulfide bridges that are formed post-translationally between their cysteine residues. This protein modification plays an important role in bacterial pathogenesis, and is facilitated by the Dsb (disulfide bond) family of the redox proteins. These proteins function in two parallel pathways in the periplasmic space: an oxidation pathway and an isomerization pathway. The Dsb oxidative pathway in Campylobacter jejuni is more complex than the one in the laboratory E. coli K-12 strain. In the C. jejuni 81-176 genome, the dsb genes of the oxidative pathway are arranged in three transcriptional units: dsbA2-dsbB-astA, dsbA1 and dba-dsbI. Their transcription responds to an environmental stimulus - iron availability - and is regulated in a Fur-dependent manner. Fur involvement in dsb gene regulation was proven by a reporter gene study in a C. jejuni wild type strain and its isogenic fur mutant. An electrophoretic mobility shift assay (EMSA) confirmed that analyzed genes are members of the Fur regulon but each of them is regulated by a disparate mechanism, and both the iron-free and the iron-complexed Fur are able to bind in vitro to the C. jejuni promoter regions. This study led to identification of a new iron- and Fur-regulated promoter that drives dsbA1 gene expression in an indirect way. Moreover, the present work documents that synthesis of DsbI oxidoreductase is controlled by the mechanism of translational coupling. The importance of a secondary dba-dsbI mRNA structure for dsbI mRNA translation was verified by estimating individual dsbI gene expression from its own promoter. The present work shows that iron concentration is a significant factor in dsb gene transcription. These results support the concept that iron concentration - also through its influence on dsb gene expression - might control the abundance of extracytoplasmic proteins during different stages of infection. Our work further shows that synthesis of the DsbI membrane oxidoreductase is controlled by a translational coupling mechanism. The dba expression is not only essential for the translation of the downstream dsbI gene, but also Dba protein that is produced might regulate the activity and/or stability of DsbI.

The extracellular matrix of the oleolytic biofilms of Marinobacter hydrocarbonoclasticus comprises cytoplasmic proteins and T2SS effectors that promote growth on hydrocarbons and lipids.

PubMed

Ennouri, Habiba; d'Abzac, Paul; Hakil, Florence; Branchu, Priscilla; Naïtali, Murielle; Lomenech, Anne-Marie; Oueslati, Ridha; Desbrières, Jacques; Sivadon, Pierre; Grimaud, Régis

2017-01-01

The assimilation of the nearly water insoluble substrates hydrocarbons and lipids by bacteria entails specific adaptations such as the formation of oleolytic biofilms. The present article reports that the extracellular matrix of an oleolytic biofilm formed by Marinobacter hydrocarbonoclasticus at n-hexadecane-water interfaces is largely composed of proteins typically cytoplasmic such as translation factors and chaperones, and a lesser amount of proteins of unknown function that are predicted extra-cytoplasmic. Matrix proteins appear to form a structured film on hydrophobic interfaces and were found mandatory for the development of biofilms on lipids, alkanes and polystyrene. Exo-proteins secreted through the type-2 secretion system (T2SS) were shown to be essential for the formation of oleolytic biofilms on both alkanes and triglycerides. The T2SS effector involved in biofilm formation on triglycerides was identified as a lipase. In the case of biofilm formation on n-hexadecane, the T2SS effector is likely involved in the mass transfer, capture or transport of alkanes. We propose that M. hydrocarbonoclasticus uses cytoplasmic proteins released by cell lysis to form a proteinaceous matrix and dedicated proteins secreted through the T2SS to act specifically in the assimilation pathways of hydrophobic substrates. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Burkholderia cepacia rpoE gene is not involved in exopolysaccharide production and onion pathogenicity.

PubMed

Devescovi, Giulia; Venturi, Vittorio

2006-03-01

Burkholderia cepacia was originally described as the causative agent of bacterial rot of onions, and it has now emerged as an important opportunistic pathogen causing severe chronic lung infections in patients having cystic fibrosis. Burkholderia cepacia is now classified into nine very closely related species (previously designated as genomovars), all of which have been isolated from both environmental and clinical sources and are collectively known as the B. cepacia complex. The alternative extracytoplasmic function sigma factor, sigmaE, has been determined in several bacterial species as making substantial contributions to bacterial survival under stress conditions. Here, we report the identification and characterization of the rpoE gene, encoding sigmaE, of B. cepacia. It is highly similar to sigmaE of other bacteria, including Escherichia coli and Pseudomonas aeruginosa. Studies using an rpoE knockout mutant of B. cepacia revealed that many stress adaptations, including osmotic, oxidative, desiccation, carbon, and nitrogen stress, were independent of sigmaE. Similarly, biofilm formation; production of exopolysaccharides, N-acyl homoserine lactones, and several exoenzymes; and onion pathogenicity were not affected by the absence of sigmaE. In contrast, sigmaE contributed to the adaptation to heat stress and phosphate starvation.

Circuitry linking the global Csr and σE-dependent cell envelope stress response systems.

PubMed

Yakhnin, Helen; Aichele, Robert; Ades, Sarah E; Romeo, Tony; Babitzke, Paul

2017-09-18

CsrA of Escherichia coli is an RNA-binding protein that globally regulates a wide variety of cellular processes and behaviors including carbon metabolism, motility, biofilm formation, and the stringent response. CsrB and CsrC are sRNAs that sequester CsrA, thereby preventing CsrA-mRNA interaction. RpoE (σ E ) is the extracytoplasmic stress response sigma factor of E. coli Previous RNA-seq studies identified rpoE mRNA as a CsrA target. Here we explored the regulation of rpoE by CsrA and found that CsrA represses rpoE translation. Gel mobility shift, footprint and toeprint studies identified three CsrA binding sites in the rpoE leader transcript, one of which overlaps the rpoE Shine-Dalgarno (SD) sequence, while another overlaps the rpoE translation initiation codon. Coupled in vitro transcription-translation experiments showed that CsrA represses rpoE translation by binding to these sites. We further demonstrate that σ E indirectly activates transcription of csrB and csrC , leading to increased sequestration of CsrA such that repression of rpoE by CsrA is reduced. We propose that the Csr system fine-tunes the σ E -dependent cell envelope stress response. We also identified a 51 amino acid coding sequence whose stop codon overlaps the rpoE start codon, and demonstrate that rpoE is translationally coupled with this upstream open reading frame (ORF51). Loss of coupling reduces rpoE translation by more than 50%. Identification of a translationally coupled ORF upstream of rpoE suggests that this previously unannotated protein may participate in the cell envelope stress response. In keeping with existing nomenclature, we name ORF51 as rseD , resulting in an operon arrangement of rseD-rpoE-rseA-rseB-rseC IMPORTANCE CsrA posttranscriptionally represses genes required for bacterial stress responses, including the stringent response, catabolite repression, and the RpoS (σ S )-mediated general stress response. We show that CsrA represses translation of rpoE , encoding the extracytoplasmic stress response sigma factor and that σ E indirectly activates transcription of csrB and csrC , resulting in reciprocal regulation of these two global regulatory systems. These findings suggest that extracytoplasmic stress leads to derepression of rpoE translation by CsrA, and CsrA-mediated repression helps to reset RpoE abundance to pre-stress levels once envelope damage is repaired. The discovery of an ORF, RseD, translationally coupled with rpoE adds further complexity to translational control of rpoE . Copyright © 2017 American Society for Microbiology.

Ultrastructure and LSU rDNA-based phylogeny of Peridinium lomnickii and description of Chimonodinium gen. nov. (Dinophyceae).

PubMed

Craveiro, Sandra C; Calado, António J; Daugbjerg, Niels; Hansen, Gert; Moestrup, Øjvind

2011-10-01

Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences. Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Serial section examination of Scrippsiella trochoidea, here taken to represent typical Scrippsiella characters, revealed no peduncle and no associated microtubular strands. The molecular phylogeny placed C. lomnickii comb. nov. as a sister group to a clade composed of Thoracosphaera and the pfiesteriaceans. Whereas the lack of information on fine structure of the swimming stage of Thoracosphaera leaves its affinities unexplained, C. lomnickii shares with the pfiesteriaceans the presence of a microtubular basket and the unusual connection between two plates on the left side of the sulcus, involving extra-cytoplasmic fibres. Copyright © 2011 Elsevier GmbH. All rights reserved.

Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation

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

Li, Jie; Nakayasu, Ernesto S.; Overall, Christopher C.

The alternative sigma factor E (σ E) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σ E-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σ E may indirectly participate in post-transcriptional regulation. Here in this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by σ E in Salmonella. We analysed samples from wild type and isogenic rpoE mutant Salmonella cultivated in three different conditions; nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of themore » observed proteome was regulated by σ E combining all three conditions. In different growth conditions, σ E affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by σ E and found that post-transcriptional regulation was responsible for a majority of changes observed in the σ E-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that σ E–mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.« less

Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation

DOE PAGES

Li, Jie; Nakayasu, Ernesto S.; Overall, Christopher C.; ...

2015-02-16

The alternative sigma factor E (σ E) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σ E-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σ E may indirectly participate in post-transcriptional regulation. Here in this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by σ E in Salmonella. We analysed samples from wild type and isogenic rpoE mutant Salmonella cultivated in three different conditions; nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of themore » observed proteome was regulated by σ E combining all three conditions. In different growth conditions, σ E affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by σ E and found that post-transcriptional regulation was responsible for a majority of changes observed in the σ E-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that σ E–mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.« less

Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ E-regulated SPI-2 gene expression

DOE PAGES

Li, Jie; Overall, Christopher C.; Nakayasu, Ernesto S.; ...

2015-02-10

The extracytoplasmic functioning sigma factor σ E is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well characterized, especially during infection. Here we used microarray to identify genes regulated by σ E in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σ E regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression ofmore » genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σ E in at least one of the three conditions. An important finding is that σ E up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σ E is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σ E and SPI-2 genes, combined with the global regulatory effect of σ E, may account for the lethality of rpoE-deficient Salmonella in murine infection.« less

Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ E-regulated SPI-2 gene expression

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

Li, Jie; Overall, Christopher C.; Nakayasu, Ernesto S.

The extracytoplasmic functioning sigma factor σ E is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well characterized, especially during infection. Here we used microarray to identify genes regulated by σ E in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σ E regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression ofmore » genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σ E in at least one of the three conditions. An important finding is that σ E up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σ E is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σ E and SPI-2 genes, combined with the global regulatory effect of σ E, may account for the lethality of rpoE-deficient Salmonella in murine infection.« less

Crystal structures of two Bordetella pertussis periplasmic receptors contribute to defining a novel pyroglutamic acid binding DctP subfamily.

PubMed

Rucktooa, Prakash; Antoine, Rudy; Herrou, Julien; Huvent, Isabelle; Locht, Camille; Jacob-Dubuisson, Françoise; Villeret, Vincent; Bompard, Coralie

2007-06-29

Gram-negative bacteria have developed several different transport systems for solute uptake. One of these, the tripartite ATP independent periplasmic transport system (TRAP-T), makes use of an extracytoplasmic solute receptor (ESR) which captures specific solutes with high affinity and transfers them to their partner permease complex located in the bacterial inner membrane. We hereby report the structures of DctP6 and DctP7, two such ESRs from Bordetella pertussis. These two proteins display a high degree of sequence and structural similarity and possess the "Venus flytrap" fold characteristic of ESRs, comprising two globular alpha/beta domains hinged together to form a ligand binding cleft. DctP6 and DctP7 both show a closed conformation due to the presence of one pyroglutamic acid molecule bound by highly conserved residues in their respective ligand binding sites. BLAST analyses have revealed that the DctP6 and DctP7 residues involved in ligand binding are strictly present in a number of predicted TRAP-T ESRs from other bacteria. In most cases, the genes encoding these TRAP-T systems are located in the vicinity of a gene coding for a pyroglutamic acid metabolising enzyme. Both the high degree of conservation of these ligand binding residues and the genomic context of these TRAP-T-coding operons in a number of bacterial species, suggest that DctP6 and DctP7 constitute the prototypes of a novel TRAP-T DctP subfamily involved in pyroglutamic acid transport.

The atypical two-subunit σ factor from Bacillus subtilis is regulated by an integral membrane protein and acid stress.

PubMed

Davis, Maria C; Smith, Logan K; MacLellan, Shawn R

2016-02-01

Extracytoplasmic function (ECF) σ factors constitute a major component of the physicochemical sensory apparatus in bacteria. Most ECF σ factors are co-expressed with a negative regulator called an anti-σ factor that binds to its cognate σ factor and sequesters it from productive association with core RNA polymerase (RNAP). Anti-σ factors constitute an important element of signal transduction pathways that mediate an appropriate transcriptional response to changing environmental conditions. The Bacillus subtilis genome encodes seven canonical ECF σ factors and six of these are co-expressed with experimentally verified anti-σ factors. B. subtilis also expresses an ECF-like atypical two-subunit σ factor composed of subunits SigO and RsoA that becomes active after exposure to certain cell-wall-acting antibiotics and to growth under acidic conditions. This work describes the identification and preliminary characterization of a protein (RsiO, formerly YvrL) that constitutes the anti-σ factor cognate to SigO-RsoA. Synthesis of RsiO represses SigO-RsoA-dependent transcription initiation by binding the N-terminus of SigO under neutral (pH 7) conditions. Reconstitution of the SigO-RsoA-RsiO regulatory system into a heterologous host reveals that the imposition of acid stress (pH 5.4) abolishes the ability of RsiO to repress SigO-RsoA-dependent transcription and this correlates with loss of RsiO binding affinity for SigO. A current model for RsiO function indicates that RsiO responds, either directly or indirectly, to increased extracytoplasmic hydrogen ion concentration and becomes inactivated. This results in the release of SigO into the cytoplasm, where it productively associates with RsoA and core RNAP to initiate transcription from target promoters in the cell.

Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019

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

Johnston, Jason W.; Coussens, Nathan P.; Allen, Simon

Nontypeable Haemophilus influenzae is an opportunistic human pathogen causing otitis media in children and chronic bronchitis and pneumonia in patients with chronic obstructive pulmonary disease. The outer membrane of nontypeable H. influenzae is dominated by lipooligosaccharides (LOS), many of which incorporate sialic acid as a terminal nonreducing sugar. Sialic acid has been demonstrated to be an important factor in the survival of the bacteria within the host environment. H. influenzae is incapable of synthesizing sialic acid and is dependent on scavenging free sialic acid from the host environment. To achieve this, H. influenzae utilizes a tripartite ATP-independent periplasmic transporter. Inmore » this study, we characterize the binding site of the extracytoplasmic solute receptor (SiaP) from nontypeable H. influenzae strain 2019. A crystal structure of N-acetyl-5-neuraminic acid (Neu5Ac)-bound SiaP was determined to 1.4 {angstrom} resolution. Thermodynamic characterization of Neu5Ac binding shows this interaction is enthalpically driven with a substantial unfavorable contribution from entropy. This is expected because the binding of SiaP to Neu5Ac is mediated by numerous hydrogen bonds and has several buried water molecules. Point mutations targeting specific amino acids were introduced in the putative binding site. Complementation with the mutated siaP constructs resulted either in full, partial, or no complementation, depending on the role of specific residues. Mass spectrometry analysis of the O-deacylated LOS of the R127K point mutation confirmed the observation of reduced incorporation of Neu5Ac into the LOS. The decreased ability of H. influenzae to import sialic acid had negative effects on resistance to complement-mediated killing and viability of biofilms in vitro, confirming the importance of sialic acid transport to the bacterium.« less

Global variation in elevational diversity patterns

Treesearch

Qinfeng Guo; Douglas A. Kelt; Zhongyu Sun; Hongxiao Liu; Liangjun Hu; Hai Ren; Jun We

2013-01-01

While horizontal gradients of biodiversity have been examined extensively in the past, vertical diversity gradients (elevation, water depth) are attracting increasing attention. We compiled data from 443 elevational gradients involving diverse organisms worldwide to investigate how elevational diversity patterns may vary between the Northern and Southern hemispheres...

Cosmic ray intensity gradients in the solar system

NASA Technical Reports Server (NTRS)

Mckibben, R. B.

1975-01-01

Recent progress in the determination of cosmic-ray intensity gradients is reviewed. Direct satellite measurements of the integral gradient are described together with various types of indirect measurements, including measurements of the Ar-37/Ar-39 ratio in samples from the Lost City meteorite, studies of anisotropies in neutron-monitor counting rates, and analysis of the sidereal diurnal anisotropy observed at a single point on earth. Nucleonic radial gradients and electron gradients measured by satellites in differential energy windows are discussed, and theoretical studies of the physical processes involved in these gradients are summarized. Observations of intensity gradients in heliographic latitude are reported.

Analysis of the link between the redox state and enzymatic activity of the HtrA (DegP) protein from Escherichia coli.

PubMed

Koper, Tomasz; Polit, Agnieszka; Sobiecka-Szkatula, Anna; Wegrzyn, Katarzyna; Scire, Andrea; Figaj, Donata; Kadzinski, Leszek; Zarzecka, Urszula; Zurawa-Janicka, Dorota; Banecki, Bogdan; Lesner, Adam; Tanfani, Fabio; Lipinska, Barbara; Skorko-Glonek, Joanna

2015-01-01

Bacterial HtrAs are proteases engaged in extracytoplasmic activities during stressful conditions and pathogenesis. A model prokaryotic HtrA (HtrA/DegP from Escherichia coli) requires activation to cleave its substrates efficiently. In the inactive state of the enzyme, one of the regulatory loops, termed LA, forms inhibitory contacts in the area of the active center. Reduction of the disulfide bond located in the middle of LA stimulates HtrA activity in vivo suggesting that this S-S bond may play a regulatory role, although the mechanism of this stimulation is not known. Here, we show that HtrA lacking an S-S bridge cleaved a model peptide substrate more efficiently and exhibited a higher affinity for a protein substrate. An LA loop lacking the disulfide was more exposed to the solvent; hence, at least some of the interactions involving this loop must have been disturbed. The protein without S-S bonds demonstrated lower thermal stability and was more easily converted to a dodecameric active oligomeric form. Thus, the lack of the disulfide within LA affected the stability and the overall structure of the HtrA molecule. In this study, we have also demonstrated that in vitro human thioredoxin 1 is able to reduce HtrA; thus, reduction of HtrA can be performed enzymatically.

Contributions of the σ(W) , σ(M) and σ(X) regulons to the lantibiotic resistome of Bacillus subtilis.

PubMed

Kingston, Anthony W; Liao, Xiaojie; Helmann, John D

2013-11-01

In Bacillus subtilis, the extracytoplasmic function (ECF) σ factors σ(M) , σ(W) and σ(X) all contribute to resistance against lantibiotics. Nisin, a model lantibiotic, has a dual mode of action: it inhibits cell wall synthesis by binding lipid II, and this complex also forms pores in the cytoplasmic membrane. These activities can be separated in a nisin hinge-region variant (N20P M21P) that binds lipid II, but no longer permeabilizes membranes. The major contribution of σ(M) to nisin resistance is expression of ltaSa, encoding a stress-activated lipoteichoic acid synthase, and σ(X) functions primarily by activation of the dlt operon controlling d-alanylation of teichoic acids. Together, σ(M) and σ(X) regulate cell envelope structure to decrease access of nisin to its lipid II target. In contrast, σ(W) is principally involved in protection against membrane permeabilization as it provides little protection against the nisin hinge region variant. σ(W) contributes to nisin resistance by regulation of a signal peptide peptidase (SppA), phage shock proteins (PspA and YvlC, a PspC homologue) and tellurite resistance related proteins (YceGHI). These defensive mechanisms are also effective against other lantibiotics such as mersacidin, gallidermin and subtilin and comprise an important subset of the intrinsic antibiotic resistome of B. subtilis. © 2013 John Wiley & Sons Ltd.

Contributions of the σW, σM, and σX Regulons to the Lantibiotic Resistome of Bacillus subtilis

PubMed Central

Kingston, Anthony W.; Liao, Xiaojie; Helmann, John D.

2014-01-01

Summary In Bacillus subtilis, the extracytoplasmic function (ECF) σ factors σM, σW, and σX all contribute to resistance against lantibiotics. Nisin, a model lantibiotic, has a dual mode of action: it inhibits cell wall synthesis by binding lipid II, and this complex also forms pores in the cytoplasmic membrane. These activities can be separated in a nisin hinge-region variant (N20P M21P) that binds lipid II, but no longer permeabilizes membranes. The major contribution of σM to nisin resistance is expression of ltaSa, encoding a stress-activated lipoteichoic acid synthase, and σX functions primarily by activation of the dlt operon controlling D-alanylation of teichoic acids. Together, σM and σX regulate cell envelope structure to decrease access of nisin to its lipid II target. In contrast, σW is principally involved in protection against membrane permeabilization as it provides little protection against the nisin hinge region variant. σW contributes to nisin resistance by regulation of a signal peptide peptidase (SppA), phage shock proteins (PspA and YvlC, a PspC homolog), and tellurite resistance related proteins (YceGHI). These defensive mechanisms are also effective against other lantibiotics such as mersacidin, gallidermin, and subtilin and comprise an important subset of the intrinsic antibiotic resistome of B. subtilis. PMID:23980836

Mutational Pathway Determines Whether Drug Gradients Accelerate Evolution of Drug-Resistant Cells

NASA Astrophysics Data System (ADS)

Greulich, Philip; Waclaw, Bartłomiej; Allen, Rosalind J.

2012-08-01

Drug gradients are believed to play an important role in the evolution of bacteria resistant to antibiotics and tumors resistant to anticancer drugs. We use a statistical physics model to study the evolution of a population of malignant cells exposed to drug gradients, where drug resistance emerges via a mutational pathway involving multiple mutations. We show that a nonuniform drug distribution has the potential to accelerate the emergence of resistance when the mutational pathway involves a long sequence of mutants with increasing resistance, but if the pathway is short or crosses a fitness valley, the evolution of resistance may actually be slowed down by drug gradients. These predictions can be verified experimentally, and may help to improve strategies for combating the emergence of resistance.

AKAP3 synthesis is mediated by RNA binding proteins and PKA signaling during mouse spermiogenesis.

PubMed

Xu, Kaibiao; Yang, Lele; Zhao, Danyun; Wu, Yaoyao; Qi, Huayu

2014-06-01

Mammalian spermatogenesis is regulated by coordinated gene expression in a spatiotemporal manner. The spatiotemporal regulation of major sperm proteins plays important roles during normal development of the male gamete, of which the underlying molecular mechanisms are poorly understood. A-kinase anchoring protein 3 (AKAP3) is one of the major components of the fibrous sheath of the sperm tail that is formed during spermiogenesis. In the present study, we analyzed the expression of sperm-specific Akap3 and the potential regulatory factors of its protein synthesis during mouse spermiogenesis. Results showed that the transcription of Akap3 precedes its protein synthesis by about 2 wk. Nascent AKAP3 was found to form protein complex with PKA and RNA binding proteins (RBPs), including PIWIL1, PABPC1, and NONO, as revealed by coimmunoprecipitation and protein mass spectrometry. RNA electrophoretic gel mobility shift assay showed that these RBPs bind sperm-specific mRNAs, of which proteins are synthesized during the elongating stage of spermiogenesis. Biochemical and cell biological experiments demonstrated that PIWIL1, PABPC1, and NONO interact with each other and colocalize in spermatids' RNA granule, the chromatoid body. In addition, NONO was found in extracytoplasmic granules in round spermatids, whereas PIWIL1 and PABPC1 were diffusely localized in cytoplasm of elongating spermatids, indicating their participation at different steps of mRNA metabolism during spermatogenesis. Interestingly, type I PKA subunits colocalize with PIWIL1 and PABPC1 in the cytoplasm of elongating spermatids and cosediment with the RBPs in polysomal fractions on sucrose gradients. Further biochemical analyses revealed that activation of PKA positively regulates AKAP3 protein synthesis without changing its mRNA level in elongating spermatids. Taken together, these results indicate that PKA signaling directly participates in the regulation of protein translation in postmeiotic male germ cells, underscoring molecular mechanisms that regulate protein synthesis during mouse spermiogenesis. © 2014 by the Society for the Study of Reproduction, Inc.

ςBldN, an Extracytoplasmic Function RNA Polymerase Sigma Factor Required for Aerial Mycelium Formation in Streptomyces coelicolor A3(2)

PubMed Central

Bibb, Maureen J.; Molle, Virginie; Buttner, Mark J.

2000-01-01

Sporulation mutants of Streptomyces coelicolor appear white because they are defective in the synthesis of the gray polyketide spore pigment, and such white (whi) mutants have been used to define 13 sporulation loci. whiN, one of five new whi loci identified in a recent screen of NTG (N-methyl-N′-nitro-N-nitrosoguanidine)-induced whi strains (N. J. Ryding et al., J. Bacteriol. 181:5419–5425, 1999), was defined by two mutants, R112 and R650. R650 produced frequent spores that were longer than those of the wild type. In contrast, R112 produced long, straight, undifferentiated hyphae, although rare spore chains were observed, sometimes showing highly irregular septum placement. Subcloning and sequencing showed that whiN encodes a member of the extracytoplasmic function subfamily of RNA polymerase sigma factors and that the sigma factor has an unusual N-terminal extension of approximately 86 residues that is not present in other sigma factors. A constructed whiN null mutant failed to form aerial mycelium (the “bald” phenotype) and, as a consequence, whiN was renamed bldN. This observation was not totally unexpected because, on some media, the R112 point mutant produced substantially less aerial mycelium than its parent, M145. The bldN null mutant did not fit simply into the extracellular signaling cascade proposed for S. coelicolor bld mutants. Expression of bldN was analyzed during colony development in wild-type and aerial mycelium-deficient bld strains. bldN was transcribed from a single promoter, bldNp. bldN transcription was developmentally regulated, commencing approximately at the time of aerial mycelium formation, and depended on bldG and bldH, but not on bldA, bldB, bldC, bldF, bldK, or bldJ or on bldN itself. Transcription from the p1 promoter of the response-regulator gene bldM depended on bldN in vivo, and the bldMp1 promoter was shown to be a direct biochemical target for ςBldN holoenzyme in vitro. PMID:10913095

Enhancing early detection of exotic pests in agricultural and forest ecosystems using an urban-gradient framework

Treesearch

Manuel Colunga-Garcia; Roger A. Magarey; Robert A. Haack; Stuart H. Gage; Jiaquo Qi

2010-01-01

Urban areas are hubs of international transport and therefore are major gateways for exotic pests. Applying an urban gradient to analyze this pathway could provide insight into the ecological processes involved in human-mediated invasions. We defined an urban gradient for agricultural and forest ecosystems in the contiguous United States to (1) assess whether...

76 FR 67200 - Prospective Grant of Exclusive License: Electron Paramagnetic Resonance Devices and Systems for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-31

... that is a unique combination of: (1) multi-gradient Single Point Imaging involving global phase...-encoding gradients. The combination approach of single point imaging with the spin-echo signal detection...

ChIP-seq analysis of the σ E regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response

DOE PAGES

Li, Jie; Overall, Christopher C.; Johnson, Rudd C.; ...

2015-09-21

The alternative sigma factor σ E functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σ E in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σ E–binding sites inSalmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σ E–binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cellmore » division factor, and a signal transduction modulator. The consensus sequence identified for σ E in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σ E–binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σ E modulates transcription. By dissecting direct and indirect modes of σ E-mediated regulation, we found that σ E activates gene expression through recognition of both canonical and reversed consensus sequence. Lastly, new σ E regulated genes ( greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.« less

Characterization of lptA and lptB, two essential genes implicated in lipopolysaccharide transport to the outer membrane of Escherichia coli.

PubMed

Sperandeo, Paola; Cescutti, Rachele; Villa, Riccardo; Di Benedetto, Cristiano; Candia, Daniela; Dehò, Gianni; Polissi, Alessandra

2007-01-01

The outer membrane (OM) of gram-negative bacteria is an asymmetric lipid bilayer that protects the cell from toxic molecules. Lipopolysaccharide (LPS) is an essential component of the OM in most gram-negative bacteria, and its structure and biosynthesis are well known. Nevertheless, the mechanisms of transport and assembly of this molecule in the OM are poorly understood. To date, the only proteins implicated in LPS transport are MsbA, responsible for LPS flipping across the inner membrane, and the Imp/RlpB complex, involved in LPS targeting to the OM. Here, we present evidence that two Escherichia coli essential genes, yhbN and yhbG, now renamed lptA and lptB, respectively, participate in LPS biogenesis. We show that mutants depleted of LptA and/or LptB not only produce an anomalous LPS form, but also are defective in LPS transport to the OM and accumulate de novo-synthesized LPS in a novel membrane fraction of intermediate density between the inner membrane (IM) and the OM. In addition, we show that LptA is located in the periplasm and that expression of the lptA-lptB operon is controlled by the extracytoplasmic sigma factor RpoE. Based on these data, we propose that LptA and LptB are implicated in the transport of LPS from the IM to the OM of E. coli.

Characterization of lptA and lptB, Two Essential Genes Implicated in Lipopolysaccharide Transport to the Outer Membrane of Escherichia coli▿

PubMed Central

Sperandeo, Paola; Cescutti, Rachele; Villa, Riccardo; Di Benedetto, Cristiano; Candia, Daniela; Dehò, Gianni; Polissi, Alessandra

2007-01-01

The outer membrane (OM) of gram-negative bacteria is an asymmetric lipid bilayer that protects the cell from toxic molecules. Lipopolysaccharide (LPS) is an essential component of the OM in most gram-negative bacteria, and its structure and biosynthesis are well known. Nevertheless, the mechanisms of transport and assembly of this molecule in the OM are poorly understood. To date, the only proteins implicated in LPS transport are MsbA, responsible for LPS flipping across the inner membrane, and the Imp/RlpB complex, involved in LPS targeting to the OM. Here, we present evidence that two Escherichia coli essential genes, yhbN and yhbG, now renamed lptA and lptB, respectively, participate in LPS biogenesis. We show that mutants depleted of LptA and/or LptB not only produce an anomalous LPS form, but also are defective in LPS transport to the OM and accumulate de novo-synthesized LPS in a novel membrane fraction of intermediate density between the inner membrane (IM) and the OM. In addition, we show that LptA is located in the periplasm and that expression of the lptA-lptB operon is controlled by the extracytoplasmic σ factor RpoE. Based on these data, we propose that LptA and LptB are implicated in the transport of LPS from the IM to the OM of E. coli. PMID:17056748

ChIP-seq analysis of the σ E regulon of Salmonella enterica serovar typhimurium reveals new genes implicated in heat shock and oxidative stress response

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

Li, Jie; Overall, Christopher C.; Johnson, Rudd C.

The alternative sigma factor σ E functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σ E in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σ E–binding sites inSalmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σ E–binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cellmore » division factor, and a signal transduction modulator. The consensus sequence identified for σ E in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σ E–binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σ E modulates transcription. By dissecting direct and indirect modes of σ E-mediated regulation, we found that σ E activates gene expression through recognition of both canonical and reversed consensus sequence. Lastly, new σ E regulated genes ( greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.« less

Stronger tests of mechanisms underlying geographic gradients of biodiversity: insights from the dimensionality of biodiversity.

PubMed

Stevens, Richard D; Tello, J Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km(2) grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota.

Stronger Tests of Mechanisms Underlying Geographic Gradients of Biodiversity: Insights from the Dimensionality of Biodiversity

PubMed Central

Stevens, Richard D.; Tello, J. Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km2 grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota. PMID:23451099

Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients.

PubMed

Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W

2004-01-01

Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation. We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers. Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively. However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results. Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses. This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems.

Solitary plasma rings and magnetic field generation involving gravity and differential rotation

NASA Astrophysics Data System (ADS)

Coppi, B.

2012-12-01

A new theoretical framework for describing how magnetic fields are generated and amplified is provided by finding magneto-gravitational modes that involve gravity, density gradients, and differential rotation in an essential way. Other factors, such as the presence of a high temperature particle population or of a temperature gradient, can contribute to their excitation. These modes identified by a linearized analysis are shown to be important for the evolution of plasma disks surrounding black holes toward different configurations. Since the nonlinear development of these modes can lead to radially localized regions with a relatively small differential rotation, new stationary structures have been identified, in the (fully) nonlinear limit, which are localized radially over regions with negligible gradients of the rotation frequency. These structures, characterized by solitary plasma rings, do not involve a pre-existing "seed" magnetic field, unlike other configurations found previously. The relevant magnetic energy density is comparable to the gravitationally confined plasma pressure. The "source" of these configurations is the combination of the gravitational force and of the plasma density gradient orthogonal to it that is an important factor in the theory of magneto-gravitational modes, another important factor being an anisotropy of the plasma pressure.

Involvement of the Golgi apparatus in the synthesis and secretion of hydroxyproline-rich cell wall glycoproteins. [carrot

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

Gardiner, M.; Chrispeels, M.J.

1975-01-01

Pulse labeling of carrot root phloem parenchyma (Daucus carota L. ev. Nantes) tissue with /sup 14/C-proline followed by fractionation of the cytoplasmic organelles on sucrose gradients was used to determine the identiy of the membranous organelles involved in the secretion of the hydroxyproline-rich glycoproteins of the cell wall. Identification of the organelles was done through electron-microscopical observations and through the localization of marker enzymes on the sucrose gradients. Enrichment of the organelles involved in secretion was determined by measuring the percentage of the incorporated radioactivity present as /sup 14/C-hydroxyproline. The Golgi apparatus (dictyosome) was found to be a major sitemore » of glycoprotein transport. This identification was based on the observed enrichment of dictyosomes paralleling the purification of newly synthesized cell-wall glycoproteins. A marker enzyme for the Golgi apparatus, inosinediphosphatase, banded with the newly synthesized cell wall glycoproteins on sequential isopycnic and rate zonal sucrose gradients. Marker enzymes for the endoplasmic reticulum and the plasma memebrane were clearly separated from the dictyosome-rich fraction. UDP-arabinose arabinosyl transferase, an enzyme involved in the glycosylation of the peptide moiety of this glycoprotein, also banded with the dictyosomes on both kinds of gradients. The results suggest an important role of the Golgi apparatus in the biosynthesis and the secretion of the cell wall glycoproteins of higher plants. (auth)« less

Chemotaxis of Molecular Dyes in Polymer Gradients in Solution.

PubMed

Guha, Rajarshi; Mohajerani, Farzad; Collins, Matthew; Ghosh, Subhadip; Sen, Ayusman; Velegol, Darrell

2017-11-08

Chemotaxis provides a mechanism for directing the transport of molecules along chemical gradients. Here, we show the chemotactic migration of dye molecules in response to the gradients of several different neutral polymers. The magnitude of chemotactic response depends on the structure of the monomer, polymer molecular weight and concentration, and the nature of the solvent. The mechanism involves cross-diffusion up the polymer gradient, driven by favorable dye-polymer interaction. Modeling allows us to quantitatively evaluate the strength of the interaction and the effect of the various parameters that govern chemotaxis.

Simple and Efficient Numerical Evaluation of Near-Hypersingular Integrals

NASA Technical Reports Server (NTRS)

Fink, Patrick W.; Wilton, Donald R.; Khayat, Michael A.

2007-01-01

Recently, significant progress has been made in the handling of singular and nearly-singular potential integrals that commonly arise in the Boundary Element Method (BEM). To facilitate object-oriented programming and handling of higher order basis functions, cancellation techniques are favored over techniques involving singularity subtraction. However, gradients of the Newton-type potentials, which produce hypersingular kernels, are also frequently required in BEM formulations. As is the case with the potentials, treatment of the near-hypersingular integrals has proven more challenging than treating the limiting case in which the observation point approaches the surface. Historically, numerical evaluation of these near-hypersingularities has often involved a two-step procedure: a singularity subtraction to reduce the order of the singularity, followed by a boundary contour integral evaluation of the extracted part. Since this evaluation necessarily links basis function, Green s function, and the integration domain (element shape), the approach ill fits object-oriented programming concepts. Thus, there is a need for cancellation-type techniques for efficient numerical evaluation of the gradient of the potential. Progress in the development of efficient cancellation-type procedures for the gradient potentials was recently presented. To the extent possible, a change of variables is chosen such that the Jacobian of the transformation cancels the singularity. However, since the gradient kernel involves singularities of different orders, we also require that the transformation leaves remaining terms that are analytic. The terms "normal" and "tangential" are used herein with reference to the source element. Also, since computational formulations often involve the numerical evaluation of both potentials and their gradients, it is highly desirable that a single integration procedure efficiently handles both.

Experimental feasibility of investigating acoustic waves in Couette flow with entropy and pressure gradients

NASA Technical Reports Server (NTRS)

Parrott, Tony L.; Zorumski, William E.; Rawls, John W., Jr.

1990-01-01

The feasibility is discussed for an experimental program for studying the behavior of acoustic wave propagation in the presence of strong gradients of pressure, temperature, and flow. Theory suggests that gradients effects can be experimentally observed as resonant frequency shifts and mode shape changes in a waveguide. A convenient experimental geometry for such experiments is the annular region between two co-rotating cylinders. Radial temperature gradients in a spinning annulus can be generated by differentially heating the two cylinders via electromagnetic induction. Radial pressure gradients can be controlled by varying the cylinder spin rates. Present technology appears adequate to construct an apparatus to allow independent control of temperature and pressure gradients. A complicating feature of a more advanced experiment, involving flow gradients, is the requirement for independently controlled cylinder spin rates. Also, the boundary condition at annulus terminations must be such that flow gradients are minimally disturbed. The design and construction of an advanced apparatus to include flow gradients will require additional technology development.

Mangrove forests

Treesearch

Ariel E. Lugo; Ernesto Medina

2014-01-01

The mangrove environment is not globally homogeneous, but involves many environmental gradients to which mangrove species must adapt and overcome to maintain the familiar structure and physiognomy associated with the mangrove ecosystem. The stature of mangroves, measured by tree height, decreases along the following environmental gradients from low to high salinity,...

Numerical optimization in Hilbert space using inexact function and gradient evaluations

NASA Technical Reports Server (NTRS)

Carter, Richard G.

1989-01-01

Trust region algorithms provide a robust iterative technique for solving non-convex unstrained optimization problems, but in many instances it is prohibitively expensive to compute high accuracy function and gradient values for the method. Of particular interest are inverse and parameter estimation problems, since function and gradient evaluations involve numerically solving large systems of differential equations. A global convergence theory is presented for trust region algorithms in which neither function nor gradient values are known exactly. The theory is formulated in a Hilbert space setting so that it can be applied to variational problems as well as the finite dimensional problems normally seen in trust region literature. The conditions concerning allowable error are remarkably relaxed: relative errors in the gradient error condition is automatically satisfied if the error is orthogonal to the gradient approximation. A technique for estimating gradient error and improving the approximation is also presented.

Conjugate gradient based projection - A new explicit methodology for frictional contact

NASA Technical Reports Server (NTRS)

Tamma, Kumar K.; Li, Maocheng; Sha, Desong

1993-01-01

With special attention towards the applicability to parallel computation or vectorization, a new and effective explicit approach for linear complementary formulations involving a conjugate gradient based projection methodology is proposed in this study for contact problems with Coulomb friction. The overall objectives are focussed towards providing an explicit methodology of computation for the complete contact problem with friction. In this regard, the primary idea for solving the linear complementary formulations stems from an established search direction which is projected to a feasible region determined by the non-negative constraint condition; this direction is then applied to the Fletcher-Reeves conjugate gradient method resulting in a powerful explicit methodology which possesses high accuracy, excellent convergence characteristics, fast computational speed and is relatively simple to implement for contact problems involving Coulomb friction.

Non-Gradient Blue Native Polyacrylamide Gel Electrophoresis.

PubMed

Luo, Xiaoting; Wu, Jinzi; Jin, Zhen; Yan, Liang-Jun

2017-02-02

Gradient blue native polyacrylamide gel electrophoresis (BN-PAGE) is a well established and widely used technique for activity analysis of high-molecular-weight proteins, protein complexes, and protein-protein interactions. Since its inception in the early 1990s, a variety of minor modifications have been made to this gradient gel analytical method. Here we provide a major modification of the method, which we call non-gradient BN-PAGE. The procedure, similar to that of non-gradient SDS-PAGE, is simple because there is no expensive gradient maker involved. The non-gradient BN-PAGE protocols presented herein provide guidelines on the analysis of mitochondrial protein complexes, in particular, dihydrolipoamide dehydrogenase (DLDH) and those in the electron transport chain. Protocols for the analysis of blood esterases or mitochondrial esterases are also presented. The non-gradient BN-PAGE method may be tailored for analysis of specific proteins according to their molecular weight regardless of whether the target proteins are hydrophobic or hydrophilic. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

A glimpse into the proteome of phototrophic bacterium Rhodobacter capsulatus.

PubMed

Onder, Ozlem; Aygun-Sunar, Semra; Selamoglu, Nur; Daldal, Fevzi

2010-01-01

A first glimpse into the proteome of Rhodobacter capsulatus revealed more than 450 (with over 210 cytoplasmic and 185 extracytoplasmic known as well as 55 unknown) proteins that are identified with high degree of confidence using nLC-MS/MS analyses. The accumulated data provide a solid platform for ongoing efforts to establish the proteome of this species and the cellular locations of its constituents. They also indicate that at least 40 of the identified proteins, which were annotated in genome databases as unknown hypothetical proteins, correspond to predicted translation products that are indeed present in cells under the growth conditions used in this work. In addition, matching the identification labels of the proteins reported between the two available R. capsulatus genome databases (ERGO-light with RRCxxxxx and NT05 with NT05RCxxxx numbers) indicated that 11 such proteins are listed only in the latter database.

Characterization of Uranium Tolerance and Biomineralization Potential of Caulobacter crescentus

NASA Astrophysics Data System (ADS)

Park, D.

2015-12-01

Due to its high toxicity and mobility, U(VI) poses a major environmental threat to ecosystems. The ubiquitous aerobic bacterium Caulobacter cresecentus is an attractive candidate for U(VI) bioremediation because of its ability to survive in low-nutrient environments (5, 6), tolerate high U concentrations and mineralize U(VI) aerobically through the formation of uranyl phosphate (U-Pi) precipitates. Despite these attractive environmental properties, both a systems level understanding of the adaptive response pathways involved in U tolerance and the environmental conditions affecting the biomineralization process and stability of biogenic U-Pi minerals remain limited. By measuring changes in both mRNA and protein expression during exposure to high U levels, we have identified the core stress response pathways involved in U tolerance. Pathways associated with heat shock, lipospolysaccharide biosynthesis and transport, outer membrane lipoprotein transport and outermembrane assembly were highly induced at both the RNA and protein levels. Correspondingly, removal of integral components of proteolysis pathways including clpA, clpS and degP significantly reduced U tolerance under biomineralization conditions. Surprisingly, in contrast to many other heavy metals, U did not cause oxidative stress or DNA damage. Together, these analyses indicate that U predominately targets the outermembrane and causes mis-folding of both cytoplasmic and extracytoplasmic proteins. Efforts are currently underway to characterize the morphological and structural properties of biogenic U-Pi minerals and the environmental factors that influence their production and stability. Preliminary AFM studies suggest that U-Pi minerals formed under biomineralization conditions appear morphologically distinct from those formed abiotically between U(VI) and inorganic phosphate. Additionally, we observed that biomineralization tolerates a wide pH range (pH 6-9). Our long-range goal is the development of a conceptual model of the role of microbes in U cycling under oxidizing conditions across the DOE complex, and ultimately, provide DOE with the scientific basis to support decisions for the remediation of legacy sites.

Involvement of Transient Receptor Potential Vanilloid (TRPV) 4 in mouse sperm thermotaxis.

PubMed

Hamano, Koh-Ichi; Kawanishi, Tae; Mizuno, Atsuko; Suzuki, Makoto; Takagi, Yuji

2016-08-25

Transient Receptor Potential Vanilloid (TRPV) 4 is one of the temperature-sensitive ion channels involved in temperature receptors, and it is known to be activated from 35 to 40ºC. Here we analyzed sperm motility function of Trpv4 knockout (KO) mouse in temperature-gradient conditions to elucidate the thermotaxis of mouse sperm and the involvement of TRPV4 in thermotaxis. The sperm were introduced at the vertical column end of a T-shaped chamber filled with medium in a plastic dish, and we measured the number of sperm that arrived at both ends of the wide column where we had established a temperature gradient of approx. 2ºC, and we evaluated the sperm's thermotaxis. Large numbers of wild-type (WT) mouse sperm migrated into the high level of the temperature gradient that was set in the wide column, and thermotaxis was confirmed. The ratio of migrated sperm at the high temperature level of the T-shaped chamber was decreased in the KO sperm and Ruthenium red (a TRPV antagonist) treated sperm compared with the WT sperm. The thermotaxis of the mouse sperm was confirmed, and the involvement of TRPV4 in this thermotaxis was suggested.

Determination of Acidity Constants by Gradient Flow-Injection Titration

ERIC Educational Resources Information Center

Conceicao, Antonio C. L.; Minas da Piedade, Manuel E.

2006-01-01

A three-hour laboratory experiment, designed for an advanced undergraduate course in instrumental analysis that illustrates the application of the gradient chamber flow-injection titration (GCFIT) method with spectrophotometric detection to determine acidity constants is presented. The procedure involves the use of an acid-base indicator to obtain…

Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa.

PubMed

Koide, Tie; Vêncio, Ricardo Z N; Gomes, Suely L

2006-08-01

Xylella fastidiosa is a phytopathogenic bacterium that is responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the better characterized stress responses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation and to promote degradation of the irreversibly denatured polypeptides. To investigate X. fastidiosa genes involved in the heat shock response, we performed a whole-genome microarray analysis in a time course experiment. Globally, 261 genes were induced (9.7%) and 222 genes were repressed (8.3%). The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative reverse transcription-PCR experiments. We determined the transcription start sites of six heat shock-inducible genes and analyzed their promoter regions, which allowed us to propose a putative consensus for sigma(32) promoters in Xylella and to suggest additional genes as putative members of this regulon. Besides the induction of classical heat shock protein genes, we observed the up-regulation of virulence-associated genes such as vapD and of genes for hemagglutinins, hemolysin, and xylan-degrading enzymes, which may indicate the importance of heat stress to bacterial pathogenesis. In addition, we observed the repression of genes related to fimbriae, aerobic respiration, and protein biosynthesis and the induction of genes related to the extracytoplasmic stress response and some phage-related genes, revealing the complex network of genes that work together in response to heat shock.

Multiple functions of the leucine-rich repeat protein LrrA of Treponema denticola.

PubMed

Ikegami, Akihiko; Honma, Kiyonobu; Sharma, Ashu; Kuramitsu, Howard K

2004-08-01

The gene lrrA, encoding a leucine-rich repeat protein, LrrA, that contains eight consensus tandem repeats of 23 amino acid residues, has been identified in Treponema denticola ATCC 35405. A leucine-rich repeat is a generally useful protein-binding motif, and proteins containing this repeat are typically involved in protein-protein interactions. Southern blot analysis demonstrated that T. denticola ATCC 35405 expresses the lrrA gene, but the gene was not identified in T. denticola ATCC 33520. In order to analyze the functions of LrrA in T. denticola, an lrrA-inactivated mutant of strain ATCC 35405 and an lrrA gene expression transformant of strain ATCC 33520 were constructed. Characterization of the mutant and transformant demonstrated that LrrA is associated with the extracytoplasmic fraction of T. denticola and expresses multifunctional properties. It was demonstrated that the attachment of strain ATCC 35405 to HEp-2 cell cultures and coaggregation with Tannerella forsythensis were attenuated by the lrrA mutation. In addition, an in vitro binding assay demonstrated specific binding of LrrA to a portion of the Tannerella forsythensis leucine-rich repeat protein, BspA, which is mediated by the N-terminal region of LrrA. It was also observed that the lrrA mutation caused a reduction of swarming in T. denticola ATCC 35405 and consequently attenuated tissue penetration. These results suggest that the leucine-rich repeat protein LrrA plays a role in the attachment and penetration of human epithelial cells and coaggregation with Tannerella forsythensis. These properties may play important roles in the virulence of T. denticola.

The sigmaR regulon of Streptomyces coelicolor A32 reveals a key role in protein quality control during disulphide stress.

PubMed

Kallifidas, Dimitris; Thomas, Derek; Doughty, Phillip; Paget, Mark S B

2010-06-01

Diamide is an artificial disulphide-generating electrophile that mimics an oxidative shift in the cellular thiol-disulphide redox state (disulphide stress). The Gram-positive bacterium Streptomyces coelicolor senses and responds to disulphide stress through the sigma(R)-RsrA system, which comprises an extracytoplasmic function (ECF) sigma factor and a redox-active anti-sigma factor. Known targets that aid in the protection and recovery from disulphide stress include the thioredoxin system and genes involved in producing the major thiol buffer mycothiol. Here we determine the global response to diamide in wild-type and sigR mutant backgrounds to understand the role of sigma(R) in this response and to reveal additional regulatory pathways that allow cells to cope with disulphide stress. In addition to thiol oxidation, diamide was found to cause protein misfolding and aggregation, which elicited the induction of the HspR heat-shock regulon. Although this response is sigma(R)-independent, sigma(R) does directly control Clp and Lon ATP-dependent AAA(+) proteases, which may partly explain the reduced ability of a sigR mutant to resolubilize protein aggregates. sigma(R) also controls msrA and msrB methionine sulphoxide reductase genes, implying that sigma(R)-RsrA is responsible for the maintenance of both cysteine and methionine residues during oxidative stress. This work shows that the sigma(R)-RsrA system plays a more significant role in protein quality control than previously realized, and emphasizes the importance of controlling the cellular thiol-disulphide redox balance.

Activity-dependent formation of a vesicular inhibitory amino acid transporter gradient in the superior olivary complex of NMRI mice.

PubMed

Ebbers, Lena; Weber, Maren; Nothwang, Hans Gerd

2017-10-26

In the mammalian superior olivary complex (SOC), synaptic inhibition contributes to the processing of binaural sound cues important for sound localization. Previous analyses demonstrated a tonotopic gradient for postsynaptic proteins mediating inhibitory neurotransmission in the lateral superior olive (LSO), a major nucleus of the SOC. To probe, whether a presynaptic molecular gradient exists as well, we investigated immunoreactivity against the vesicular inhibitory amino acid transporter (VIAAT) in the mouse auditory brainstem. Immunoreactivity against VIAAT revealed a gradient in the LSO and the superior paraolivary nucleus (SPN) of NMRI mice, with high expression in the lateral, low frequency processing limb and low expression in the medial, high frequency processing limb of both nuclei. This orientation is opposite to the previously reported gradient of glycine receptors in the LSO. Other nuclei of the SOC showed a uniform distribution of VIAAT-immunoreactivity. No gradient was observed for the glycine transporter GlyT2 and the neuronal protein NeuN. Formation of the VIAAT gradient was developmentally regulated and occurred around hearing-onset between postnatal days 8 and 16. Congenital deaf Claudin14 -/- mice bred on an NMRI background showed a uniform VIAAT-immunoreactivity in the LSO, whereas cochlear ablation in NMRI mice after hearing-onset did not affect the gradient. Additional analysis of C57Bl6/J, 129/SvJ and CBA/J mice revealed a strain-specific formation of the gradient. Our results identify an activity-regulated gradient of VIAAT in the SOC of NRMI mice. Its absence in other mouse strains adds a novel layer of strain-specific features in the auditory system, i.e. tonotopic organization of molecular gradients. This calls for caution when comparing data from different mouse strains frequently used in studies involving transgenic animals. The presence of strain-specific differences offers the possibility of genetic mapping to identify molecular factors involved in activity-dependent developmental processes in the auditory system. This would provide an important step forward concerning improved auditory rehabilitation in cases of congenital deafness.

Dual fuel gradients in uranium silicide plates

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

Pace, B.W.

1997-08-01

Babcock & Wilcox has been able to achieve dual gradient plates with good repeatability in small lots of U{sub 3}Si{sub 2} plates. Improvements in homogeneity and other processing parameters and techniques have allowed the development of contoured fuel within the cladding. The most difficult obstacles to overcome have been the ability to evaluate the bidirectional fuel loadings in comparison to the perfect loading model and the different methods of instilling the gradients in the early compact stage. The overriding conclusion is that to control the contour of the fuel, a known relationship between the compact, the frames and final coremore » gradient must exist. Therefore, further development in the creation and control of dual gradients in fuel plates will involve arriving at a plausible gradient requirement and building the correct model between the compact configuration and the final contoured loading requirements.« less

BACTERIOPHAGE AND MICROSPHERE TRANSPORT IN SATURATED POROUS MEDIA: FORCED-GRADIENT EXPERIMENT AT BORDEN, ONTARIO

EPA Science Inventory

A two-well forced-gradient experiment involving virus and microsphere transport was carried out in a sandy aquifer in Borden, Ontario, Canada. Virus traveled at least a few meters in the experiment, but virus concentrations at observation points 1 and 2.54 m away from the injecti...

Quantification and Compensation of Eddy-Current-Induced Magnetic Field Gradients

PubMed Central

Spees, William M.; Buhl, Niels; Sun, Peng; Ackerman, Joseph J.H.; Neil, Jeffrey J.; Garbow, Joel R.

2011-01-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or 6-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom’s free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner’s gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. PMID:21764614

Quantification and compensation of eddy-current-induced magnetic-field gradients.

PubMed

Spees, William M; Buhl, Niels; Sun, Peng; Ackerman, Joseph J H; Neil, Jeffrey J; Garbow, Joel R

2011-09-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or six-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom's free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner's gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. Copyright © 2011 Elsevier Inc. All rights reserved.

Tested Demonstrations.

ERIC Educational Resources Information Center

Gilbert, George L., Ed.

1985-01-01

Background information, procedures, and typical results obtained are provided for two demonstrations. The first involves the colorful complexes of copper(II). The second involves reverse-phase separation of Food, Drug, and Cosmetic (FD & C) dyes using a solvent gradient. (JN)

Optimal trajectories for aeroassisted orbital transfer

NASA Technical Reports Server (NTRS)

Miele, A.; Venkataraman, P.

1983-01-01

Consideration is given to classical and minimax problems involved in aeroassisted transfer from high earth orbit (HEO) to low earth orbit (LEO). The transfer is restricted to coplanar operation, with trajectory control effected by means of lift modulation. The performance of the maneuver is indexed to the energy expenditure or, alternatively, the time integral of the heating rate. Firist-order optimality conditions are defined for the classical approach, as are a sequential gradient-restoration algorithm and a combined gradient-restoration algorithm. Minimization techniques are presented for the aeroassisted transfer energy consumption and time-delay integral of the heating rate, as well as minimization of the pressure. It is shown that the eigenvalues of the Jacobian matrix of the differential system is both stiff and unstable, implying that the sequential gradient restoration algorithm in its present version is unsuitable. A new method, involving a multipoint approach to the two-poing boundary value problem, is recommended.

Intracellular diffusion of oxygen and hypoxic sensing: role of mitochondrial respiration.

PubMed

Takahashi, Eiji; Sato, Michihiko

2010-01-01

In vivo, diffusional O(2) gradients from the capillary blood to the intracellular space determine O(2) availability at the O(2) sensing molecules in the cell. With a novel technique for imaging intracellular O(2) levels using green fluorescent protein (GFP), we examined the possibility that diffusional O(2) concentration gradients might be involved in the cellular hypoxic sensing in cultured Hep3B cells. In the present study, we failed to demonstrate significant gradients of intracellular O(2) when mitochondrial respiration was maximally elevated by an uncoupler of oxidative phosphorylation. Thus, we conclude that intracellular O(2) gradients may be negligible at normal mitochondrial O(2) demand in these cells.

Gradients of microhabitat and crappie (Pomoxis spp.) distributions in reservoir coves

USGS Publications Warehouse

Kaczka, Levi J.; Miranda, Leandro E.

2013-01-01

Embayments are among the most widespread littoral habitats found in Mississippi flood-control reservoirs. These macrohabitats represent commonly used nursery zones for age-0 crappies, Pomoxis spp., despite barren and eroded shorelines formed over 60–70 years of annual water level fluctuations. We tested if embayments displayed microhabitat gradients linked to the effect of water level fluctuations on riparian vegetation and if these gradients were paralleled by gradients in age-0 crappie distribution. Habitat composition changed longitudinally along the embayments with the most pronounced gradient representing a shift from nonvegetated mudflats near the mouth of embayments to herbaceous material upstream. The degree of habitat change depended on the water level. Similarly, catch rates of crappies increased upstream toward the rear of embayments, differing among water levels and reservoirs, but the longitudinal pattern persisted. Our results indicate that habitat composition gradients occur in embayments of northwest Mississippi flood-control reservoirs and that these gradients may influence a similar gradient in age-0 crappie distribution. While the biotic interactions behind the gradients may be less clear, we speculate that water level is the main factor influencing the observed gradients in habitat composition and fish. Management to benefit age-0 crappies may involve habitat improvement along embayment shorelines and water level regimes that foster growth of herbaceous plants.

Microgravity Particle Dynamics

NASA Technical Reports Server (NTRS)

Clark, Ivan O.; Johnson, Edward J.

1996-01-01

This research seeks to identify the experiment design parameters for future flight experiments to better resolve the effects of thermal and velocity gradients on gas-solid flows. By exploiting the reduced body forces and minimized thermal convection current of reduced gravity experiments, features of gas-solid flow normally masked by gravitationally induced effects can be studied using flow regimes unattainable under unigravity. This paper assesses the physical scales of velocity, length, time, thermal gradient magnitude, and velocity gradient magnitude likely to be involved in laminar gas-solid multiphase flight experiments for 1-100 micro-m particles.

Collective gradient sensing and chemotaxis: modeling and recent developments

NASA Astrophysics Data System (ADS)

Camley, Brian A.

2018-06-01

Cells measure a vast variety of signals, from their environment’s stiffness to chemical concentrations and gradients; physical principles strongly limit how accurately they can do this. However, when many cells work together, they can cooperate to exceed the accuracy of any single cell. In this topical review, I will discuss the experimental evidence showing that cells collectively sense gradients of many signal types, and the models and physical principles involved. I also propose new routes by which experiments and theory can expand our understanding of these problems.

How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient.

PubMed

Blomberg, Margareta R A; Siegbahn, Per E M

2015-03-01

Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiscale design and synthesis of biomimetic gradient protein/biosilica composites for interfacial tissue engineering.

PubMed

Guo, Jin; Li, Chunmei; Ling, Shengjie; Huang, Wenwen; Chen, Ying; Kaplan, David L

2017-11-01

Continuous gradients present at tissue interfaces such as osteochondral systems, reflect complex tissue functions and involve changes in extracellular matrix compositions, cell types and mechanical properties. New and versatile biomaterial strategies are needed to create suitable biomimetic engineered grafts for interfacial tissue engineering. Silk protein-based composites, coupled with selective peptides with mineralization domains, were utilized to mimic the soft-to-hard transition in osteochondral interfaces. The gradient composites supported tunable mineralization and mechanical properties corresponding to the spatial concentration gradient of the mineralization domains (R5 peptide). The composite system exhibited continuous transitions in terms of composition, structure and mechanical properties, as well as cytocompatibility and biodegradability. The gradient silicified silk/R5 composites promoted and regulated osteogenic differentiation of human mesenchymal stem cells in an osteoinductive environment in vitro. The cells differentiated along the composites in a manner consistent with the R5-gradient profile. This novel biomimetic gradient biomaterial design offers a useful approach to meet a broad range of needs in regenerative medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microfluidic Synthesis of Composite Cross-Gradient Materials for Investigating Cell–Biomaterial Interactions

PubMed Central

He, Jiankang; Du, Yanan; Guo, Yuqi; Hancock, Matthew J.; Wang, Ben; Shin, Hyeongho; Wu, Jinhui; Li, Dichen; Khademhosseini, Ali

2010-01-01

Combinatorial material synthesis is a powerful approach for creating composite material libraries for the high-throughput screening of cell–material interactions. Although current combinatorial screening platforms have been tremendously successful in identifying target (termed “hit”) materials from composite material libraries, new material synthesis approaches are needed to further optimize the concentrations and blending ratios of the component materials. Here we employed a microfluidic platform to rapidly synthesize composite materials containing cross-gradients of gelatin and chitosan for investigating cell–biomaterial interactions. The microfluidic synthesis of the cross-gradient was optimized experimentally and theoretically to produce quantitatively controllable variations in the concentrations and blending ratios of the two components. The anisotropic chemical compositions of the gelatin/chitosan cross-gradients were characterized by Fourier transform infrared spectrometry and X-ray photoelectron spectrometry. The three-dimensional (3D) porous gelatin/chitosan cross-gradient materials were shown to regulate the cellular morphology and proliferation of smooth muscle cells (SMCs) in a gradient-dependent manner. We envision that our microfluidic cross-gradient platform may accelerate the material development processes involved in a wide range of biomedical applications. PMID:20721897

The covariance between genetic and environmental influences across ecological gradients: reassessing the evolutionary significance of countergradient and cogradient variation.

PubMed

Conover, David O; Duffy, Tara A; Hice, Lyndie A

2009-06-01

Patterns of phenotypic change across environmental gradients (e.g., latitude, altitude) have long captivated the interest of evolutionary ecologists. The pattern and magnitude of phenotypic change is determined by the covariance between genetic and environmental influences across a gradient. Cogradient variation (CoGV) occurs when covariance is positive: that is, genetic and environmental influences on phenotypic expression are aligned and their joint influence accentuates the change in mean trait value across the gradient. Conversely, countergradient variation (CnGV) occurs when covariance is negative: that is, genetic and environmental influences on phenotypes oppose one another, thereby diminishing the change in mean trait expression across the gradient. CnGV has so far been found in at least 60 species, with most examples coming from fishes, amphibians, and insects across latitudinal or altitudinal gradients. Traits that display CnGV most often involve metabolic compensation, that is, the elevation of various physiological rates processes (development, growth, feeding, metabolism, activity) to counteract the dampening effect of reduced temperature, growing season length, or food supply. Far fewer examples of CoGV have been identified (11 species), and these most often involve morphological characters. Increased knowledge of spatial covariance patterns has furthered our understanding of Bergmann size clines, phenotypic plasticity, species range limits, tradeoffs in juvenile growth rate, and the design of conservation strategies for wild species. Moreover, temporal CnGV explains some cases of an apparent lack of phenotypic response to directional selection and provides a framework for predicting evolutionary responses to climate change.

A gradient of auxin and auxin-dependent transcription precedes tropic growth responses.

PubMed

Esmon, C Alex; Tinsley, Amanda G; Ljung, Karin; Sandberg, Goran; Hearne, Leonard B; Liscum, Emmanuel

2006-01-03

Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny-Went theory [Went, F. W. & Thimann, K. V. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced genes in Brassica oleracea that are responsive to an auxin gradient and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny-Went theory and suggest that morphologically graded transcription represents an important mechanism for interpreting tropically stimulated gradients of auxin. Intriguingly, two of the tropic stimulus-induced genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are up-regulated before curvature in the flank that will elongate. This observation suggests that morphologically graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.

Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond.

PubMed

Erb-Downward, John R; Sadighi Akha, Amir A; Wang, Juan; Shen, Ning; He, Bei; Martinez, Fernando J; Gyetko, Margaret R; Curtis, Jeffrey L; Huffnagle, Gary B

2012-01-01

This study investigated the use of direct gradient analysis of bacterial 16S pyrosequencing surveys to identify relevant bacterial community signals in the midst of a "noisy" background, and to facilitate hypothesis-testing both within and beyond the realm of ecological surveys. The results, utilizing 3 different real world data sets, demonstrate the utility of adding direct gradient analysis to any analysis that draws conclusions from indirect methods such as Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA). Direct gradient analysis produces testable models, and can identify significant patterns in the midst of noisy data. Additionally, we demonstrate that direct gradient analysis can be used with other kinds of multivariate data sets, such as flow cytometric data, to identify differentially expressed populations. The results of this study demonstrate the utility of direct gradient analysis in microbial ecology and in other areas of research where large multivariate data sets are involved.

Gradient Scouting in Reversed-Phase HPLC Revisited

ERIC Educational Resources Information Center

Alcazar, A.; Jurado, J. M.; Gonzalez, A. G.

2011-01-01

Gradient scouting is the best way to decide the most suitable elution mode in reversed-phase high-performance liquid chromatography (RP-HPLC). A simple rule for this decision involves the evaluation of the ratio [delta]t/t[subscript G] (where [delta]t is the difference in the retention time between the last and the first peak and t[subscript G] is…

Complex physiological and molecular processes underlying root gravitropism

NASA Technical Reports Server (NTRS)

Chen, Rujin; Guan, Changhui; Boonsirichai, Kanokporn; Masson, Patrick H.

2002-01-01

Gravitropism allows plant organs to guide their growth in relation to the gravity vector. For most roots, this response to gravity allows downward growth into soil where water and nutrients are available for plant growth and development. The primary site for gravity sensing in roots includes the root cap and appears to involve the sedimentation of amyloplasts within the columella cells. This process triggers a signal transduction pathway that promotes both an acidification of the wall around the columella cells, an alkalinization of the columella cytoplasm, and the development of a lateral polarity across the root cap that allows for the establishment of a lateral auxin gradient. This gradient is then transmitted to the elongation zones where it triggers a differential cellular elongation on opposite flanks of the central elongation zone, responsible for part of the gravitropic curvature. Recent findings also suggest the involvement of a secondary site/mechanism of gravity sensing for gravitropism in roots, and the possibility that the early phases of graviresponse, which involve differential elongation on opposite flanks of the distal elongation zone, might be independent of this auxin gradient. This review discusses our current understanding of the molecular and physiological mechanisms underlying these various phases of the gravitropic response in roots.

A comparison of methods for computing the sigma-coordinate pressure gradient force for flow over sloped terrain in a hybrid theta-sigma model

NASA Technical Reports Server (NTRS)

Johnson, D. R.; Uccellini, L. W.

1983-01-01

In connection with the employment of the sigma coordinates introduced by Phillips (1957), problems can arise regarding an accurate finite-difference computation of the pressure gradient force. Over steeply sloped terrain, the calculation of the sigma-coordinate pressure gradient force involves computing the difference between two large terms of opposite sign which results in large truncation error. To reduce the truncation error, several finite-difference methods have been designed and implemented. The present investigation has the objective to provide another method of computing the sigma-coordinate pressure gradient force. Phillips' method is applied for the elimination of a hydrostatic component to a flux formulation. The new technique is compared with four other methods for computing the pressure gradient force. The work is motivated by the desire to use an isentropic and sigma-coordinate hybrid model for experiments designed to study flow near mountainous terrain.

Iterative solution of the inverse Cauchy problem for an elliptic equation by the conjugate gradient method

NASA Astrophysics Data System (ADS)

Vasil'ev, V. I.; Kardashevsky, A. M.; Popov, V. V.; Prokopev, G. A.

2017-10-01

This article presents results of computational experiment carried out using a finite-difference method for solving the inverse Cauchy problem for a two-dimensional elliptic equation. The computational algorithm involves an iterative determination of the missing boundary condition from the override condition using the conjugate gradient method. The results of calculations are carried out on the examples with exact solutions as well as at specifying an additional condition with random errors are presented. Results showed a high efficiency of the iterative method of conjugate gradients for numerical solution

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

DOE PAGES

Sychantha, David; Jones, Carys S.; Little, Dustin J.; ...

2017-10-27

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain.more » We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens.« less

The twin-arginine translocation pathway of Mycobacterium smegmatis is functional and required for the export of mycobacterial beta-lactamases.

PubMed

McDonough, Justin A; Hacker, Kari E; Flores, Anthony R; Pavelka, Martin S; Braunstein, Miriam

2005-11-01

The twin-arginine translocation (Tat) pathway exports folded proteins across the bacterial cytoplasmic membrane and is responsible for the proper extracytoplasmic localization of proteins involved in a variety of cellular functions, including pathogenesis. The Mycobacterium tuberculosis and Mycobacterium smegmatis genomes contain open reading frames with homology to components of the Tat export system (TatABC) as well as potential Tat-exported proteins possessing N-terminal signal sequences with the characteristic twin-arginine motif. Due to the importance of exported virulence factors in the pathogenesis of M. tuberculosis and the limited understanding of mycobacterial protein export systems, we sought to determine the functional nature of the Tat export pathway in mycobacteria. Here we describe phenotypic analyses of DeltatatA and DeltatatC deletion mutants of M. smegmatis, which demonstrated that tatA and tatC encode components of a functional Tat system capable of exporting characteristic Tat substrates. Both mutants displayed a growth defect on agar medium and hypersensitivity to sodium dodecyl sulfate. The mutants were also defective in the export of active beta-lactamases of M. smegmatis (BlaS) and M. tuberculosis (BlaC), both of which possess twin-arginine signal sequences. The Tat-dependent nature of BlaC was further revealed by mutation of the twin-arginine motif. Finally, we demonstrated that replacement of the native signal sequence of BlaC with the predicted Tat signal sequences of M. tuberculosis phospholipase C proteins (PlcA and PlcB) resulted in the Tat-dependent export of an enzymatically active 'BlaC. Thus, 'BlaC can be used as a genetic reporter for Tat-dependent export in mycobacteria.

Transcriptomic analysis of the response of Pseudomonas fluorescens to epigallocatechin gallate by RNA-seq

PubMed Central

Liu, Xiaoxiang; Shen, Bimiao; Du, Peng; Wang, Nan; Wang, Jiaxue; Li, Jianrong

2017-01-01

Epigallocatechin gallate (EGCG) is a main constituent of green tea polyphenols that are widely used as food preservatives and are considered to be safe for consumption. However, the underlying antimicrobial mechanism of EGCG and the bacterial response to EGCG are not clearly understood. In the present study, a genome-wide transcriptional analysis of a typical spoilage bacterium, Pseudomonas fluorescens that responded to EGCG was performed using RNA-seq technology. A total of 26,365,414 and 23,287,092 clean reads were generated from P. fluorescens treated with or without 1 mM EGCG and the clean reads were aligned to the reference genome. Differential expression analysis revealed 291 upregulated genes and 134 downregulated genes and the differentially expressed genes (DEGs) were verified using RT-qPCR. Most of the DGEs involved in iron uptake, antioxidation, DNA repair, efflux system, cell envelope and cell-surface component synthesis were significantly upregulated by EGCG treatment, while most genes associated with energy production were downregulated. These transcriptomic changes are likely to be adaptive responses of P. fluorescens to iron limitation and oxidative stress, as well as DNA and envelope damage caused by EGCG. The expression of specific genes encoding the extra-cytoplasmic function sigma factor (PvdS, RpoE and AlgU) and the two-component sensor histidine kinase (BaeS and RpfG) were markedly changed by EGCG treatment, which may play important roles in regulating the stress responses of P. fluorescens to EGCG. The present data provides important insights into the molecular action of EGCG and the possible cross-resistance mediated by EGCG on P. fluorescens, which may ultimately contribute to the optimal application of green tea polyphenols in food preservation. PMID:28545064

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

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

Sychantha, David; Jones, Carys S.; Little, Dustin J.

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain.more » We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens.« less

Complex regulation of AprA metalloprotease in Pseudomonas fluorescens M114: evidence for the involvement of iron, the ECF sigma factor, PbrA and pseudobactin M114 siderophore.

PubMed

Maunsell, Bláithín; Adams, Claire; O'Gara, Fergal

2006-01-01

In the soil bacterium Pseudomonas fluorescens M114, extracellular proteolytic activity and fluorescent siderophore (pseudobactin M114) production were previously shown to be co-ordinately negatively regulated in response to environmental iron levels. An iron-starvation extracytoplasmic function sigma factor, PbrA, required for the transcription of siderophore biosynthetic genes, was also implicated in M114 protease regulation. The current study centred on the characterization and genetic regulation of the gene(s) responsible for protease production in M114. A serralysin-type metalloprotease gene, aprA, was identified and found to encode the major, if not only, extracellular protease produced by this strain. The expression of aprA and its protein product were found to be subject to complex regulation. Transcription analysis confirmed that PbrA was required for full aprA transcription under low iron conditions, while the ferric uptake regulator, Fur, was implicated in aprA repression under high iron conditions. Interestingly, the iron regulation of AprA was dependent on culture conditions, with PbrA-independent AprA-mediated proteolytic activity observed on skim milk agar supplemented with yeast extract, when supplied with iron or purified pseudobactin M114. These effects were not observed on skim milk agar without yeast extract. PbrA-independent aprA expression was also observed from a truncated transcriptional fusion when grown in sucrose asparagine tryptone broth supplied with iron or purified pseudobactin M114. Thus, experimental evidence suggested that iron mediated its effects via transcriptional activation by PbrA under low iron conditions, while an as-yet-unidentified sigma factor(s) may be required for the PbrA-independent aprA expression and AprA proteolytic activity induced by siderophore and iron.

In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)

PubMed Central

Sychantha, David; Jones, Carys S.; Little, Dustin J.; Howell, P. Lynne

2017-01-01

The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain. We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens. PMID:29077761

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.

Mycobacterium tuberculosis two-component systems and implications in novel vaccines and drugs.

PubMed

Zhou, PeiFu; Long, QuanXin; Zhou, YeXin; Wang, HongHai; Xie, JianPing

2012-01-01

Communication is vital for nearly all organisms to survive and thrive. For some particularly successful intracellular pathogens, a robust and precise signal transduction system is imperative for handling the complex, volatile, and harsh niche. The communication network of the etiology of tuberculosis, Mycobacterium tuberculosis (M.tb), namely two-component system (TCS), the eukaryotic-like Ser/Thr protein kinases(STPKs) system, the protein tyrosine kinase(PTK) system and the extracytoplasmic function σ(ECF-σ) system, determine how the pathogen responds to environmental fluctuations. At least 12 pair TCSs and four orphan proteins (three response regulators, Rv2884, Rv0260c, Rv0818, and one putative sensory transduction protein, Rv3143) can be found in the M.tb H37Rv genome. They regulate various aspects of M.tb, including virulence, dormancy, persistence, and drug resistance. This review focuses on the physiological roles of TCSs and the network of M.tb TCSs from a systems biology perspective. The implications of TCSs for better vaccine and new drug targets against tuberculosis are also examined.

Prediction of the Mechanism of Action of Fusaricidin on Bacillus subtilis

PubMed Central

Yu, Wen-Bang; Yin, Chun-Yun; Zhou, Ying; Ye, Bang-Ce

2012-01-01

Long-term use of antibiotics has engendered a large number of resistant pathogens, which pose a serious threat to human health. Here, we investigated the mechanism of fusaricidin antibacterial activity toward Bacillus subtilis and characterized the pathways responsible for drug resistance. We found that σw, an extracytoplasmic function sigma factor, plays an important role in the resistance to fusaricidins during the initial 5 minutes of drug addition. Approximately 18 genes were induced more than 3-fold, of which 66.7% are known to be regulated by σw. Over the following 3 h, fusaricidins induced 194 genes more than three-fold, and most were associated with classes of antibiotic-responsive stimulons. Moreover, the fusaricidin treatment increased the catabolism of fatty and amino acids but strongly repressed glucose decomposition and gluconeogenesis. In summary, our data provide insight into the mechanism of fusaricidin activity, on which we based our suggested strategies for the development of novel antibiotic agents. PMID:23185515

Prediction of the mechanism of action of fusaricidin on Bacillus subtilis.

PubMed

Yu, Wen-Bang; Yin, Chun-Yun; Zhou, Ying; Ye, Bang-Ce

2012-01-01

Long-term use of antibiotics has engendered a large number of resistant pathogens, which pose a serious threat to human health. Here, we investigated the mechanism of fusaricidin antibacterial activity toward Bacillus subtilis and characterized the pathways responsible for drug resistance. We found that σ(w), an extracytoplasmic function sigma factor, plays an important role in the resistance to fusaricidins during the initial 5 minutes of drug addition. Approximately 18 genes were induced more than 3-fold, of which 66.7% are known to be regulated by σ(w). Over the following 3 h, fusaricidins induced 194 genes more than three-fold, and most were associated with classes of antibiotic-responsive stimulons. Moreover, the fusaricidin treatment increased the catabolism of fatty and amino acids but strongly repressed glucose decomposition and gluconeogenesis. In summary, our data provide insight into the mechanism of fusaricidin activity, on which we based our suggested strategies for the development of novel antibiotic agents.

Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

DOE PAGES

Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; ...

2016-04-06

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly builtmore » computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.« less

Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

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

Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly builtmore » computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.« less

Random forests and stochastic gradient boosting for predicting tree canopy cover: Comparing tuning processes and model performance

Treesearch

E. Freeman; G. Moisen; J. Coulston; B. Wilson

2014-01-01

Random forests (RF) and stochastic gradient boosting (SGB), both involving an ensemble of classification and regression trees, are compared for modeling tree canopy cover for the 2011 National Land Cover Database (NLCD). The objectives of this study were twofold. First, sensitivity of RF and SGB to choices in tuning parameters was explored. Second, performance of the...

AmeriFlux US-SCg Southern California Climate Gradient - Grassland

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

Goulden, Mike

This is the AmeriFlux version of the carbon flux data for the site US-SCg Southern California Climate Gradient - Grassland. Site Description - Half hourly data are available at https://www.ess.uci.edu/~california/. This site is one of six Southern California Climate Gradient flux towers operated along an elevation gradient (sites are US-SCg, US-SCs, US-SCf, US-SCw, US-SCc, US-SCd). This site is a grassland that was historically dominated by exotic annuals and that underwent restoration with a focus on native bunch grasses in the 2010s. The site has historically burned every 10-20 years, with a wildfire in October 2007. The restoration involved several yearsmore » of mowing and herbicide application to suppress exotics followed by dense planting of Nasella bunch grasses.« less

Pure phase encode magnetic field gradient monitor.

PubMed

Han, Hui; MacGregor, Rodney P; Balcom, Bruce J

2009-12-01

Numerous methods have been developed to measure MRI gradient waveforms and k-space trajectories. The most promising new strategy appears to be magnetic field monitoring with RF microprobes. Multiple RF microprobes may record the magnetic field evolution associated with a wide variety of imaging pulse sequences. The method involves exciting one or more test samples and measuring the time evolution of magnetization through the FIDs. Two critical problems remain. The gradient waveform duration is limited by the sample T(2)*, while the k-space maxima are limited by gradient dephasing. The method presented is based on pure phase encode FIDs and solves the above two problems in addition to permitting high strength gradient measurement. A small doped water phantom (1-3 mm droplet, T(1), T(2), T(2)* < 100 micros) within a microprobe is excited by a series of closely spaced broadband RF pulses each followed by FID single point acquisition. Two trial gradient waveforms have been chosen to illustrate the technique, neither of which could be measured by the conventional RF microprobe measurement. The first is an extended duration gradient waveform while the other illustrates the new method's ability to measure gradient waveforms with large net area and/or high amplitude. The new method is a point monitor with simple implementation and low cost hardware requirements.

Increased dimensionality of cell-cell communication can decrease the precision of gradient sensing

NASA Astrophysics Data System (ADS)

Smith, Tyler; Levchenko, Andre; Nemenman, Ilya; Mugler, Andrew

Gradient sensing is a biological computation that involves comparison of concentrations measured in at least two different locations. As such, the pre- cision of gradient sensing is limited by the intrinsic stochasticity in the com- munication that brings such distributed information to the same location. We have recently analyzed such limitations experimentally and theoretically in multicellular gradient sensing in mammary epithelial cell organoids. For 1d chains of collectively sensing cells, the communication noise puts a se- vere constraint on how the accuracy of gradient sensing increases with the number of cells in the sensor. A question remains as to whether the effect of the noise can be mitigated by the extra spatial averaging allowed in sensing by 2d and 3d cellular organoids. Here we show using computer simulations that, counterintuitively, such spatial averaging decreases gradient sensitiv- ity (while it increases concentration sensitivity). We explain the findings analytically and propose that a recently introduced Regional Excitation - Global Inhibition model of gradient sensing can overcome this limitation and use 2d or 3d spatial averaging to improve the sensing accuracy. Supported by NSF Grant PHY/1410978 and James S. McDonnell Foundation Grant # 220020321.

Tracing the social gradient in the health of Canadians: primary and secondary determinants.

PubMed

Kosteniuk, Julie G; Dickinson, Harley D

2003-07-01

The social gradient in heath refers to the fact that inequalities in population health status are related to inequalities in social status. This study advances and tests a model of the relationships between what we term primary and secondary determinants of the social gradient in health. The primary determinants of health include socioeconomic and demographic indicators. Secondary determinants include stressors, control, self-esteem, social support, and social involvement. Health status is indicated by measures of physical health, self-reported health status, and mental distress. Data are taken from the Canadian National Population Health (NPH) Survey (1994-1995). The study sample consists of 7720 men and 9269 women 15 to over 80 years of age. Using path analysis, we found that higher household income, being retired and growing older are significantly associated with lower stressor levels. Higher stressor levels are associated with lower levels of control, self-esteem, and social support. Higher income Canadians experience greater levels of control and social support, while older Canadians experience lower rates of social support but higher rates of social involvement. Being employed and caring for one's family are positively associated with better physical and self-reported health status. Higher household income, being retired, and aging are associated with better physical health and lower mental distress when accounting for their role in lowering stressor levels and bolstering control, self-esteem, social support, and social involvement. Replicating this study with future samples of the NPH Survey should be of benefit in ascertaining whether the social gradient in Canadians' health status shows signs of declining.

Spectral-Element Simulations of Wave Propagation in Porous Media: Finite-Frequency Sensitivity Kernels Based Upon Adjoint Methods

NASA Astrophysics Data System (ADS)

Morency, C.; Tromp, J.

2008-12-01

The mathematical formulation of wave propagation in porous media developed by Biot is based upon the principle of virtual work, ignoring processes at the microscopic level, and does not explicitly incorporate gradients in porosity. Based on recent studies focusing on averaging techniques, we derive the macroscopic porous medium equations from the microscale, with a particular emphasis on the effects of gradients in porosity. In doing so, we are able to naturally determine two key terms in the momentum equations and constitutive relationships, directly translating the coupling between the solid and fluid phases, namely a drag force and an interfacial strain tensor. In both terms, gradients in porosity arise. One remarkable result is that when we rewrite this set of equations in terms of the well known Biot variables us, w), terms involving gradients in porosity are naturally accommodated by gradients involving w, the fluid motion relative to the solid, and Biot's formulation is recovered, i.e., it remains valid in the presence of porosity gradients We have developed a numerical implementation of the Biot equations for two-dimensional problems based upon the spectral-element method (SEM) in the time domain. The SEM is a high-order variational method, which has the advantage of accommodating complex geometries like a finite-element method, while keeping the exponential convergence rate of (pseudo)spectral methods. As in the elastic and acoustic cases, poroelastic wave propagation based upon the SEM involves a diagonal mass matrix, which leads to explicit time integration schemes that are well-suited to simulations on parallel computers. Effects associated with physical dispersion & attenuation and frequency-dependent viscous resistance are addressed by using a memory variable approach. Various benchmarks involving poroelastic wave propagation in the high- and low-frequency regimes, and acoustic-poroelastic and poroelastic-poroelastic discontinuities have been successfully performed. We present finite-frequency sensitivity kernels for wave propagation in porous media based upon adjoint methods. We first show that the adjoint equations in porous media are similar to the regular Biot equations upon defining an appropriate adjoint source. Then we present finite-frequency kernels for seismic phases in porous media (e.g., fast P, slow P, and S). These kernels illustrate the sensitivity of seismic observables to structural parameters and form the basis of tomographic inversions. Finally, we show an application of this imaging technique related to the detection of buried landmines and unexploded ordnance (UXO) in porous environments.

Integrating the Gradient of the Thin Wire Kernel

NASA Technical Reports Server (NTRS)

Champagne, Nathan J.; Wilton, Donald R.

2008-01-01

A formulation for integrating the gradient of the thin wire kernel is presented. This approach employs a new expression for the gradient of the thin wire kernel derived from a recent technique for numerically evaluating the exact thin wire kernel. This approach should provide essentially arbitrary accuracy and may be used with higher-order elements and basis functions using the procedure described in [4].When the source and observation points are close, the potential integrals over wire segments involving the wire kernel are split into parts to handle the singular behavior of the integrand [1]. The singularity characteristics of the gradient of the wire kernel are different than those of the wire kernel, and the axial and radial components have different singularities. The characteristics of the gradient of the wire kernel are discussed in [2]. To evaluate the near electric and magnetic fields of a wire, the integration of the gradient of the wire kernel needs to be calculated over the source wire. Since the vector bases for current have constant direction on linear wire segments, these integrals reduce to integrals of the form

Global gradient estimates for divergence-type elliptic problems involving general nonlinear operators

NASA Astrophysics Data System (ADS)

Cho, Yumi

2018-05-01

We study nonlinear elliptic problems with nonstandard growth and ellipticity related to an N-function. We establish global Calderón-Zygmund estimates of the weak solutions in the framework of Orlicz spaces over bounded non-smooth domains. Moreover, we prove a global regularity result for asymptotically regular problems which are getting close to the regular problems considered, when the gradient variable goes to infinity.

Functional integrative levels in the human interactome recapitulate organ organization.

PubMed

Souiai, Ouissem; Becker, Emmanuelle; Prieto, Carlos; Benkahla, Alia; De las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This 'Largest Common Interactome Network' represents a 'functional interactome core'. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization.

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

PubMed Central

Bocian-Ostrzycka, Katarzyna M.; Łasica, Anna M.; Dunin-Horkawicz, Stanisław; Grzeszczuk, Magdalena J.; Drabik, Karolina; Dobosz, Aneta M.; Godlewska, Renata; Nowak, Elżbieta; Collet, Jean-Francois; Jagusztyn-Krynicka, Elżbieta K.

2015-01-01

Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity. PMID:26500620

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain.

PubMed

Bocian-Ostrzycka, Katarzyna M; Łasica, Anna M; Dunin-Horkawicz, Stanisław; Grzeszczuk, Magdalena J; Drabik, Karolina; Dobosz, Aneta M; Godlewska, Renata; Nowak, Elżbieta; Collet, Jean-Francois; Jagusztyn-Krynicka, Elżbieta K

2015-01-01

Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation - periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.

Towards ultra-high ductility TRIP-assisted multiphase steels controlled by strain gradient plasticity effects

NASA Astrophysics Data System (ADS)

Hatami, M. K.; Pardoen, T.; Lacroix, G.; Berke, P.; Jacques, P. J.; Massart, T. J.

2017-01-01

TRansformation Induced Plasticity (TRIP) is a very effective mechanism to increase the strain hardening capacity of multiphase steels containing a fraction of metastable austenite, leading to both high strength and large uniform elongation. Excellent performances have been reached in the past 20 years, with recent renewed interest through the development of the 3rd generation of high strength steels often involving a TRIP effect. The microstructure and composition optimization is complex due to the interplay of coupled effects on the transformation kinetics and work hardening such as phase stability, size of retained austenite grains, temperature and loading path. In particular, recent studies have shown that the TRIP effect can only be quantitatively captured for realistic microstructures if strain gradient plasticity effects are taken into account, although direct experimental validation of this claim is missing. Here, an original computational averaging scheme is developed for predicting the elastoplastic response of TRIP aided multiphase steels based on a strain gradient plasticity model. The microstructure is represented by an aggregate of many elementary unit cells involving each a fraction of retained austenite with a specified stability. The model parameters, involving the transformation kinetics, are identified based on experimental tensile tests performed at different temperatures. The model is further assessed towards original experiments, involving temperature changes during deformation. A classical size independent plasticity model is shown unable to capture the TRIP effect on the mechanical response. Conversely, the strain gradient formulation properly predicts substantial variations of the strain hardening with deformation and temperature, hence of the uniform elongation in good agreement with the experiments. A parametric study is performed to get more insight on the effect of the material length scale as well as to determine optimum transformation kinetics to reach the highest possible strength-ductility balance. It is shown that the uniform elongation can potentially be increased by 50% or more, paving the way towards future microstructure engineering efforts.

Designing in vivo concentration gradients with discrete controlled release: a computational model

NASA Astrophysics Data System (ADS)

Walker, Edgar Y.; Barbour, Dennis L.

2010-08-01

One promising neurorehabilitation therapy involves presenting neurotrophins directly into the brain to induce growth of new neural connections. The precise control of neurotrophin concentration gradients deep within neural tissue that would be necessary for such a therapy is not currently possible, however. Here we evaluate the theoretical potential of a novel method of drug delivery, discrete controlled release (DCR), to control effective neurotrophin concentration gradients in an isotropic region of neocortex. We do so by constructing computational models of neurotrophin concentration profiles resulting from discrete release locations into the cortex and then optimizing their design for uniform concentration gradients. The resulting model indicates that by rationally selecting initial neurotrophin concentrations for drug-releasing electrode coatings in a square 16-electrode array, nearly uniform concentration gradients (i.e. planar concentration profiles) from one edge of the electrode array to the other should be obtainable. DCR therefore represents a promising new method of precisely directing neuronal growth in vivo over a wider spatial profile than would be possible with single release points.

Finite element analysis of gradient z-coil induced eddy currents in a permanent MRI magnet.

PubMed

Li, Xia; Xia, Ling; Chen, Wufan; Liu, Feng; Crozier, Stuart; Xie, Dexin

2011-01-01

In permanent magnetic resonance imaging (MRI) systems, pulsed gradient fields induce strong eddy currents in the conducting structures of the magnet body. The gradient field for image encoding is perturbed by these eddy currents leading to MR image distortions. This paper presents a comprehensive finite element (FE) analysis of the eddy current generation in the magnet conductors. In the proposed FE model, the hysteretic characteristics of ferromagnetic materials are considered and a scalar Preisach hysteresis model is employed. The developed FE model was applied to study gradient z-coil induced eddy currents in a 0.5 T permanent MRI device. The simulation results demonstrate that the approach could be effectively used to investigate eddy current problems involving ferromagnetic materials. With the knowledge gained from this eddy current model, our next step is to design a passive magnet structure and active gradient coils to reduce the eddy current effects. Copyright © 2010 Elsevier Inc. All rights reserved.

Theory of Epithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.

PubMed

Dasbiswas, Kinjal; Hannezo, Edouard; Gov, Nir S

2018-02-27

Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner-and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Postphloem, Nonvascular Transfer in Citrus

PubMed Central

Koch, Karen E.; Avigne, Wayne T.

1990-01-01

Postphloem, nonvascular assimilate transport occurs over an unusually long area in citrus fruit and thus facilitates investigation of this process relative to sugar entry into many sink structures. Labeled photosynthates moving into juice tissues of grapefruit (Citrus paradisi Macf.) slowed dramatically after entering the postphloem transport path (parenchyma cells, narrow portions of segment epidermis, and hair-like, parenchymatous stalks of juice sacs). Kinetic, metabolic, and compositional data indicated that transfer through the nonvascular area was delayed many hours by temporary storage and/or equilibration with sugars in compartments along the postphloem path. Labeled assimilates were generally recovered as sucrose throughout the path, and extent of hexose formation enroute bore no apparent relationship to the assimilate transfer process. Even after 24 hours, radiolabel was restricted to discrete, highly localized areas directly between vascular bundles and juice sacs. Postphloem transfer occurred against an ascending sucrose concentration gradient in young fruit, whereas a descending gradient (favoring diffusion/cytoplasmic streaming) developed only later in maturation. Involvement of a postphloem bulk flow is complicated in the present instance by the extremely limited water loss from juice sacs either via transpiration or fluid backflow. Nonetheless, tissue expansion can account for a collective water inflow of at least 1.0 milliliter per day throughout the majority of juice sac development, thus providing a modest, but potentially important means of nonvascular solution flow. Overall, data indicate postphloem transfer (a) can follow highly localized paths through sizable nonvascular areas (up to 3.0 centimeters total), (b) appears to involve temporary storage and/or equilibration with compartmentalized sugars enroute, (c) can occur either against an overall up-hill sugar gradient (young tissues) or along a descending gradient (near full expansion), and (d) appears to involve at least some contribution by nonvascular mass flow accommodated by tissue expansion. Images Figure 1 Figure 4 PMID:16667632

Enhancing early detection of exotic pests in agricultural and forest ecosystems using an urban-gradient framework.

PubMed

Colunga-Garcia, Manuel; Magarey, Roger A; Haack, Robert A; Gage, Stuart H; Qi, Jiaquo

2010-03-01

Urban areas are hubs of international transport and therefore are major gateways for exotic pests. Applying an urban gradient to analyze this pathway could provide insight into the ecological processes involved in human-mediated invasions. We defined an urban gradient for agricultural and forest ecosystems in the contiguous United States to (1) assess whether ecosystems nearer more urbanized areas were at greater risk of invasion, and (2) apply this knowledge to enhance early detection of exotic pests. We defined the gradient using the tonnage of imported products in adjacent urban areas and their distance to nearby agricultural or forest land. County-level detection reports for 39 exotic agricultural and forest pests of major economic importance were used to characterize invasions along the gradient. We found that counties with more exotic pests were nearer the urban end of the gradient. Assuming that the exotic species we analyzed represent typical invaders, then early detection efforts directed at 21-26% of U.S. agricultural and forest land would likely be able to detect 70% of invaded counties and 90% of the selected species. Applying an urban-gradient framework to current monitoring strategies should enhance early detection efforts of exotic pests, facilitating optimization in allocating resources to areas at greater risk of future invasions.

Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria.

PubMed

Boiangiu, Clara D; Jayamani, Elamparithi; Brügel, Daniela; Herrmann, Gloria; Kim, Jihoe; Forzi, Lucia; Hedderich, Reiner; Vgenopoulou, Irini; Pierik, Antonio J; Steuber, Julia; Buckel, Wolfgang

2005-01-01

Anaerobic bacteria ferment glutamate via two different pathways to ammonia, carbon dioxide, acetate, butyrate and molecular hydrogen. The coenzyme B12-dependent pathway in Clostridium tetanomorphum via 3-methylaspartate involves pyruvate:ferredoxin oxidoreductase and a novel enzyme, a membrane-bound NADH:ferredoxin oxidoreductase. The flavin- and iron-sulfur-containing enzyme probably uses the energy difference between reduced ferredoxin and NADH to generate an electrochemical Na+ gradient, which drives transport processes. The other pathway via 2-hydroxyglutarate in Acidaminococcus fermentans and Fusobacterium nucleatum involves glutaconyl-CoA decarboxylase, which uses the free energy of decarboxylation to generate also an electrochemical Na+ gradient. In the latter two organisms, similar membrane-bound NADH:ferredoxin oxidoreductases have been characterized. We propose that in the hydroxyglutarate pathway these oxidoreductases work in the reverse direction, whereby the reduction of ferredoxin by NADH is driven by the Na+ gradient. The reduced ferredoxin is required for hydrogen production and the activation of radical enzymes. Further examples show that reduced ferredoxin is an agent, whose reducing energy is about 1 ATP 'richer' than that of NADH. Copyright 2005 S. Karger AG, Basel.

A mathematical model for the generation and control of a pH gradient in an immobilized enzyme system involving acid generation.

PubMed

Chen, G; Fournier, R L; Varanasi, S

1998-02-20

An optimal pH control technique has been developed for multistep enzymatic synthesis reactions where the optimal pH differs by several units for each step. This technique separates an acidic environment from a basic environment by the hydrolysis of urea within a thin layer of immobilized urease. With this technique, a two-step enzymatic reaction can take place simultaneously, in proximity to each other, and at their respective optimal pH. Because a reaction system involving an acid generation represents a more challenging test of this pH control technique, a number of factors that affect the generation of such a pH gradient are considered in this study. The mathematical model proposed is based on several simplifying assumptions and represents a first attempt to provide an analysis of this complex problem. The results show that, by choosing appropriate parameters, the pH control technique still can generate the desired pH gradient even if there is an acid-generating reaction in the system. Copyright 1998 John Wiley & Sons, Inc.

On the physics of the pressure and temperature gradients in the edge of tokamak plasmas

NASA Astrophysics Data System (ADS)

Stacey, Weston M.

2018-04-01

An extended plasma fluid theory including atomic physics, radiation, electromagnetic and themodynamic forces, external sources of particles, momentum and energy, and kinetic ion orbit loss is employed to derive theoretical expressions that display the role of the various factors involved in the determination of the pressure and temperature gradients in the edge of tokamak plasmas. Calculations for current experiments are presented to illustrate the magnitudes of various effects including strong radiative and atomic physics edge cooling effects and strong reduction in ion particle and energy fluxes due to ion orbit loss in the plasma edge. An important new insight is the strong relation between rotation and the edge pressure gradient.

Experimental evidence of temperature gradients in cavitating microflows seeded with thermosensitive nanoprobes

NASA Astrophysics Data System (ADS)

Ayela, Frédéric; Medrano-Muñoz, Manuel; Amans, David; Dujardin, Christophe; Brichart, Thomas; Martini, Matteo; Tillement, Olivier; Ledoux, Gilles

2013-10-01

Thermosensitive fluorescent nanoparticles seeded in deionized water combined with confocal microscopy enables thermal mapping over three dimensions of the liquid phase flowing through a microchannel interrupted by a microdiaphragm. This experiment reveals the presence of a strong thermal gradient up to ˜105 K/m only when hydrodynamic cavitation is present. Here hydrodynamic cavitation is the consequence of high shear rates downstream in the diaphragm. This temperature gradient is located in vortical structures associated with eddies in the shear layers. We attribute such overheating to the dissipation involved by the cavitating flow regime. Accordingly, we demonstrate that the microsizes of the device enhance the intensity of the thermal gap.

Stream-profile analysis and stream-gradient index

USGS Publications Warehouse

Hack, John T.

1973-01-01

The generally regular three-dimensional geometry of drainage networks is the basis for a simple method of terrain analysis providing clues to bedrock conditions and other factors that determine topographic forms. On a reach of any stream, a gradient-index value can be obtained which allows meaningful comparisons of channel slope on streams of different sizes. The index is believed to reflect stream power or competence and is simply the product of the channel slope at a point and channel length measured along the longest stream above the pointwhere the calculation is made. In an adjusted topography, changes in gradient-index values along a stream generally correspond to differences in bedrock or introduced load. In any landscape the gradient index of a stream is related to total relief and stream regimen. Thus, climate, tectonic events, and geomorphic history must be considered in using the gradient index. Gradient-index values can be obtained quickly by simple measurements on topographic maps, or they can be obtained by more sophisticated photogrammetric measurements that involve simple computer calculations from x, y, z coordinates.

Adipocyte induction of preadipocyte differentiation in a gradient chamber.

PubMed

Lai, Ning; Sims, James K; Jeon, Noo Li; Lee, Kyongbum

2012-12-01

Adipose tissue expansion involves enlargement of mature adipocytes and the formation of new adipocytes through the differentiation of locally resident preadipocytes. Factors released by the enlarged adipocytes are potential cues that induce the differentiation of the preadipocytes. Currently, there are limited options to investigate these cues in isolation from confounding systemic influences. A gradient generating microfluidic channel-based cell culture system was designed to enable solution patterning, while supporting long-term culture and differentiation of preadipocytes. Solution patterning was confirmed by selectively staining a fraction of uniformly seeded preadipocytes. An adipogenic cocktail gradient was used to induce the differentiation of a fraction of uniformly seeded preadipocytes and establish a spatially defined coculture of adipocytes and preadipocytes. Varying the adipogenic cocktail gradient generated cocultures of preadipocytes and adipocytes with different compositions. Transient application of the cocktail gradient, followed by basal medium treatment showed a biphasic induction of differentiation. The two phases of differentiation correlated with a spatial gradient in adipocyte size. Our results provide in vitro data supporting the size-dependent release of preadipocyte differentiation factors by enlarged adipocytes. Prospectively, the coculture system developed in this study could facilitate controlled, yet physiologically meaningful studies on paracrine interactions between adipocytes and preadipocytes during adipose tissue development.

Automated Processing of Plasma Samples for Lipoprotein Separation by Rate-Zonal Ultracentrifugation.

PubMed

Peters, Carl N; Evans, Iain E J

2016-12-01

Plasma lipoproteins are the primary means of lipid transport among tissues. Defining alterations in lipid metabolism is critical to our understanding of disease processes. However, lipoprotein measurement is limited to specialized centers. Preparation for ultracentrifugation involves the formation of complex density gradients that is both laborious and subject to handling errors. We created a fully automated device capable of forming the required gradient. The design has been made freely available for download by the authors. It is inexpensive relative to commercial density gradient formers, which generally create linear gradients unsuitable for rate-zonal ultracentrifugation. The design can easily be modified to suit user requirements and any potential future improvements. Evaluation of the device showed reliable peristaltic pump accuracy and precision for fluid delivery. We also demonstrate accurate fluid layering with reduced mixing at the gradient layers when compared to usual practice by experienced laboratory personnel. Reduction in layer mixing is of critical importance, as it is crucial for reliable lipoprotein separation. The automated device significantly reduces laboratory staff input and reduces the likelihood of error. Overall, this device creates a simple and effective solution to formation of complex density gradients. © 2015 Society for Laboratory Automation and Screening.

OSMOSIS: A CAUSE OF APPARENT DEVIATIONS FROM DARCY'S LAW.

USGS Publications Warehouse

Olsen, Harold W.

1985-01-01

This review of the existing evidence shows that osmosis causes intercepts in flow rate versus hydraulic gradient relationships that are consistent with the observed deviations from Darcy's law at very low gradients. Moreover, it is suggested that a natural cause of osmosis in laboratory samples could be chemical reactions such as those involved in aging effects. This hypothesis is analogous to the previously proposed occurrence of electroosmosis in nature generated by geochemical weathering reactions. Refs.

Composition Influences the Pathway but not the Outcome of the Metabolic Response of Bacterioplankton to Resource Shifts

PubMed Central

Comte, Jérôme; del Giorgio, Paul A.

2011-01-01

Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations. PMID:21980410

Concentration gradient induced morphology evolution of silica nanostructure growth on photoresist-derived carbon micropatterns

NASA Astrophysics Data System (ADS)

Liu, Dan; Shi, Tielin; Xi, Shuang; Lai, Wuxing; Liu, Shiyuan; Li, Xiaoping; Tang, Zirong

2012-09-01

The evolution of silica nanostructure morphology induced by local Si vapor source concentration gradient has been investigated by a smart design of experiments. Silica nanostructure or their assemblies with different morphologies are obtained on photoresist-derived three-dimensional carbon microelectrode array. At a temperature of 1,000°C, rope-, feather-, and octopus-like nanowire assemblies can be obtained along with the Si vapor source concentration gradient flow. While at 950°C, stringlike assemblies, bamboo-like nanostructures with large joints, and hollow structures with smaller sizes can be obtained along with the Si vapor source concentration gradient flow. Both vapor-liquid-solid and vapor-quasiliquid-solid growth mechanisms have been applied to explain the diverse morphologies involving branching, connecting, and batch growth behaviors. The present approach offers a potential method for precise design and controlled synthesis of nanostructures with different features.

Gradient-based Optimization for Poroelastic and Viscoelastic MR Elastography

PubMed Central

Tan, Likun; McGarry, Matthew D.J.; Van Houten, Elijah E.W.; Ji, Ming; Solamen, Ligin; Weaver, John B.

2017-01-01

We describe an efficient gradient computation for solving inverse problems arising in magnetic resonance elastography (MRE). The algorithm can be considered as a generalized ‘adjoint method’ based on a Lagrangian formulation. One requirement for the classic adjoint method is assurance of the self-adjoint property of the stiffness matrix in the elasticity problem. In this paper, we show this property is no longer a necessary condition in our algorithm, but the computational performance can be as efficient as the classic method, which involves only two forward solutions and is independent of the number of parameters to be estimated. The algorithm is developed and implemented in material property reconstructions using poroelastic and viscoelastic modeling. Various gradient- and Hessian-based optimization techniques have been tested on simulation, phantom and in vivo brain data. The numerical results show the feasibility and the efficiency of the proposed scheme for gradient calculation. PMID:27608454

Functional Integrative Levels in the Human Interactome Recapitulate Organ Organization

PubMed Central

Prieto, Carlos; Benkahla, Alia; De Las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This ‘Largest Common Interactome Network’ represents a ‘functional interactome core’. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization. PMID:21799769

Carrier-Mediated Transport of Nicotine Across the Inner Blood-Retinal Barrier: Involvement of a Novel Organic Cation Transporter Driven by an Outward H(+) Gradient.

PubMed

Tega, Yuma; Kubo, Yoshiyuki; Yuzurihara, Chihiro; Akanuma, Shin-Ichi; Hosoya, Ken-Ichi

2015-09-01

The present study was carried out to investigate the blood-to-retina transport of nicotine across the inner blood-retinal barrier (BRB). Using the in vivo vascular injection method, the blood-to-retina influx clearance of nicotine across the BRB was determined as 131 μL/(min?g retina), which is much higher than that of a nonpermeable paracellular marker, and blood-to-retina transport of nicotine was inhibited by organic cations such as pyrilamine and verapamil. The nicotine uptake by a conditionally immortalized rat retinal capillary endothelial cell line (TR-iBRB2 cells), an in vitro model of the inner BRB, exhibited time, temperature, and concentration dependence with a Km of 492 μM. These results suggest the involvement of a carrier-mediated transport process in nicotine transport in the inner BRB. The nicotine uptake by TR-iBRB2 cells was stimulated by an outwardly directed H(+) gradient, and the uptake was significantly inhibited by bulky and hydrophobic cationic drugs, whereas inhibitors of organic cation transporters did not show inhibitory effect. These results suggest that the novel organic cation transport system driven by an outwardly directed H(+) gradient is involved in the blood-to-retina transport of nicotine across the inner BRB. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

A Novel Computational Model Predicts Key Regulators of Chemokine Gradient Formation in Lymph Nodes and Site-Specific Roles for CCL19 and ACKR4

PubMed Central

Brook, Bindi S.

2017-01-01

The chemokine receptor CCR7 drives leukocyte migration into and within lymph nodes (LNs). It is activated by chemokines CCL19 and CCL21, which are scavenged by the atypical chemokine receptor ACKR4. CCR7-dependent navigation is determined by the distribution of extracellular CCL19 and CCL21, which form concentration gradients at specific microanatomical locations. The mechanisms underpinning the establishment and regulation of these gradients are poorly understood. In this article, we have incorporated multiple biochemical processes describing the CCL19–CCL21–CCR7–ACKR4 network into our model of LN fluid flow to establish a computational model to investigate intranodal chemokine gradients. Importantly, the model recapitulates CCL21 gradients observed experimentally in B cell follicles and interfollicular regions, building confidence in its ability to accurately predict intranodal chemokine distribution. Parameter variation analysis indicates that the directionality of these gradients is robust, but their magnitude is sensitive to these key parameters: chemokine production, diffusivity, matrix binding site availability, and CCR7 abundance. The model indicates that lymph flow shapes intranodal CCL21 gradients, and that CCL19 is functionally important at the boundary between B cell follicles and the T cell area. It also predicts that ACKR4 in LNs prevents CCL19/CCL21 accumulation in efferent lymph, but does not control intranodal gradients. Instead, it attributes the disrupted interfollicular CCL21 gradients observed in Ackr4-deficient LNs to ACKR4 loss upstream. Our novel approach has therefore generated new testable hypotheses and alternative interpretations of experimental data. Moreover, it acts as a framework to investigate gradients at other locations, including those that cannot be visualized experimentally or involve other chemokines. PMID:28807994

Development of morphogen gradient: The role of dimension and discreteness

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

Teimouri, Hamid; Kolomeisky, Anatoly B.

2014-02-28

The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen gradients is a result of complex processes that involve diffusion and degradation of locally produced signaling molecules. We developed a multi-dimensional discrete-state stochastic approach for investigating the corresponding reaction-diffusion models. It provided a full analytical description for stationary profiles and for important dynamic properties such as local accumulation times, variances, and mean first-passage times. The role of discreteness in developing of morphogen gradients is analyzed by comparing with available continuummore » descriptions. It is found that the continuum models prediction about multiple time scales near the source region in two-dimensional and three-dimensional systems is not supported in our analysis. Using ideas that view the degradation process as an effective potential, the effect of dimensionality on establishment of morphogen gradients is also discussed. In addition, we investigated how these reaction-diffusion processes are modified with changing the size of the source region.« less

Derivatives of logarithmic stationary distributions for policy gradient reinforcement learning.

PubMed

Morimura, Tetsuro; Uchibe, Eiji; Yoshimoto, Junichiro; Peters, Jan; Doya, Kenji

2010-02-01

Most conventional policy gradient reinforcement learning (PGRL) algorithms neglect (or do not explicitly make use of) a term in the average reward gradient with respect to the policy parameter. That term involves the derivative of the stationary state distribution that corresponds to the sensitivity of its distribution to changes in the policy parameter. Although the bias introduced by this omission can be reduced by setting the forgetting rate gamma for the value functions close to 1, these algorithms do not permit gamma to be set exactly at gamma = 1. In this article, we propose a method for estimating the log stationary state distribution derivative (LSD) as a useful form of the derivative of the stationary state distribution through backward Markov chain formulation and a temporal difference learning framework. A new policy gradient (PG) framework with an LSD is also proposed, in which the average reward gradient can be estimated by setting gamma = 0, so it becomes unnecessary to learn the value functions. We also test the performance of the proposed algorithms using simple benchmark tasks and show that these can improve the performances of existing PG methods.

Analytic Formulation and Numerical Implementation of an Acoustic Pressure Gradient Prediction

NASA Technical Reports Server (NTRS)

Lee, Seongkyu; Brentner, Kenneth S.; Farassat, F.; Morris, Philip J.

2008-01-01

Two new analytical formulations of the acoustic pressure gradient have been developed and implemented in the PSU-WOPWOP rotor noise prediction code. The pressure gradient can be used to solve the boundary condition for scattering problems and it is a key aspect to solve acoustic scattering problems. The first formulation is derived from the gradient of the Ffowcs Williams-Hawkings (FW-H) equation. This formulation has a form involving the observer time differentiation outside the integrals. In the second formulation, the time differentiation is taken inside the integrals analytically. This formulation avoids the numerical time differentiation with respect to the observer time, which is computationally more efficient. The acoustic pressure gradient predicted by these new formulations is validated through comparison with available exact solutions for a stationary and moving monopole sources. The agreement between the predictions and exact solutions is excellent. The formulations are applied to the rotor noise problems for two model rotors. A purely numerical approach is compared with the analytical formulations. The agreement between the analytical formulations and the numerical method is excellent for both stationary and moving observer cases.

Evaluation of hydrothermal resources of North Dakota. Phase II. Final report

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

Harris, K.L.; Howell, F.L.; Winczewski, L.M.

1981-06-01

The Phase II activities dealt with three main topical areas: geothermal gradient and heat-flow studies, stratigraphic studies, and water quality studies. Efforts were concentrated on Mesozoic and Cenozoic rocks. The geothermal gradient and heat-flow studies involved running temperature logs in groundwater observation holes in areas of interest, and locating, obtaining access to, and casing holes of convenience to be used as heat-flow determination sites. The stratigraphic and water quality studies involved two main efforts: updating and expanding WELLFILE and assembling a computer library system (WELLCAT) for all water wells drilled in the state. WATERCAT combines data from the United Statesmore » Geological Survey Water Resources Division's WATSTOR and GWST computer libraries; and includes physical, stratigraphic, and water quality data. Goals, methods, and results are presented.« less

Relocalization of the calcium gradient and a dihydropyridine receptor is involved in upward bending by bulging of Chara protonemata, but not in downward bending by bowing of Chara rhizoids.

PubMed

Braun, M; Richter, P

1999-10-01

The localization of cytoplasmic free calcium and a dihydropyridine (DHP) receptor, a putative calcium channel, was recorded during the opposite graviresponses of tip-growing Chara rhizoids and Chara protonemata by using the calcium indicator Calcium Crimson and a fluorescently labeled dihydropyridine (FL-DHP). In upward (negatively gravitropically) growing protonemata and downward (positively gravitropically) growing rhizoids, a steep Ca2+ gradient and DHP receptors were found to be symmetrically localized in the tip. However, the localization of the Ca2+ gradient and DHP receptors differed considerably during the gravitropic responses upon horizontal positioning of the two cell types. During the graviresponse of rhizoids, a continuous bowing downward by differential flank growth, the Ca2+ gradient and DHP receptors remained symmetrically localized in the tip at the centre of growth. However, after tilting protonemata into a horizontal position, there was a drastic displacement of the Ca2+ gradient and FL-DHP to the upper flank of the apical dome. This displacement occurred after the apical intrusion and sedimentation of the statoliths but clearly before the change in the growth direction became evident. In protonemata, the reorientation of the growth direction started with the appearance of a bulge on that site of the upper flank which was predicted by the asymmetrically displaced Ca2+ gradient. With the upward shift of the cell tip, which is suggested to result from a statolith-induced displacement of the growth centre, the Ca2+ gradient and DHP receptors became symmetrically relocalized in the apical dome. No major asymmetrical rearrangement was observed during the following phase of gravitropic curvature which is characterized by slower rates of bending. Labeling with FL-DHP was completely inhibited by a non-fluorescently labeled dihydropyridine. From these results it is suggested that FL-DHP labels calcium channels in rhizoids and protonemata. In rhizoids, positive gravitropic curvature is caused by differential growth limited to the opposite subapical flanks of the apical dome, a process which does not involve displacement of the growth centre, the calcium gradient or calcium channels. In protonemata, however, it is proposed that a statolith-induced asymmetrical relocalization of calcium channels and the Ca2+ gradient precedes, and might mediate, the rearrangement of the centre of growth, most likely by the displacement of the Spitzenkorper, to the upper flank, which results in the negative gravitropic reorientation of the growth direction.

Efficiency of unconstrained minimization techniques in nonlinear analysis

NASA Technical Reports Server (NTRS)

Kamat, M. P.; Knight, N. F., Jr.

1978-01-01

Unconstrained minimization algorithms have been critically evaluated for their effectiveness in solving structural problems involving geometric and material nonlinearities. The algorithms have been categorized as being zeroth, first, or second order depending upon the highest derivative of the function required by the algorithm. The sensitivity of these algorithms to the accuracy of derivatives clearly suggests using analytically derived gradients instead of finite difference approximations. The use of analytic gradients results in better control of the number of minimizations required for convergence to the exact solution.

High gradient magnetic beneficiation of dry pulverized coal via upwardly directed recirculating fluidization

DOEpatents

Eissenberg, David M.; Liu, Yin-An

1980-01-01

This invention relates to an improved device and method for the high gradient magnetic beneficiation of dry pulverized coal, for the purpose of removing sulfur and ash from the coal whereby the product is a dry environmentally acceptable, low-sulfur fuel. The process involves upwardly directed recirculating air fluidization of selectively sized powdered coal in a separator having sections of increasing diameters in the direction of air flow, with magnetic field and flow rates chosen for optimum separations depending upon particulate size.

REPLICATIONS AND EXTENSIONS IN AROUSAL ASSESSMENT FOR SEX OFFENDERS WITH DEVELOPMENTAL DISABILITIES

PubMed Central

Reyes, Jorge R; Vollmer, Timothy R; Hall, Astrid

2011-01-01

Three adult male sex offenders with developmental disabilities participated in phallometric assessments that involved repeated measures of arousal when exposed to various stimuli. Arousal assessment outcomes were similar to those obtained by Reyes et al. (2006). Additional data-analysis methods provided further information about sexual preferences, thus replicating and extending previous research. The results provide preliminary data for establishing a preference gradient by age. Implications for the use of repeated measures and preference gradients in arousal assessments are discussed. PMID:21709795

Magnetic Field Generation Processes Involving Gravity and Differential Rotation. Solitary Plasma Rings Formation around Black Holes

NASA Astrophysics Data System (ADS)

Coppi, Bruno

2012-10-01

A clear theoretical framework to describe how magnetic fields are generated and amplified is provided by the magneto-gravitational modes that involve both differential rotation and gravity and for which other factors such as temperature gradients can contribute to their excitation. These modes are shown to be important for the evolution of plasma disks surrounding black holes.footnotetextB. Coppi, Phys. Plasmas 18, 032901 (2011) Non-linear and axi-symmetric plasmas and associated field configurations are found under stationary conditions that do not involve the presence of a pre-existing ``seed'' magnetic field unlike other configurations found previously.footnotetextIbid. The relevant magnetic energy density is of the order of the gravitationally confined plasma pressure. The solitary plasma rings that characterize these configurations are localized radially over regions with vanishing differential rotation and can be envisioned as the saturated state of magneto-gravitational modes. The ``source'' of these configurations is the combination of the gravitational force and of the plasma density gradient orthogonal to it.

Theoretical analysis of degradation mechanisms in the formation of morphogen gradients

NASA Astrophysics Data System (ADS)

Bozorgui, Behnaz; Teimouri, Hamid; Kolomeisky, Anatoly B.

2015-07-01

Fundamental biological processes of development of tissues and organs in multicellular organisms are governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in the concentration profiles of signaling molecules, which are frequently referred as morphogen gradients, lead to a cell differentiation via activating specific genes in a concentration-dependent manner. It is widely accepted that the establishment of the morphogen gradients involves multiple biochemical reactions and diffusion processes. One of the critical elements in the formation of morphogen gradients is a degradation of signaling molecules. We develop a new theoretical approach that provides a comprehensive description of the degradation mechanisms. It is based on the idea that the degradation works as an effective potential that drives the signaling molecules away from the source region. Utilizing the method of first-passage processes, the dynamics of the formation of morphogen gradients for various degradation mechanisms is explicitly evaluated. It is found that linear degradation processes lead to a dynamic behavior specified by times to form the morphogen gradients that depend linearly on the distance from the source. This is because the effective potential due to the degradation is quite strong. At the same time, nonlinear degradation mechanisms yield a quadratic scaling in the morphogen gradients formation times since the effective potentials are much weaker. Physical-chemical explanations of these phenomena are presented.

A microfluidics-based turning assay reveals complex growth cone responses to integrated gradients of substrate-bound ECM molecules and diffusible guidance cues.

PubMed

Joanne Wang, C; Li, Xiong; Lin, Benjamin; Shim, Sangwoo; Ming, Guo-Li; Levchenko, Andre

2008-02-01

Neuronal growth cones contain sophisticated molecular machinery precisely regulating their migration in response to complex combinatorial gradients of diverse external cues. The details of this regulation are still largely unknown, in part due to limitations of the currently available experimental techniques. Microfluidic devices have been shown to be capable of generating complex, stable and precisely controlled chemical gradients, but their use in studying growth cone migration has been limited in part due to the effects of shear stress. Here we describe a microfluidics-based turning-assay chip designed to overcome this issue. In addition to generating precise gradients of soluble guidance cues, the chip can also fabricate complex composite gradients of diffusible and surface-bound guidance cues that mimic the conditions the growth cones realistically counter in vivo. Applying this assay to Xenopus embryonic spinal neurons, we demonstrate that the presence of a surface-bound laminin gradient can finely tune the polarity of growth cone responses (repulsion or attraction) to gradients of brain-derived neurotrophic factor (BDNF), with the guidance outcome dependent on the mean BDNF concentration. The flexibility inherent in this assay holds significant potential for refinement of our understanding of nervous system development and regeneration, and can be extended to elucidate other cellular processes involving chemotaxis of shear sensitive cells.

Optical ray tracing method for simulating beam-steering effects during laser diagnostics in turbulent media.

PubMed

Wang, Yejun; Kulatilaka, Waruna D

2017-04-10

In most coherent spectroscopic methods used in gas-phase laser diagnostics, multiple laser beams are focused and crossed at a specific location in space to form the probe region. The desired signal is then generated as a result of nonlinear interactions between the beams in this overlapped region. When such diagnostic schemes are implemented in practical devices having turbulent reacting flow fields with refractive index gradients, the resulting beam steering can give rise to large measurement uncertainties. The objective of this work is to simulate beam-steering effects arising from pressure and temperature gradients in gas-phase media using an optical ray tracing approach. The ZEMAX OpticStudio software package is used to simulate the beam crossing and uncrossing effects in the presence of pressure and temperature gradients, specifically the conditions present in high-pressure, high-temperature combustion devices such as gas turbine engines. Specific cases involving two-beam and three-beam crossing configurations are simulated. The model formulation, the effects of pressure and temperature gradients, and the resulting beam-steering effects are analyzed. The results show that thermal gradients in the range of 300-3000 K have minimal effects, while pressure gradients in the range of 1-50 atm result in pronounced beam steering and the resulting signal fluctuations in the geometries investigated. However, with increasing pressures, the temperature gradients can also have a pronounced effect on the resultant signal levels.

Learning Incoherent Sparse and Low-Rank Patterns from Multiple Tasks

PubMed Central

Chen, Jianhui; Liu, Ji; Ye, Jieping

2013-01-01

We consider the problem of learning incoherent sparse and low-rank patterns from multiple tasks. Our approach is based on a linear multi-task learning formulation, in which the sparse and low-rank patterns are induced by a cardinality regularization term and a low-rank constraint, respectively. This formulation is non-convex; we convert it into its convex surrogate, which can be routinely solved via semidefinite programming for small-size problems. We propose to employ the general projected gradient scheme to efficiently solve such a convex surrogate; however, in the optimization formulation, the objective function is non-differentiable and the feasible domain is non-trivial. We present the procedures for computing the projected gradient and ensuring the global convergence of the projected gradient scheme. The computation of projected gradient involves a constrained optimization problem; we show that the optimal solution to such a problem can be obtained via solving an unconstrained optimization subproblem and an Euclidean projection subproblem. We also present two projected gradient algorithms and analyze their rates of convergence in details. In addition, we illustrate the use of the presented projected gradient algorithms for the proposed multi-task learning formulation using the least squares loss. Experimental results on a collection of real-world data sets demonstrate the effectiveness of the proposed multi-task learning formulation and the efficiency of the proposed projected gradient algorithms. PMID:24077658

Learning Incoherent Sparse and Low-Rank Patterns from Multiple Tasks.

PubMed

Chen, Jianhui; Liu, Ji; Ye, Jieping

2012-02-01

We consider the problem of learning incoherent sparse and low-rank patterns from multiple tasks. Our approach is based on a linear multi-task learning formulation, in which the sparse and low-rank patterns are induced by a cardinality regularization term and a low-rank constraint, respectively. This formulation is non-convex; we convert it into its convex surrogate, which can be routinely solved via semidefinite programming for small-size problems. We propose to employ the general projected gradient scheme to efficiently solve such a convex surrogate; however, in the optimization formulation, the objective function is non-differentiable and the feasible domain is non-trivial. We present the procedures for computing the projected gradient and ensuring the global convergence of the projected gradient scheme. The computation of projected gradient involves a constrained optimization problem; we show that the optimal solution to such a problem can be obtained via solving an unconstrained optimization subproblem and an Euclidean projection subproblem. We also present two projected gradient algorithms and analyze their rates of convergence in details. In addition, we illustrate the use of the presented projected gradient algorithms for the proposed multi-task learning formulation using the least squares loss. Experimental results on a collection of real-world data sets demonstrate the effectiveness of the proposed multi-task learning formulation and the efficiency of the proposed projected gradient algorithms.

A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.

PubMed

Chao, Yanjie; Vogel, Jörg

2016-02-04

Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an alternative biogenesis pathway releasing the conserved mRNA 3' UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3' UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol. Copyright © 2016 Elsevier Inc. All rights reserved.

Some infectious causes of diarrhea in young farm animals.

PubMed Central

Holland, R E

1990-01-01

Escherichia coli, rotaviruses, and Cryptosporidium parvum are discussed in this review as they relate to enteric disease in calves, lambs, and pigs. These microorganisms are frequently incriminated as causative agents in diarrheas among neonatal food animals, and in some cases different strains or serotypes of the same organism cause diarrhea in humans. E. coli causes diarrhea by mechanisms that include production of heat-labile or heat-stable enterotoxins and synthesis of potent cytotoxins, and some strains cause diarrhea by yet undetermined mechanisms. Rotaviruses and C. parvum induce various degrees of villous atrophy. Rotaviruses infect and replicate within the cytoplasm of enterocytes, whereas C. parvum resides in an intracellular, extracytoplasmic location. E. coli, rotavirus, and C. parvum infections are of concern to producers, veterinarians, and public health officials. These agents are a major cause of economic loss to the producer because of costs associated with therapy, reduced performance, and high morbidity and mortality rates. Moreover, diarrheic animals may harbor, incubate, and act as a source to healthy animals and humans of some of these agents. Images PMID:2224836

Complex oligosaccharides are N-linked to Kv3 voltage-gated K+ channels in rat brain.

PubMed

Cartwright, Tara A; Corey, Melissa J; Schwalbe, Ruth A

2007-04-01

Neuronal Kv3 voltage-gated K(+) channels have two absolutely conserved N-glycosylation sites. Here, it is shown that Kv3.1, 3.3, and 3.4 channels are N-glycosylated in rat brain. Digestion of total brain membranes with peptide N glycosidase F (PNGase F) produced faster migrating immunobands than those of undigested membranes. Additionally, partial PNGase F digests showed that both sites are occupied by oligosaccharides. Neuraminidase treatment produced a smaller immunoband shift relative to PNGase F treatment. These results indicate that both sites are highly available and occupied by N-linked oligosaccharides for Kv3.1, 3.3, and 3.4 in rat brain, and furthermore that at least one oligosaccharide is of complex type. Additionally, these results point to an extracytoplasmic S1-S2 linker in Kv3 proteins expressed in native membranes. We suggest that N-glycosylation processing of Kv3 channels is critical for the expression of K(+) currents at the surface of neurons, and perhaps contributes to the pathophysiology of congenital disorders of glycosylation.

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective.

PubMed

Greene, Nicholas P; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.

The Bacillus subtilis GntR family repressor YtrA responds to cell wall antibiotics.

PubMed

Salzberg, Letal I; Luo, Yun; Hachmann, Anna-Barbara; Mascher, Thorsten; Helmann, John D

2011-10-01

The transglycosylation step of cell wall synthesis is a prime antibiotic target because it is essential and specific to bacteria. Two antibiotics, ramoplanin and moenomycin, target this step by binding to the substrate lipid II and the transglycosylase enzyme, respectively. Here, we compare the ramoplanin and moenomycin stimulons in the Gram-positive model organism Bacillus subtilis. Ramoplanin strongly induces the LiaRS two-component regulatory system, while moenomycin almost exclusively induces genes that are part of the regulon of the extracytoplasmic function (ECF) σ factor σ(M). Ramoplanin additionally induces the ytrABCDEF and ywoBCD operons, which are not part of a previously characterized antibiotic-responsive regulon. Cluster analysis reveals that these two operons are selectively induced by a subset of cell wall antibiotics that inhibit lipid II function or recycling. Repression of both operons requires YtrA, which recognizes an inverted repeat in front of its own operon and in front of ywoB. These results suggest that YtrA is an additional regulator of cell envelope stress responses.

The Bacillus subtilis GntR Family Repressor YtrA Responds to Cell Wall Antibiotics▿§

PubMed Central

Salzberg, Letal I.; Luo, Yun; Hachmann, Anna-Barbara; Mascher, Thorsten; Helmann, John D.

2011-01-01

The transglycosylation step of cell wall synthesis is a prime antibiotic target because it is essential and specific to bacteria. Two antibiotics, ramoplanin and moenomycin, target this step by binding to the substrate lipid II and the transglycosylase enzyme, respectively. Here, we compare the ramoplanin and moenomycin stimulons in the Gram-positive model organism Bacillus subtilis. Ramoplanin strongly induces the LiaRS two-component regulatory system, while moenomycin almost exclusively induces genes that are part of the regulon of the extracytoplasmic function (ECF) σ factor σM. Ramoplanin additionally induces the ytrABCDEF and ywoBCD operons, which are not part of a previously characterized antibiotic-responsive regulon. Cluster analysis reveals that these two operons are selectively induced by a subset of cell wall antibiotics that inhibit lipid II function or recycling. Repression of both operons requires YtrA, which recognizes an inverted repeat in front of its own operon and in front of ywoB. These results suggest that YtrA is an additional regulator of cell envelope stress responses. PMID:21856850

The sensitivity of Bacillus subtilis to diverse antimicrobial compounds is influenced by Abh.

PubMed

Murray, Ewan J; Stanley-Wall, Nicola R

2010-12-01

Abh is a transition state regulator of Bacillus subtilis that controls biofilm formation and the production of several diverse antimicrobial compounds. Using a high-throughput non-biased technique, we show for the first time that Abh influences the sensitivity of B. subtilis to diverse antimicrobial compounds. Following up on these findings with a combination of classical genetics and antibiotic susceptibility assays, we demonstrate that Abh influences cellular processes such as the remodelling of the cell wall. We present data demonstrating that the extracytoplasmic function sigma factor σ(X) controls resistance to β-lactam antibiotics by activating abh transcription. Downstream from Abh, activation of slrR expression by Abh is responsible for controlling the sensitivity of B. subtilis to such antibiotics due to the role that SlrR plays in regulating autolysin biosynthesis. The abh mutant additionally exhibits increased resistance to aminoglycoside antimicrobials. We confirm that aminoglycoside killing of B. subtilis is likely to be caused by oxidative damage but rule out the possibility that the increased resistance of the abh mutant to aminoglycosides is due to a general increase in resistance to oxidative stress.

Fabrication process for a gradient index x-ray lens

DOEpatents

Bionta, R.M.; Makowiecki, D.M.; Skulina, K.M.

1995-01-17

A process is disclosed for fabricating high efficiency x-ray lenses that operate in the 0.5-4.0 keV region suitable for use in biological imaging, surface science, and x-ray lithography of integrated circuits. The gradient index x-ray optics fabrication process broadly involves co-sputtering multi-layers of film on a wire, followed by slicing and mounting on block, and then ion beam thinning to a thickness determined by periodic testing for efficiency. The process enables the fabrication of transmissive gradient index x-ray optics for the 0.5-4.0 keV energy range. This process allows the fabrication of optical elements for the next generation of imaging and x-ray lithography instruments in the soft x-ray region. 13 figures.

Matrix elements of N-particle explicitly correlated Gaussian basis functions with complex exponential parameters

NASA Astrophysics Data System (ADS)

Bubin, Sergiy; Adamowicz, Ludwik

2006-06-01

In this work we present analytical expressions for Hamiltonian matrix elements with spherically symmetric, explicitly correlated Gaussian basis functions with complex exponential parameters for an arbitrary number of particles. The expressions are derived using the formalism of matrix differential calculus. In addition, we present expressions for the energy gradient that includes derivatives of the Hamiltonian integrals with respect to the exponential parameters. The gradient is used in the variational optimization of the parameters. All the expressions are presented in the matrix form suitable for both numerical implementation and theoretical analysis. The energy and gradient formulas have been programed and used to calculate ground and excited states of the He atom using an approach that does not involve the Born-Oppenheimer approximation.

Matrix elements of N-particle explicitly correlated Gaussian basis functions with complex exponential parameters.

PubMed

Bubin, Sergiy; Adamowicz, Ludwik

2006-06-14

In this work we present analytical expressions for Hamiltonian matrix elements with spherically symmetric, explicitly correlated Gaussian basis functions with complex exponential parameters for an arbitrary number of particles. The expressions are derived using the formalism of matrix differential calculus. In addition, we present expressions for the energy gradient that includes derivatives of the Hamiltonian integrals with respect to the exponential parameters. The gradient is used in the variational optimization of the parameters. All the expressions are presented in the matrix form suitable for both numerical implementation and theoretical analysis. The energy and gradient formulas have been programmed and used to calculate ground and excited states of the He atom using an approach that does not involve the Born-Oppenheimer approximation.

Diversity and Seasonal Dynamics of an Assemblage of Sarcophagid Diptera in a Gradient of Urbanization

PubMed Central

Mulieri, Pablo R.; Patitucci, Luciano D.; Schnack, Juan A; Mariluis, Juan C.

2011-01-01

Sarcophagid species inhabiting different locations in a rural-urban gradient were surveyed in the east central Argentine district of the Almirante Brown, Buenos Aires province. The main objectives of this research were to identify the most prevalent sarcophagid species and to describe community richness and diversity according to the degree of urbanization and the environmental variables measured in three locations within a rural-urban gradient sampled during two years from May 2005 to April 2007. Spatial and seasonal variations were the main factors involved in structuring the sarcophagid communities. Diversity was lower in urbanized areas than in rural ones. Bait and microhabitat preferences (sunny or shady places) and seasonal fluctuations were described for 17 sarcophagid species. PMID:21870984

Fabrication process for a gradient index x-ray lens

DOEpatents

Bionta, Richard M.; Makowiecki, Daniel M.; Skulina, Kenneth M.

1995-01-01

A process for fabricating high efficiency x-ray lenses that operate in the 0.5-4.0 keV region suitable for use in biological imaging, surface science, and x-ray lithography of integrated circuits. The gradient index x-ray optics fabrication process broadly involves co-sputtering multi-layers of film on a wire, followed by slicing and mounting on block, and then ion beam thinning to a thickness determined by periodic testing for efficiency. The process enables the fabrication of transmissive gradient index x-ray optics for the 0.5-4.0 keV energy range. This process allows the fabrication of optical elements for the next generation of imaging and x-ray lithography instruments m the soft x-ray region.

Gradient twinned 304 stainless steels for high strength and high ductility

DOE PAGES

Chen, Aiying; Liu, Jiabin; Wang, Hongtao; ...

2016-04-23

Gradient materials often have attractive mechanical properties that outperform uniform microstructure counterparts. It remains a difficult task to investigate and compare the performance of various gradient microstructures due to the difficulty of fabrication, the wide range of length scales involved, and their respective volume percentage variations. We have investigated four types of gradient microstructures in 304 stainless steels that utilize submicrotwins, nanotwins, nanocrystalline-, ultrafine- and coarse-grains as building blocks. Tensile tests reveal that the gradient microstructure consisting of submicrotwins and nanotwins has a persistent and stable work hardening rate and yields an impressive combination of high strength and high ductility,more » leading to a toughness that is nearly 50% higher than that of the coarse-grained counterpart. Ex- and in-situ transmission electron microscopy indicates that nanoscale and submicroscale twins help to suppress and limit martensitic phase transformation via the confinement of martensite within the twin lamellar. Twinning and detwinning remain active during tensile deformation and contribute to the work hardening behavior. We discuss the advantageous properties of using submicrotwins as the main load carrier and nanotwins as the strengthening layers over those coarse and nanocrystalline grains. Furthermore, our work uncovers a new gradient design strategy to help metals and alloys achieve high strength and high ductility.« less

Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

PubMed Central

Fitzpatrick, Matthew C.; Sanders, Nathan J.; Normand, Signe; Svenning, Jens-Christian; Ferrier, Simon; Gove, Aaron D.; Dunn, Robert R.

2013-01-01

A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel method that accommodates variation in rates of species turnover along gradients and between different gradients, to compare environmental and spatial controls on the floras of two regions with contrasting evolutionary and climatic histories: southwest Australia and northern Europe. We find stronger signals of climate history in the northern European flora and demonstrate that variation in rates of species turnover is persistent across regions, taxa and different gradients. Such variation may represent an important but often overlooked component of biodiversity that complicates comparisons of distance–decay relationships and underscores the importance of using methods that accommodate the curvilinear relationships expected when modelling beta diversity. Determining how rates of species turnover vary along and between gradients is relevant to understanding the sensitivity of ecological systems to environmental change. PMID:23926147

Conjugation of gold nanoparticles and recombinant human endostatin modulates vascular normalization via interruption of anterior gradient 2-mediated angiogenesis.

PubMed

Pan, Fan; Yang, Wende; Li, Wei; Yang, Xiao-Yan; Liu, Shuhao; Li, Xin; Zhao, Xiaoxu; Ding, Hui; Qin, Li; Pan, Yunlong

2017-07-01

Several studies have revealed the potential of normalizing tumor vessels in anti-angiogenic treatment. Recombinant human endostatin is an anti-angiogenic agent which has been applied in clinical tumor treatment. Our previous research indicated that gold nanoparticles could be a nanoparticle carrier for recombinant human endostatin delivery. The recombinant human endostatin-gold nanoparticle conjugates normalized vessels, which improved chemotherapy. However, the mechanism of recombinant human endostatin-gold nanoparticle-induced vascular normalization has not been explored. Anterior gradient 2 has been reported to be over-expressed in many malignant tumors and involved in tumor angiogenesis. To date, the precise efficacy of recombinant human endostatin-gold nanoparticles on anterior gradient 2-mediated angiogenesis or anterior gradient 2-related signaling cohort remained unknown. In this study, we aimed to explore whether recombinant human endostatin-gold nanoparticles could normalize vessels in metastatic colorectal cancer xenografts, and we further elucidated whether recombinant human endostatin-gold nanoparticles could interrupt anterior gradient 2-induced angiogenesis. In vivo, it was indicated that recombinant human endostatin-gold nanoparticles increased pericyte expression while inhibit vascular endothelial growth factor receptor 2 and anterior gradient 2 expression in metastatic colorectal cancer xenografts. In vitro, we uncovered that recombinant human endostatin-gold nanoparticles reduced cell migration and tube formation induced by anterior gradient 2 in human umbilical vein endothelial cells. Treatment with recombinant human endostatin-gold nanoparticles attenuated anterior gradient 2-mediated activation of MMP2, cMyc, VE-cadherin, phosphorylation of p38, and extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) in human umbilical vein endothelial cells. Our findings demonstrated recombinant human endostatin-gold nanoparticles might normalize vessels by interfering anterior gradient 2-mediated angiogenesis in metastatic colorectal cancer.

Electrochemical measurements and thermodynamic calculations of redox equilibria in pallasite meteorites - Implications for the eucrite parent body

NASA Technical Reports Server (NTRS)

Righter, Kevin; Arculus, Richard J.; Paslick, Cassi; Delano, John W.

1990-01-01

The intrinsic oxygen fugacity (IOF) of olivine separates from the Salta, Springwater, and Eagle Station pallasites was measured between 850 and 1150 C using oxygen-specific solid zirconia electrolytes at 100,000 Pa. Thermodynamic calculations of redox equilibria involving equalibrium pallasite assemblages are in good agreement with the experimental results and provide a lower limit to pallasite redox stability; others involving disequilibrium assemblages, suggest that pallasites experienced localized, late-stage oxidation and reduction effects. Consideration of the redox buffer metal-olivine-orthopyroxene utilizing calculated Eucrite Parent Body (EPB) mantle phase compositions indicates that small redox gradients may have existed in the EPB. Such gradients may have produced strong compositional variation within the EPB. In addition, there is apparently significant redox heterogeneity in the source area of Eagle Station Trio pallasites and Bocaiuva iron meteorites.

A novel polymerase chain reaction (PCR) - denaturing gradient gel electrophoresis (DGGE) for the identification of Micrococcaceae strains involved in meat fermentations. Its application to naturally fermented Italian sausages.

PubMed

Cocolin, L; Manzano, M; Aggio, D; Cantoni, C; Comi, G

2001-05-01

A new molecular method consisting of polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis (DGGE) of a small fragment from the 16S rRNA gene identified the Micrococcaceae strains isolated from natural fermented Italian sausages. Lactic acid bacteria, total aerobic mesophilic flora, Enterobacteriaceae and faecal enterococci were also monitored. Micrococcaceaea control strains from international collections were used to optimise the method and 90 strains, isolated from fermented sausages, were identified by biochemical tests and PCR-DGGE. No differences were observed between the methods used. The results reported in this paper prove that Staphylococcus xylosus is the main bacterium involved in fermented sausage production, representing, from the tenth day of ripening, the only Micrococcaceaea species isolated.

Using absolute gravimeter data to determine vertical gravity gradients

USGS Publications Warehouse

Robertson, D.S.

2001-01-01

The position versus time data from a free-fall absolute gravimeter can be used to estimate the vertical gravity gradient in addition to the gravity value itself. Hipkin has reported success in estimating the vertical gradient value using a data set of unusually good quality. This paper explores techniques that may be applicable to a broader class of data that may be contaminated with "system response" errors of larger magnitude than were evident in the data used by Hipkin. This system response function is usually modelled as a sum of exponentially decaying sinusoidal components. The technique employed here involves combining the x0, v0 and g parameters from all the drops made during a site occupation into a single least-squares solution, and including the value of the vertical gradient and the coefficients of system response function in the same solution. The resulting non-linear equations must be solved iteratively and convergence presents some difficulties. Sparse matrix techniques are used to make the least-squares problem computationally tractable.

Patterns of premature physeal arrest: MR imaging of 111 children.

PubMed

Ecklund, Kirsten; Jaramillo, Diego

2002-04-01

The purpose of this study was to use MR imaging, especially fat-suppressed three-dimensional (3D) spoiled gradient-recalled echo sequences, to identify patterns of growth arrest after physeal insult in children. We evaluated 111 children with physeal bone bridges (median age, 11.4 years) using MR imaging to analyze bridge size, location in physis, signal intensity, growth recovery lines, avascular necrosis, and metaphyseal cartilage tongues. Fifty-eight patients underwent fat-suppressed 3D spoiled gradient-recalled echo imaging with physeal mapping. The cause, bone involved, radiographic appearance, and surgical interventions (60/111) were also correlated. Data were analyzed with the two-tailed Fisher's exact test. Posttraumatic bridges, accounting for 70% (78/111) of patients, were most often distal, especially of the tibia (n = 43) and femur (n = 14), whereas those due to the other miscellaneous causes were more frequently proximal (p < 0.0001). The position of the bridge in the physis was related to the bone involved (p < 0.0001). Sixty-five percent of distal tibial bridges involved the anteromedial physis, whereas 60% of the distal femoral arrests were central. Larger bridges had higher T1 signal intensity (p < 0.008). Oblique growth recovery lines were seen exclusively with bridges involving the peripheral physis (p = 0.002) and smaller, more potentially resectable bridges. Metaphyseal cartilaginous tongues were seen with all causes, but avascular necrosis was exclusively posttraumatic (p = 0.03). Signal characteristics and bridge size did not vary with the cause. Premature physeal bony bridging in children is most often posttraumatic and disproportionately involves the distal tibia and femur where bridges tend to develop at the sites of earliest physiologic closure, namely anteromedially and centrally, respectively. MR imaging, especially with the use of fat-suppressed 3D spoiled gradient-recalled echo imaging, exquisitely shows the growth disturbance and associated abnormalities that may follow physeal injury and guides surgical management.

Proposed gravity-gradient dynamics experiments in lunar orbit using the RAE-B spacecraft

NASA Technical Reports Server (NTRS)

Blanchard, D. L.; Walden, H.

1973-01-01

A series of seven gravity-gradient dynamics experiments is proposed utilizing the Radio Astronomy Explorer (RAE-B) spacecraft in lunar orbit. It is believed that none of the experiments will impair the spacecraft structure or adversely affect the continuation of the scientific mission of the satellite. The first experiment is designed to investigate the spacecraft dynamical behavior in the absence of libration damper action and inertia. It requires stable gravity-gradient capture of the spacecraft in lunar orbit with small amplitude attitude librations as a prerequisite. Four subsequent experiments involve partial retraction, ultimately followed by full redeployment, of one or two of the 230-meter booms forming the lunar-directed Vee-antenna. These boom length change operations will induce moderate amplitude angular librations of the spacecraft.

The Transition from Stiff to Compliant Materials in Squid Beaks

PubMed Central

Miserez, Ali; Schneberk, Todd; Sun, Chengjun; Zok, Frank W.; Waite, J. Herbert

2009-01-01

The beak of the Humboldt squid Dosidicus gigas represents one of the hardest and stiffest wholly organic materials known. As it is deeply embedded within the soft buccal envelope, the manner in which impact forces are transmitted between beak and envelope is a matter of considerable scientific interest. Here, we show that the hydrated beak exhibits a large stiffness gradient, spanning two orders of magnitude from the tip to the base. This gradient is correlated with a chemical gradient involving mixtures of chitin, water, and His-rich proteins that contain 3,4-dihydroxyphenyl-l-alanine (dopa) and undergo extensive stabilization by histidyl-dopa cross-link formation. These findings may serve as a foundation for identifying design principles for attaching mechanically mismatched materials in engineering and biological applications. PMID:18369144

The transition from stiff to compliant materials in squid beaks.

PubMed

Miserez, Ali; Schneberk, Todd; Sun, Chengjun; Zok, Frank W; Waite, J Herbert

2008-03-28

The beak of the Humboldt squid Dosidicus gigas represents one of the hardest and stiffest wholly organic materials known. As it is deeply embedded within the soft buccal envelope, the manner in which impact forces are transmitted between beak and envelope is a matter of considerable scientific interest. Here, we show that the hydrated beak exhibits a large stiffness gradient, spanning two orders of magnitude from the tip to the base. This gradient is correlated with a chemical gradient involving mixtures of chitin, water, and His-rich proteins that contain 3,4-dihydroxyphenyl-L-alanine (dopa) and undergo extensive stabilization by histidyl-dopa cross-link formation. These findings may serve as a foundation for identifying design principles for attaching mechanically mismatched materials in engineering and biological applications.

The Transition from Stiff to Compliant Materials in Squid Beaks

NASA Astrophysics Data System (ADS)

Miserez, Ali; Schneberk, Todd; Sun, Chengjun; Zok, Frank W.; Waite, J. Herbert

2008-03-01

The beak of the Humboldt squid Dosidicus gigas represents one of the hardest and stiffest wholly organic materials known. As it is deeply embedded within the soft buccal envelope, the manner in which impact forces are transmitted between beak and envelope is a matter of considerable scientific interest. Here, we show that the hydrated beak exhibits a large stiffness gradient, spanning two orders of magnitude from the tip to the base. This gradient is correlated with a chemical gradient involving mixtures of chitin, water, and His-rich proteins that contain 3,4-dihydroxyphenyl-L-alanine (dopa) and undergo extensive stabilization by histidyl-dopa cross-link formation. These findings may serve as a foundation for identifying design principles for attaching mechanically mismatched materials in engineering and biological applications.

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

Chen, Aiying; Liu, Jiabin; Wang, Hongtao

Gradient materials often have attractive mechanical properties that outperform uniform microstructure counterparts. It remains a difficult task to investigate and compare the performance of various gradient microstructures due to the difficulty of fabrication, the wide range of length scales involved, and their respective volume percentage variations. We have investigated four types of gradient microstructures in 304 stainless steels that utilize submicrotwins, nanotwins, nanocrystalline-, ultrafine- and coarse-grains as building blocks. Tensile tests reveal that the gradient microstructure consisting of submicrotwins and nanotwins has a persistent and stable work hardening rate and yields an impressive combination of high strength and high ductility,more » leading to a toughness that is nearly 50% higher than that of the coarse-grained counterpart. Ex- and in-situ transmission electron microscopy indicates that nanoscale and submicroscale twins help to suppress and limit martensitic phase transformation via the confinement of martensite within the twin lamellar. Twinning and detwinning remain active during tensile deformation and contribute to the work hardening behavior. We discuss the advantageous properties of using submicrotwins as the main load carrier and nanotwins as the strengthening layers over those coarse and nanocrystalline grains. Furthermore, our work uncovers a new gradient design strategy to help metals and alloys achieve high strength and high ductility.« less

Fabrication and microstructures of functional gradient SiBCN–Nb composite by hot pressing

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

Sun, Min, E-mail: lcxsunmin@163.com; Fu, Ruoyu; Chen, Jun

2016-04-15

A functional gradient material with five layers composed of SiBCN ceramic and niobium (Nb) was prepared successfully by hot pressing. The phase composition, morphology features and microstructures were investigated in each layer of the gradient material. The Nb-containing compounds involving NbC, Nb{sub 6}C{sub 5}, Nb{sub 4}C{sub 3}, Nb{sub 5}Si{sub 3} and NbN increase with the volume fraction of Nb increasing in the sub-layer. They are randomly scattered (≤ 25 vol.% Nb), then strip-like, and finally distribute continuously (≥ 75 vol.% Nb). The size of BN(C) and SiC grains in Nb-containing layers is larger than in 100% SiBCN layer due tomore » the loss of the capsule-like structures. No distinct interfaces form in the transition regions indicating the gradual changes in phase composition and microstructures. - Highlights: • A functional gradient SiBCN–Nb material was prepared successfully by hot pressing. • Phase composition, morphology features and microstructures were investigated. • Thermodynamic calculation was used to aid in the phase analysis. • No distinct interfaces form typical of the functional gradient material.« less

Magnetic Control of Concentration Gradient in Microgravity

NASA Technical Reports Server (NTRS)

Leslie, Fred; Ramachandran, Narayanan

2005-01-01

A report describes a technique for rapidly establishing a fluid-concentration gradient that can serve as an initial condition for an experiment on solutal instabilities associated with crystal growth in microgravity. The technique involves exploitation of the slight attractive or repulsive forces exerted on most fluids by a magnetic-field gradient. Although small, these forces can dominate in microgravity and therefore can be used to hold fluids in position in preparation for an experiment. The magnetic field is applied to a test cell, while a fluid mixture containing a concentration gradient is prepared by introducing an undiluted solution into a diluting solution in a mixing chamber. The test cell is then filled with the fluid mixture. Given the magnetic susceptibilities of the undiluted and diluting solutions, the magnetic-field gradient must be large enough that the magnetic force exceeds both (1) forces associated with the flow of the fluid mixture during filling of the test cell and (2) forces imposed by any residual gravitation and fluctuations thereof. Once the test cell has been filled with the fluid mixture, the magnetic field is switched off so that the experiment can proceed, starting from the proper initial conditions.

Gradient Mn-La-Pt Catalysts with Three-layered Structure for Li-O2 battery

PubMed Central

Cai, Kedi; Yang, Rui; Lang, Xiaoshi; Zhang, Qingguo; Wang, Zhenhua; He, Tieshi

2016-01-01

Gradient Mn-La-Pt catalysts with three-layered structure of manganese dioxide (MnO2), lanthanum oxide (La2O3), and Platinum (Pt) for Li-O2 battery are prepared in this study. The mass ratio of the catalysts is respectively 5:2:3, 4:2:4, and 3:2:5 (MnO2: La2O3: Pt) which is start from the side of the electrolyte. The relationship between morphology structure and electrochemical performance of gradient catalyst is investigated by energy dispersive spectrometry and constant current charge/discharge test. The Li-O2 battery based on gradient Mn-La-Pt catalysts shows high discharge specific capacity (2707 mAh g−1), specific energy density (8400 Wh kg−1) and long cycle life (56 cycles). The improvement of the Li-O2 battery discharge capacity is attributed to the gradient distribution of MnO2 and Pt and the involvement of La2O3 that can improve the energy density of the battery. More important, this work will also provide new ideas and methods for the research of other metal-air battery. PMID:27731340

Treating convection in sequential solvers

NASA Technical Reports Server (NTRS)

Shyy, Wei; Thakur, Siddharth

1992-01-01

The treatment of the convection terms in the sequential solver, a standard procedure found in virtually all pressure based algorithms, to compute the flow problems with sharp gradients and source terms is investigated. Both scalar model problems and one-dimensional gas dynamics equations have been used to study the various issues involved. Different approaches including the use of nonlinear filtering techniques and adoption of TVD type schemes have been investigated. Special treatments of the source terms such as pressure gradients and heat release have also been devised, yielding insight and improved accuracy of the numerical procedure adopted.

Anti-sigma factor YlaD regulates transcriptional activity of sigma factor YlaC and sporulation via manganese-dependent redox-sensing molecular switch in Bacillus subtilis.

PubMed

Kwak, Min-Kyu; Ryu, Han-Bong; Song, Sung-Hyun; Lee, Jin-Won; Kang, Sa-Ouk

2018-05-14

YlaD, a membrane-anchored anti-sigma factor of Bacillus subtilis , contains a HX 3 CXXC motif that functions as a redox-sensing domain and belongs to one of the zinc-coordinated anti-sigma factor families. Despite previously showing that the YlaC transcription is controlled by YlaD, experimental evidence of how the YlaC-YlaD interaction is affected by active cysteines and/or metal ions is lacking. Here, we showed that the P yla promoter is autoregulated solely by YlaC. Moreover, reduced YlaD contained zinc and iron, while oxidized YlaD did not. Cysteine substitution in YlaD led to changes in its secondary structure; Cys3 had important structural functions in YlaD, and its mutation caused dissociation from YlaC, indicating the essential requirement of a HX 3 CXXC motif for regulating interactions of YlaC with YlaD. Analyses of the far-UV CD spectrum and metal content revealed that the addition of Mn ions to Zn-YlaD changed its secondary structure and that iron was substituted for manganese. The ylaC gene expression using βGlu activity from P yla : gusA was observed at the late-exponential and early-stationary phase and the ylaC -overexpressing mutant constitutively expressed gene transcripts of clpP and sigH , an important alternative sigma factor regulated by ClpXP. Collectively, our data demonstrated that YlaD senses redox changes and elicits increase in manganese ion concentrations and that, in turn, YlaD-mediated transcriptional activity of YlaC regulates sporulation initiation under oxidative stress and manganese-substituted conditions by regulating clpP gene transcripts. This is the first report of the involvement of oxidative stress-responsive B. subtilis extracytoplasmic function sigma factors during sporulation via a manganese-dependent redox-sensing molecular switch. ©2018 The Author(s).

Point mutations in the extracytosolic loop between transmembrane segments M5 and M6 of the yeast Pma1 H+-ATPase: alanine-scanning mutagenesis.

PubMed

Petrov, Valery V

2015-01-01

Membrane-spanning segments M4, M5, M6, and M8 of the H(+)-, Ca(2+)-, and K(+), Na(+)-ATPases, which belong to the P2-type pumps are the core through which cations are transported. M5 and M6 loop is a short extracytoplasmic stretch of the seven amino acid residues (714-DNSLDID) connecting two of these segments, M5 and M6, where residues involved in the formation of the proton-binding site(s) are located. In the present study, we have used alanine-scanning mutagenesis to explore the structural and functional relationships within this loop of the yeast plasma membrane Pma1 H(+)-ATPase. Of the 7 Ala mutants made, substitution for the most conserved residue (Leu-717) has led to a severe misfolding and complete block in biogenesis of the mutant enzyme. The replacement of Asp-714 has also caused misfolding leading to significant decrease in the expression of the mutant and loss of activity. The remaining mutants were expressed in secretory vesicles at 21-119% of the wild-type level and were active enough to be analyzed in detail. One of these mutants (I719A) showed five- to threefold decrease in both expression and ATP hydrolyzing and H(+) pumping activities and also threefold reduction in the coupling ratio between ATP hydrolysis and H(+) transport. Thus, Ala substitutions at three positions of the seven seriously affected biogenesis, folding, stability and/or functioning of the enzyme. Taken together, these results lead to suggestion that M5 and M6 loop play an important role in the protein stability and function and is responsible for proper arrangement of transmembrane segments M5 and M6 and probably other domains of the enzyme. Results for additional conserved substitutions (Asn and Glu) at Asp-714 and Asp-720 confirmed this suggestion.

Seismic anisotropy of 70 Ma Pacific-plate upper mantle

NASA Astrophysics Data System (ADS)

Mark, H. F.; Lizarralde, D.; Collins, J. A.; Miller, N. C.; Hirth, G.; Gaherty, J. B.; Evans, R. L.

2017-12-01

We present a new measurement of seismic anisotropy and velocity gradients in the Pacific-plate upper mantle based on data from the NoMelt experiment. The seismic velocity structure of oceanic lithosphere reflects the processes involved in its formation at mid-ocean ridges and subsequent evolution off-axis. Increasing mantle depletion with depth due to melt extraction predicts negative velocity gradients, as does cooling with age. Alignment of olivine by corner flow predicts azimuthal anisotropy. Some models predict the strength of anisotropy should decrease with depth. Measurements of uppermost mantle velocities have not fully verified these predictions. Observations of direct Pn phases demonstrate that positive velocity gradients exist; and anisotropy measurements, while consistent with strain-induced olivine alignment, vary widely and generally suggest weaker fabric development than is observed in ophiolite samples. These discrepancies raise questions about the extent to which mantle structure evolves through time due to processes such as cracking and alteration, and hinder the use of seismic measurements to make more detailed inferences on aspects of lithospheric formation processes. We have measured anisotropy and vertical velocity gradients to 10 km below the Moho on 70 Ma lithosphere between the Clarion and Clipperton fracture zones. The lithosphere at the study site has not been obviously affected by tectonic or magmatic events since its formation. We find 6.2% anisotropy at the Moho with a mean velocity of 8.14 km/s and the fast direction parallel to paleospreading. Velocity gradients are estimated at 0.02 km/s/km in the fast direction and near 0 km/s/km in the slow direction. The gradient estimates can be explained by aligned microcracks oriented perpendicular to spreading that close with depth. Cracks are expected to close by 10 km below the Moho. At that depth the strength of anisotropy increases to 9%, close to the strength estimated from ophiolite fabrics. These results are consistent with observed olivine fabrics and the predicted effects of lithospheric formation processes, and suggest that lithospheric evolution is modest even at 70 Ma, involving microcracks oriented by a stress field consistent with thermal contraction.

Development and kinetic analysis of cobalt gradient formation in WC-Co composites

NASA Astrophysics Data System (ADS)

Guo, Jun

2011-12-01

Functionally graded cemented tungsten carbide (FG WC-Co) is one of the main research directions in the field of WC-Co over decades. Although it has long been recognized that FG WC-Co could outperform conventional homogeneous WC-Co owing to its potentially superior combinations of mechanical properties, until recently there has been a lack of effective and economical methods to make such materials. The lack of the technology has prevented the manufacturing and industrial applications of FG WC-Co from becoming a reality. This dissertation is a comprehensive study of an innovative atmosphere heat treatment process for producing FG WC-Co with a surface cobalt compositional gradient. The process exploited a triple phase field in W-C-Co phase diagram among three phases (solid WC, solid Co, and liquid Co) and the dependence of the migration of liquid Co on temperature and carbon content. WC-Co with a graded surface cobalt composition can be achieved by controlling the diffusion of carbon transported from atmosphere during sintering or during postsintering heat treatment. The feasibility of the process was validated by the successful preparations of FG WC-Co via both carburization and decarburization process following conventional liquid phase sintering. A study of the carburization process was undertaken to further understand and quantitatively modeled this process. The effects of key processing parameters (including heat treating temperature, atmosphere, and time) and key materials variables (involving Co content, WC grain size, and addition of grain growth inhibitors) on the formation of Co gradients were examined. Moreover, a carbon-diffusion controlled kinetic model was developed for simulating the formation of the gradient during the process. The parameters involved in this model were determined by thermodynamic calculations and regression-fit of simulation results with experimental data. In summary, this research first demonstrated the principle of the approach. Second, a model was developed to predict the gradients produced by the carbon-controlled atmosphere heat treatment process, which is useful for manufacturing WC-Co with designed gradients. FG WC-Co materials produced using this method are expected to exhibit superior performance in many applications and to have a profound impact on the manufacturing industries that use tungsten carbide tools.

Cell–cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis

PubMed Central

Ellison, David; Mugler, Andrew; Brennan, Matthew D.; Lee, Sung Hoon; Huebner, Robert J.; Shamir, Eliah R.; Woo, Laura A.; Kim, Joseph; Amar, Patrick; Nemenman, Ilya; Ewald, Andrew J.; Levchenko, Andre

2016-01-01

Collective cell responses to exogenous cues depend on cell–cell interactions. In principle, these can result in enhanced sensitivity to weak and noisy stimuli. However, this has not yet been shown experimentally, and little is known about how multicellular signal processing modulates single-cell sensitivity to extracellular signaling inputs, including those guiding complex changes in the tissue form and function. Here we explored whether cell–cell communication can enhance the ability of cell ensembles to sense and respond to weak gradients of chemotactic cues. Using a combination of experiments with mammary epithelial cells and mathematical modeling, we find that multicellular sensing enables detection of and response to shallow epidermal growth factor (EGF) gradients that are undetectable by single cells. However, the advantage of this type of gradient sensing is limited by the noisiness of the signaling relay, necessary to integrate spatially distributed ligand concentration information. We calculate the fundamental sensory limits imposed by this communication noise and combine them with the experimental data to estimate the effective size of multicellular sensory groups involved in gradient sensing. Functional experiments strongly implicated intercellular communication through gap junctions and calcium release from intracellular stores as mediators of collective gradient sensing. The resulting integrative analysis provides a framework for understanding the advantages and limitations of sensory information processing by relays of chemically coupled cells. PMID:26792522

Spatial and temporal variations in mango colour, acidity, and sweetness in relation to temperature and ethylene gradients within the fruit.

PubMed

Nordey, Thibault; Léchaudel, Mathieu; Génard, Michel; Joas, Jacques

2014-11-01

Managing fruit quality is complex because many different attributes have to be taken into account, which are themselves subjected to spatial and temporal variations. Heterogeneous fruit quality has been assumed to be partly related to temperature and maturity gradients within the fruit. To test this assumption, we measured the spatial variability of certain mango fruit quality traits: colour of the peel and of the flesh, and sourness and sweetness, at different stages of fruit maturity using destructive methods as well as vis-NIR reflectance. The spatial variability of mango quality traits was compared to internal variations in thermal time, simulated by a physical model, and to internal variations in maturity, using ethylene content as an indicator. All the fruit quality indicators analysed showed significant spatial and temporal variations, regardless of the measurement method used. The heterogeneity of internal fruit quality traits was not correlated with the marked internal temperature gradient we modelled. However, variations in ethylene content revealed a strong internal maturity gradient which was correlated with the spatial variations in measured mango quality traits. Nonetheless, alone, the internal maturity gradient did not explain the variability of fruit quality traits, suggesting that other factors, such as gas, abscisic acid and water gradients, are also involved. Copyright © 2014 Elsevier GmbH. All rights reserved.

3D joint inversion of gravity-gradient and borehole gravity data

NASA Astrophysics Data System (ADS)

Geng, Meixia; Yang, Qingjie; Huang, Danian

2017-12-01

Borehole gravity is increasingly used in mineral exploration due to the advent of slim-hole gravimeters. Given the full-tensor gradiometry data available nowadays, joint inversion of surface and borehole data is a logical next step. Here, we base our inversions on cokriging, which is a geostatistical method of estimation where the error variance is minimised by applying cross-correlation between several variables. In this study, the density estimates are derived using gravity-gradient data, borehole gravity and known densities along the borehole as a secondary variable and the density as the primary variable. Cokriging is non-iterative and therefore is computationally efficient. In addition, cokriging inversion provides estimates of the error variance for each model, which allows direct assessment of the inverse model. Examples are shown involving data from a single borehole, from multiple boreholes, and combinations of borehole gravity and gravity-gradient data. The results clearly show that the depth resolution of gravity-gradient inversion can be improved significantly by including borehole data in addition to gravity-gradient data. However, the resolution of borehole data falls off rapidly as the distance between the borehole and the feature of interest increases. In the case where the borehole is far away from the target of interest, the inverted result can be improved by incorporating gravity-gradient data, especially all five independent components for inversion.

Visualization of an endogenous retinoic acid gradient across embryonic development.

PubMed

Shimozono, Satoshi; Iimura, Tadahiro; Kitaguchi, Tetsuya; Higashijima, Shin-Ichi; Miyawaki, Atsushi

2013-04-18

In vertebrate development, the body plan is determined by primordial morphogen gradients that suffuse the embryo. Retinoic acid (RA) is an important morphogen involved in patterning the anterior-posterior axis of structures, including the hindbrain and paraxial mesoderm. RA diffuses over long distances, and its activity is spatially restricted by synthesizing and degrading enzymes. However, gradients of endogenous morphogens in live embryos have not been directly observed; indeed, their existence, distribution and requirement for correct patterning remain controversial. Here we report a family of genetically encoded indicators for RA that we have termed GEPRAs (genetically encoded probes for RA). Using the principle of fluorescence resonance energy transfer we engineered the ligand-binding domains of RA receptors to incorporate cyan-emitting and yellow-emitting fluorescent proteins as fluorescence resonance energy transfer donor and acceptor, respectively, for the reliable detection of ambient free RA. We created three GEPRAs with different affinities for RA, enabling the quantitative measurement of physiological RA concentrations. Live imaging of zebrafish embryos at the gastrula and somitogenesis stages revealed a linear concentration gradient of endogenous RA in a two-tailed source-sink arrangement across the embryo. Modelling of the observed linear RA gradient suggests that the rate of RA diffusion exceeds the spatiotemporal dynamics of embryogenesis, resulting in stability to perturbation. Furthermore, we used GEPRAs in combination with genetic and pharmacological perturbations to resolve competing hypotheses on the structure of the RA gradient during hindbrain formation and somitogenesis. Live imaging of endogenous concentration gradients across embryonic development will allow the precise assignment of molecular mechanisms to developmental dynamics and will accelerate the application of approaches based on morphogen gradients to tissue engineering and regenerative medicine.

Assessing public health policy approaches to level-up the gradient in health inequalities: the Gradient Evaluation Framework.

PubMed

Davies, J K; Sherriff, N S

2014-03-01

This paper seeks to introduce and analyse the development of the Gradient Evaluation Framework (GEF) to facilitate evaluation of policy actions for their current or future use in terms of their 'gradient friendliness'. In particular, this means their potential to level-up the gradient in health inequalities by addressing the social determinants of health and thereby reducing decision-makers' chances of error when developing such policy actions. A qualitative developmental study to produce a policy-based evaluation framework. The scientific basis of GEF was developed using a comprehensive consensus-building process. This process followed an initial narrative review, based on realist review principles, which highlighted the need for production of a dedicated evaluation framework. The consensus-building process included expert workshops, a pretesting phase, and external peer review, together with support from the Gradient project Scientific Advisory Group and all Gradient project partners, including its Project Steering Committee. GEF is presented as a flexible policy tool resulting from a consensus-building process involving experts from 13 European countries. The theoretical foundations which underpin GEF are discussed, together with a range of practical challenges. The importance of systematic evaluation at each stage of the policy development and implementation cycle is highlighted, as well as the socio-political context in which policy actions are located. GEF offers potentially a major contribution to the public health field in the form of a practical, policy-relevant and common frame of reference for the evaluation of public health interventions that aim to level-up the social gradient in health inequalities. Further research, including the need for practical field testing of GEF and the exploration of alternative presentational formats, is recommended. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

A Study of Wake Development and Structure in Constant Pressure Gradients

NASA Technical Reports Server (NTRS)

Thomas, Flint O.; Nelson, R. C.; Liu, Xiaofeng

2000-01-01

Motivated by the application to high-lift aerodynamics for commercial transport aircraft, a systematic investigation into the response of symmetric/asymmetric planar turbulent wake development to constant adverse, zero, and favorable pressure gradients has been conducted. The experiments are performed at a Reynolds number of 2.4 million based on the chord of the wake generator. A unique feature of this wake study is that the pressure gradients imposed on the wake flow field are held constant. The experimental measurements involve both conventional LDV and hot wire flow field surveys of mean and turbulent quantities including the turbulent kinetic energy budget. In addition, similarity analysis and numerical simulation have also been conducted for this wake study. A focus of the research has been to isolate the effects of both pressure gradient and initial wake asymmetry on the wake development. Experimental results reveal that the pressure gradient has a tremendous influence on the wake development, despite the relatively modest pressure gradients imposed. For a given pressure gradient, the development of an initially asymmetric wake is different from the initially symmetric wake. An explicit similarity solution for the shape parameters of the symmetric wake is obtained and agrees with the experimental results. The turbulent kinetic energy budget measurements of the symmetric wake demonstrate that except for the convection term, the imposed pressure gradient does not change the fundamental flow physics of turbulent kinetic energy transport. Based on the turbulent kinetic energy budget measurements, an approach to correct the bias error associated with the notoriously difficult dissipation estimate is proposed and validated through the comparison of the experimental estimate with a direct numerical simulation result.

Characteristics of a Recent and Prehistoric Landslides in the Pine River Valley, BC: a Mapping Effort

NASA Astrophysics Data System (ADS)

Heijenk, R.; Geertsema, M.; Miller, B.; de Jong, S. M.

2015-12-01

Spreads and other low gradient landslides are common in glacial lake sediments in north eastern British Columbia. Both pre and post glacial lake sediments, largely derived from shale bedrock are susceptible to low-gradient landslides. Bank erosion by rivers and streams and high pore pressures, have contributed to the landslides. We used LiDAR for mapping the extent of the glaciolacustrine sediments and map and characterise landslides in the Pine River valley, near Chetwynd, British Columbia. We included metrics such as travel angle, length, area, and elevation to distinguish rotational and translational landslides. We mapped 45 landslides in the Pine River valley distinguishing between rotational and translational landslides. The rotational landslides commonly have a smaller area and smaller travel length than translational landslides. Most rotational slides involved overlying alluvial fans, while most translational slides involved terraces.

Root gravitropism

NASA Technical Reports Server (NTRS)

Masson, P. H.

1995-01-01

When a plant root is reoriented within the gravity field, it responds by initiating a curvature which eventually results in vertical growth. Gravity sensing occurs primarily in the root tip. It may involve amyloplast sedimentation in the columella cells of the root cap, or the detection of forces exerted by the mass of the protoplast on opposite sides of its cell wall. Gravisensing activates a signal transduction cascade which results in the asymmetric redistribution of auxin and apoplastic Ca2+ across the root tip, with accumulation at the bottom side. The resulting lateral asymmetry in Ca2+ and auxin concentration is probably transmitted to the elongation zone where differential cellular elongation occurs until the tip resumes vertical growth. The Cholodny-Went theory proposes that gravity-induced auxin redistribution across a gravistimulated plant organ is responsible for the gravitropic response. However, recent data indicate that the gravity-induced reorientation is more complex, involving both auxin gradient-dependent and auxin gradient-independent events.

On the electromagnetic scattering from infinite rectangular grids with finite conductivity

NASA Technical Reports Server (NTRS)

Christodoulou, C. G.; Kauffman, J. F.

1986-01-01

A variety of methods can be used in constructing solutions to the problem of mesh scattering. However, each of these methods has certain drawbacks. The present paper is concerned with a new technique which is valid for all spacings. The new method involved, called the fast Fourier transform-conjugate gradient method (FFT-CGM), represents an iterative technique which employs the conjugate gradient method to improve upon each iterate, utilizing the fast Fourier transform. The FFT-CGM method provides a new accurate model which can be extended and applied to the more difficult problems of woven mesh surfaces. The formulation of the FFT-conjugate gradient method for aperture fields and current densities for a planar periodic structure is considered along with singular operators, the formulation of the FFT-CG method for thin wires with finite conductivity, and reflection coefficients.

A compressible two-phase model for dispersed particle flows with application from dense to dilute regimes

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

McGrath, Thomas P., E-mail: thomas.p.mcgrath@navy.mil; St Clair, Jeffrey G.; Department of Mechanical and Aerospace Engineering, University of Florida, 231 MAE-A, P.O. Box 116250, Gainesville, Florida 32611

2016-05-07

Multiphase flows are present in many important fields ranging from multiphase explosions to chemical processing. An important subset of multiphase flow applications involves dispersed materials, such as particles, droplets, and bubbles. This work presents an Eulerian–Eulerian model for multiphase flows containing dispersed particles surrounded by a continuous media such as air or water. Following a large body of multiphase literature, the driving force for particle acceleration is modeled as a direct function of both the continuous-phase pressure gradient and the gradient of intergranular stress existing within the particle phase. While the application of these two components of driving force ismore » well accepted in much of the literature, other models exist in which the particle-phase pressure gradient itself drives particle motion. The multiphase model treats all phases as compressible and is derived to ensure adherence to the 2nd Law of Thermodynamics. The governing equations are presented and discussed, and a characteristic analysis shows the model to be hyperbolic, with a degeneracy in the case that the intergranular stress, which is modeled as a configuration pressure, is zero. Finally, results from a two sample problems involving shock-induced particle dispersion are presented. The results agree well with experimental measurements, providing initial confidence in the proposed model.« less

Data analysis of a dense GPS network operated during the ESCOMPTE campaign: first results

NASA Astrophysics Data System (ADS)

Walpersdorf, A.; Bock, O.; Doerflinger, E.; Masson, F.; van Baelen, J.; Somieski, A.; Bürki, B.

The experiment GPS/H 2O involving 17 GPS receivers has been operated for two weeks in June 2001 in a dense network around Marseille. This project was integrated into the ESCOMPTE campaign. This paper will focus on the GPS analysis in preparation of the tomographic inversion of GPS slant delays. As first results, GPS tropospheric parameters zenith delays and horizontal gradients have been extracted. For a first visualization of the humidity field overlying the network, zenith delays have been transformed into precipitable water. Successive humidity fields are presented for a period of sudden drop in humidity, indicating some spatial resolution in the small network. The time series of horizontal gradients evaluated at individual sites are compared to correlated zenith delay variations over the whole network (horizontal gradient of zenith delays), showing that in the small size network horizontal atmospheric structure is reflected by both types of parameters. To compare these two quantities, scaling of zenith delays due to different station altitudes was necessary. In this way, a GPS internal validation of the individual gradients by comparison with the horizontal gradient of zenith delays has been established. Differential features along transects across the network indicate a good spatial resolution of tropospheric phenomena, encouraging for the further tomographic exploitation of the data. Moreover, individual and zenith delay gradients weight differently atmospheric horizontal gradients occurring at different heights. This different sensitivity has been used for a first identification of a vertical atmospheric structure from GPS tropospheric delays, by observing an inclined frontal zone crossing the network.

Transcoronary gradients of HDL-associated MicroRNAs in unstable coronary artery disease.

PubMed

Choteau, Sébastien A; Cuesta Torres, Luisa F; Barraclough, Jennifer Y; Elder, Alexander M M; Martínez, Gonzalo J; Chen Fan, William Y; Shrestha, Sudichhya; Ong, Kwok L; Barter, Philip J; Celermajer, David S; Rye, Kerry-Anne; Patel, Sanjay; Tabet, Fatiha

2018-02-15

MicroRNAs (miRNAs) are transported on high-density lipoproteins (HDLs) and HDL-associated miRNAs are involved in intercellular communication. We explored HDL-associated miRNAs concentration gradients across the coronary circulation in stable and unstable coronary artery disease patients and whether changes in the transcoronary gradient were associated with changes in HDL composition and size. Acute coronary syndrome (ACS, n=17) patients, those with stable coronary artery disease (stable CAD, n=19) and control subjects without CAD (n=6) were studied. HDLs were isolated from plasma obtained from the coronary sinus (CS), aortic root (arterial blood) and right atrium (venous blood). HDL-associated miRNAs (miR-16, miR-20a, miR-92a, miR-126, miR-222 and miR-223) were quantified by TaqMan miRNA assays. HDL particle sizes were determined by non-denaturing polyacrylamide gradient gel electrophoresis. HDL composition was measured immunoturbidometrically or enzymatically. A concentration gradient across the coronary circulation was observed for all the HDL-associated miRNAs. In ACS patients, there was a significant inverse transcoronary gradient for HDL-associated miR-16, miR-92a and miR-223 (p<0.05) compared to patients with stable CAD. Changes in HDL-miRNA transcoronary gradients were not associated with changes in HDL composition or size. HDLs are depleted of miR-16, miR-92a and miR-223 during the transcoronary passage in patients with ACS compared to patients with stable CAD. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

The Contribution of Drug Overdose to Educational Gradients in Life Expectancy in the United States, 1992-2011.

PubMed

Ho, Jessica Y

2017-06-01

Since the mid-1990s, the United States has witnessed a dramatic rise in drug overdose mortality. Educational gradients in life expectancy widened over the same period, and drug overdose likely plays a role in this widening, particularly for non-Hispanic whites. The contemporary drug epidemic is distinctive in terms of its scope, the nature of the substances involved, and its geographic patterning, which influence how it impacts different education groups. I use vital statistics and National Health Interview Survey data to examine the contribution of drug overdose to educational gradients in life expectancy from 1992-2011. I find that over this period, years of life lost due to drug overdose increased for all education groups and for both males and females. The contribution of drug overdose to educational gradients in life expectancy has increased over time and is greater for non-Hispanic whites than for the population as a whole. Drug overdose accounts for a sizable proportion of the increases in educational gradients in life expectancy, particularly at the prime adult ages (ages 30-60), where it accounts for 25 % to 100 % of the widening in educational gradients between 1992 and 2011. Drug overdose mortality has increased more rapidly for females than for males, leading to a gender convergence. These findings shed light on the processes driving recent changes in educational gradients in life expectancy and suggest that effective measures to address the drug overdose epidemic should take into account its differential burden across education groups.

Retention prediction and separation optimization under multilinear gradient elution in liquid chromatography with Microsoft Excel macros.

PubMed

Fasoula, S; Zisi, Ch; Gika, H; Pappa-Louisi, A; Nikitas, P

2015-05-22

A package of Excel VBA macros have been developed for modeling multilinear gradient retention data obtained in single or double gradient elution mode by changing organic modifier(s) content and/or eluent pH. For this purpose, ten chromatographic models were used and four methods were adopted for their application. The methods were based on (a) the analytical expression of the retention time, provided that this expression is available, (b) the retention times estimated using the Nikitas-Pappa approach, (c) the stepwise approximation, and (d) a simple numerical approximation involving the trapezoid rule for integration of the fundamental equation for gradient elution. For all these methods, Excel VBA macros have been written and implemented using two different platforms; the fitting and the optimization platform. The fitting platform calculates not only the adjustable parameters of the chromatographic models, but also the significance of these parameters and furthermore predicts the analyte elution times. The optimization platform determines the gradient conditions that lead to the optimum separation of a mixture of analytes by using the Solver evolutionary mode, provided that proper constraints are set in order to obtain the optimum gradient profile in the minimum gradient time. The performance of the two platforms was tested using experimental and artificial data. It was found that using the proposed spreadsheets, fitting, prediction, and optimization can be performed easily and effectively under all conditions. Overall, the best performance is exhibited by the analytical and Nikitas-Pappa's methods, although the former cannot be used under all circumstances. Copyright © 2015 Elsevier B.V. All rights reserved.

The Contribution of Drug Overdose to Educational Gradients in Life Expectancy in the United States, 1992–2011

PubMed Central

Ho, Jessica Y.

2017-01-01

Over the past two decades, the United States has witnessed a dramatic rise in drug overdose mortality. Educational gradients in life expectancy widened over the same period, and it is likely that drug overdose plays a role in this widening, particularly for non-Hispanic whites. The contemporary drug epidemic is distinctive in terms of its scope, the nature of the substances involved, and its geographic patterning, which influence how it impacts different education groups. I use data from vital statistics and from the National Health Interview Survey to examine the contribution of drug overdose to educational gradients in life expectancy from 1992–2011. I find that over this period, years of life lost due to drug overdose increased for all education groups and for both males and females. The contribution of drug overdose to educational gradients in life expectancy has increased over time and is greater for non-Hispanic whites than for the population as a whole. Drug overdose accounts for a sizeable proportion of the increases in educational gradients in life expectancy, particularly at the prime adult ages (ages 30–60) where it accounts for 25–100% of the widening in educational gradients between 1992–2011. Over time, drug overdose mortality has increased more rapidly for females than for males, leading to a gender convergence. These findings shed light on the processes driving recent changes in educational gradients in life expectancy and suggest that effective measures to address the drug overdose epidemic should take into account its differential burden across education groups. PMID:28324483

Closed circuit TV system monitors welding operations

NASA Technical Reports Server (NTRS)

Gilman, M.

1967-01-01

TV camera system that has a special vidicon tube with a gradient density filter is used in remote monitoring of TIG welding of stainless steel. The welding operations involve complex assembly welding tools and skates in areas of limited accessibility.

A fast pulse design for parallel excitation with gridding conjugate gradient.

PubMed

Feng, Shuo; Ji, Jim

2013-01-01

Parallel excitation (pTx) is recognized as a crucial technique in high field MRI to address the transmit field inhomogeneity problem. However, it can be time consuming to design pTx pulses which is not desirable. In this work, we propose a pulse design with gridding conjugate gradient (CG) based on the small-tip-angle approximation. The two major time consuming matrix-vector multiplications are substituted by two operators which involves with FFT and gridding only. Simulation results have shown that the proposed method is 3 times faster than conventional method and the memory cost is reduced by 1000 times.

The flares of August 1972

NASA Technical Reports Server (NTRS)

Zirin, H.; Tanaka, K.

1972-01-01

Analysis is made of observations of the August, 1972 flares at Big Bear and Tel Aviv, involving monochromatic movies, magnetograms, and spectra. In each flare the observations fit a model of particle acceleration in the chromosphere with emission produced by impart and by heating by the energetic electrons and protons. The region showed twisted flux and high gradients from birth, and flares appear due to strong magnetic shears and gradients across the neutral line produced by sunspot motions. Post flare loops show a strong change from sheared, force-free fields parallel to potential-field-like loops, perpendicular to the neutral line above the surface.

Measurement of magnetic field gradients using Raman spectroscopy in a fountain

NASA Astrophysics Data System (ADS)

Srinivasan, Arvind; Zimmermann, Matthias; Efremov, Maxim A.; Davis, Jon P.; Narducci, Frank A.

2017-02-01

In many experiments involving cold atoms, it is crucial to know the strength of the magnetic field and/or the magnetic field gradient at the precise location of a measurement. While auxiliary sensors can provide some of this information, the sensors are usually not perfectly co-located with the atoms and so can only provide an approximation to the magnetic field strength. In this article, we describe a technique to measure the magnetic field, based on Raman spectroscopy, using the same atomic fountain source that will be used in future magnetically sensitive measurements.

Diffusion with chemical reaction: An attempt to explain number density anomalies in experiments involving alkali vapor

NASA Technical Reports Server (NTRS)

Snow, W. L.

1974-01-01

The mutual diffusion of two reacting gases is examined which takes place in a bath of inert gas atoms. Solutions are obtained between concentric spheres, each sphere acting as a source for one of the reactants. The calculational model is used to illustrate severe number density gradients observed in absorption experiments with alkali vapor. Severe gradients result when sq root k/D R is approximately 5 where k, D, and R are respectively the second order rate constant, the multicomponent diffusion constant, and the geometrical dimension of the experiment.

Large scale micro-photometry for high resolution pH-characterization during electro-osmotic pumping and modular micro-swimming

NASA Astrophysics Data System (ADS)

Niu, Ran; Khodorov, Stanislav; Weber, Julian; Reinmüller, Alexander; Palberg, Thomas

2017-11-01

Micro-fluidic pumps as well as artificial micro-swimmers are conveniently realized exploiting phoretic solvent flows based on local gradients of temperature, electrolyte concentration or pH. We here present a facile micro-photometric method for monitoring pH gradients and demonstrate its performance and scope on different experimental situations including an electro-osmotic pump and modular micro-swimmers assembled from ion exchange resin beads and polystyrene colloids. In combination with the present microscope and DSLR camera our method offers a 2 μm spatial resolution at video frame rate over a field of view of 3920 × 2602 μm2. Under optimal conditions we achieve a pH-resolution of 0.05 with about equal contributions from statistical and systematical uncertainties. Our quantitative micro-photometric characterization of pH gradients which develop in time and reach out several mm is anticipated to provide valuable input for reliable modeling and simulations of a large variety of complex flow situations involving pH-gradients including artificial micro-swimmers, microfluidic pumping or even electro-convection.

Texturing of high T(sub c) superconducting polycrystalline fibers/wires by laser-driven directional solidification in an thermal gradient

NASA Technical Reports Server (NTRS)

Varshney, Usha; Eichelberger, B. Davis, III

1995-01-01

This paper summarizes the technique of laser-driven directional solidification in a controlled thermal gradient of yttria stabilized zirconia core coated Y-Ba-Cu-O materials to produce textured high T(sub c) superconducting polycrystalline fibers/wires with improved critical current densities in the extended range of magnetic fields at temperatures greater than 77 K. The approach involves laser heating to minimize phase segregation by heating very rapidly through the two-phase incongruent melt region to the single phase melt region and directionally solidifying in a controlled thermal gradient to achieve highly textured grains in the fiber axis direction. The technique offers a higher grain growth rate and a lower thermal budget compared with a conventional thermal gradient and is amenable as a continuous process for improving the J(sub c) of high T(sub c) superconducting polycrystalline fibers/wires. The technique has the advantage of suppressing weak-link behavior by orientation of crystals, formation of dense structures with enhanced connectivity, formation of fewer and cleaner grain boundaries, and minimization of phase segregation in the incongruent melt region.

Fine-scale features in the far-field of a turbulent jet

NASA Astrophysics Data System (ADS)

Buxton, Oliver; Ganapathisubramani, Bharathram

2008-11-01

The structure of a fully turbulent axisymmetric jet, at Reynolds number based on jet exit conditions of 5000, is investigated with cinematographic (1 kHz) stereoscopic PIV in a plane normal to the jet axis. Taylor's hypothesis is employed to calculate all three velocity gradients in the axial direction. The technique's resolution allows all terms of the velocity gradient tensor, hence strain rate tensor and kinetic energy dissipation, to be computed at each point within the plane. The data reveals that the vorticity field is dominated by high enstrophy tube-like structures. Conversely, the dissipation field appears to consist of sheet-like structures. Several criteria for isolating these strongly swirling vortical structures from the background turbulence were employed. One such technique involves isolating points in which the velocity gradient tensor has a real and a pair of complex conjugate eigenvectors. Once identified, the alignment of the various structures with relation to the vorticity vector and the real velocity gradient tensor eigenvector is investigated. The effect of the strain field on the geometry of the structures is also examined.

Working principle and application of magnetic separation for biomedical diagnostic at high- and low-field gradients.

PubMed

Leong, Sim Siong; Yeap, Swee Pin; Lim, JitKang

2016-12-06

Magnetic separation is a versatile technique used in sample preparation for diagnostic purpose. For such application, an external magnetic field is applied to drive the separation of target entity (e.g. bacteria, viruses, parasites and cancer cells) from a complex raw sample in order to ease the subsequent task(s) for disease diagnosis. This separation process not only can be achieved via the utilization of high magnetic field gradient, but also, in most cases, low magnetic field gradient with magnitude less than 100 T m -1 is equally feasible. It is the aim of this review paper to summarize the usage of both high gradient magnetic separation and low gradient magnetic separation (LGMS) techniques in this area of research. It is noteworthy that effectiveness of the magnetic separation process not only determines the outcome of a diagnosis but also directly influences its accuracy as well as sensing time involved. Therefore, understanding the factors that simultaneously influence the efficiency of both magnetic separation process and target detection is necessary. Moreover, for LGMS, there are several important considerations that should be taken into account in order to ensure its successful implementation. Hence, this review paper aims to provide an overview to relate all this crucial information by linking the magnetic separation theory to biomedical diagnostic applications.

CNT based thermal Brownian motor to pump water in nanodevices

NASA Astrophysics Data System (ADS)

Oyarzua, Elton; Zambrano, Harvey; Walther, J. H.

2016-11-01

Brownian molecular motors are nanoscale machines that exploit thermal fluctuations for directional motion by employing mechanisms such as the Feynman-Smoluchowski ratchet. In this study, using Non Equilibrium Molecular Dynamics, we propose a novel thermal Brownian motor for pumping water through Carbon Nanotubes (CNTs). To achieve this we impose a thermal gradient along the axis of a CNT filled with water and impose, in addition, a spatial asymmetry by fixing specific zones on the CNT in order to modify the vibrational modes of the CNT. We find that the temperature gradient and imposed spatial asymmetry drive the water flow in a preferential direction. We systematically modified the magnitude of the applied thermal gradient and the axial position of the fixed points. The analysis involves measurement of the vibrational modes in the CNTs using a Fast Fourier Transform (FFT) algorithm. We observed water flow in CNTs of 0.94, 1.4 and 2.0 nm in diameter, reaching a maximum velocity of 5 m/s for a thermal gradient of 3.3 K/nm. The proposed thermal motor is capable of delivering a continuous flow throughout a CNT, providing a useful tool for driving liquids in nanofluidic devices by exploiting thermal gradients. We aknowledge partial support from Fondecyt project 11130559.

Atmospheric gradients from GNSS, VLBI, and DORIS analyses and from Numerical Weather Models during CONT14

NASA Astrophysics Data System (ADS)

Heinkelmann, Robert; Dick, Galina; Nilsson, Tobias; Soja, Benedikt; Wickert, Jens; Zus, Florian; Schuh, Harald

2015-04-01

Observations from space-geodetic techniques are nowadays increasingly used to derive atmospheric information for various commercial and scientific applications. A prominent example is the operational use of GNSS data to improve global and regional weather forecasts, which was started in 2006. Atmosphere gradients describe the azimuthal asymmetry of zenith delays. Estimates of geodetic and other parameters significantly improve when atmosphere gradients are determined in addition. Here we assess the capability of several space geodetic techniques (GNSS, VLBI, DORIS) to determine atmosphere gradients of refractivity. For this purpose we implement and compare various strategies for gradient estimation, such as different values for the temporal resolution and the corresponding parameter constraints. Applying least squares estimation the gradients are usually deterministically modelled as constants or piece-wise linear functions. In our study we compare this approach with a stochastic approach modelling atmosphere gradients as random walk processes and applying a Kalman Filter for parameter estimation. The gradients, derived from space geodetic techniques are verified by comparison with those derived from Numerical Weather Models (NWM). These model data were generated using raytracing calculations based on European Centre for Medium-Range Weather Forecast (ECMWF) and National Centers for Environmental Prediction (NCEP) analyses with different spatial resolutions. The investigation of the differences between the ECMWF and NCEP gradients hereby in addition allow for an empirical assessment of the quality of model gradients and how suitable the NWM data are for verification. CONT14 (2014-05-06 until 2014-05-20) is the youngest two week long continuous VLBI campaign carried out by IVS (International VLBI Service for Geodesy and Astrometry). It presents the state-of-the-art VLBI performance in terms of number of stations and number of observations and presents thus an excellent test period for comparisons with other space geodetic techniques. During the VLBI campaign CONT14 the HOBART12 and HOBART26 (Hobart, Tasmania, Australia) VLBI antennas were involved that co-locate with each other. The investigation of the gradient estimate differences from these co-located antennas allows for a valuable empirical quality assessment. Another quality criterion for gradient estimates are the differences of parameters at the borders of adjacent 24h-sessions. Both are investigated in our study.

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective

PubMed Central

Greene, Nicholas P.; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking. PMID:29892271

Reductive dehalogenation of 3,5-dibromo-4-hydroxybenzoate by an aerobic strain of Delftia sp. EOB-17.

PubMed

Chen, Kai; Jian, Shanshan; Huang, Linglong; Ruan, Zhepu; Li, Shunpeng; Jiang, Jiandong

2015-12-01

To confirm the reductive dehalogenation ability of the aerobic strain of Delftia sp. EOB-17, finding more evidences to support the hypothesis that reductive dehalogenation may occur extensively in aerobic bacteria. Delftia sp. EOB-17, isolated from terrestrial soil contaminated with halogenated aromatic compounds, completely degraded 0.2 mM DBHB in 28 h and released two equivalents of bromides under aerobic conditions in the presence of sodium succinate. LC-MS analysis revealed that DBHB was transformed to 4-hydroxybenzoate via 3-bromo-4-hydroxybenzoate by successive reductive dehalogenation. Highly conserved DBHB-degrading genes, including reductive dehalogenase gene (bhbA3) and the extra-cytoplasmic binding receptor gene (bhbB3), were also found in strain EOB-17 by genome sequencing. The optimal temperature and pH for DBHB reductive dehalogenation activity are 30 °C and 8, respectively, and 0.1 mM Cd(2+), Cu(2+), Hg(2+) and Zn(2+) strongly inhibited dehalogenation activity. The aerobic strain of Delftia sp. EOB-17 was confirmed to reductively dehalogenate DBHB under aerobic conditions, providing another evidence to support the hypothesis that reductive dehalogenation occurs extensively in aerobic bacteria.

Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters

PubMed Central

Rhodius, Virgil A; Segall-Shapiro, Thomas H; Sharon, Brian D; Ghodasara, Amar; Orlova, Ekaterina; Tabakh, Hannah; Burkhardt, David H; Clancy, Kevin; Peterson, Todd C; Gross, Carol A; Voigt, Christopher A

2013-01-01

Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti-σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti-σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti-σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome-scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well-characterized regulatory parts will enable the construction of sophisticated gene expression programs. PMID:24169405

Strain gradient drives shear banding in metallic glasses

NASA Astrophysics Data System (ADS)

Tian, Zhi-Li; Wang, Yun-Jiang; Chen, Yan; Dai, Lan-Hong

2017-09-01

Shear banding is a nucleation-controlled process in metallic glasses (MGs) involving multiple temporal-spatial scales, which hinders a concrete understanding of its structural origin down to the atomic scale. Here, inspired by the morphology of composite materials, we propose a different perspective of MGs as a hard particle-reinforced material based on atomic-scale structural heterogeneity. The local stable structures indicated by a high level of local fivefold symmetry (L5FS) act as hard "particles" which are embedded in the relatively soft matrix. We demonstrate this concept by performing atomistic simulations of shear banding in CuZr MG. A shear band is prone to form in a sample with a high degree of L5FS which is slowly quenched from the liquid. An atomic-scale analysis on strain and the structural evolution reveals that it is the strain gradient effect that has originated from structural heterogeneity that facilitates shear transformation zones (STZs) to mature shear bands. An artificial composite model with a high degree of strain gradient, generated by inserting hard MG strips into a soft MG matrix, demonstrates a great propensity for shear banding. It therefore confirms the critical role strain gradient plays in shear banding. The strain gradient effect on shear banding is further quantified with a continuum model and a mechanical instability analysis. These physical insights might highlight the strain gradient as the hidden driving force in transforming STZs into shear bands in MGs.

Electroneutral, HCO3(-)-independent, pH gradient-dependent uphill transport of Cl- by ileal brush-border membrane vesicles. Possible role in the pathogenesis of chloridorrhea.

PubMed Central

Vasseur, M; Caüzac, M; Alvarado, F

1989-01-01

By applying a rapid filtration technique to isolated brush border membrane vesicles from guinea pig ileum, 36Cl uptake was quantified in the presence and absence of electrical, pH and alkali-metal ion gradients. A mixture of 20 mM-Hepes and 40 mM-citric acid, adjusted to the desired pH with Tris base, was found to be the most suitable buffer. Malate and Mes could be used to replace the citrate, but succinate, acetate and maleate proved to be unsuitable. In the absence of a pH gradient (pHout:pHin = 7.5:7.5), Cl- uptake increased slightly when an inside-positive membrane potential was applied, but uphill transport was never observed. A pH gradient (pHout:pHin = 5.0:7.5) induced both a 400% increase in the initial Cl- influx rate and a long-lasting (20 to 300 s) overshoot, indicating that a proton gradient can furnish the driving force for uphill Cl- transport. Under pH gradient conditions, initial Cl- entry rates had the following characteristics. (1) They were unaffected by cis-Na+ and/or -K+, indicating the absence of Cl-/K+, Cl-/Na+ or Cl-/K+/Na+ symport activity. (2) Inhibition by 20-100 mM-trans-Na+ and/or -K+ occurred, independent of the existence of an ion gradient. (3) Cl- entry was practically unaffected by short-circuiting the membrane potential with equilibrated potassium and valinomycin. (4) Carbonyl cyanide m-chlorophenylhydrazone was strongly inhibitory and so, to a lesser extent, was 4-acetamido-4'-isothiocyanostilbene-2,2'-disulphonic acid [(SITS)], independent of the sign and size of the membrane potential. (5) Cl- entry was negligibly increased (less than 30%) by either trans-Cl- or -HCO3-, indicating the absence of an obligatory Cl-/anion antiport activity. In contrast, the height of the overshoot at 60 s was increased by trans-Cl-, indicating time-dependent inhibition of 36Cl efflux. That competitive inhibition of 36Cl fluxes by anions is involved here is supported by initial influx rate experiments demonstrating: (1) the saturability of Cl- influx, which was found to exhibit Michaelis-Menten kinetics; and (2) competitive inhibition of influx by cis-Cl- and -Br-. Quantitatively, the conclusion is warranted that over 85% of the total initial Cl- uptake energized by a pH gradient involves an electroneutral Cl-/H+ symporter or its physicochemical equivalent, a Cl-/OH- antiporter, exhibiting little Cl- uniport and either Cl-/Cl- or Cl-/HCO3- antiport activities.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2597129

Effect of pulmonary vein isolation on the left-to-right atrial dominant frequency gradient in human atrial fibrillation.

PubMed

Lazar, Sorin; Dixit, Sanjay; Callans, David J; Lin, David; Marchlinski, Francis E; Gerstenfeld, Edward P

2006-08-01

We previously demonstrated the existence of a left-to-right atrial dominant frequency gradient during paroxysmal but not persistent atrial fibrillation (AF) in humans. One possible mechanism of the left-to-right dominant frequency gradient involves the role of the pulmonary veins (PVs) in AF maintenance. The purpose of this study was to examine the effect of PV isolation on the dominant frequency gradient and outcome after PV isolation. Patients with either paroxysmal or persistent AF were studied. Recordings were made from catheters in the coronary sinus (CS), posterior right atrium (RA), and posterior left atrium (LA) during AF before and after PV isolation. Mean left-to-right dominant frequency gradient was measured before and after segmental PV isolation. Patients were followed for AF recurrence after PV isolation. Twenty-seven patients with paroxysmal (n = 15) or persistent (n = 12) AF were studied. In the paroxysmal group, baseline dominant frequency was greatest in the posterior LA with a significant left-to-right atrial dominant frequency gradient (posterior LA = 6.2 +/- 0.9 Hz, CS = 5.8 +/- 0.8 Hz, posterior RA = 5.4 +/- 0.9 Hz; P <.001). After PV isolation, there was no regional difference in dominant frequency (5.9 +/- 0.7 Hz vs 5.7 +/- 0.6 Hz vs 5.7 +/- 0.7 Hz, respectively; P = NS). In the persistent AF group, there was no overall difference in dominant frequency among sites before or after PV isolation (P = NS); however, patients with long-term freedom from AF after PV isolation had a higher left-to-right dominant frequency gradient compared with patients with recurrent AF (0.4 vs 0.1 Hz; P <.05). PV isolation results in a loss in the left-to-right dominant frequency gradient in patients with paroxysmal AF. This finding supports the critical role of PVs in the maintenance of ongoing paroxysmal AF. Patients with persistent AF and a baseline left-to-right dominant frequency gradient have a better success rate with PV isolation alone compared with patients without a dominant frequency gradient.

Directional transport of colloids inside a bath of self-propelling walkers.

PubMed

Merlitz, Holger; Wu, Chenxu; Sommer, Jens-Uwe

2017-05-24

We present a setup in which passive colloids inside a solvent are moved to the boundaries of the container. The directional transport is facilitated by self-propelling microparticles ("walkers") with an activity gradient, which reduces their propulsion in the vicinity of bounding walls. An attractive interaction leads to the adsorption of walkers onto the colloid-surfaces in regions of low walker activity. It is shown that the activity gradient generates a free energy gradient which in turn acts as a driving force on the passive colloids. We carry out molecular dynamics simulations and present approaches to a theoretical description of the involved processes. Although the simulation data are not reproduced on a fully quantitative level, their qualitative features are covered by the model. The effect described here may be applied to facilitate a directional transport of drugs or to eliminate pollutants.

Split gradient coils for simultaneous PET-MRI

PubMed Central

Poole, Michael; Bowtell, Richard; Green, Dan; Pittard, Simon; Lucas, Alun; Hawkes, Rob; Carpenter, Adrian

2015-01-01

Combining positron emission tomography (PET) and MRI necessarily involves an engineering tradeoff as the equipment needed for the two modalities vies for the space closest to the region where the signals originate. In one recently described scanner configuration for simultaneous positron emission tomography–MRI, the positron emission tomography detection scintillating crystals reside in an 80-mm gap between the 2 halves of a 1-T split-magnet cryostat. A novel set of gradient and shim coils has been specially designed for this split MRI scanner to include an 110-mm gap from which wires are excluded so as not to interfere with positron detection. An inverse boundary element method was necessarily employed to design the three orthogonal, shielded gradient coils and shielded Z0 shim coil. The coils have been constructed and tested in the hybrid positron emission tomography-MRI system and successfully used in simultaneous positron emission tomography-MRI experiments. PMID:19780167

Possible influence of the Kuramoto length in a photo-catalytic water splitting reaction revealed by Poisson-Nernst-Planck equations involving ionization in a weak electrolyte

NASA Astrophysics Data System (ADS)

Suzuki, Yohichi; Seki, Kazuhiko

2018-03-01

We studied ion concentration profiles and the charge density gradient caused by electrode reactions in weak electrolytes by using the Poisson-Nernst-Planck equations without assuming charge neutrality. In weak electrolytes, only a small fraction of molecules is ionized in bulk. Ion concentration profiles depend on not only ion transport but also the ionization of molecules. We considered the ionization of molecules and ion association in weak electrolytes and obtained analytical expressions for ion densities, electrostatic potential profiles, and ion currents. We found the case that the total ion density gradient was given by the Kuramoto length which characterized the distance over which an ion diffuses before association. The charge density gradient is characterized by the Debye length for 1:1 weak electrolytes. We discuss the role of these length scales for efficient water splitting reactions using photo-electrocatalytic electrodes.

Recent identification of an ERK signal gradient governing planarian regeneration.

PubMed

Agata, Kiyokazu; Tasaki, Junichi; Nakajima, Elizabeth; Umesono, Yoshihiko

2014-06-01

Planarians have strong regenerative abilities derived from their adult pluripotent stem cell (neoblast) system. However, the molecular mechanisms involved in planarian regeneration have long remained a mystery. In particular, no anterior-specifying factor(s) could be found, although Wnt family proteins had been successfully identified as posterior-specifying factors during planarian regeneration (Gurley et al., 2008; Petersen and Reddien, 2008). A recent textbook of developmental biology therefore proposes a Wnt antagonist as a putative anterior factor (Gilbert, 2013). That is, planarian regeneration was supposed to be explained by a single decreasing gradient of the β-catenin signal from tail to head. However, recently we succeeded in demonstrating that in fact the extracellular-signal regulated kinases (ERK) form a decreasing gradient from head to tail to direct the reorganization of planarian body regionality after amputation (Umesono et al., 2013). Copyright © 2014 Elsevier GmbH. All rights reserved.

Wnt, Ptk7, and FGFRL expression gradients control trunk positional identity in planarian regeneration.

PubMed

Lander, Rachel; Petersen, Christian P

2016-04-13

Mechanisms enabling positional identity re-establishment are likely critical for tissue regeneration. Planarians use Wnt/beta-catenin signaling to polarize the termini of their anteroposterior axis, but little is known about how regeneration signaling restores regionalization along body or organ axes. We identify three genes expressed constitutively in overlapping body-wide transcriptional gradients that control trunk-tail positional identity in regeneration. ptk7 encodes a trunk-expressed kinase-dead Wnt co-receptor, wntP-2 encodes a posterior-expressed Wnt ligand, and ndl-3 encodes an anterior-expressed homolog of conserved FGFRL/nou-darake decoy receptors. ptk7 and wntP-2 maintain and allow appropriate regeneration of trunk tissue position independently of canonical Wnt signaling and with suppression of ndl-3 expression in the posterior. These results suggest that restoration of regional identity in regeneration involves the interpretation and re-establishment of axis-wide transcriptional gradients of signaling molecules.

Data-driven gradient algorithm for high-precision quantum control

NASA Astrophysics Data System (ADS)

Wu, Re-Bing; Chu, Bing; Owens, David H.; Rabitz, Herschel

2018-04-01

In the quest to achieve scalable quantum information processing technologies, gradient-based optimal control algorithms (e.g., grape) are broadly used for implementing high-precision quantum gates, but their performance is often hindered by deterministic or random errors in the system model and the control electronics. In this paper, we show that grape can be taught to be more effective by jointly learning from the design model and the experimental data obtained from process tomography. The resulting data-driven gradient optimization algorithm (d-grape) can in principle correct all deterministic gate errors, with a mild efficiency loss. The d-grape algorithm may become more powerful with broadband controls that involve a large number of control parameters, while other algorithms usually slow down due to the increased size of the search space. These advantages are demonstrated by simulating the implementation of a two-qubit controlled-not gate.

Automated apparatus for producing gradient gels

DOEpatents

Anderson, N.L.

1983-11-10

Apparatus for producing a gradient gel which serves as a standard medium for a two-dimensional analysis of proteins, the gel having a density gradient along its height formed by a variation in gel composition, with the apparatus including first and second pumping means each including a plurality of pumps on a common shaft and driven by a stepping motor capable of providing small incremental changes in pump outputs for the gel ingredients, the motors being controlled, by digital signals from a digital computer, a hollow form or cassette for receiving the gel composition, means for transferring the gel composition including a filler tube extending near the bottom of the cassette, adjustable horizontal and vertical arms for automatically removing and relocating the filler tube in the next cassette, and a digital computer programmed to automatically control the stepping motors, arm movements, and associated sensing operations involving the filling operation.

Automated apparatus for producing gradient gels

DOEpatents

Anderson, Norman L.

1986-01-01

Apparatus for producing a gradient gel which serves as a standard medium for a two-dimensional analysis of proteins, the gel having a density gradient along its height formed by a variation in gel composition, with the apparatus including first and second pumping means each including a plurality of pumps on a common shaft and driven by a stepping motor capable of providing small incremental changes in pump outputs for the gel ingredients, the motors being controlled, by digital signals from a digital computer, a hollow form or cassette for receiving the gel composition, means for transferring the gel composition including a filler tube extending near the bottom of the cassette, adjustable horizontal and vertical arms for automatically removing and relocating the filler tube in the next cassette, and a digital computer programmed to automatically control the stepping motors, arm movements, and associated sensing operations involving the filling operation.

Salt-gradient Solar Ponds: Summary of US Department of Energy Sponsored Research

NASA Technical Reports Server (NTRS)

French, R. L.; Johnson, D. H.; Jones, G. F.; Zangrando, F.

1984-01-01

The solar pond research program conducted by the United States Department of Energy was discontinued after 1983. This document summarizes the results of the program, reviews the state of the art, and identifies the remaining outstanding issues. Solar ponds is a generic term but, in the context of this report, the term solar pond refers specifically to saltgradient solar pond. Several small research solar ponds have been built and successfully tested. Procedures for filling the pond, maintaining the gradient, adjusting the zone boundaries, and extracting heat were developed. Theories and models were developed and verified. The major remaining unknowns or issues involve the physical behavior of large ponds; i.e., wind mixing of the surface, lateral range or reach of horizontally injected fluids, ground thermal losses, and gradient zone boundary erosion caused by pumping fluid for heat extraction. These issues cannot be scaled and must be studied in a large outdoor solar pond.

Areal-averaged trace gas emission rates from long-range open-path measurements in stable boundary layer conditions

NASA Astrophysics Data System (ADS)

Schäfer, K.; Grant, R. H.; Emeis, S.; Raabe, A.; von der Heide, C.; Schmid, H. P.

2012-07-01

Measurements of land-surface emission rates of greenhouse and other gases at large spatial scales (10 000 m2) are needed to assess the spatial distribution of emissions. This can be readily done using spatial-integrating micro-meteorological methods like flux-gradient methods which were evaluated for determining land-surface emission rates of trace gases under stable boundary layers. Non-intrusive path-integrating measurements are utilized. Successful application of a flux-gradient method requires confidence in the gradients of trace gas concentration and wind, and in the applicability of boundary-layer turbulence theory; consequently the procedures to qualify measurements that can be used to determine the flux is critical. While there is relatively high confidence in flux measurements made under unstable atmospheres with mean winds greater than 1 m s-1, there is greater uncertainty in flux measurements made under free convective or stable conditions. The study of N2O emissions of flat grassland and NH3 emissions from a cattle lagoon involves quality-assured determinations of fluxes under low wind, stable or night-time atmospheric conditions when the continuous "steady-state" turbulence of the surface boundary layer breaks down and the layer has intermittent turbulence. Results indicate that following the Monin-Obukhov similarity theory (MOST) flux-gradient methods that assume a log-linear profile of the wind speed and concentration gradient incorrectly determine vertical profiles and thus flux in the stable boundary layer. An alternative approach is considered on the basis of turbulent diffusivity, i.e. the measured friction velocity as well as height gradients of horizontal wind speeds and concentrations without MOST correction for stability. It is shown that this is the most accurate of the flux-gradient methods under stable conditions.

ISOLATION OF CHICKEN FOLLICULAR DENDRITIC CELLS

USDA-ARS?s Scientific Manuscript database

The aim of the present study was to isolate chicken follicular dendritic cells (FDC). A combination of methods involving panning, iodixanol density gradient centrifugation, and magnetic cell separation technology made it possible to obtain functional FDC from the cecal tonsils from chickens, which h...

Turbulent kinetic energy and a possible hierarchy of length scales in a generalization of the Navier-Stokes alpha theory.

PubMed

Fried, Eliot; Gurtin, Morton E

2007-05-01

We present a continuum-mechanical formulation and generalization of the Navier-Stokes alpha theory based on a general framework for fluid-dynamical theories with gradient dependencies. Our flow equation involves two additional problem-dependent length scales alpha and beta. The first of these scales enters the theory through the internal kinetic energy, per unit mass, alpha2|D|2, where D is the symmetric part of the gradient of the filtered velocity. The remaining scale is associated with a dissipative hyperstress which depends linearly on the gradient of the filtered vorticity. When alpha and beta are equal, our flow equation reduces to the Navier-Stokes alpha equation. In contrast to the original derivation of the Navier-Stokes alpha equation, which relies on Lagrangian averaging, our formulation delivers boundary conditions. For a confined flow, our boundary conditions involve an additional length scale l characteristic of the eddies found near walls. Based on a comparison with direct numerical simulations for fully developed turbulent flow in a rectangular channel of height 2h, we find that alphabeta approximately Re(0.470) and lh approximately Re(-0.772), where Re is the Reynolds number. The first result, which arises as a consequence of identifying the internal kinetic energy with the turbulent kinetic energy, indicates that the choice alpha=beta required to reduce our flow equation to the Navier-Stokes alpha equation is likely to be problematic. The second result evinces the classical scaling relation eta/L approximately Re(-3/4) for the ratio of the Kolmogorov microscale eta to the integral length scale L . The numerical data also suggests that l < or = beta . We are therefore led to conjecture a tentative hierarchy, l < or = beta < alpha , involving the three length scales entering our theory.

An Overview of the Thermal Challenges of Designing Microgravity Furnaces

NASA Technical Reports Server (NTRS)

Westra, Douglas G.

2001-01-01

Marshall Space Flight Center is involved in a wide variety of microgravity projects that require furnaces, with hot zone temperatures ranging from 300 C to 2300 C, requirements for gradient processing and rapid quench, and both semi-conductor and metal materials. On these types of projects, the thermal engineer is a key player in the design process. Microgravity furnaces present unique challenges to the thermal designer. One challenge is designing a sample containment assembly that achieves dual containment, yet allows a high radial heat flux. Another challenge is providing a high axial gradient but a very low radial gradient. These furnaces also present unique challenges to the thermal analyst. First, there are several orders of magnitude difference in the size of the thermal 'conductors' between various parts of the model. A second challenge is providing high fidelity in the sample model, and connecting the sample with the rest of the furnace model, yet maintaining some sanity in the number of total nodes in the model. The purpose of this paper is to present an overview of the challenges involved in designing and analyzing microgravity furnaces and how some of these challenges have been overcome. The thermal analysis tools presently used to analyze microgravity furnaces and will be listed. Challenges for the future and a description of future analysis tools will be given.

Reynolds and Maxwell stress measurements in the reversed field pinch experiment Extrap-T2R

NASA Astrophysics Data System (ADS)

Vianello, N.; Antoni, V.; Spada, E.; Spolaore, M.; Serianni, G.; Cavazzana, R.; Bergsåker, H.; Cecconello, M.; Drake, J. R.

2005-08-01

The complete Reynolds stress (RS) has been measured in the edge region of the Extrap-T2R reversed field pinch experiment. The RS exhibits a strong gradient in the region where a high E × B shear takes place. Experimental results show this gradient to be almost entirely due to the electrostatic contribution. This has been interpreted as experimental evidence of flow generation via turbulence mechanism. The scales involved in flow generation are deduced from the frequency decomposition of RS tensor. They are found related to magnetohydrodynamic activity but are different with respect to the scales responsible for turbulent transport.

A class of fractional differential hemivariational inequalities with application to contact problem

NASA Astrophysics Data System (ADS)

Zeng, Shengda; Liu, Zhenhai; Migorski, Stanislaw

2018-04-01

In this paper, we study a class of generalized differential hemivariational inequalities of parabolic type involving the time fractional order derivative operator in Banach spaces. We use the Rothe method combined with surjectivity of multivalued pseudomonotone operators and properties of the Clarke generalized gradient to establish existence of solution to the abstract inequality. As an illustrative application, a frictional quasistatic contact problem for viscoelastic materials with adhesion is investigated, in which the friction and contact conditions are described by the Clarke generalized gradient of nonconvex and nonsmooth functionals, and the constitutive relation is modeled by the fractional Kelvin-Voigt law.

U(1) current from the AdS/CFT: diffusion, conductivity and causality

NASA Astrophysics Data System (ADS)

Bu, Yanyan; Lublinsky, Michael; Sharon, Amir

2016-04-01

For a holographically defined finite temperature theory, we derive an off-shell constitutive relation for a global U(1) current driven by a weak external non-dynamical electromagnetic field. The constitutive relation involves an all order gradient expansion resummed into three momenta-dependent transport coefficient functions: diffusion, electric conductivity, and "magnetic" conductivity. These transport functions are first computed analytically in the hydrodynamic limit, up to third order in the derivative expansion, and then numerically for generic values of momenta. We also compute a diffusion memory function, which, as a result of all order gradient resummation, is found to be causal.

Macrophyte Community Response to Nitrogen Loading and Thermal Stressors: Water Residence Time Ameliorates Eutrophication Symptom Expression

EPA Science Inventory

Empirical determination of nutrient loading thresholds that negatively impact seagrass communities have been elusive due to the multitude of factors involved. Using a mesocosm system that simulated Pacific Northwest estuaries, we evaluated macrophyte metrics across gradients of ...

Factors associated with single-vehicle and multi-vehicle road traffic collision injuries in Ireland.

PubMed

Donnelly-Swift, Erica; Kelly, Alan

2016-12-01

Generalised linear regression models were used to identify factors associated with fatal/serious road traffic collision injuries for single- and multi-vehicle collisions. Single-vehicle collisions and multi-vehicle collisions occurring during the hours of darkness or on a wet road surface had reduced likelihood of a fatal/serious injury. Single-vehicle 'driver with passengers' collisions occurring at junctions or on a hill/gradient were less likely to result in a fatal/serious injury. Multi-vehicle rear-end/angle collisions had reduced likelihood of a fatal/serious injury. Single-vehicle 'driver only' collisions and multi-vehicle collisions occurring on a public/bank holiday or on a hill/gradient were more likely to result in a fatal/serious injury. Single-vehicle collisions involving male drivers had increased likelihood of a fatal/serious injury and single-vehicle 'driver with passengers' collisions involving drivers under the age of 25 years also had increased likelihood of a fatal/serious injury. Findings can enlighten decision-makers to circumstances leading to fatal/serious injuries.

Transient Flow Dynamics in Optical Micro Well Involving Gas Bubbles

NASA Technical Reports Server (NTRS)

Johnson, B.; Chen, C. P.; Jenkins, A.; Spearing, S.; Monaco, L. A.; Steele, A.; Flores, G.

2006-01-01

The Lab-On-a-Chip Application Development (LOCAD) team at NASA s Marshall Space Flight Center is utilizing Lab-On-a-Chip to support technology development specifically for Space Exploration. In this paper, we investigate the transient two-phase flow patterns in an optic well configuration with an entrapped bubble through numerical simulation. Specifically, the filling processes of a liquid inside an expanded chamber that has bubbles entrapped. Due to the back flow created by channel expansion, the entrapped bubbles tend to stay stationary at the immediate downstream of the expansion. Due to the huge difference between the gas and liquid densities, mass conservation issues associated with numerical diffusion need to be specially addressed. The results are presented in terms of the movement of the bubble through the optic well. Bubble removal strategies are developed that involve only pressure gradients across the optic well. Results show that for the bubble to be moved through the well, pressure pulsations must be utilized in order to create pressure gradients across the bubble itself.

Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe): A new radiomics descriptor.

PubMed

Prasanna, Prateek; Tiwari, Pallavi; Madabhushi, Anant

2016-11-22

In this paper, we introduce a new radiomic descriptor, Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe) for capturing subtle differences between benign and pathologic phenotypes which may be visually indistinguishable on routine anatomic imaging. CoLlAGe seeks to capture and exploit local anisotropic differences in voxel-level gradient orientations to distinguish similar appearing phenotypes. CoLlAGe involves assigning every image voxel an entropy value associated with the co-occurrence matrix of gradient orientations computed around every voxel. The hypothesis behind CoLlAGe is that benign and pathologic phenotypes even though they may appear similar on anatomic imaging, will differ in their local entropy patterns, in turn reflecting subtle local differences in tissue microarchitecture. We demonstrate CoLlAGe's utility in three clinically challenging classification problems: distinguishing (1) radiation necrosis, a benign yet confounding effect of radiation treatment, from recurrent tumors on T1-w MRI in 42 brain tumor patients, (2) different molecular sub-types of breast cancer on DCE-MRI in 65 studies and (3) non-small cell lung cancer (adenocarcinomas) from benign fungal infection (granulomas) on 120 non-contrast CT studies. For each of these classification problems, CoLlAGE in conjunction with a random forest classifier outperformed state of the art radiomic descriptors (Haralick, Gabor, Histogram of Gradient Orientations).

Working principle and application of magnetic separation for biomedical diagnostic at high- and low-field gradients

PubMed Central

Yeap, Swee Pin; Lim, JitKang

2016-01-01

Magnetic separation is a versatile technique used in sample preparation for diagnostic purpose. For such application, an external magnetic field is applied to drive the separation of target entity (e.g. bacteria, viruses, parasites and cancer cells) from a complex raw sample in order to ease the subsequent task(s) for disease diagnosis. This separation process not only can be achieved via the utilization of high magnetic field gradient, but also, in most cases, low magnetic field gradient with magnitude less than 100 T m−1 is equally feasible. It is the aim of this review paper to summarize the usage of both high gradient magnetic separation and low gradient magnetic separation (LGMS) techniques in this area of research. It is noteworthy that effectiveness of the magnetic separation process not only determines the outcome of a diagnosis but also directly influences its accuracy as well as sensing time involved. Therefore, understanding the factors that simultaneously influence the efficiency of both magnetic separation process and target detection is necessary. Moreover, for LGMS, there are several important considerations that should be taken into account in order to ensure its successful implementation. Hence, this review paper aims to provide an overview to relate all this crucial information by linking the magnetic separation theory to biomedical diagnostic applications. PMID:27920891

Role of central and peripheral opiate receptors in the effects of fentanyl on analgesia, ventilation and arterial blood-gas chemistry in conscious rats

PubMed Central

Henderson, Fraser; May, Walter J.; Gruber, Ryan B.; Discala, Joseph F.; Puscovic, Veljko; Young, Alex P.; Baby, Santhosh M.; Lewis, Stephen J.

2015-01-01

This study determined the effects of the peripherally restricted µ-opiate receptor (µ-OR) antagonist, naloxone methiodide (NLXmi) on fentanyl (25 µg/kg, i.v.)-induced changes in (1) analgesia, (2) arterial blood gas chemistry (ABG) and alveolar-arterial gradient (A-a gradient), and (3) ventilatory parameters, in conscious rats. The fentanyl-induced increase in analgesia was minimally affected by a 1.5 mg/kg of NLXmi but was attenuated by a 5.0 mg/kg dose. Fentanyl decreased arterial blood pH, pO2 and sO2 and increased pCO2 and A-a gradient. These responses were markedly diminished in NLXmi (1.5 mg/kg)-pretreated rats. Fentanyl caused ventilatory depression (e.g., decreases in tidal volume and peak inspiratory flow). Pretreatment with NLXmi (1.5 mg/kg, i.v.) antagonized the fentanyl decrease in tidal volume but minimally affected the other responses. These findings suggest that (1) the analgesia and ventilatory depression caused by fentanyl involve peripheral µ-ORs and (2) NLXmi prevents the fentanyl effects on ABG by blocking the negative actions of the opioid on tidal volume and A-a gradient. PMID:24284037

Field-gradient partitioning for fracture and frictional contact in the material point method: Field-gradient partitioning for fracture and frictional contact in the material point method [Fracture and frictional contact in material point method using damage-field gradients for velocity-field partitioning

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

Homel, Michael A.; Herbold, Eric B.

Contact and fracture in the material point method require grid-scale enrichment or partitioning of material into distinct velocity fields to allow for displacement or velocity discontinuities at a material interface. We present a new method which a kernel-based damage field is constructed from the particle data. The gradient of this field is used to dynamically repartition the material into contact pairs at each node. Our approach avoids the need to construct and evolve explicit cracks or contact surfaces and is therefore well suited to problems involving complex 3-D fracture with crack branching and coalescence. A straightforward extension of this approachmore » permits frictional ‘self-contact’ between surfaces that are initially part of a single velocity field, enabling more accurate simulation of granular flow, porous compaction, fragmentation, and comminution of brittle materials. Finally, numerical simulations of self contact and dynamic crack propagation are presented to demonstrate the accuracy of the approach.« less

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

PubMed Central

Finarelli, John A.; Badgley, Catherine

2010-01-01

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earth's history. PMID:20427339

Field-gradient partitioning for fracture and frictional contact in the material point method: Field-gradient partitioning for fracture and frictional contact in the material point method [Fracture and frictional contact in material point method using damage-field gradients for velocity-field partitioning

DOE PAGES

Homel, Michael A.; Herbold, Eric B.

2016-08-15

Contact and fracture in the material point method require grid-scale enrichment or partitioning of material into distinct velocity fields to allow for displacement or velocity discontinuities at a material interface. We present a new method which a kernel-based damage field is constructed from the particle data. The gradient of this field is used to dynamically repartition the material into contact pairs at each node. Our approach avoids the need to construct and evolve explicit cracks or contact surfaces and is therefore well suited to problems involving complex 3-D fracture with crack branching and coalescence. A straightforward extension of this approachmore » permits frictional ‘self-contact’ between surfaces that are initially part of a single velocity field, enabling more accurate simulation of granular flow, porous compaction, fragmentation, and comminution of brittle materials. Finally, numerical simulations of self contact and dynamic crack propagation are presented to demonstrate the accuracy of the approach.« less

A Study of the Development of Steady and Periodic Unsteady Turbulent Wakes Through Curved Channels at Positive, Zero, and Negative Streamwise Pressure Gradients, Part 1

NASA Technical Reports Server (NTRS)

Schobeiri, M. T.; John, J.

1996-01-01

The turbomachinery wake flow development is largely influenced by streamline curvature and streamwise pressure gradient. The objective of this investigation is to study the development of the wake under the influence of streamline curvature and streamwise pressure gradient. The experimental investigation is carried out in two phases. The first phase involves the study of the wake behind a stationary circular cylinder (steady wake) in curved channels at positive, zero, and negative streamwise pressure gradients. The mean velocity and Reynolds stress components are measured using a X-hot-film probe. The measured quantities obtained in probe coordinates are transformed to a curvilinear coordinate system along the wake centerline and are presented in similarity coordinates. The results of the steady wakes suggest strong asymmetry in velocity and Reynolds stress components. However, the velocity defect profiles in similarity coordinates are almost symmetrical and follow the same distribution as the zero pressure gradient straight wake. The results of Reynolds stress distributions show higher values on the inner side of the wake than the outer side. Other quantities, including the decay of maximum velocity defect, growth of wake width, and wake integral parameters, are also presented for the three different pressure gradient cases of steady wake. The decay rate of velocity defect is fastest for the negative streamwise pressure gradient case and slowest for the positive pressure gradient case. Conversely, the growth of the wake width is fastest for the positive streamwise pressure gradient case and slowest for the negative streamwise pressure gradient. The second phase studies the development of periodic unsteady wakes generated by the circular cylinders of the rotating wake generator in a curved channel at zero streamwise pressure gradient. Instantaneous velocity components of the periodic unsteady wakes, measured with a stationary X-hot-film probe, are analyzed by the phase averaging techniques. The temporal distribution of velocity and Reynolds stress components obtained in a stationary frame of reference are transformed to a spatial distribution in a relative frame of reference. Profiles of phase-averaged velocity and Reynolds stress distributions in the relative frame of reference and similarity coordinates are presented. The velocity defect and Reynolds stress distributions agree with the results of the wake development behind a stationary cylinder in the curved channel at zero streamwise pressure gradient. The phase-averaged third-order correlations, presented in the relative frame of reference and similarity coordinates, show pronounced asymmetric features.

Mass Dependency of Isotope Fractionation of Gases Under Thermal Gradient and Its Possible Implications for Planetary Atmosphere Escaping Process

NASA Technical Reports Server (NTRS)

Sun, Tao; Niles, Paul; Bao, Huiming; Socki, Richard

2014-01-01

Physical processes that unmix elements/isotopes of gas molecules involve phase changes, diffusion (chemical or thermal), effusion and gravitational settling. Some of those play significant roles for the evolution of chemical and isotopic compositions of gases in planetary bodies which lead to better understanding of surface paleoclimatic conditions, e.g. gas bubbles in Antarctic ice, and planetary evolution, e.g. the solar-wind erosion induced gas escaping from exosphere on terrestrial planets.. A mass dependent relationship is always expected for the kinetic isotope fractionations during these simple physical processes, according to the kinetic theory of gases by Chapman, Enskog and others [3-5]. For O-bearing (O16, -O17, -O18) molecules the alpha O-17/ alpha O-18 is expected at 0.5 to 0.515, and for S-bearing (S32,-S33. -S34, -S36) molecules, the alpha S-33/ alpha S-34 is expected at 0.5 to 0.508, where alpha is the isotope fractionation factor associated with unmixing processes. Thus, one isotope pair is generally proxied to yield all the information for the physical history of the gases. However, we recently] reported the violation of mass law for isotope fractionation among isotope pairs of multiple isotope system during gas diffusion or convection under thermal gradient (Thermal Gradient Induced Non-Mass Dependent effect, TGI-NMD). The mechanism(s) that is responsible to such striking observation remains unanswered. In our past studies, we investigated polyatomic molecules, O2 and SF6, and we suggested that nuclear spin effect could be responsible to the observed NMD effect in a way of changing diffusion coefficients of certain molecules, owing to the fact of negligible delta S-36 anomaly for SF6.. On the other hand, our results also showed that for both diffusion and convection under thermal gradient, this NMD effect is increased by lower gas pressure, bigger temperature gradient and lower average temperature, which indicate that the nuclear spin effect may not be the significant contributor as the energies involved in the hyperfine effect are much smaller than those with molecular collisions, especially under convective conditions.

Cell wall and enzyme changes during the graviresponse of the leaf-sheath pulvinus of oat (Avena sativa)

NASA Technical Reports Server (NTRS)

Gibeaut, David M.; Karuppiah, Nadarajah; Chang, S.-R.; Brock, Thomas G.; Vadlamudi, Babu; Kim, Donghern; Ghosheh, Najati S.; Rayle, David L.; Carpita, Nicholas C.; Kaufman, Peter B.

1990-01-01

The graviresponse of the leaf-sheath pulvinus of oat (Avena sativa) involves an asymmetric growth response and asymmetric processes involving degradation of starch and cell wall synthesis. Cellular and biochemical events were studied by investigation of the activities of related enzymes and changes in cell walls and their constituents. It is suggested that an osmotic potential gradient acts as the driving factor for growth, while wall extensibility is a limiting factor in pulvinus growth.

A Useful Laboratory Tool

ERIC Educational Resources Information Center

Johnson, Samuel A.; Tutt, Tye

2008-01-01

Recently, a high school Science Club generated a large number of questions involving temperature. Therefore, they decided to construct a thermal gradient apparatus in order to conduct a wide range of experiments beyond the standard "cookbook" labs. They felt that this apparatus could be especially useful in future ninth-grade biology classes, in…

From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees

Treesearch

Glenn T. Howe; Sally N. Aitken; David B. Neale; Kathleen D. Jermstad; Nicholas C. Wheeler; Tony H.H Chen

2003-01-01

Adaptation to winter cold in temperate and boreal trees involves complex genetic, physiological, and developmental processes. Genecological studies demonstrate the existence of steep genetic clines for cold adaptation traits in relation to environmental (mostly temperature related) gradients. Population differentiation is generally stronger for cold adaptation traits...

Phytoextraction potential of poplar (Populus alba L. var. pyramidalis Bunge) from calcareous agricultural soils contaminated by cadmium.

PubMed

Hu, Yahu; Nan, Zhongren; Jin, Cheng; Wang, Ning; Luo, Huanzhang

2014-01-01

To investigate the phytoextraction potential of Populus alba L. var. pyramidalis Bunge for cadmium (Cd) contaminated calcareous soils, a concentration gradient experiment and a field sampling experiment (involving poplars of different ages) were conducted. The translocation factors for all experiments and treatments were greater than 1. The bioconcentration factor decreased from 2.37 to 0.25 with increasing soil Cd concentration in the concentration gradient experiment and generally decreased with stand age under field conditions. The Cd concentrations in P. pyramidalis organs decreased in the order of leaves > stems > roots. The shoot biomass production in the concentration gradient experiment was not significantly reduced with soil Cd concentrations up to or slightly over 50 mg kg(-1). The results show that the phytoextraction efficiency of P. pyramidalis depends on both the soil Cd concentration and the tree age. Populus pyramidalis is most suitable for remediation of slightly Cd contaminated calcareous soils through the combined harvest of stems and leaves under actual field conditions.

Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid[C][W][OPEN

PubMed Central

Pěnčík, Aleš; Simonovik, Biljana; Petersson, Sara V.; Henyková, Eva; Simon, Sibu; Greenham, Kathleen; Zhang, Yi; Kowalczyk, Mariusz; Estelle, Mark; Zažímalová, Eva; Novák, Ondřej; Sandberg, Göran; Ljung, Karin

2013-01-01

The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type–specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms. PMID:24163311

Mesenchymal chemotaxis requires selective inactivation of Myosin II at the leading edge via a non-canonical PLCγ/PKCα pathway

PubMed Central

Asokan, Sreeja B.; Johnson, Heath E.; Rahman, Anisur; King, Samantha J.; Rotty, Jeremy D.; Lebedeva, Irina P.; Haugh, Jason M.; Bear, James E.

2014-01-01

Summary Chemotaxis, migration towards soluble chemical cues, is critical for processes such as wound healing and immune surveillance, and is exhibited by various cell types from rapidly-migrating leukocytes to slow-moving mesenchymal cells. To interrogate the mechanisms involved in mesenchymal chemotaxis, we observed cell migration in microfluidic chambers that generate stable gradients of the chemoattractant PDGF. Surprisingly, we found that pathways implicated in amoeboid chemotaxis, such as PI3K and mTOR signaling, are dispensable for chemotaxis to PDGF. Instead, we find that local inactivation of Myosin IIA, through a non-canonical Ser1/2 phosphorylation of the regulatory light chain, is essential. This site is phosphorylated by PKCα, which is activated by an intracellular gradient of diacylglycerol generated by PLCγ. Using a combination of TIRF imaging and gradients of activators/inhibitors in the microfluidic chambers, we demonstrate that this signaling pathway and subsequent inhibition of Myosin II activity at the leading edge is required for mesenchymal chemotaxis. PMID:25482883

Wnt, Ptk7, and FGFRL expression gradients control trunk positional identity in planarian regeneration

PubMed Central

Lander, Rachel; Petersen, Christian P

2016-01-01

Mechanisms enabling positional identity re-establishment are likely critical for tissue regeneration. Planarians use Wnt/beta-catenin signaling to polarize the termini of their anteroposterior axis, but little is known about how regeneration signaling restores regionalization along body or organ axes. We identify three genes expressed constitutively in overlapping body-wide transcriptional gradients that control trunk-tail positional identity in regeneration. ptk7 encodes a trunk-expressed kinase-dead Wnt co-receptor, wntP-2 encodes a posterior-expressed Wnt ligand, and ndl-3 encodes an anterior-expressed homolog of conserved FGFRL/nou-darake decoy receptors. ptk7 and wntP-2 maintain and allow appropriate regeneration of trunk tissue position independently of canonical Wnt signaling and with suppression of ndl-3 expression in the posterior. These results suggest that restoration of regional identity in regeneration involves the interpretation and re-establishment of axis-wide transcriptional gradients of signaling molecules. DOI: http://dx.doi.org/10.7554/eLife.12850.001 PMID:27074666

Purification of Peroxisomes and Mitochondria from Spinach Leaf by Percoll Gradient Centrifugation 1

PubMed Central

Schwitzguebel, Jean-Paul; Siegenthaler, Paul-André

1984-01-01

A procedure was developed to purify simultaneously peroxisomes and mitochondria from spinach (Spinacia oleracea L.) leaf under isoosmotic and low viscosity conditions. This method involved differential centrifugation and density gradient centrifugation on four layers of Percoll. Chlorophyll-free preparations of highly intact and active organelles were obtained and cross-contamination was negligible. Both organelles were stable for several hours, even if they remained in Percoll. Purified mitochondria were able to carry out the oxidation of different substrates with excellent respiratory control and ADP:O ratios. The method described in the present work was also suitable to purify mitochondria and peroxisomes from potato (Solanum tuberosum L.) tubers. PMID:16663685

Optical-Near-infrared Color Gradients and Merging History of Elliptical Galaxies

NASA Astrophysics Data System (ADS)

Kim, Duho; Im, Myungshin

2013-04-01

It has been suggested that merging plays an important role in the formation and the evolution of elliptical galaxies. While gas dissipation by star formation is believed to steepen metallicity and color gradients of the merger products, mixing of stars through dissipation-less merging (dry merging) is believed to flatten them. In order to understand the past merging history of elliptical galaxies, we studied the optical-near-infrared (NIR) color gradients of 204 elliptical galaxies. These galaxies are selected from the overlap region of the Sloan Digital Sky Survey (SDSS) Stripe 82 and the UKIRT Infrared Deep Sky Survey (UKIDSS) Large Area Survey (LAS). The use of optical and NIR data (g, r, and K) provides large wavelength baselines, and breaks the age-metallicity degeneracy, allowing us to derive age and metallicity gradients. The use of the deep SDSS Stripe 82 images makes it possible for us to examine how the color/age/metallicity gradients are related to merging features. We find that the optical-NIR color and the age/metallicity gradients of elliptical galaxies with tidal features are consistent with those of relaxed ellipticals, suggesting that the two populations underwent a similar merging history on average and that mixing of stars was more or less completed before the tidal features disappeared. Elliptical galaxies with dust features have steeper color gradients than the other two types, even after masking out dust features during the analysis, which can be due to a process involving wet merging. More importantly, we find that the scatter in the color/age/metallicity gradients of the relaxed and merging feature types decreases as their luminosities (or masses) increase at M > 1011.4 M ⊙ but stays large at lower luminosities. Mean metallicity gradients appear nearly constant over the explored mass range, but a possible flattening is observed at the massive end. According to our toy model that predicts how the distribution of metallicity gradients changes as a result of major dry merging, the mean metallicity gradient should flatten by 40% and its scatter becomes smaller by 80% per a mass-doubling scale if ellipticals evolve only through major dry merger. Our result, although limited by a number statistics at the massive end, is consistent with the picture that major dry merging is an important mechanism for the evolution for ellipticals at M > 1011.4 M ⊙, but is less important at the lower mass range.

OPTICAL-NEAR-INFRARED COLOR GRADIENTS AND MERGING HISTORY OF ELLIPTICAL GALAXIES

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

Kim, Duho; Im, Myungshin

2013-04-01

It has been suggested that merging plays an important role in the formation and the evolution of elliptical galaxies. While gas dissipation by star formation is believed to steepen metallicity and color gradients of the merger products, mixing of stars through dissipation-less merging (dry merging) is believed to flatten them. In order to understand the past merging history of elliptical galaxies, we studied the optical-near-infrared (NIR) color gradients of 204 elliptical galaxies. These galaxies are selected from the overlap region of the Sloan Digital Sky Survey (SDSS) Stripe 82 and the UKIRT Infrared Deep Sky Survey (UKIDSS) Large Area Surveymore » (LAS). The use of optical and NIR data (g, r, and K) provides large wavelength baselines, and breaks the age-metallicity degeneracy, allowing us to derive age and metallicity gradients. The use of the deep SDSS Stripe 82 images makes it possible for us to examine how the color/age/metallicity gradients are related to merging features. We find that the optical-NIR color and the age/metallicity gradients of elliptical galaxies with tidal features are consistent with those of relaxed ellipticals, suggesting that the two populations underwent a similar merging history on average and that mixing of stars was more or less completed before the tidal features disappeared. Elliptical galaxies with dust features have steeper color gradients than the other two types, even after masking out dust features during the analysis, which can be due to a process involving wet merging. More importantly, we find that the scatter in the color/age/metallicity gradients of the relaxed and merging feature types decreases as their luminosities (or masses) increase at M > 10{sup 11.4} M{sub Sun} but stays large at lower luminosities. Mean metallicity gradients appear nearly constant over the explored mass range, but a possible flattening is observed at the massive end. According to our toy model that predicts how the distribution of metallicity gradients changes as a result of major dry merging, the mean metallicity gradient should flatten by 40% and its scatter becomes smaller by 80% per a mass-doubling scale if ellipticals evolve only through major dry merger. Our result, although limited by a number statistics at the massive end, is consistent with the picture that major dry merging is an important mechanism for the evolution for ellipticals at M > 10{sup 11.4} M{sub Sun }, but is less important at the lower mass range.« less

Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

PubMed

Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

2012-08-01

Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Intestinal transport: studies with isolated epithelial cells

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

Kimmich, G.A.

1979-12-01

Isolated intestinal epithelial cells have been extremely useful for characterizing the nature of intestinal absorption processes and for providing insight into the energetics of Na/sup +/-dependent transport systems. This report describes a number of experimental approaches which have been used for investigating the specific epithelial transport systems involved in sugar absorption, but provides information which ultimately should prove useful for characterizing a number of different intestinal transport events. Similar experiments should also prove useful for exploring the effect of environmental agents on the function of intestinal tissue. In the case of sugars, net absorption is accomplished via a mucosal, Na/supmore » +/-dependent concentrative transport system acting in sequence with a passive serosal system which does not require Na/sup +/. The serosal system limits the full gradient-forming capability of the muscosal system. Agents such as phloretin or cytochalasin B which inhibit serosal transport allow the cells to establish sugar gradients as high as 70 fold in contrast to 10 to 15 fold gradients observed for control cells. Sevety-fold sugar gradients cannot be explained in terms of the energy available in the electrochemical potential for Na/sup +/ if the Na/sub 2/: sugar coupling stoichiometry is 1:1 as commonly assumed. New information indicates that the true Na/sup +/:sugar stoichiometry is in fact 2:1. Flow of two Na/sup +/ ions per sugar molecule down the transmembrane electrochemical potential for Na/sup +/ provides more than sufficient energy to account for observed 70 fold sugar gradients. If flow of sugar by other routes could be completely inhibited, theoretical sugar gradients as high as 400 could be achieved assuming that the cells maintain a membrane potential of -36 mV as measured for intact tissue.« less

Geothermal Gradient impact on Induced Seismicity in Raton Basin, Colorado and New Mexico

NASA Astrophysics Data System (ADS)

Pfeiffer, K.; Ge, S.

2017-12-01

Since 1999, Raton Basin, located in southeastern Colorado and northern New Mexico, is the site of wastewater injection for disposing a byproduct of coal bed methane production. During 1999-2016, 29 wastewater injection wells were active in Raton Basin. Induced seismicity began in 2001 and the largest recorded earthquake, an M5.3, occurred in August 2011. Although most injection occurs in the Dakota Formation, the majority of the seismicity has been located in the crystalline basement. Previous studies involving Raton Basin focused on high injection rates and high volume wells to determine their effect on increased pore pressure. However, the geothermal gradient has yet to be studied as a potential catalyst of seismicity. Enhanced Geothermal Systems throughout the world have experienced similar seismicity problems due to water injection. Raton's geothermal gradient, which averages 49± 12°C/km, is much higher then other areas experiencing seismicity. Thermal differences between the hot subsurface and cooler wastewater injection have the potential to affect the strength of the rock and allow for failure. Therefore, we hypothesis that wells in high geothermal gradient areas will produce more frequent earthquakes due to thermal contrast from relatively cold wastewater injection. We model the geothermal gradient in the surrounding areas of the injection sites in Raton Basin to assess potential spatial relationship between high geothermal gradient and earthquakes. Preliminary results show that the fluid pressure increase from injecting cool water is above the threshold of 0.1MPa, which has been shown to induce earthquakes. In addition, temperatures in the subsurface could decrease up to 2°C at approximately 80 m from the injection well, with a temperature effect reaching up to 100 m away from the injection well.

Culture-Independent Analysis of Probiotic Products by Denaturing Gradient Gel Electrophoresis

PubMed Central

Temmerman, R.; Scheirlinck, I.; Huys, G.; Swings, J.

2003-01-01

In order to obtain functional and safe probiotic products for human consumption, fast and reliable quality control of these products is crucial. Currently, analysis of most probiotics is still based on culture-dependent methods involving the use of specific isolation media and identification of a limited number of isolates, which makes this approach relatively insensitive, laborious, and time-consuming. In this study, a collection of 10 probiotic products, including four dairy products, one fruit drink, and five freeze-dried products, were subjected to microbial analysis by using a culture-independent approach, and the results were compared with the results of a conventional culture-dependent analysis. The culture-independent approach involved extraction of total bacterial DNA directly from the product, PCR amplification of the V3 region of the 16S ribosomal DNA, and separation of the amplicons on a denaturing gradient gel. Digital capturing and processing of denaturing gradient gel electrophoresis (DGGE) band patterns allowed direct identification of the amplicons at the species level. This whole culture-independent approach can be performed in less than 30 h. Compared with culture-dependent analysis, the DGGE approach was found to have a much higher sensitivity for detection of microbial strains in probiotic products in a fast, reliable, and reproducible manner. Unfortunately, as reported in previous studies in which the culture-dependent approach was used, a rather high percentage of probiotic products suffered from incorrect labeling and yielded low bacterial counts, which may decrease their probiotic potential. PMID:12513998

A Comparison of Forest Survey Data with Forest Dynamics Simulators FORCLIM and ZELIG along Climatic Gradients in the Pacific Northwest

USGS Publications Warehouse

Busing, Richard T.; Solomon, Allen M.

2004-01-01

Two forest dynamics simulators are compared along climatic gradients in the Pacific Northwest. The ZELIG and FORCLIM models are tested against forest survey data from western Oregon. Their ability to generate accurate patterns of forest basal area and species composition is evaluated for series of sites with contrasting climate. Projections from both models approximate the basal area and composition patterns for three sites along the elevation gradient at H.J. Andrews Experimental Forest in the western Cascade Range. The ZELIG model is somewhat more accurate than FORCLIM at the two low-elevation sites. Attempts to project forest composition along broader climatic gradients reveal limitations of ZELIG, however. For example, ZELIG is less accurate than FORCLIM at projecting the average composition of a west Cascades ecoregion selected for intensive analysis. Also, along a gradient consisting of several sites on an east to west transect at 44.1oN latitude, both the FORCLIM model and the actual data show strong changes in composition and total basal area, but the ZELIG model shows a limited response. ZELIG does not simulate the declines in forest basal area and the diminished dominance of mesic coniferous species east of the Cascade crest. We conclude that ZELIG is suitable for analyses of certain sites for which it has been calibrated. FORCLIM can be applied in analyses involving a range of climatic conditions without requiring calibration for specific sites.

Image Motion Detection And Estimation: The Modified Spatio-Temporal Gradient Scheme

NASA Astrophysics Data System (ADS)

Hsin, Cheng-Ho; Inigo, Rafael M.

1990-03-01

The detection and estimation of motion are generally involved in computing a velocity field of time-varying images. A completely new modified spatio-temporal gradient scheme to determine motion is proposed. This is derived by using gradient methods and properties of biological vision. A set of general constraints is proposed to derive motion constraint equations. The constraints are that the second directional derivatives of image intensity at an edge point in the smoothed image will be constant at times t and t+L . This scheme basically has two stages: spatio-temporal filtering, and velocity estimation. Initially, image sequences are processed by a set of oriented spatio-temporal filters which are designed using a Gaussian derivative model. The velocity is then estimated for these filtered image sequences based on the gradient approach. From a computational stand point, this scheme offers at least three advantages over current methods. The greatest advantage of the modified spatio-temporal gradient scheme over the traditional ones is that an infinite number of motion constraint equations are derived instead of only one. Therefore, it solves the aperture problem without requiring any additional assumptions and is simply a local process. The second advantage is that because of the spatio-temporal filtering, the direct computation of image gradients (discrete derivatives) is avoided. Therefore the error in gradients measurement is reduced significantly. The third advantage is that during the processing of motion detection and estimation algorithm, image features (edges) are produced concurrently with motion information. The reliable range of detected velocity is determined by parameters of the oriented spatio-temporal filters. Knowing the velocity sensitivity of a single motion detection channel, a multiple-channel mechanism for estimating image velocity, seldom addressed by other motion schemes in machine vision, can be constructed by appropriately choosing and combining different sets of parameters. By applying this mechanism, a great range of velocity can be detected. The scheme has been tested for both synthetic and real images. The results of simulations are very satisfactory.

Crystal structures and atomic model of NADPH oxidase.

PubMed

Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea

2017-06-27

NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.

Inhibition and dispersal of Agrobacterium tumefaciens biofilms by a small diffusible Pseudomonas aeruginosa exoproduct(s).

PubMed

Hibbing, Michael E; Fuqua, Clay

2012-06-01

Environmental biofilms often contain mixed populations of different species. In these dense communities, competition between biofilm residents for limited nutrients such as iron can be fierce, leading to the evolution of competitive factors that affect the ability of competitors to grow or form biofilms. We have discovered a compound(s) present in the conditioned culture fluids of Pseudomonas aeruginosa that disperses and inhibits the formation of biofilms produced by the facultative plant pathogen Agrobacterium tumefaciens. The inhibitory activity is strongly induced when P. aeruginosa is cultivated in iron-limited conditions, but it does not function through iron sequestration. In addition, the production of the biofilm inhibitory activity is not regulated by the global iron regulatory protein Fur, the iron-responsive extracytoplasmic function σ factor PvdS, or three of the recognized P. aeruginosa quorum-sensing systems. In addition, the compound(s) responsible for the inhibition and dispersal of A. tumefaciens biofilm formation is likely distinct from the recently identified P. aeruginosa dispersal factor, cis-2-decenoic acid (CDA), as dialysis of the culture fluids showed that the inhibitory compound was larger than CDA and culture fluids that dispersed and inhibited biofilm formation by A. tumefaciens had no effect on biofilm formation by P. aeruginosa.

Inhibition and dispersal of Agrobacterium tumefaciens biofilms by a small diffusible Pseudomonas aeruginosa exoproduct(s)

PubMed Central

Hibbing, Michael E.; Fuqua, Clay

2013-01-01

Environmental biofilms often contain mixed populations of different species. In these dense communities, competition between biofilm residents for limited nutrients such as iron, can be fierce, leading to the evolution of competitive factors that affect the ability of competitors to grow or form biofilms. We have discovered a compound(s) present in the conditioned culture fluids of Pseudomonas aeruginosa that disperses and inhibits the formation of biofilms produced by the facultative plant pathogen Agrobacterium tumefaciens. The inhibitory activity is strongly induced when P. aeruginosa is cultivated in iron-limited conditions, but it does not function through iron sequestration. In addition, the production of the inhibitory activity is not regulated by the global iron regulatory protein Fur, the iron-responsive extra-cytoplasmic function (ECF) σ factor PvdS, or three of the recognized P. aeruginosa quorum sensing systems. In addition, the compound(s) responsible for the inhibition and dispersal of A. tumefaciens biofilm formation is likely distinct from the recently identified P. aeruginosa dispersal factor, cis-2-decenoic acid (CDA), as dialysis of the culture fluids showed that the inhibitory compound was larger than CDA and culture fluids that dispersed and inhibited biofilm formation by A. tumefaciens had no effect on biofilm formation by P. aeruginosa. PMID:22105093

The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1T as revealed by whole genome comparisons.

PubMed

Lombardot, Thierry; Bauer, Margarete; Teeling, Hanno; Amann, Rudolf; Glöckner, Frank Oliver

2005-01-01

Rhodopirellula baltica (strain SH 1T) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum Planctomycetes. Little is known about the regulatory strategies of free-living bacteria with large (7.15 Mb) genomes. Therefore, a consistent, quantitative and qualitative description was produced by comparing R. baltica's transcriptional regulator pool with that of 123 publicly available bacterial genomes. The overall results are congruous with earlier observations that in Bacteria, the proportion of genes encoding transcriptional regulators generally increases with genome size. However, R. baltica distinctly stands out from this trend with only 2.4% (174) of all genes predicted to encode transcriptional regulators. The qualitative investigation of R. baltica's transcriptional regulators revealed a clear shift towards high numbers of two-component systems (66) as well as high numbers of sigma factors (49), with more than 76% (37) belonging to the extra-cytoplasmic function subfamily of sigma-70. Only one predicted sigma factor showed a relatively close phylogenetic relationship to that of another bacterium, the sigma factor SigZ of Bacillus subtilis. In summary, analysis of the R. baltica genome revealed disparate regulatory mechanisms and a clear bias towards direct environmental sensing. This strategy might provide a selective advantage for organisms living in habitats with frequently changing environmental conditions.

Evaluating the role of phage-shock protein A in Burkholderia pseudomallei.

PubMed

Southern, Stephanie J; Male, Abigail; Milne, Timothy; Sarkar-Tyson, Mitali; Tavassoli, Ali; Oyston, Petra C F

2015-11-01

The phage-shock protein (Psp) response is an extracytoplasmic response system that is vital for maintenance of the cytoplasmic membrane when the cell encounters stressful conditions. The paradigm of the Psp response has been established in Escherichia coli. The response has been shown to be important for survival during the stationary phase, maintenance of the proton motive force across membranes and implicated in virulence. In this study, we identified a putative PspA homologue in Burkholderia pseudomallei, annotated as BPSL2105. Similar to the induction of PspA in E. coli, the expression of B. pseudomallei BPSL2105 was induced by heat shock. Deletion of BPSL2105 resulted in a survival defect in the late stationary phase coincident with dramatic changes in the pH of the culture medium. The B. pseudomallei BPSL2105 deletion mutant also displayed reduced survival in macrophage infection - the first indication that the Psp response plays a role during intracellular pathogenesis in this species. The purified protein formed large oligomeric structures similar to those observed for the PspA protein of E. coli, and PspA homologues in Bacillus, cyanobacteria and higher plants, providing further evidence to support the identification of BPSL2105 as a PspA-like protein in B. pseudomallei.

Wall ingrowth deposition in phloem parenchyma transfer cells in Arabidopsis: Heteroblastic variations and a potential role in pathogen defence.

PubMed

Nguyen, Suong T T; McCurdy, David W

2017-06-03

Transfer cell (TCs) develop unique wall ingrowth networks which amplify plasma membrane surface area and thus maximize nutrient transporter density at key anatomic sites for nutrient exchange within plants and their external environment. These sites fall into 4 main groups corresponding to 4 categories of trans-membrane flux: absorption/secretion of solutes from or to the external environment, and absorption/secretion of solutes from or to internal, extra-cytoplasmic compartments. Research on TC biology over recent decades has demonstrated correlations between wall ingrowth deposition in TCs and enhanced transport capacity in many major agricultural species such as pea, fava bean, cotton and maize. Consequently, there is general consensus that the existence of wall ingrowth morphology implies an augmentation in membrane transport capacity. However, this may not be entirely applicable for phloem parenchyma (PP) TCs in Arabidopsis. Our recent survey of PP TC abundance and distribution in Arabidopsis veins indicated that PP TC development reflects heteroblastic status. A consequence of this observation is the suggestion that PP TCs, or at least wall ingrowth deposition in these cells, potentially act as a physical barrier to defend access of invading pathogens to sugar-rich sieve elements rather than solely in facilitating the export of photoassimilate from collection phloem in leaves.

An Extracytoplasmic Function Sigma Factor-Mediated Cell Surface Signaling System in Pseudomonas syringae pv. tomato DC3000 Regulates Gene Expression in Response to Heterologous Siderophores ▿ †

PubMed Central

Markel, Eric; Maciak, Charlene; Butcher, Bronwyn G.; Myers, Christopher R.; Stodghill, Paul; Bao, Zhongmeng; Cartinhour, Sam; Swingle, Bryan

2011-01-01

The diversity of regulatory systems encoded by bacteria provides an indication of the variety of stresses and interactions that these organisms encounter in nature. We have been investigating how the plant pathogen Pseudomonas syringae pv. tomato DC3000 responds to iron limitation and have focused on the iron starvation (IS) sigma factors to identify regulon members and to explore the mechanistic details of genetic control for this class of regulators. In the study described in this report, we used chromatin immunoprecipitation paired with high-throughput sequencing (ChIP-Seq) to screen the genome for locations associated with binding of the P. syringae IS sigma factor PSPTO_1203. We used multiple methods to demonstrate differential regulation of two genes identified in the ChIP-Seq screen and characterize the promoter elements that facilitate PSPTO_1203-dependent regulation. The genes regulated by PSPTO_1203 encode a TonB-dependent transducer (PSPTO_1206) and a cytoplasmic membrane protein (PSPTO_2145), which is located in the P. syringae pyoverdine cluster. Additionally, we identified siderophores that induce the activity of PSPTO_1203 and used this information to investigate the functional components of the signal transduction cascade. PMID:21840980

Comparative In Situ Measurements of Plasma Instabilities in the Equatorial and Auroral Electrojets

NASA Technical Reports Server (NTRS)

Pfaff, Robert F.

2008-01-01

This presentation provides a comparison of in situ measurements of plasma instabilities gathered by rocket-borne probes in the equatorial and auroral electrojets. Specifically, using detailed measurements of the DC electric fields, current density, and plasma number density within the unstable daytime equatorial electrojet from Brazil (Guara Campaign) and in the auroral electrojet from Sweden (ERRIS Campaign), we present comparative observations and general conclusions regarding the observed physical properties of Farley-Buneman two-stream waves and large scale, gradient drift waves. The two stream observations reveal coherent-like waves propagating near the E x B direction but at reduced speeds (nearer to the presumed acoustic velocity) with wavelengths of approximately 5-10m in both the equatorial and auroral electrojet, as measured using the spaced-receiver technique. The auroral electrojet data generally shows extensions to shorter wavelengths, in concert with the fact that these waves are driven harder. With respect to gradient-drift driven waves, observations of this instability are much more pronounced in the equatorial electrojet, given the more favorable geometry for growth provided by the vertical gradient and horizontal magnetic field lines. We present new analysis of Guara rocket observations of electric field and plasma density data that reveal considerable structuring in the middle and lower portion of the electrojet (90-105 km) where the ambient plasma density gradient is unstable. Although the electric field amplitudes are largest (approximately 10-15 mV/m) in the zonal direction, considerable structure (approximately 5-10 mV/m) is also observed in the vertical electric field component as well, implying that the dominant large scale waves involve significant vertical interaction and coupling within the narrow altitude range where they are observed. Furthermore, a detailed examination of the phase of the waveforms show that on some, but not all occasions, locally enhanced eastward fields are associated with locally enhanced upwards (polarization) electric fields. The measurements are discussed in terms of theories involving the non-linear evolution and structuring of plasma waves.

Direct Determination of the Dependence of the Surface Shear and Dilatational Viscosities on the Thermodynamic State of the Interface: Theoretical Foundations.

PubMed

Lopez; Hirsa

1998-10-01

Recent developments in nonlinear optical techniques for noninvasive probing of a surfactant influenced gas/liquid interface allow for the measurement of the surfactant surface concentration, c, and thus provide new opportunities for the direct determination of its intrinsic viscosities. Here, we present the theoretical foundations, based on the Boussinesq-Scriven surface model without the usual simplification of constant viscosities, for an experimental technique to directly measure the surface shear (µs) and dilatational (kappas) viscosities of a Newtonian interface as functions of the surfactant surface concentration. This ability to directly measure the surfactant concentration permits the use of a simple surface flow for the measurement of the surface viscosities. The requirements are that the interface must be nearly flat, and the flow steady, axisymmetric, and swirling; these flow conditions can be achieved in the deep-channel viscometer driven at relatively fast rates. The tangential stress balance on such an interface leads to two equations; the balance in the azimuthal direction involves only µs and its gradients, and the balance in the radial direction involves both µs and kappas and their gradients. By further exploiting recent developments in laser-based flow measuring techniques, the surface velocities and their gradients which appear in the two equations can be measured directly. The surface tension gradient, which appears in the radial balance equation, is incorporated from the equation of state for the surfactant system and direct measurements of the surfactant surface concentration distribution. The stress balance equations are then ordinary differential equations in the surface viscosities as functions of radial position, which can be readily integrated. Since c is measured as a function of radial position, we then have a direct measurement of µs and kappas as functions of c. Numerical computations of the Navier-Stokes equations are performed to determine the appropriate conditions to achieve the requisite secondary flow. Copyright 1998 Academic Press.

Role of central and peripheral opiate receptors in the effects of fentanyl on analgesia, ventilation and arterial blood-gas chemistry in conscious rats.

PubMed

Henderson, Fraser; May, Walter J; Gruber, Ryan B; Discala, Joseph F; Puskovic, Veljko; Young, Alex P; Baby, Santhosh M; Lewis, Stephen J

2014-01-15

This study determined the effects of the peripherally restricted μ-opiate receptor (μ-OR) antagonist, naloxone methiodide (NLXmi) on fentanyl (25μg/kg, i.v.)-induced changes in (1) analgesia, (2) arterial blood gas chemistry (ABG) and alveolar-arterial gradient (A-a gradient), and (3) ventilatory parameters, in conscious rats. The fentanyl-induced increase in analgesia was minimally affected by a 1.5mg/kg of NLXmi but was attenuated by a 5.0mg/kg dose. Fentanyl decreased arterial blood pH, pO2 and sO2 and increased pCO2 and A-a gradient. These responses were markedly diminished in NLXmi (1.5mg/kg)-pretreated rats. Fentanyl caused ventilatory depression (e.g., decreases in tidal volume and peak inspiratory flow). Pretreatment with NLXmi (1.5mg/kg, i.v.) antagonized the fentanyl decrease in tidal volume but minimally affected the other responses. These findings suggest that (1) the analgesia and ventilatory depression caused by fentanyl involve peripheral μ-ORs and (2) NLXmi prevents the fentanyl effects on ABG by blocking the negative actions of the opioid on tidal volume and A-a gradient. Copyright © 2013 Elsevier B.V. All rights reserved.

Role of a texture gradient in the perception of relative size.

PubMed

Tozawa, Junko

2010-01-01

Two theories regarding the role of a texture gradient in the perception of the relative size of objects are compared. Relational theory states that relative size is directly specified by the projective ratio of the numbers of texture elements spanned by objects. Distance calibration theory assumes that relative size is a product of visual angle and distance, once the distance is specified by the texture. Experiment 1 involved three variables: background (no texture, texture gradient patterns), the ratio of heights of the comparison stimulus to a standard (three levels), and angular vertical separation of the standard stimulus below the horizon (two levels). The effect of the retinal length of the comparison stimulus was examined in experiment 2. In both experiments, participants judged both the apparent size and distance of a comparison stimulus relative to a standard stimulus. Results suggest that the cues selected by observers to judge relative size were to some degree different from those used to judge relative distance. Relative size was strongly affected by a texture gradient and the retinal length of a comparison stimulus whereas relative distance perception was affected by relative height. When dominant cues that specify size are different from those which specify distance, relational theory might provide a better account of relative size perception than distance calibration theory.

The role of the geothermal gradient in the emplacement and replenishment of ground ice on Mars

NASA Technical Reports Server (NTRS)

Clifford, Stephen M.

1993-01-01

Knowledge of the mechanisms by which ground ice is emplaced, removed, and potentially replenished, are critical to understanding the climatic and hydrologic behavior of water on Mars, as well as the morphologic evolution of its surface. Because of the strong temperature dependence of the saturated vapor pressure of H2O, the atmospheric emplacement or replenishment of ground ice is prohibited below the depth at which crustal temperatures begin to monotonically increase due to geothermal heating. In contrast, the emplacement and replenishment of ground ice from reservoirs of H2O residing deep within the crust can occur by at least three different thermally-driven processes, involving all three phases of water. In this regard, Clifford has discussed how the presence of a geothermal gradient as small as 15 K/km can give rise to a corresponding vapor pressure gradient sufficient to drive the vertical transport of 1 km of water from a reservoir of ground water at depth to the base of the cryosphere every 10(exp 6) - 10(exp 7) years. This abstract expands on this earlier treatment by considering the influence of thermal gradients on the transport of H2O at temperatures below the freezing point.

Macroinvertebrate colonization dynamics on artificial substrates along an algal resource gradient

Treesearch

A. Braccia; S.L. Eggert; N. King

2014-01-01

Riparian canopy removal and land use may introduce multiple stressors that can alter food and habitat for stream organisms, but the influence of these alterations on macroinvertebrate colonization dynamics is less well known. A field study involving the simultaneous placement and removal of artificial substrates was performed to examine how macroinvertebrate...

Soil fauna and plant litter decomposition in tropical and subalpine forests

Treesearch

G. Gonzalez; T.R. Seastedt

2001-01-01

The decomposition of plant residues is influenced by their chemical composition, the physical-chemical environment, and the decomposer organisms. Most studies interested in latitudinal gradients of decomposition have focused on substrate quality and climate effects on decomposition, and have excluded explicit recognition of the soil organisms involved in the process....

Sparse matrix methods based on orthogonality and conjugacy

NASA Technical Reports Server (NTRS)

Lawson, C. L.

1973-01-01

A matrix having a high percentage of zero elements is called spares. In the solution of systems of linear equations or linear least squares problems involving large sparse matrices, significant saving of computer cost can be achieved by taking advantage of the sparsity. The conjugate gradient algorithm and a set of related algorithms are described.

Data for prediction of mechanical properties of aspen flakeboards

Treesearch

C. G. Carll; P. Wang

1983-01-01

This research compared two methods of producing flakeboards with uniform density distribution (which could then be used to predict bending properties of flakeboards with density gradients). One of the methods was suspected of producing weak boards because it involved exertion of high pressures on cold mats. Although differences were found in mechanical properties of...

Ethanol and thermotolerance in the bioconversion of xylose by yeasts

Treesearch

Thomas W. Jeffries; Yong-Su Jin

2000-01-01

The mechanisms underlying ethanol and heat tolerance are complex. Many different genes are involved, and the exact basis is not fully understood. The integrity of cytoplasmic and mitochondrial membranes is critical to maintain proton gradients for metabolic energy and nutrient uptake. Heat and ethanol stress adversely affect membrane integrity. These factors are...

Molecular diagnostics of periodontitis.

PubMed

Korona-Głowniak, Izabela; Siwiec, Radosław; Berger, Marcin; Malm, Anna; Szymańska, Jolanta

2017-01-28

The microorganisms that form dental plaque are the main cause of periodontitis. Their identification and the understanding of the complex relationships and interactions that involve these microorganisms, environmental factors and the host's health status enable improvement in diagnostics and targeted therapy in patients with periodontitis. To this end, molecular diagnostics techniques (both techniques based on the polymerase chain reaction and those involving nucleic acid analysis via hybridization) come increasingly into use. On the basis of a literature review, the following methods are presented: polymerase chain reaction (PCR), real-time polymerase chain reaction (real-time PCR), 16S rRNA-encoding gene sequencing, checkerboard and reverse-capture checkerboard hybridization, microarrays, denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), as well as terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). The advantages and drawbacks of each method in the examination of periopathogens are indicated. The techniques listed above allow fast detection of even small quantities of pathogen present in diagnostic material and prove particularly useful to detect microorganisms that are difficult or impossible to grow in a laboratory.

Towards an Integrated QR Code Biosensor: Light-Driven Sample Acquisition and Bacterial Cellulose Paper Substrate.

PubMed

Yuan, Mingquan; Jiang, Qisheng; Liu, Keng-Ku; Singamaneni, Srikanth; Chakrabartty, Shantanu

2018-06-01

This paper addresses two key challenges toward an integrated forward error-correcting biosensor based on our previously reported self-assembled quick-response (QR) code. The first challenge involves the choice of the paper substrate for printing and self-assembling the QR code. We have compared four different substrates that includes regular printing paper, Whatman filter paper, nitrocellulose membrane and lab synthesized bacterial cellulose. We report that out of the four substrates bacterial cellulose outperforms the others in terms of probe (gold nanorods) and ink retention capability. The second challenge involves remote activation of the analyte sampling and the QR code self-assembly process. In this paper, we use light as a trigger signal and a graphite layer as a light-absorbing material. The resulting change in temperature due to infrared absorption leads to a temperature gradient that then exerts a diffusive force driving the analyte toward the regions of self-assembly. The working principle has been verified in this paper using assembled biosensor prototypes where we demonstrate higher sample flow rate due to light induced thermal gradients.

Latent hardening size effect in small-scale plasticity

NASA Astrophysics Data System (ADS)

Bardella, Lorenzo; Segurado, Javier; Panteghini, Andrea; Llorca, Javier

2013-07-01

We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view.

Marangoni-driven chemotaxis, chemotactic collapse, and the Keller-Segel equation

NASA Astrophysics Data System (ADS)

Shelley, Michael; Masoud, Hassan

2013-11-01

Almost by definition, chemotaxis involves the biased motion of motile particles along gradients of a chemical concentration field. Perhaps the most famous model for collective chemotaxis in mathematical biology is the Keller-Segel model, conceived to describe collective aggregation of slime mold colonies in response to an intrinsically produced, and diffusing, chemo-attractant. Heavily studied, particularly in 2D where the system is ``super-critical'', it has been proved that the KS model can develop finite-time singularities - so-called chemotactic collapse - of delta-function type. Here, we study the collective dynamics of immotile particles bound to a 2D interface above a 3D fluid. These particles are chemically active and produce a diffusing field that creates surface-tension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. Remarkably, we show that this system involving 3D diffusion and fluid dynamics, exactly yields the 2D Keller-Segel model for the surface-flow of active particles. We discuss the consequences of collapse on the 3D fluid dynamics, and generalizations of the fluid-dynamical model.

Reactive Oxygen Species-Inducible ECF σ Factors of Bradyrhizobium japonicum

PubMed Central

Masloboeva, Nadezda; Reutimann, Luzia; Stiefel, Philipp; Follador, Rainer; Leimer, Nadja; Hennecke, Hauke; Mesa, Socorro; Fischer, Hans-Martin

2012-01-01

Extracytoplasmic function (ECF) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. The genome of Bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ECF σ factors belonging to nine different ECF σ factor families. The genes for two of them, ecfQ (bll1028) and ecfF (blr3038), are highly induced in response to the reactive oxygen species hydrogen peroxide (H2O2) and singlet oxygen (1O2). The ecfF gene is followed by the predicted anti-σ factor gene osrA (blr3039). Mutants lacking EcfQ, EcfF plus OsrA, OsrA alone, or both σ factors plus OsrA were phenotypically characterized. While the symbiotic properties of all mutants were indistinguishable from the wild type, they showed increased sensitivity to singlet oxygen under free-living conditions. Possible target genes of EcfQ and EcfF were determined by microarray analyses, and candidate genes were compared with the H2O2-responsive regulon. These experiments disclosed that the two σ factors control rather small and, for the most part, distinct sets of genes, with about half of the genes representing 13% of the members of H2O2-responsive regulon. To get more insight into transcriptional regulation of both σ factors, the 5′ ends of ecfQ and ecfF mRNA were determined. The presence of conserved sequence motifs in the promoter region of ecfQ and genes encoding EcfQ-like σ factors in related α-proteobacteria suggests regulation via a yet unknown transcription factor. By contrast, we have evidence that ecfF is autoregulated by transcription from an EcfF-dependent consensus promoter, and its product is negatively regulated via protein-protein interaction with OsrA. Conserved cysteine residues 129 and 179 of OsrA are required for normal function of OsrA. Cysteine 179 is essential for release of EcfF from an EcfF-OsrA complex upon H2O2 stress while cysteine 129 is possibly needed for EcfF-OsrA interaction. PMID:22916258

Calcium dynamics in tomato pollen tubes using the Yellow Cameleon 3.6 sensor.

PubMed

Barberini, María Laura; Sigaut, Lorena; Huang, Weijie; Mangano, Silvina; Juarez, Silvina Paola Denita; Marzol, Eliana; Estevez, José; Obertello, Mariana; Pietrasanta, Lía; Tang, Weihua; Muschietti, Jorge

2018-06-01

In vitro tomato pollen tubes show a cytoplasmic calcium gradient that oscillates with the same period as growth. Pollen tube growth requires coordination between the tip-focused cytoplasmic calcium concentration ([Ca 2+ ] cyt ) gradient and the actin cytoskeleton. This [Ca 2+ ] cyt gradient is necessary for exocytosis of small vesicles, which contributes to the delivery of new membrane and cell wall at the pollen tube tip. The mechanisms that generate and maintain this [Ca 2+ ] cyt gradient are not completely understood. Here, we studied calcium dynamics in tomato (Solanum lycopersicum) pollen tubes using transgenic tomato plants expressing the Yellow Cameleon 3.6 gene under the pollen-specific promoter LAT52. We use tomato as an experimental model because tomato is a Solanaceous plant that is easy to transform, and has an excellent genomic database and genetic stock center, and unlike Arabidopsis, tomato pollen is a good system to do biochemistry. We found that tomato pollen tubes showed an oscillating tip-focused [Ca 2+ ] cyt gradient with the same period as growth. Then, we used a pharmacological approach to disturb the intracellular Ca 2+ homeostasis, evaluating how the [Ca 2+ ] cyt gradient, pollen germination and in vitro pollen tube growth were affected. We found that cyclopiazonic acid (CPA), a drug that inhibits plant P IIA -type Ca 2+ -ATPases, increased [Ca 2+ ] cyt in the subapical zone, leading to the disappearance of the Ca 2+ oscillations and inhibition of pollen tube growth. In contrast, 2-aminoethoxydiphenyl borate (2-APB), an inhibitor of Ca 2+ released from the endoplasmic reticulum to the cytoplasm in animals cells, completely reduced [Ca 2+ ] cyt at the tip of the tube, blocked the gradient and arrested pollen tube growth. Although both drugs have antagonistic effects on [Ca 2+ ] cyt , both inhibited pollen tube growth triggering the disappearance of the [Ca 2+ ] cyt gradient. When CPA and 2-APB were combined, their individual inhibitory effects on pollen tube growth were partially compensated. Finally, we found that GsMTx-4, a peptide from spider venom that blocks stretch-activated Ca 2+ channels, inhibited tomato pollen germination and had a heterogeneous effect on pollen tube growth, suggesting that these channels are also involved in the maintenance of the [Ca 2+ ] cyt gradient. All these results indicate that tomato pollen tube is an excellent model to study calcium dynamics.

On the distinction between large deformation and large distortion for anisotropic materials

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

BRANNON,REBECCA M.

2000-02-24

A motion involves large distortion if the ratios of principal stretches differ significantly from unity. A motion involves large deformation if the deformation gradient tensor is significantly different from the identity. Unfortunately, rigid rotation fits the definition of large deformation, and models that claim to be valid for large deformation are often inadequate for large distortion. An exact solution for the stress in an idealized fiber-reinforced composite is used to show that conventional large deformation representations for transverse isotropy give errant results. Possible alternative approaches are discussed.

High left ventricular outflow tract gradient: Aortic stenosis, obstructive hypertrophic cardiomyopathy or both?

PubMed

Almeida, Inês; Caetano, Francisca; Trigo, Joana; Mota, Paula; Marques, António Leitão

2015-05-01

The authors report the case of a patient diagnosed with both hypertrophic cardiomyopathy and aortic stenosis. Due to clinical deterioration, additional investigation was performed, and a high left ventricular outflow tract gradient was identified. Correct identification of the condition causing the symptoms was challenging, and involved several imaging techniques, the contribution of transesophageal echocardiography being crucial. The final diagnosis of severe aortic stenosis led to successful valve replacement surgery. The presence of these two conditions in the same patient has been documented, although it is uncommon. This association poses particular diagnostic and therapeutic challenges, which are discussed in this paper. Copyright © 2015 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

Contributions on the Subject of Longitudinal Movements of Aircraft in Wind Shears. Ph.D. Thesis - Technischen Univ., 1983

NASA Technical Reports Server (NTRS)

Krauspe, P.

1985-01-01

The effect of downburst-type wind shears on the longitudinal dynamic behavior of an unguided aircraft is simulated numerically on the basis of published meteorological data and the flight characteristics of an A300-B passenger jet. The nonlinear differential equations of the aircraft motion are linearized by conventional methods, and the wind effects are introduced via the linear derivatives of the wind components referred to the wind gradients to obtain simplified technical models of the longitudinal response to all possible types of constant-gradient wind shears during the first 20-60 sec. Graphs, maps, and diagrams are provided, and a number of accidents presumed to have involved wind shears are analyzed in detail.

Time-resolved lateral spin-caloric transport of optically generated spin packets in n-GaAs

NASA Astrophysics Data System (ADS)

Göbbels, Stefan; Güntherodt, Gernot; Beschoten, Bernd

2018-05-01

We report on lateral spin-caloric transport (LSCT) of electron spin packets which are optically generated by ps laser pulses in the non-magnetic semiconductor n-GaAs at K. LSCT is driven by a local temperature gradient induced by an additional cw heating laser. The spatio-temporal evolution of the spin packets is probed using time-resolved Faraday rotation. We demonstrate that the local temperature-gradient induced spin diffusion is solely driven by a non-equilibrium hot spin distribution, i.e. without involvement of phonon drag effects. Additional electric field-driven spin drift experiments are used to verify directly the validity of the non-classical Einstein relation for moderately doped semiconductors at low temperatures for near band-gap excitation.

Corotating solar wind structures and recurrent trains of enhanced diurnal variation in galactic cosmic rays

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

Yeeram, T.; Ruffolo, D.; Sáiz, A.

Data from the Princess Sirindhorn Neutron Monitor at Doi Inthanon, Thailand, with a vertical cutoff rigidity of 16.8 GV, were utilized to determine the diurnal anisotropy (DA) of Galactic cosmic rays (GCRs) near Earth during solar minimum conditions between 2007 November and 2010 November. We identified trains of enhanced DA over several days, which often recur after a solar rotation period (∼27 days). By investigating solar coronal holes as identified from synoptic maps and solar wind parameters, we found that the intensity and anisotropy of cosmic rays are associated with the high-speed streams (HSSs) in the solar wind, which aremore » in turn related to the structure and evolution of coronal holes. An enhanced DA was observed after the onset of some, but not all, HSSs. During time periods of recurrent trains, the DA was often enhanced or suppressed according to the sign of the interplanetary magnetic field B, which suggests a contribution from a mechanism involving a southward gradient in the GCR density, n, and a gradient anisotropy along B × ∇n. In one non-recurrent and one recurrent sequence, an HSS from an equatorial coronal hole was merged with that from a trailing mid-latitude extension of a polar coronal hole, and the slanted HSS structure in space with suppressed GCR density can account for the southward GCR gradient. We conclude that the gradient anisotropy is a source of temporary changes in the GCR DA under solar minimum conditions, and that the latitudinal GCR gradient can sometimes be explained by the coronal hole morphology.« less

Optical imaging measurements of oxygen transport fluctuations and gradients in tumor microvascular networks

NASA Astrophysics Data System (ADS)

Sorg, Brian S.; Hardee, Matthew E.; Moeller, Benjamin J.; Dewhirst, Mark W.

2006-02-01

It is well established that hypoxia can influence tumor biology and physiology, gene expression, metastatic potential, treatment efficacy, and patient survival. Most human solid tumors have been shown to have some hypoxic regions, thus there is a strong motivation to understand the various causes of hypoxia. One key to understanding tumor hypoxia involves the study of oxygen transport to tumors, and the connection between hypoxia, tumor microvasculature, and the tumor microenvironment. Recent research has suggested that the causes of tumor hypoxia are much more complex than indicated by the classical paradigms ("chronic" and "acute" hypoxia), and several potential factors have been identified. Two such factors are temporal fluctuations in tissue pO II and longitudinal gradients in oxygen transport. Research has shown the existence of low frequency (<2 cycles per minute) fluctuations in tumor pO II without cessation of blood flow that can lead to transient hypoxia. In addition, longitudinal gradients in tumor pO II along the arteriolar afferent direction have been documented in window chamber tumors. However, the causes of the pO II temporal fluctuations and longitudinal gradients are not exactly known, and the clinical significance of these observations is not well understood. In this preliminary study, we demonstrate the potential of optical imaging measurements of hemoglobin saturation to add new information in these areas. Slow temporal fluctuations of hemoglobin saturation (HbSat) and gradients in the average HbSat were observed in some 4T1 mouse mammary carcinoma microvessels. With additional research, the mechanisms behind these phenomena and insights into their clinical significance may be revealed.

Influence on cell death of high frequency motion of magnetic nanoparticles during magnetic hyperthermia experiments

NASA Astrophysics Data System (ADS)

Hallali, N.; Clerc, P.; Fourmy, D.; Gigoux, V.; Carrey, J.

2016-07-01

Studies with transplanted tumors in animals and clinical trials have provided the proof-of-concept of magnetic hyperthermia (MH) therapy of cancers using iron oxide nanoparticles. Interestingly, in several studies, the application of an alternating magnetic field (AMF) to tumor cells having internalized and accumulated magnetic nanoparticles (MNPs) into their lysosomes can induce cell death without detectable temperature increase. To explain these results, among other hypotheses, it was proposed that cell death could be due to the high-frequency translational motion of MNPs under the influence of the AMF gradient generated involuntarily by most inductors. Such mechanical actions of MNPs might cause cellular damages and participate in the induction of cell death under MH conditions. To test this hypothesis, we developed a setup maximizing this effect. It is composed of an anti-Helmholtz coil and two permanent magnets, which produce an AMF gradient and a superimposed static MF. We have measured the MNP heating power and treated tumor cells by a standard AMF and by an AMF gradient, on which was added or not a static magnetic field. We showed that the presence of a static magnetic field prevents MNP heating and cell death in standard MH conditions. The heating power of MNPs in an AMF gradient is weak, position-dependent, and related to the presence of a non-zero AMF. Under an AMF gradient and a static field, no MNP heating and cell death were measured. Consequently, the hypothesis that translational motions could be involved in cell death during MH experiments is ruled out by our experiments.

Fluoroquinolone resistance of Serratia marcescens: involvement of a proton gradient-dependent efflux pump.

PubMed

Kumar, Ayush; Worobec, Elizabeth A

2002-10-01

To determine the presence of a proton gradient-dependent efflux of fluoroquinolone drugs in Serratia marcescens. Thirteen clinical isolates of S. marcescens were screened for resistance to four fluoroquinolones: ofloxacin, ciprofloxacin, norfloxacin and nalidixic acid by determining MICs. The presence of a proton gradient-dependent efflux mechanism was assessed using ethidium bromide accumulation assays. Drug accumulation studies for norfloxacin, ciprofloxacin and ofloxacin were performed to determine the drug specificity of efflux. Western transfer of cellular proteins, followed by immunodetection using anti-AcrA (Escherichia coli) antibodies were used to demonstrate the presence of a resistance-nodulation-cell division (RND) pump protein. PCR was used to identify a RND pump-encoding gene using primers for two conserved motifs within inner membrane components of RND proteins. A mutant strain of S. marcescens, UOC-67WL, was isolated by culturing the wild-type strain in the presence of ciprofloxacin in T-soy media and was subjected to the same studies as described above for the clinical isolates. Ethidium bromide accumulation assays confirmed the presence of a proton gradient-dependent efflux mechanism in S. marcescens. One clinical isolate, T-861, and the mutant strain, UOC-67WL, were found to efflux ciprofloxacin and ofloxacin. Western immunoblot results confirmed overexpression of an AcrA-like protein in T-861 and UOC-67WL. Sequencing of the PCR product showed the presence of a mexF-like gene, which is overexpressed in nfxC mutants of Pseudomonas aeruginosa. This study reports the presence of a proton gradient-dependent efflux mechanism in S. marcescens.

Response of oxidative stress transcripts in the brain of wild yellow perch (Perca flavescens) exposed to an environmental gradient of methylmercury.

PubMed

Graves, Stephanie D; Kidd, Karen A; Batchelar, Katharina L; Cowie, Andrew M; O'Driscoll, Nelson J; Martyniuk, Christopher J

2017-02-01

Methylmercury (MeHg) exposure and adverse health effects in fishes have been documented, but the molecular mechanisms involved in toxicity have not been fully characterized. The objectives of the current study were to (1) determine whether total Hg (THg) in the muscle was predictive of MeHg concentrations in the brain of wild female yellow perch (Perca flavescens) collected from four lakes in Kejimkujik National Park, a known biological mercury (Hg) hotspot in Nova Scotia, Canada and (2) to determine whether transcripts involved in the oxidative stress response were altered in abundance in fish collected across five lakes representing a MeHg gradient. In female yellow perch, MeHg in whole brain (0.38 to 2.00μg/g wet weight) was positively associated with THg in muscle (0.18 to 2.13μg/g wet weight) (R 2 =0.61, p<0.01), suggesting that muscle THg may be useful for predicting MeHg concentrations in the brain. Catalase (cat) mRNA levels were significantly lower in brains of perch collected from lakes with high Hg when compared to those individuals from lakes with relatively lower Hg (p=0.02). Other transcripts (cytochrome c oxidase, glutathione peroxidase, glutathione-s-transferase, heat shock protein 70, protein disulfide isomerase, and superoxide dismutase) did not show differential expression in the brain over the gradient. These findings suggest that MeHg may be inversely associated with catalase mRNA abundance in the central nervous system of wild fishes. Copyright © 2016 Elsevier Inc. All rights reserved.

Cortical networks for encoding near and far space in the non-human primate.

PubMed

Cléry, Justine; Guipponi, Olivier; Odouard, Soline; Wardak, Claire; Ben Hamed, Suliann

2018-08-01

While extra-personal space is often erroneously considered as a unique entity, early neuropsychological studies report a dissociation between near and far space processing both in humans and in monkeys. Here, we use functional MRI in a naturalistic 3D environment to describe the non-human primate near and far space cortical networks. We describe the co-occurrence of two extended functional networks respectively dedicated to near and far space processing. Specifically, far space processing involves occipital, temporal, parietal, posterior cingulate as well as orbitofrontal regions not activated by near space, possibly subserving the processing of the shape and identity of objects. In contrast, near space processing involves temporal, parietal, prefrontal and premotor regions not activated by far space, possibly subserving the preparation of an arm/hand mediated action in this proximal space. Interestingly, this network also involves somatosensory regions, suggesting a cross-modal anticipation of touch by a nearby object. Last, we also describe cortical regions that process both far and near space with a preference for one or the other. This suggests a continuous encoding of relative distance to the body, in the form of a far-to-near gradient. We propose that these cortical gradients in space representation subserve the physically delineable peripersonal spaces described in numerous psychology and psychophysics studies. Copyright © 2018 Elsevier Inc. All rights reserved.

Reproductive allometry in three species of Dusky Salamanders

Treesearch

Richard C. Bruce

2014-01-01

Desmognathus comprises 21 currently recognized species of salamanders in eastern North America. Assemblages of 3–6 species occur in the Appalachian Mountains, wherein the larger species are more aquatic and the smaller more terrestrial. Adaptive divergence along the habitat gradient from stream to forest involves variation in such life-history traits as age and size at...

Teaching Simulation and Computer-Aided Separation Optimization in Liquid Chromatography by Means of Illustrative Microsoft Excel Spreadsheets

ERIC Educational Resources Information Center

Fasoula, S.; Nikitas, P.; Pappa-Louisi, A.

2017-01-01

A series of Microsoft Excel spreadsheets were developed to simulate the process of separation optimization under isocratic and simple gradient conditions. The optimization procedure is performed in a stepwise fashion using simple macros for an automatic application of this approach. The proposed optimization approach involves modeling of the peak…

Revisiting and Re-Representing Scaffolding: The Two Gradient Model

ERIC Educational Resources Information Center

Malik, Shoaib Ahmed

2017-01-01

In this paper I intend to illustrate Vygotsky's Zone of Proximal Development (ZPD) and then extend the discussion to scaffolding and its relationship with the ZPD. This is then followed by some concerns raised in literature regarding scaffolding as a concept and as a metaphor which involves analysing the arguments for regarding the role of…

Developmental Differences for Word Processing in the Ventral Stream

ERIC Educational Resources Information Center

Olulade, Olumide A.; Flowers, D. Lynn; Napoliello, Eileen M.; Eden, Guinevere F.

2013-01-01

The visual word form system (VWFS), located in the occipito-temporal cortex, is involved in orthographic processing of visually presented words (Cohen et al., 2002). Recent fMRI studies in children and adults have demonstrated a gradient of increasing word-selectivity along the posterior-to-anterior axis of this system (Vinckier et al., 2007), yet…

Formation of non-wettable soils...involves heat transfer mechanism

Treesearch

Leonardo F. Debano

1966-01-01

After a wiIdfire, some brushland soils in southern California have been found to include a non-wettable layer. This formation may be the result of hydrophobic material volatilizing and later condensing. In burning experiments, hydrophobic substances from ceanothus litter and non-wettable soil were moved downward into an underlying wettable sand by temperature gradients...

Dispatched mediates Hedgehog basolateral release to form the long-range morphogenetic gradient in the Drosophila wing disk epithelium

PubMed Central

Callejo, Ainhoa; Bilioni, Aphrodite; Mollica, Emanuela; Gorfinkiel, Nicole; Andrés, Germán; Ibáñez, Carmen; Torroja, Carlos; Doglio, Laura; Sierra, Javier; Guerrero, Isabel

2011-01-01

Hedgehog (Hh) moves from the producing cells to regulate the growth and development of distant cells in a variety of tissues. Here, we have investigated the mechanism of Hh release from the producing cells to form a morphogenetic gradient in the Drosophila wing imaginal disk epithelium. We describe that Hh reaches both apical and basolateral plasma membranes, but the apical Hh is subsequently internalized in the producing cells and routed to the basolateral surface, where Hh is released to form a long-range gradient. Functional analysis of the 12-transmembrane protein Dispatched, the glypican Dally-like (Dlp) protein, and the Ig-like and FNNIII domains of protein Interference Hh (Ihog) revealed that Dispatched could be involved in the regulation of vesicular trafficking necessary for basolateral release of Hh, Dlp, and Ihog. We also show that Dlp is needed in Hh-producing cells to allow for Hh release and that Ihog, which has been previously described as an Hh coreceptor, anchors Hh to the basolateral part of the disk epithelium. PMID:21690386

Preferential paths in yield stress fluid flow through a porous medium

NASA Astrophysics Data System (ADS)

Guasto, Jeffrey; Waisbord, Nicolas; Stoop, Norbert; Dunkel, Jörn

2016-11-01

A broad range of biological, geological, and industrial materials with complex rheological properties are subjected to flow through porous media in applications ranging from oil recovery to food manufacturing. In this experimental study, we examine the flow of a model yield stress fluid (Carbopol micro-gel) through a quasi-2D porous medium, fabricated in a microfluidic channel. The flow is driven by applying a precisely-controlled pressure gradient and measured by particle tracking velocimetry, and our observations are complemented by a pore-network model of the yield stress fluid flow. While remaining unyielded at small applied pressure, the micro-gel begins to yield at a critical pressure gradient, exhibiting a single preferential flow path that percolates through the porous medium. As the applied pressure gradient increases, we observe a subsequent coarsening and invasion of the yielded, fluidized network. An examination of both the yielded network topology and pore-scale flow reveal that two cooperative phenomena are involved in sculpting the preferential flow paths: (1) the geometry of the porous microstructure, and (2) the adhesive surface interactions between the micro-gel and substrate. NSF CBET-1511340.

Spatially Correlated Gene Expression in Bacterial Groups: The Role of Lineage History, Spatial Gradients, and Cell-Cell Interactions.

PubMed

van Vliet, Simon; Dal Co, Alma; Winkler, Annina R; Spriewald, Stefanie; Stecher, Bärbel; Ackermann, Martin

2018-04-25

Gene expression levels in clonal bacterial groups have been found to be spatially correlated. These correlations can partly be explained by the shared lineage history of nearby cells, although they could also arise from local cell-cell interactions. Here, we present a quantitative framework that allows us to disentangle the contributions of lineage history, long-range spatial gradients, and local cell-cell interactions to spatial correlations in gene expression. We study pathways involved in toxin production, SOS stress response, and metabolism in Escherichia coli microcolonies and find for all pathways that shared lineage history is the main cause of spatial correlations in gene expression levels. However, long-range spatial gradients and local cell-cell interactions also contributed to spatial correlations in SOS response, amino acid biosynthesis, and overall metabolic activity. Together, our data show that the phenotype of a cell is influenced by its lineage history and population context, raising the question of whether bacteria can arrange their activities in space to perform functions they cannot achieve alone. Copyright © 2018 Elsevier Inc. All rights reserved.

The use of superconductivity in magnetic balance design

NASA Technical Reports Server (NTRS)

Moss, F. E.

1973-01-01

The magnetic field and field gradient requirements for magnetic suspension in a Mach 3, 6-in. diameter wind tunnel are stated, along with the power requirements for gradient coil pairs wound of copper operating at room temperature and aluminum cooled to 20 K. The power dissipated is large enough that the use of superconductivity in the coil design becomes an attractive alternative. The problems of stability and ac losses are outlined along with the properties of stabilized superconductors. A brief review of a simplified version of the critical state model of C. P. Bean is presented, and the problems involved in calculations of the ac losses in superconducting coils are outlined. A summary of ac loss data taken on pancake coils wound of commercially available Nb3Sn partially stabilized tape is presented and shown as leading to the U.Va. gradient coil design. The actual coil performance is compared with predictions based on the BNL results. Finally, some remarks are presented concerning scaling of the ac losses to larger magnetic suspension systems as well as prospects for improved performance using newer multifilament superconductors.

Meropenem/colistin synergy testing for multidrug-resistant Acinetobacter baumannii strains by a two-dimensional gradient technique applicable in routine microbiology.

PubMed

van Belkum, Alex; Halimi, Diane; Bonetti, Eve-Julie; Renzi, Gesuele; Cherkaoui, Abdessalam; Sauvonnet, Véronique; Martelin, Roland; Durand, Géraldine; Chatellier, Sonia; Zambardi, Gilles; Engelhardt, Anette; Karlsson, Åsa; Schrenzel, Jacques

2015-01-01

Precise assessment of potential therapeutic synergy, antagonism or indifference between antimicrobial agents currently depends on time-consuming and hard-to-standardize in vitro chequerboard titration methods. We here present a method based on a novel two-dimensional antibiotic gradient technique named Xact™. We used a test comprising a combination of perpendicular gradients of meropenem and colistin in a single quadrant. We compared test outcomes with those obtained with classical chequerboard microbroth dilution testing in a study involving 27 unique strains of multidrug-resistant Acinetobacter baumannii from diverse origins. We were able to demonstrate 92% concordance between the new technology and classical chequerboard titration using the A. baumannii collection. Two strains could not be analysed by Xact™ due to their out-of-range MIC of meropenem (>128 mg/L). The new test was shown to be diagnostically useful, easy to implement and less labour intensive than the classical method. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Prediction of the chromatographic retention of acid-base compounds in pH buffered methanol-water mobile phases in gradient mode by a simplified model.

PubMed

Andrés, Axel; Rosés, Martí; Bosch, Elisabeth

2015-03-13

Retention of ionizable analytes under gradient elution depends on the pH of the mobile phase, the pKa of the analyte and their evolution along the programmed gradient. In previous work, a model depending on two fitting parameters was recommended because of its very favorable relationship between accuracy and required experimental work. It was developed using acetonitrile as the organic modifier and involves pKa modeling by means of equations that take into account the acidic functional group of the compound (carboxylic acid, protonated amine, etc.). In this work, the two-parameter predicting model is tested and validated using methanol as the organic modifier of the mobile phase and several compounds of higher pharmaceutical relevance and structural complexity as testing analytes. The results have been quite good overall, showing that the predicting model is applicable to a wide variety of acid-base compounds using mobile phases prepared with acetonitrile or methanol. Copyright © 2015 Elsevier B.V. All rights reserved.

The use of the ion probe mass spectrometer in the measurement of hydrogen concentration gradients in Monel K 500

NASA Technical Reports Server (NTRS)

Truhan, J. J., Jr.; Hehemann, R. F.

1974-01-01

The ion probe mass spectrometer was used to measure hydrogen concentration gradients in cathodically charged Monel K 500. Initial work with the ion probe involved the calibration of the instrument and the establishment of a suitable experimental procedure for this application. Samples of Monel K 500 were cathodically charged in a weak sulfuric acid solution. By varying the current density, different levels of hydrogen were introduced into the samples. Hydrogen concentration gradients were taken by ion sputtering on the surface of these samples and monitoring the behavior of the hydrogen mass peak as a function of time. An attempt was made to determine the relative amounts of hydrogen in the bulk and grain boundaries by analyzing a fresh fracture surface with a higher proportion of grain boundary area. It was found that substantially more hydrogen was detected in the grain boundaries than in the bulk, confirming the predictions of previous workers. A sputter rate determination was made in order to establish the rate of erosion.

Representing Matrix Cracks Through Decomposition of the Deformation Gradient Tensor in Continuum Damage Mechanics Methods

NASA Technical Reports Server (NTRS)

Leone, Frank A., Jr.

2015-01-01

A method is presented to represent the large-deformation kinematics of intraply matrix cracks and delaminations in continuum damage mechanics (CDM) constitutive material models. The method involves the additive decomposition of the deformation gradient tensor into 'crack' and 'bulk material' components. The response of the intact bulk material is represented by a reduced deformation gradient tensor, and the opening of an embedded cohesive interface is represented by a normalized cohesive displacement-jump vector. The rotation of the embedded interface is tracked as the material deforms and as the crack opens. The distribution of the total local deformation between the bulk material and the cohesive interface components is determined by minimizing the difference between the cohesive stress and the bulk material stress projected onto the cohesive interface. The improvements to the accuracy of CDM models that incorporate the presented method over existing approaches are demonstrated for a single element subjected to simple shear deformation and for a finite element model of a unidirectional open-hole tension specimen. The material model is implemented as a VUMAT user subroutine for the Abaqus/Explicit finite element software. The presented deformation gradient decomposition method reduces the artificial load transfer across matrix cracks subjected to large shearing deformations, and avoids the spurious secondary failure modes that often occur in analyses based on conventional progressive damage models.

Merging Marine Ecosystem Models and Genomics

NASA Astrophysics Data System (ADS)

Coles, V.; Hood, R. R.; Stukel, M. R.; Moran, M. A.; Paul, J. H.; Satinsky, B.; Zielinski, B.; Yager, P. L.

2015-12-01

oceanography. One of the grand challenges of oceanography is to develop model techniques to more effectively incorporate genomic information. As one approach, we developed an ecosystem model whose community is determined by randomly assigning functional genes to build each organism's "DNA". Microbes are assigned a size that sets their baseline environmental responses using allometric response cuves. These responses are modified by the costs and benefits conferred by each gene in an organism's genome. The microbes are embedded in a general circulation model where environmental conditions shape the emergent population. This model is used to explore whether organisms constructed from randomized combinations of metabolic capability alone can self-organize to create realistic oceanic biogeochemical gradients. Realistic community size spectra and chlorophyll-a concentrations emerge in the model. The model is run repeatedly with randomly-generated microbial communities and each time realistic gradients in community size spectra, chlorophyll-a, and forms of nitrogen develop. This supports the hypothesis that the metabolic potential of a community rather than the realized species composition is the primary factor setting vertical and horizontal environmental gradients. Vertical distributions of nitrogen and transcripts for genes involved in nitrification are broadly consistent with observations. Modeled gene and transcript abundance for nitrogen cycling and processing of land-derived organic material match observations along the extreme gradients in the Amazon River plume, and they help to explain the factors controlling observed variability.

Magnetothermal Convection of Water with the Presence or Absence of a Magnetic Force Acting on the Susceptibility Gradient.

PubMed

Maki, Syou

2016-01-01

Heat transfer of magnetothermal convection with the presence or absence of the magnetic force acting on the susceptibility gradient (fsc) was examined by three-dimensional numerical computations. Thermal convection of water enclosed in a shallow cylindrical vessel (diameter over vessel height = 6.0) with the Rayleigh-Benard model was adopted as the model, under the conditions of Prandtl number 6.0 and Ra number 7000, respectively. The momentum equations of convection were nondimensionalized, which involved the term of fsc and the term of magnetic force acting on the magnetic field gradient (fb). All the computations resulted in axisymmetric steady rolls. The values of the averaged Nu, the averaged velocity components U, V, and W, and the isothermal distributions and flow patterns were almost completely the same, regardless of the presence or absence of the term of fsc. As a result, we found that the effect of fsc was extremely small, although much previous research emphasized the effect with paramagnetic solutions under an unsteady state. The magnitude of fsc depends not only on magnetic conditions (magnitudes of magnetic susceptibility and magnetic flux density), but also on the thermal properties of the solution (thermal conductivity, thermal diffusivity, and viscosity). Therefore the effect of fb becomes dominant on the magnetothermal convection. Active control over the density gradient with temperature will be required to advance heat transfer with the effect of fsc.

Distribution and movement of Caenorhabditis elegans on a thermal gradient.

PubMed

Yamada, Yohko; Ohshima, Yasumi

2003-08-01

To analyze thermal responses of Caenorhabditis elegans in detail, distribution of a worm population and movement of individual worms were examined on a linear, reproducible and broad temperature gradient. Assay methods were improved compared with those reported previously to ensure good motility and dispersion of worms. Well-fed, wild-type worms distributed over a wide temperature range of up to 10 degrees C, and, within this range, worms migrated in both directions of the gradient at similar frequencies without any specific response to the growth temperature in most cases. By contrast, worms migrated down the gradient if put in a region warmer than the warm boundary of distribution. The distribution range changed depending on the growth temperature and starvation, but active avoidance of a starvation temperature was not detected. These findings contradict previous hypotheses of taxis or migration to the growth temperature in association with food and instead indicate avoidance of a warm temperature. Our results favor a model for thermal response of C. elegans that postulates a single drive based on warm sensation rather than downward and upward drives in the physiological temperature range. Mutants in ttx-3, tax-2, tax-4 or egl-4 genes showed abnormal thermal responses, suggesting that these genes are involved in warm avoidance. Laser ablation and gene expression studies suggest that AFD neurons are not important, and tax-4 expression in neurons other than AFD is required, for warm avoidance.

Is Team-Based Primary Care Associated with Less Access Problems and Self-Reported Unmet Need in Canada?

PubMed

Zygmunt, Austin; Asada, Yukiko; Burge, Frederick

2017-10-01

As in many jurisdictions, the delivery of primary care in Canada is being transformed from solo practice to team-based care. In Canada, team-based primary care involves general practitioners working with nurses or other health care providers, and it is expected to improve equity in access to care. This study examined whether team-based care is associated with fewer access problems and less unmet need and whether socioeconomic gradients in access problems and unmet need are smaller in team-based care than in non-team-based care. Data came from the 2008 Canadian Survey of Experiences with Primary Health Care (sample size: 10,858). We measured primary care type as team-based or non-team-based and socioeconomic status by income and education. We created four access problem variables and four unmet need variables (overall and three specific components). For each, we ran separate logistic regression models to examine their associations with primary care type. We examined socioeconomic gradients in access problems and unmet need stratified by primary care type. Primary care type had no statistically significant, independent associations with access problems or unmet need. Among those with non-team-based care, a statistically significant education gradient for overall access problems existed, whereas among those with team-based care, no statistically significant socioeconomic gradients existed.

Joint reconstruction via coupled Bregman iterations with applications to PET-MR imaging

NASA Astrophysics Data System (ADS)

Rasch, Julian; Brinkmann, Eva-Maria; Burger, Martin

2018-01-01

Joint reconstruction has recently attracted a lot of attention, especially in the field of medical multi-modality imaging such as PET-MRI. Most of the developed methods rely on the comparison of image gradients, or more precisely their location, direction and magnitude, to make use of structural similarities between the images. A challenge and still an open issue for most of the methods is to handle images in entirely different scales, i.e. different magnitudes of gradients that cannot be dealt with by a global scaling of the data. We propose the use of generalized Bregman distances and infimal convolutions thereof with regard to the well-known total variation functional. The use of a total variation subgradient respectively the involved vector field rather than an image gradient naturally excludes the magnitudes of gradients, which in particular solves the scaling behavior. Additionally, the presented method features a weighting that allows to control the amount of interaction between channels. We give insights into the general behavior of the method, before we further tailor it to a particular application, namely PET-MRI joint reconstruction. To do so, we compute joint reconstruction results from blurry Poisson data for PET and undersampled Fourier data from MRI and show that we can gain a mutual benefit for both modalities. In particular, the results are superior to the respective separate reconstructions and other joint reconstruction methods.

Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 2: Computer controlled pH gradients in the presence of urea provide improved separation of proteins: Stability influenced anion and cation exchange chromatography.

PubMed

Hirsh, Allen G; Tsonev, Latchezar I

2017-04-28

This paper details the use of a method of creating controlled pH gradients (pISep) to improve the separation of protein isoforms on ion exchange (IEX) stationary phases in the presence of various isocratic levels of urea. The pISep technology enables the development of computer controlled pH gradients on both cationic (CEX) and anionic (AEX) IEX stationary phases over the very wide pH range from 2 to 12. In pISep, titration curves generated by proportional mixing of the acidic and basic pISep working buffers alone, or in the presence of non-buffering solutes such as the neutral salt NaCl (0-1M), polar organics such as urea (0-8M) or acetonitrile (0-80 Vol%), can be fitted with high fidelity using high order polynomials which, in turn allows construction of a mathematical manifold %A (% acidic pISep buffer) vs. pH vs. [non-buffering solute], permitting precise computer control of pH and the non-buffering solute concentration allowing formation of dual uncoupled liquid chromatographic (LC) gradients of arbitrary shape (Hirsh and Tsonev, 2012 [1]). The separation of protein isoforms examined in this paper by use of such pH gradients in the presence of urea demonstrates the fractionation power of a true single step two dimensional liquid chromatography which we denote as Stability-Influenced Ion Exchange Chromatography (SIIEX). We present evidence that SIIEX is capable of increasing the resolution of protein isoforms difficult to separate by ordinary pH gradient IEX, and potentially simplifying the development of laboratory and production purification strategies involving on-column simultaneous pH and urea unfolding or refolding of targeted proteins. We model some of the physics implied by the dynamics of the observed protein fractionations as a function of both urea concentration and pH assuming that urea-induced native state unfolding competes with native state electrostatic interaction binding to an IEX stationary phase. Implications for in vivo protein-membrane interactions are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Elevational Gradients in Fish Diversity in the Himalaya: Water Discharge Is the Key Driver of Distribution Patterns

PubMed Central

Bhatt, Jay P.; Manish, Kumar; Pandit, Maharaj K.

2012-01-01

Background Studying diversity and distribution patterns of species along elevational gradients and understanding drivers behind these patterns is central to macroecology and conservation biology. A number of studies on biogeographic gradients are available for terrestrial ecosystems, but freshwater ecosystems remain largely neglected. In particular, we know very little about the species richness gradients and their drivers in the Himalaya, a global biodiversity hotspot. Methodology/Principal Findings We collated taxonomic and distribution data of fish species from 16 freshwater Himalayan rivers and carried out empirical studies on environmental drivers and fish diversity and distribution in the Teesta river (Eastern Himalaya). We examined patterns of fish species richness along the Himalayan elevational gradients (50–3800 m) and sought to understand the drivers behind the emerging patterns. We used generalized linear models (GLM) and generalized additive models (GAM) to examine the richness patterns; GLM was used to investigate relationship between fish species richness and various environmental variables. Regression modelling involved stepwise procedures, including elimination of collinear variables, best model selection, based on the least Akaike’s information criterion (AIC) and the highest percentage of deviance explained (D2). This maiden study on the Himalayan fishes revealed that total and non-endemic fish species richness monotonously decrease with increasing elevation, while endemics peaked around mid elevations (700–1500 m). The best explanatory model (synthetic model) indicated that water discharge is the best predictor of fish species richness patterns in the Himalayan rivers. Conclusions/Significance This study, carried out along one of the longest bioclimatic elevation gradients of the world, lends support to Rapoport’s elevational rule as opposed to mid domain effect hypothesis. We propose a species-discharge model and contradict species-area model in predicting fish species richness. We suggest that drivers of richness gradients in terrestrial and aquatic ecosystems are likely to be different. These studies are crucial in context of the impacts of unprecedented on-going river regulation on fish diversity and distribution in the Himalaya. PMID:23029444

Multidisciplinary design optimization using genetic algorithms

NASA Technical Reports Server (NTRS)

Unal, Resit

1994-01-01

Multidisciplinary design optimization (MDO) is an important step in the conceptual design and evaluation of launch vehicles since it can have a significant impact on performance and life cycle cost. The objective is to search the system design space to determine values of design variables that optimize the performance characteristic subject to system constraints. Gradient-based optimization routines have been used extensively for aerospace design optimization. However, one limitation of gradient based optimizers is their need for gradient information. Therefore, design problems which include discrete variables can not be studied. Such problems are common in launch vehicle design. For example, the number of engines and material choices must be integer values or assume only a few discrete values. In this study, genetic algorithms are investigated as an approach to MDO problems involving discrete variables and discontinuous domains. Optimization by genetic algorithms (GA) uses a search procedure which is fundamentally different from those gradient based methods. Genetic algorithms seek to find good solutions in an efficient and timely manner rather than finding the best solution. GA are designed to mimic evolutionary selection. A population of candidate designs is evaluated at each iteration, and each individual's probability of reproduction (existence in the next generation) depends on its fitness value (related to the value of the objective function). Progress toward the optimum is achieved by the crossover and mutation operations. GA is attractive since it uses only objective function values in the search process, so gradient calculations are avoided. Hence, GA are able to deal with discrete variables. Studies report success in the use of GA for aircraft design optimization studies, trajectory analysis, space structure design and control systems design. In these studies reliable convergence was achieved, but the number of function evaluations was large compared with efficient gradient methods. Applicaiton of GA is underway for a cost optimization study for a launch-vehicle fuel-tank and structural design of a wing. The strengths and limitations of GA for launch vehicle design optimization is studied.

Reversible mechanosensitive ion pumping as a part of mechanoelectrical transduction.

PubMed Central

Markin, V. S.; Tsong, T. Y.

1991-01-01

To explain the ability of some mechanosensitive cells to reverse the process of mechanotransduction and to generate mechanical oscillations and emit sound, a piezo-conformational coupling model (PCC model) is proposed. The model includes a transport protein which changes either its volume (PV-coupling) or its area in the membrane (gamma A-coupling) when undergoing conformational transitions. Such a protein can interact with an oscillating pressure to pump ions and create a transmembrane gradient if the affinities of the protein for ions are different at the two sides of membrane. The frequency and concentration windows for mechanical energy transduction were determined. Under optimal conditions, the efficiency of energy transduction can approach the theoretical maximum of 100%. If the concentration gradient exceeds the static head value (quasi-equilibrium which can be built up and maintained by this transport system), the energy transduction reverses and the transporter becomes a generator of mechanical oscillations at the expense of a concentration gradient. Estimation of thermodynamic parameters of the pump shows that the PV-coupling model would require large pressure oscillations to work while the gamma A-coupling model could work in physiological conditions. The gamma A-coupling mechanism may be used by cells for two purposes. In the reverse mode, it can be a force generator for various applications. In the direct mode, it may serve bioenergetic purposes by harvesting the energy of mechanical oscillations and storing it in the form of a concentration gradient. This pump has an unusual thermodynamic feature: it can distinguish the two components of the electrochemical potential gradient,i.e., the concentration gradient and the electrical potential, the latter serving as a permissive switch to open, or close, the pump when the potential reaches the threshold value.Predictions of the PCC model and its probable involvement in biological mechanotransduction are dicussed. PMID:1873468

Directed self-assembly of proteins into discrete radial patterns

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Thundat, Thomas

2013-01-01

Unlike physical patterning of materials at nanometer scale, manipulating soft matter such as biomolecules into patterns is still in its infancy. Self-assembled monolayer (SAM) with surface density gradient has the capability to drive biomolecules in specific directions to create hierarchical and discrete structures. Here, we report on a two-step process of self-assembly of the human serum albumin (HSA) protein into discrete ring structures based on density gradient of SAM. The methodology involves first creating a 2-dimensional (2D) polyethylene glycol (PEG) islands with responsive carboxyl functionalities. Incubation of proteins on such pre-patterned surfaces results in direct self-assembly of protein molecules around PEG islands. Immobilization and adsorption of protein on such structures over time evolve into the self-assembled patterns. PMID:23719678

Absorption of the Martian regolith: Specific surface area and missing CO(sub 2)

NASA Technical Reports Server (NTRS)

Zent, A. P.; Fanale, F. P.; Postawko, S. E.

1987-01-01

For most estimates of available regolith and initial degassed CO(sub 2) inventories, it appears that any initial inventory must have been lost to space or incorporated into carbonates. Most estimates of the total available degassed CO(sub 2) inventory are only marginally sufficient to allow for a major early greenhouse effect. It is suggested that the requirements for greenhouse warming to produce old dessicated terrain would be greatly lessened if groundwater brines rather than rainfall were involved and if a higher internal gradient were involved to raise the water (brine) table, leading to more frequent sapping.

NDR proteins

PubMed Central

Jones, Alan M

2010-01-01

N-myc downregulated (NDR) genes were discovered more than fifteen years ago. Indirect evidence support a role in tumor progression and cellular differentiation, but their biochemical function is still unknown. Our detailed analyses on Arabidopsis NDR proteins (deisgnated NDR-like, NDL) show their involvement in altering auxin transport, local auxin gradients and expression level of auxin transport proteins. Animal NDL proteins may be involved in membrane recycling of E-cadherin and effector for the small GTPase. In light of these findings, we hypothesize that NDL proteins regulate vesicular trafficking of auxin transport facilitator PIN proteins by biochemically alterating the local lipid environment of PIN proteins. PMID:20724844

Genes and proteins involved in bacterial magnetic particle formation.

PubMed

Matsunaga, Tadashi; Okamura, Yoshiko

2003-11-01

Magnetic bacteria synthesize intracellular magnetosomes that impart a cellular swimming behaviour referred to as magnetotaxis. The magnetic structures aligned in chains are postulated to function as biological compass needles allowing the bacterium to migrate along redox gradients through the Earth's geomagnetic field lines. Despite the discovery of this unique group of microorganisms 28 years ago, the mechanisms of magnetic crystal biomineralization have yet to be fully elucidated. This review describes the current knowledge of the genes and proteins involved in magnetite formation in magnetic bacteria and the biotechnological applications of biomagnetites in the interdisciplinary fields of nanobiotechnology, medicine and environmental management.

Detergent-Based Isolation of Yeast Membrane Rafts: An Inquiry-Based Laboratory Series for the Undergraduate Cell Biology or Biochemistry Lab

ERIC Educational Resources Information Center

Willhite, D. Grant; Wright, Stephen E.

2009-01-01

Lipid rafts have been implicated in numerous cellular processes including cell signaling, endocytosis, and even viral infection. Isolation of these lipid rafts often involves detergent treatment of the membrane to dissolve nonraft components followed by separation of raft regions in a density gradient. We present here an inquiry-based lab series…

Vacuolar CAX1 and CAX3 influence auxin transport in guard cells via regulation of apoplastic pH

USDA-ARS?s Scientific Manuscript database

Cation exchangers CAX1 and CAX3 are vacuolar ion transporters involved in ion homeostasis in plants. Widely expressed in the plant, they mediate calcium transport from the cytosol to the vacuole lumen using the proton gradient across the tonoplast. Here, we report an unexpected role of CAX1 and CAX3...

Modeling the Hydraulics of Root Growth in Three Dimensions with Phloem Water Sources1[C][OA

PubMed Central

Wiegers, Brandy S.; Cheer, Angela Y.; Silk, Wendy K.

2009-01-01

Primary growth is characterized by cell expansion facilitated by water uptake generating hydrostatic (turgor) pressure to inflate the cell, stretching the rigid cell walls. The multiple source theory of root growth hypothesizes that root growth involves transport of water both from the soil surrounding the growth zone and from the mature tissue higher in the root via phloem and protophloem. Here, protophloem water sources are used as boundary conditions in a classical, three-dimensional model of growth-sustaining water potentials in primary roots. The model predicts small radial gradients in water potential, with a significant longitudinal gradient. The results improve the agreement of theory with empirical studies for water potential in the primary growth zone of roots of maize (Zea mays). A sensitivity analysis quantifies the functional importance of apical phloem differentiation in permitting growth and reveals that the presence of phloem water sources makes the growth-sustaining water relations of the root relatively insensitive to changes in root radius and hydraulic conductivity. Adaptation to drought and other environmental stresses is predicted to involve more apical differentiation of phloem and/or higher phloem delivery rates to the growth zone. PMID:19542299

Effects of Osmolality on Paracellular Transport in MDCK II Cells

PubMed Central

Hirai, Toyohiro; Furuse, Mikio

2016-01-01

Epithelia separate apical and basal compartments, and movement of substances via the paracellular pathway is regulated by tight junctions. Claudins are major constituents of tight junctions and involved in the regulation of tight junction permeability. On the other hand, the osmolality in the extracellular environment fluctuates in association with life activity. However, effects of osmotic changes on the permeaibility of claudins are poorly understood. Therefore, we investigated the effects of osmotic changes on the paracellular transport in MDCK II cells. Interestingly, apical hyposmolality decreased cation selectivity in the paracellular pathway gradually with time, and the elimination of the osmotic gradient promptly restored the cation selectivity. Apical hyposmolality also induced bleb formation at cell-cell contacts and changed the shape of cell-cell contacts from a jagged pattern to a slightly linear pattern. In claudin-2 knockout MDCK II cells, the decrease of cation selectivity, the bleb formation, nor the changes in the shape of cell-cell contacts was observed under the apical hyposmolality. Our findings in this study indicate that osmotic gradient between apical and basal sides is involved in the acute regulation of the cation selective property of claudin-2 channels. PMID:27855213

Links between Osmoregulation and Nitrogen-Excretion in Insects and Crustaceans.

PubMed

Weihrauch, Dirk; O'Donnell, Michael J

2015-11-01

The epithelia involved in ionoregulation and detoxification in crustaceans and insects are quite distinct: the gills, hepatopancreas, and antennal gland serve these functions in crustaceans, whereas the Malpighian tubules, hindgut, and, to some extent, the midgut, are involved in insects. This article compares the means by which the Na(+)/K(+)-ATPase and the vacuolar type H(+)-ATPase are used to energize ionoregulatory processes in both groups. The vacuolar H(+)-ATPase is particularly important as a generator of both H(+) gradients and transmembrane electrical gradients that can be used to energize electroneutral or electrogenic exchange of Na(+) and/or K(+) for H(+). In addition to cation:proton antiporters, epithelia in both groups depend upon the activity of Na(+):K(+):2Cl(-) cotransporters, Cl(-)/[Formula: see text] exchangers, and channels for K(+) and Cl(-) for transepithelial ion transport. This article also contrasts the dominant role of ammonia as the primary nitrogenous waste in crustaceans, with the excretion of ammonia, uric acid, or both in insects. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Nuclear relaxation and critical fluctuations in membranes containing cholesterol

NASA Astrophysics Data System (ADS)

McConnell, Harden

2009-04-01

Nuclear resonance frequencies in bilayer membranes depend on lipid composition. Our calculations describe the combined effects of composition fluctuations and diffusion on nuclear relaxation near a miscibility critical point. Both tracer and gradient diffusion are included. The calculations involve correlation functions and a correlation length ξ =ξ0T/(T -Tc), where T -Tc is temperature above the critical temperature and ξ0 is a parameter of molecular length. Several correlation functions are examined, each of which is related in some degree to the Ising model correlation function. These correlation functions are used in the calculation of transverse deuterium relaxation rates in magic angle spinning and quadrupole echo experiments. The calculations are compared with experiments that report maxima in deuterium and proton nuclear relaxation rates at the critical temperature [Veatch et al., Proc. Nat. Acad. Sci. U.S.A. 104, 17650 (2007)]. One Ising-model-related correlation function yields a maximum 1/T2 relaxation rate at the critical temperature for both magic angle spinning and quadrupole echo experiments. The calculated rates at the critical temperature are close to the experimental rates. The rate maxima involve relatively rapid tracer diffusion in a static composition gradient over distances of up to 10-100 nm.

Modeling the hydraulics of root growth in three dimensions with phloem water sources.

PubMed

Wiegers, Brandy S; Cheer, Angela Y; Silk, Wendy K

2009-08-01

Primary growth is characterized by cell expansion facilitated by water uptake generating hydrostatic (turgor) pressure to inflate the cell, stretching the rigid cell walls. The multiple source theory of root growth hypothesizes that root growth involves transport of water both from the soil surrounding the growth zone and from the mature tissue higher in the root via phloem and protophloem. Here, protophloem water sources are used as boundary conditions in a classical, three-dimensional model of growth-sustaining water potentials in primary roots. The model predicts small radial gradients in water potential, with a significant longitudinal gradient. The results improve the agreement of theory with empirical studies for water potential in the primary growth zone of roots of maize (Zea mays). A sensitivity analysis quantifies the functional importance of apical phloem differentiation in permitting growth and reveals that the presence of phloem water sources makes the growth-sustaining water relations of the root relatively insensitive to changes in root radius and hydraulic conductivity. Adaptation to drought and other environmental stresses is predicted to involve more apical differentiation of phloem and/or higher phloem delivery rates to the growth zone.

A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

PubMed

Jain, Dharm Skandh; Gupte, Sanket Rajan; Aduri, Raviprasad

2018-06-22

RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA. Here, we present a data-driven model for RPI prediction using a gradient boosting classifier. Amino acids and nucleotides are classified based on the high-resolution structural data of RNA protein complexes. The minimum structural unit consisting of five residues is used as the descriptor. Comparative analysis of existing methods shows the consistently higher performance of our method irrespective of the length of RNA present in the RPI. The method has been successfully applied to map RPI networks involving both long noncoding RNA as well as TERRA RNA. The method is also shown to successfully predict RNA and protein hubs present in RPI networks of four different organisms. The robustness of this method will provide a way for predicting RPI networks of yet unknown interactions for both long noncoding RNA and microRNA.

Generic equilibration dynamics of planar defects in trapped atomic superfluids

DOE PAGES

Scherpelz, Peter; Padavić, Karmela; Murray, Andy; ...

2015-03-18

Here, we investigate equilibration processes shortly after sudden perturbations are applied to ultracold trapped superfluids. We show the similarity of phase imprinting and localized density depletion perturbations, both of which initially are found to produce “phase walls”. These planar defects are associated with a sharp gradient in the phase. Importantly they relax following a quite general sequence. Our studies, based on simulations of the complex time-dependent Ginzburg-Landau equation, address the challenge posed by these experiments: how a superfluid eventually eliminatesa spatially extended planar defect. The processes involved are necessarily more complex than equilibration involving simpler line vortices. An essential mechanismmore » form relaxation involves repeated formation and loss of vortex rings near the trap edge.« less

Unsteady, one-dimensional gas dynamics computations using a TVD type sequential solver

NASA Technical Reports Server (NTRS)

Thakur, Siddharth; Shyy, Wei

1992-01-01

The efficacy of high resolution convection schemes to resolve sharp gradient in unsteady, 1D flows is examined using the TVD concept based on a sequential solution algorithm. Two unsteady flow problems are considered which include the problem involving the interaction of the various waves in a shock tube with closed reflecting ends and the problem involving the unsteady gas dynamics in a tube with closed ends subject to an initial pressure perturbation. It is concluded that high accuracy convection schemes in a sequential solution framework are capable of resolving discontinuities in unsteady flows involving complex gas dynamics. However, a sufficient amount of dissipation is required to suppress oscillations near discontinuities in the sequential approach, which leads to smearing of the solution profiles.

Diffusion of lactate and ammonium in relation to growth of Geotrichum candidum at the surface of solid media.

PubMed

Aldarf, M; Fourcade, F; Amrane, A; Prigent, Y

2004-07-05

Geotrichum candidum was cultivated at the surface of solid model media containing peptone to simulate the composition of Camembert cheese. The surface growth of G. candidum induced the diffusion of substrates from the core to the rind and the diffusion of produced metabolites from the rind to the core. In the range of pH measured during G. candidum growth, constant diffusion coefficients were found for lactate and ammonium, 0.4 and 0.8 cm(2) day(-1), respectively, determined in sterile culture medium. Growth kinetics are described using the Verlhust model and both lactate consumption and ammonium production are considered as partially linked to growth. The experimental diffusion gradients of lactate and ammonium recorded during G. candidum growth have been fitted. The diffusion/reaction model was found to match with experimental data until the end of growth, except with regard to ammonium concentration gradients in the presence of lactate in the medium. Indeed, G. candidum preferentially assimilated peptone over lactate as a carbon source, resulting in an almost cessation of ammonium release before the end of growth. On peptone, it was found that the proton transfer did not account for the ammonium concentration gradients. Indeed, amino acids, being positively charged, are involved in the proton transfer at the beginning of growth. This effect can be neglected in the presence of lactate within the medium, and the sum of both lactate consumption and ammonium release gradients corresponded well to the proton transfer gradients, confirming that both components are responsible for the pH increase observed during the ripening of soft Camembert cheese. Copyright 2004 Wiley Periodicals, Inc.

A bioenergetic basis for membrane divergence in archaea and bacteria.

PubMed

Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

2014-08-01

Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

Murine intracochlear drug delivery: reducing concentration gradients within the cochlea.

PubMed

Borkholder, David A; Zhu, Xiaoxia; Hyatt, Brad T; Archilla, Alfredo S; Livingston, William J; Frisina, Robert D

2010-09-01

Direct delivery of compounds to the mammalian inner ear is most commonly achieved by absorption or direct injection through the round window membrane (RWM), or infusion through a basal turn cochleostomy. These methods provide direct access to cochlear structures, but with a strong basal-to-apical concentration gradient consistent with a diffusion-driven distribution. This gradient limits the efficacy of therapeutic approaches for apical structures, and puts constraints on practical therapeutic dose ranges. A surgical approach involving both a basal turn cochleostomy and a posterior semicircular canal canalostomy provides opportunities for facilitated perfusion of cochlear structures to reduce concentration gradients. Infusion of fixed volumes of artificial perilymph (AP) and sodium salicylate were used to evaluate two surgical approaches in the mouse: cochleostomy-only (CO), or cochleostomy-plus-canalostomy (C+C). Cochlear function was evaluated via closed-system distortion product otoacoustic emissions (DPOAE) threshold level measurements from 8 to 49 kHz. AP infusion confirmed no surgical impact to auditory function, while shifts in DPOAE thresholds were measured during infusion of salicylate and AP (washout). Frequency dependent shifts were compared for the CO and C+C approaches. Computer simulations modeling diffusion, volume flow, interscala transport, and clearance mechanisms provided estimates of drug concentration as a function of cochlear position. Simulated concentration profiles were compared to frequency-dependent shifts in measured auditory responses using a cochlear tonotopic map. The impact of flow rate on frequency dependent DPOAE threshold shifts was also evaluated for both surgical approaches. Both the C+C approach and a flow rate increase were found to provide enhanced response for lower frequencies, with evidence suggesting the C+C approach reduces concentration gradients within the cochlea. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Murine Intracochlear Drug Delivery: Reducing Concentration Gradients within the Cochlea

PubMed Central

Borkholder, David A.; Zhu, Xiaoxia; Hyatt, Brad T.; Archilla, Alfredo S.; Livingston, William J.; Frisina, Robert D.

2010-01-01

Direct delivery of compounds to the mammalian inner ear is most commonly achieved by absorption or direct injection through the round window membrane (RWM), or infusion through a basal turn cochleostomy. These methods provide direct access to cochlear structures, but with a strong basal-to-apical concentration gradient consistent with a diffusion-driven distribution. This gradient limits the efficacy of therapeutic approaches for apical structures, and puts constraints on practical therapeutic dose ranges. A surgical approach involving both a basal turn cochleostomy and a posterior semicircular canal canalostomy provides opportunities for facilitated perfusion of cochlear structures to reduce concentration gradients. Infusion of fixed volumes of artificial perilymph (AP) and sodium salicylate were used to evaluate two surgical approaches in the mouse: cochleostomy-only (CO), or cochleostomy-plus-canalostomy (C+C). Cochlear function was evaluated via closed-system distortion product otoacoustic emissions (DPOAE) threshold level measurements from 8-49 kHz. AP infusion confirmed no surgical impact to auditory function, while shifts in DPOAE thresholds were measured during infusion of salicylate and AP (washout). Frequency dependent shifts were compared for the CO and C+C approaches. Computer simulations modeling diffusion, volume flow, interscala transport, and clearance mechanisms provided estimates of drug concentration as a function of cochlear position. Simulated concentration profiles were compared to frequency-dependent shifts in measured auditory responses using a cochlear tonotopic map. The impact of flow rate on frequency dependent DPOAE threshold shifts was also evaluated for both surgical approaches. Both the C+C approach and a flow rate increase were found to provide enhanced response for lower frequencies, with evidence suggesting the C+C approach reduces concentration gradients within the cochlea. PMID:20451593

Extracellular signal-regulated kinase activation and endothelin-1 production in human endothelial cells exposed to vibration

PubMed Central

White, Charles R; Haidekker, Mark A; Stevens, Hazel Y; Frangos, John A

2004-01-01

Hand–arm vibration syndrome is a vascular disease of occupational origin and a form of secondary Raynaud's phenomenon. Chronic exposure to hand-held vibrating tools may cause endothelial injury. This study investigates the biomechanical forces involved in the transduction of fluid vibration in the endothelium. Human endothelial cells were exposed to direct vibration and rapid low-volume fluid oscillation. Rapid low-volume fluid oscillation was used to simulate the effects of vibration by generating defined temporal gradients in fluid shear stress across an endothelial monolayer. Extracellular signal-regulated kinase (ERK1/2) phosphorylation and endothelin-1 (ET-1) release were monitored as specific biochemical markers for temporal gradients and endothelial response, respectively. Both vibrational methods were found to phosphorylate ERK1/2 in a similar pattern. At a fixed frequency of fluid oscillation where the duration of each pulse cycle remained constant, ERK1/2 phosphorylation increased with the increasing magnitude of the applied temporal gradient. However, when the frequency of flow oscillation was increased (thus decreasing the duration of each pulse cycle), ERK1/2 phosphorylation was attenuated across all temporal gradient flow profiles. Fluid oscillation significantly stimulated ET-1 release compared to steady flow, and endothelin-1 was also attenuated with the increase in oscillation frequency. Taken together, these results show that both the absolute magnitude of the temporal gradient and the frequency/duration of each pulse cycle play a role in the biomechanical transduction of fluid vibrational forces in endothelial cells. Furthermore, this study reports for the first time a link between the ERK1/2 signal transduction pathway and transmission of vibrational forces in the endothelium. PMID:14724194

A PDE Sensitivity Equation Method for Optimal Aerodynamic Design

NASA Technical Reports Server (NTRS)

Borggaard, Jeff; Burns, John

1996-01-01

The use of gradient based optimization algorithms in inverse design is well established as a practical approach to aerodynamic design. A typical procedure uses a simulation scheme to evaluate the objective function (from the approximate states) and its gradient, then passes this information to an optimization algorithm. Once the simulation scheme (CFD flow solver) has been selected and used to provide approximate function evaluations, there are several possible approaches to the problem of computing gradients. One popular method is to differentiate the simulation scheme and compute design sensitivities that are then used to obtain gradients. Although this black-box approach has many advantages in shape optimization problems, one must compute mesh sensitivities in order to compute the design sensitivity. In this paper, we present an alternative approach using the PDE sensitivity equation to develop algorithms for computing gradients. This approach has the advantage that mesh sensitivities need not be computed. Moreover, when it is possible to use the CFD scheme for both the forward problem and the sensitivity equation, then there are computational advantages. An apparent disadvantage of this approach is that it does not always produce consistent derivatives. However, for a proper combination of discretization schemes, one can show asymptotic consistency under mesh refinement, which is often sufficient to guarantee convergence of the optimal design algorithm. In particular, we show that when asymptotically consistent schemes are combined with a trust-region optimization algorithm, the resulting optimal design method converges. We denote this approach as the sensitivity equation method. The sensitivity equation method is presented, convergence results are given and the approach is illustrated on two optimal design problems involving shocks.

Shadowgraph Study of Gradient Driven Fluctuations

NASA Technical Reports Server (NTRS)

Cannell, David; Nikolaenko, Gennady; Giglio, Marzio; Vailati, Alberto; Croccolo, Fabrizio; Meyer, William

2002-01-01

A fluid or fluid mixture, subjected to a vertical temperature and/or concentration gradient in a gravitational field, exhibits greatly enhanced light scattering at small angles. This effect is caused by coupling between the vertical velocity fluctuations due to thermal energy and the vertically varying refractive index. Physically, small upward or downward moving regions will be displaced into fluid having a refractive index different from that of the moving region, thus giving rise to the enhanced scattering. The scattered intensity is predicted to vary with scattering wave vector q, as q(sup -4), for sufficiently large q, but the divergence is quenched by gravity at small q. In the absence of gravity, the long wavelength fluctuations responsible for the enhanced scattering are predicted to grow until limited by the sample dimensions. It is thus of interest to measure the mean-squared amplitude of such fluctuations in the microgravity environment for comparison with existing theory and ground based measurements. The relevant wave vectors are extremely small, making traditional low-angle light scattering difficult or impossible because of stray elastically scattered light generated by optical surfaces. An alternative technique is offered by the shadowgraph method, which is normally used to visualize fluid flows, but which can also serve as a quantitative tool to measure fluctuations. A somewhat novel shadowgraph apparatus and the necessary data analysis methods will be described. The apparatus uses a spatially coherent, but temporally incoherent, light source consisting of a super-luminescent diode coupled to a single-mode optical fiber in order to achieve extremely high spatial resolution, while avoiding effects caused by interference of light reflected from the various optical surfaces that are present when using laser sources. Results obtained for a critical mixture of aniline and cyclohexane subjected to a vertical temperature gradient will be presented. The sample was confined between two horizontal parallel sapphire plates with a vertical spacing of 1 mm. The temperatures of the sapphire plates were controlled by independent circulating water loops that used Peltier devices to add or remove heat from the room air as required. For a mixture with a temperature gradient, two effects are involved in generating the vertical refractive index gradient, namely thermal expansion and the Soret effect, which generates a concentration gradient in response to the applied temperature gradient. For the aniline/cyclohexane system, the denser component (aniline) migrates toward the colder surface. Consequently, when heating from above, both effects result in the sample density decreasing with altitude and are stabilizing in the sense that no convective motion occurs regardless of the magnitude of the applied temperature gradient. The Soret effect is strong near a binary liquid critical point, and thus the dominant effect is due to the induced concentration gradient. The results clearly show the divergence at low q and the predicted gravitational quenching. Results obtained for different applied temperature gradients at varying temperature differences from the critical temperature, clearly demonstrate the predicted divergence of the thermal diffusion ratio. Thus, the more closely the critical point is approached, the smaller becomes the temperature gradient required to generate the same signal. Two different methods have been used to generate pure concentration gradients. In the first, a sample cell was filled with a single fluid, ethylene glycol, and a denser miscible fluid, water, was added from below thus establishing a sharp interface to begin the experiment. As time went on the two fluids diffused into each other, and large amplitude fluctuations were clearly observed at low q. The effects of gravitational quenching were also evident. In the second method, the aniline/cyclohexane sample was used, and after applying a vertical temperature gradient for several hours, the top and bottom temperatures were set equal and the thermal gradient died on a time scale of seconds, leaving the Soret induced concentration gradient in place. Again, large-scale fluctuations were observed and died away slowly in amplitude as diffusion destroyed the initial concentration gradient.

DsbA Plays a Critical and Multifaceted Role in the Production of Secreted Virulence Factors by the Phytopathogen Erwinia carotovora subsp. atroseptica*S⃞

PubMed Central

Coulthurst, Sarah J.; Lilley, Kathryn S.; Hedley, Peter E.; Liu, Hui; Toth, Ian K.; Salmond, George P. C.

2008-01-01

Erwinia carotovora subsp. atroseptica is an enterobacterial phytopathogen causing economically significant soft rot disease. Pathogenesis is mediated by multiple secreted virulence factors, many of which are secreted by the type II (Out) secretion system. DsbA catalyzes the introduction of disulfide bonds into periplasmic and secreted proteins. In this study, the extracellular proteome (secretome) of wild type E. carotovora subsp. atroseptica SCRI1043, and dsbA and out mutants, was analyzed by spectral counting mass spectrometry. This revealed that dsbA inactivation had a huge impact on the secretome and identified diverse DsbA- and Out-dependent secreted proteins, representing known, predicted, and novel candidate virulence factors. Further characterization of the dsbA mutant showed that secreted enzyme activities, motility, production of the quorumsensing signal, and virulence were absent or substantially reduced. The impact of DsbA on secreted virulence factor production was mediated at multiple levels, including impacting on the Out secretion system and the virulence gene regulatory network. Transcriptome analyses revealed that the abundance of a broad, but defined, set of transcripts, including many virulence factors, was altered in the dsbA mutant, identifying a new virulence regulon responsive to extracytoplasmic conditions. In conclusion, DsbA plays a crucial, multifaceted role in the pathogenesis of E. carotovora subsp. atroseptica. PMID:18562317

In depth analysis of the mechanism of action of metal-dependent sigma factors: characterization of CorE2 from Myxococcus xanthus

PubMed Central

Marcos-Torres, Francisco Javier; Pérez, Juana; Gómez-Santos, Nuria; Moraleda-Muñoz, Aurelio; Muñoz-Dorado, José

2016-01-01

Extracytoplasmic function sigma factors represent the third pillar of signal-transduction mechanisms in bacteria. The variety of stimuli they recognize and mechanisms of action they use have allowed their classification into more than 50 groups. We have characterized CorE2 from Myxococcus xanthus, which belongs to group ECF44 and upregulates the expression of two genes when it is activated by cadmium and zinc. Sigma factors of this group contain a Cys-rich domain (CRD) at the C terminus which is essential for detecting metals. Point mutations at the six Cys residues of the CRD have revealed the contribution of each residue to CorE2 activity. Some of them are essential, while others are either dispensable or their mutations only slightly affect the activity of the protein. However, importantly, mutation of Cys174 completely shifts the specificity of CorE2 from cadmium to copper, indicating that the Cys arrangement of the CRD determines the metal specificity. Moreover, the conserved CxC motif located between the σ2 domain and the σ4.2 region has also been found to be essential for activity. The results presented here contribute to our understanding of the mechanism of action of metal-dependent sigma factors and help to define new common features of the members of this group of regulators. PMID:26951374

Subcellular localization, interactions and dynamics of the phage-shock protein-like Lia response in Bacillus subtilis.

PubMed

Domínguez-Escobar, Julia; Wolf, Diana; Fritz, Georg; Höfler, Carolin; Wedlich-Söldner, Roland; Mascher, Thorsten

2014-05-01

The liaIH operon of Bacillus subtilis is the main target of the envelope stress-inducible two-component system LiaRS. Here, we studied the localization, interaction and cellular dynamics of Lia proteins to gain insights into the physiological role of the Lia response. We demonstrate that LiaI serves as the membrane anchor for the phage-shock protein A homologue LiaH. Under non-inducing conditions, LiaI locates in highly motile membrane-associated foci, while LiaH is dispersed throughout the cytoplasm. Under stress conditions, both proteins are strongly induced and colocalize in numerous distinct static spots at the cytoplasmic membrane. This behaviour is independent of MreB and does also not correlate with the stalling of the cell wall biosynthesis machinery upon antibiotic inhibition. It can be induced by antibiotics that interfere with the membrane-anchored steps of cell wall biosynthesis, while compounds that inhibit the cytoplasmic or extracytoplasmic steps do not trigger this response. Taken together, our data are consistent with a model in which the Lia system scans the cytoplasmic membrane for envelope perturbations. Upon their detection, LiaS activates the cognate response regulator LiaR, which in turn strongly induces the liaIH operon. Simultaneously, LiaI recruits LiaH to the membrane, presumably to protect the envelope and counteract the antibiotic-induced damage. © 2014 John Wiley & Sons Ltd.

Functional Characterization of Corynebacterium glutamicum Mycothiol S-Conjugate Amidase

PubMed Central

Si, Meiru; Long, Mingxiu; Chaudhry, Muhammad Tausif; Xu, Yixiang; Zhang, Pan; Zhang, Lei; Shen, Xihui

2014-01-01

The present study focuses on the genetic and biochemical characterization of mycothiol S-conjugate amidase (Mca) of Corynebacterium glutamicum. Recombinant C. glutamicum Mca was heterologously expressed in Escherichia coli and purified to apparent homogeneity. The molecular weight of native Mca protein determined by gel filtration chromatography was 35 kDa, indicating that Mca exists as monomers in the purification condition. Mca showed amidase activity with mycothiol S-conjugate of monobromobimane (MSmB) in vivo while mca mutant lost the ability to cleave MSmB. In addition, Mca showed limited deacetylase activity with N-acetyl-D-glucosamine (GlcNAc) as substrate. Optimum pH for amidase activity was between 7.5 and 8.5, while the highest activity in the presence of Zn2+ confirmed Mca as a zinc metalloprotein. Amino acid residues conserved among Mca family members were located in C. glutamicum Mca and site-directed mutagenesis of these residues indicated that Asp14, Tyr137, His139 and Asp141 were important for activity. The mca deletion mutant showed decreased resistance to antibiotics, alkylating agents, oxidants and heavy metals, and these sensitive phenotypes were recovered in the complementary strain to a great extent. The physiological roles of Mca in resistance to various toxins were further supported by the induced expression of Mca in C. glutamicum under various stress conditions, directly under the control of the stress-responsive extracytoplasmic function-sigma (ECF-σ) factor SigH. PMID:25514023

Transpeptidase activity of penicillin-binding protein SpoVD in peptidoglycan synthesis conditionally depends on the disulfide reductase StoA.

PubMed

Bukowska-Faniband, Ewa; Hederstedt, Lars

2017-07-01

Endospore cortex peptidoglycan synthesis is not required for bacterial growth but essential for endospore heat resistance. It therefore constitutes an amenable system for research on peptidoglycan biogenesis. The Bacillus subtilis sporulation-specific class B penicillin-binding protein (PBP) SpoVD and many homologous PBPs contain two conserved cysteine residues of unknown function in the transpeptidase domain - one as residue x in the SxN catalytic site motif and the other in a flexible loop near the catalytic site. A disulfide bond between these residues blocks the function of SpoVD in cortex synthesis. With a combination of experiments with purified proteins and B. subtilis mutant cells, it was shown that in active SpoVD the two cysteine residues most probably interact by hydrogen bonding and that this is important for peptidoglycan synthesis in vivo. It was furthermore demonstrated that the sporulation-specific thiol-disulfide oxidoreductase StoA reduces SpoVD and that requirement of StoA for cortex synthesis can be suppressed by two completely different types of structural alterations in SpoVD. It is concluded that StoA plays a critical role mainly during maturation of SpoVD in the forespore outer membrane. The findings advance our understanding of essential PBPs and redox control of extra-cytoplasmic protein disulfides in bacterial cells. © 2017 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

Geometric effects on bilayer convection in cylindrical containers

NASA Astrophysics Data System (ADS)

Johnson, Duane Thomas

The study of convection in two immiscible fluid layers is of interest for reasons both theoretical as well as applied. Recently, bilayer convection has been used as a model of convection in the earth's mantle. It is also an interesting system to use in the study of pattern formation. Bilayer convection also occurs in a process known as liquid encapsulated crystal growth, which is used to grow compound semiconductors. It is the last application which motivates this study. To analyze bilayer convection, theoretical models, numerical calculations and experiments were used. One theoretical model involves the derivation of the Navier- Stokes and energy equation for two immiscible fluid layers, using the Boussinesq approximation. A weakly nonlinear analysis was also performed to study the behavior of the system slightly beyond the onset of convection. Numerical calculations were necessary to solve both models. The experiments involved a single liquid layer of silicone oil, superposed by a layer of air. The radius and height of each fluid layer were changed to observe different flow patterns at the onset of convection. From the experiments and theory, two major discoveries were made as well as several interesting observations. The first discovery is the existence of codimension-two points-particular aspect ratios where two flow patterns coexist-in cylindrical containers. At these points, dynamic switching between different flow patterns was observed. The second discovery was the effect of air convection on the flow pattern in silicone oil. Historically, air has been considered a passive medium that has no effect on the lower fluid. However, experiments were done to show that for large air heights, convection in the air can cause radial temperature gradients at the liquid interface. These temperature gradients then cause surface tension gradient-driven flows. It was also shown that changing the radius of the container can change the driving force of convection from a surface tension gradient-driven to buoyancy-driven and back again. Finally, the weakly nonlinear analysis was able to give a qualitative description of codimension-two points as well as the change in flow patterns due to the convecting air layer.

Brain Na+, K+-ATPase Activity In Aging and Disease

PubMed Central

de Lores Arnaiz, Georgina Rodríguez; Ordieres, María Graciela López

2014-01-01

Na+/K+ pump or sodium- and potassium-activated adenosine 5’-triphosphatase (Na+, K+-ATPase), its enzymatic version, is a crucial protein responsible for the electrochemical gradient across the cell membranes. It is an ion transporter, which in addition to exchange cations, is the ligand for cardenolides. This enzyme regulates the entry of K+ with the exit of Na+ from cells, being the responsible for Na+/K+ equilibrium maintenance through neuronal membranes. This transport system couples the hydrolysis of one molecule of ATP to exchange three sodium ions for two potassium ions, thus maintaining the normal gradient of these cations in animal cells. Oxidative metabolism is very active in brain, where large amounts of chemical energy as ATP molecules are consumed, mostly required for the maintenance of the ionic gradients that underlie resting and action potentials which are involved in nerve impulse propagation, neurotransmitter release and cation homeostasis. Protein phosphorylation is a key process in biological regulation. At nervous system level, protein phosphorylation is the major molecular mechanism through which the function of neural proteins is modulted in response to extracellular signals, including the response to neurotransmitter stimuli. It is the major mechanism of neural plasticity, including memory processing. The phosphorylation of Na+, K+-ATPase catalytic subunit inhibits enzyme activity whereas the inhibition of protein kinase C restores the enzyme activity. The dephosphorylation of neuronal Na+, K+-ATPase is mediated by calcineurin, a serine / threonine phosphatase. The latter enzyme is involved in a wide range of cellular responses to Ca2+ mobilizing signals, in the regulation of neuronal excitability by controlling the activity of ion channels, in the release of neurotransmitters and hormones, as well as in synaptic plasticity and gene transcription. In the present article evidence showing Na+, K+-ATPase involvement in signaling pathways, enzyme changes in diverse neurological diseases as well as during aging, have been summarized. Issues refer mainly to Na+, K+-ATPase studies in ischemia, brain injury, depression and mood disorders, mania, stress, Alzheimer´s disease, learning and memory, and neuronal hyperexcitability and epilepsy. PMID:25018677

Selection Gradients, the Opportunity for Selection, and the Coefficient of Determination

PubMed Central

Moorad, Jacob A.; Wade, Michael J.

2013-01-01

We derive the relationship between R2 (the coefficient of determination), selection gradients, and the opportunity for selection for univariate and multivariate cases. Our main result is to show that the portion of the opportunity for selection that is caused by variation for any trait is equal to the product of its selection gradient and its selection differential. This relationship is a corollary of the first and second fundamental theorems of natural selection, and it permits one to investigate the portions of the total opportunity for selection that are involved in directional selection, stabilizing (and diversifying) selection, and correlational selection, which is important to morphological integration. It also allows one to determine the fraction of fitness variation not explained by variation in measured phenotypes and therefore attributable to random (or, at least, unknown) influences. We apply our methods to a human data set to show how sex-specific mating success as a component of fitness variance can be decoupled from that owing to prereproductive mortality. By quantifying linear sources of sexual selection and quadratic sources of sexual selection, we illustrate that the former is stronger in males, while the latter is stronger in females. PMID:23448880

Cleaning by Surfactant Gradients: Particulate Removal from Porous Materials and the Significance of Rinsing in Laundry Detergency

NASA Astrophysics Data System (ADS)

Shin, Sangwoo; Warren, Patrick B.; Stone, Howard A.

2018-03-01

Removing particles from fibrous materials involves loosening via surfactants followed by particle transfer in a flow. While flow advection is commonly believed to be the major driver for pore-scale transport, small pores within the fabric do not allow any significant fluid flow inside them, thus significantly reducing the role of advection. However, rinsing the fabric with fresh water naturally establishes a surfactant gradient within the pore space, providing a suitable environment for particles to undergo diffusiophoresis. We demonstrate that this mechanism can remove particles from deep within fabric pores at an accelerated rate. The nonlinear aspect of diffusiophoresis significantly prolongs the lifetime of the phoretic motion beyond the naive solute diffusion time scale during rinsing, allowing long-lasting, continuous removal of particles. Moreover, owing to the fine balance between chemiphoresis and electrophoresis for particles in anionic surfactant concentration gradients, we show that the particle removal is sensitive to the counterion mobility, suggesting a simple route to control the effect. We thus claim to have resolved the "stagnant core problem"—a long-standing mystery in laundry detergency—and have identified a physicochemical approach to particle transport in fibrous media with broad applicability.

Cyclic Failure Mechanisms of Thermal and Environmental Barrier Coating Systems Under Thermal Gradient Test Conditions

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Lee, Kang N.; Miller, Robert A.

2002-01-01

Plasma-sprayed ZrO2-8wt%Y2O3 and mullite+BSAS/Si multilayer thermal and environmental barrier coating (TBC-EBC) systems on SiC/SiC ceramic matrix composite (CMC) substrates were thermally cyclic tested under high thermal gradients using a laser high-heat-flux rig in conjunction with furnace exposure in water-vapor environments. Coating sintering and interface damage were assessed by monitoring the real-time thermal conductivity changes during the laser heat-flux tests and by examining the microstructural changes after exposure. Sintering kinetics of the coating systems were also independently characterized using a dilatometer. It was found that the coating failure involved both the time-temperature dependent sintering and the cycle frequency dependent cyclic fatigue processes. The water vapor environments not only facilitated the initial coating conductivity increases due to enhanced sintering and interface reaction, but also promoted later conductivity reductions due to the accelerated coating cracking and delamination. The failure mechanisms of the coating systems are also discussed based on the cyclic test results and are correlated to the sintering and thermal stress behavior under the thermal gradient test conditions.

Multi-Mode Cavity Accelerator Structure

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

Jiang, Yong; Hirshfield, Jay Leonard

2016-11-10

This project aimed to develop a prototype for a novel accelerator structure comprising coupled cavities that are tuned to support modes with harmonically-related eigenfrequencies, with the goal of reaching an acceleration gradient >200 MeV/m and a breakdown rate <10 -7/pulse/meter. Phase I involved computations, design, and preliminary engineering of a prototype multi-harmonic cavity accelerator structure; plus tests of a bimodal cavity. A computational procedure was used to design an optimized profile for a bimodal cavity with high shunt impedance and low surface fields to maximize the reduction in temperature rise ΔT. This cavity supports the TM010 mode and its 2ndmore » harmonic TM011 mode. Its fundamental frequency is at 12 GHz, to benchmark against the empirical criteria proposed within the worldwide High Gradient collaboration for X-band copper structures; namely, a surface electric field E sur max< 260 MV/m and pulsed surface heating ΔT max< 56 °K. With optimized geometry, amplitude and relative phase of the two modes, reductions are found in surface pulsed heating, modified Poynting vector, and total RF power—as compared with operation at the same acceleration gradient using only the fundamental mode.« less

Selection gradients, the opportunity for selection, and the coefficient of determination.

PubMed

Moorad, Jacob A; Wade, Michael J

2013-03-01

Abstract We derive the relationship between R(2) (the coefficient of determination), selection gradients, and the opportunity for selection for univariate and multivariate cases. Our main result is to show that the portion of the opportunity for selection that is caused by variation for any trait is equal to the product of its selection gradient and its selection differential. This relationship is a corollary of the first and second fundamental theorems of natural selection, and it permits one to investigate the portions of the total opportunity for selection that are involved in directional selection, stabilizing (and diversifying) selection, and correlational selection, which is important to morphological integration. It also allows one to determine the fraction of fitness variation not explained by variation in measured phenotypes and therefore attributable to random (or, at least, unknown) influences. We apply our methods to a human data set to show how sex-specific mating success as a component of fitness variance can be decoupled from that owing to prereproductive mortality. By quantifying linear sources of sexual selection and quadratic sources of sexual selection, we illustrate that the former is stronger in males, while the latter is stronger in females.

Design optimization using adjoint of Long-time LES for the trailing edge of a transonic turbine vane

NASA Astrophysics Data System (ADS)

Talnikar, Chaitanya; Wang, Qiqi

2017-11-01

Adjoint-based design optimization methods have been applied to low-fidelity simulation methods like Reynolds Averaged Navier-Stokes (RANS) and are useful for designing fluid machinery components. But to reliably capture the complex flow phenomena involved in turbomachinery, high fidelity simulations like large eddy simulation (LES) are required. Unfortunately due to the chaotic dynamics of turbulence, the unsteady adjoint method for LES diverges and produces incorrect gradients. Using a viscosity stabilized unsteady adjoint method developed for LES, the gradient can be obtained with reasonable accuracy. In this paper, design of the trailing edge of a gas turbine inlet guide vane is performed with the objective to reduce stagnation pressure loss and heat transfer over the surface of the vane. Slight changes in the shape of trailing edge can significantly impact these quantities by altering the boundary layer development process and separation points. The trailing edge is parameterized using a linear combination of 5 convex designs. Bayesian optimization is used as a global optimizer with the objective function evaluated from the LES and gradients obtained using the viscosity adjoint method. Results from the optimization, performed on the supercomputer Mira, are presented.

Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement.

PubMed

Kravchenko-Balasha, Nataly; Shin, Young Shik; Sutherland, Alex; Levine, R D; Heath, James R

2016-05-17

Controlling cell migration is important in tissue engineering and medicine. Cell motility depends on factors such as nutrient concentration gradients and soluble factor signaling. In particular, cell-cell signaling can depend on cell-cell separation distance and can influence cellular arrangements in bulk cultures. Here, we seek a physical-based approach, which identifies a potential governed by cell-cell signaling that induces a directed cell-cell motion. A single-cell barcode chip (SCBC) was used to experimentally interrogate secreted proteins in hundreds of isolated glioblastoma brain cancer cell pairs and to monitor their relative motions over time. We used these trajectories to identify a range of cell-cell separation distances where the signaling was most stable. We then used a thermodynamics-motivated analysis of secreted protein levels to characterize free-energy changes for different cell-cell distances. We show that glioblastoma cell-cell movement can be described as Brownian motion biased by cell-cell potential. To demonstrate that the free-energy potential as determined by the signaling is the driver of motion, we inhibited two proteins most involved in maintaining the free-energy gradient. Following inhibition, cell pairs showed an essentially random Brownian motion, similar to the case for untreated, isolated single cells.

Capturing tensile size-dependency in polymer nanofiber elasticity.

PubMed

Yuan, Bo; Wang, Jun; Han, Ray P S

2015-02-01

As the name implies, tensile size-dependency refers to the size-dependent response under uniaxial tension. It defers markedly from bending size-dependency in terms of onset and magnitude of the size-dependent response; the former begins earlier but rises to a smaller value than the latter. Experimentally, tensile size-dependent behavior is much harder to capture than its bending counterpart. This is also true in the computational effort; bending size-dependency models are more prevalent and well-developed. Indeed, many have questioned the existence of tensile size-dependency. However, recent experiments seem to support the existence of this phenomenon. Current strain gradient elasticity theories can accurately predict bending size-dependency but are unable to track tensile size-dependency. To rectify this deficiency a higher-order strain gradient elasticity model is constructed by including the second gradient of the strain into the deformation energy. Tensile experiments involving 10 wt% polycaprolactone nanofibers are performed to calibrate and verify our model. The results reveal that for the selected nanofibers, their size-dependency begins when their diameters reduce to 600 nm and below. Further, their characteristic length-scale parameter is found to be 1095.8 nm. Copyright © 2014 Elsevier Ltd. All rights reserved.

Along-shelf current variability on the Catalan inner-shelf (NW Mediterranean)

USGS Publications Warehouse

Grifoll, Manel; Aretxabaleta, Alfredo L.; Espino, Manuel; Warner, John C.

2012-01-01

We examine the circulation over the inner shelf of the Catalan Sea using observations of currents obtained from three ADCPs within the inner-shelf (24 and 50 m depth) during March-April 2011. The along-shelf current fluctuations during that period are mainly controlled by the local wind stress on short time scales and by remote pressure gradients on synoptic time scales. Different forcing mechanisms are involved in the along-shelf momentum balance. During storm conditions, wind stress, sea level gradients and the non-linear terms dominate the balance. During weak wind conditions, the momentum balance is controlled by the pressure gradient, while during periods of moderate wind in the presence of considerable stratification, the balance is established between the Coriolis and wind stress terms. Vertical variations of velocity are affected by the strong observed density gradient. The increased vertical shear is accompanied by the development of stratified conditions due to local heating when the wind is not able to counteract (and destroy) stratification. The occasional influence of the Besòs river plume is observed in time scales of hours to days in a limited area in front of Barcelona. The area affected by the plume depends on the vertical extend of the fresher layer, the fast river discharge peak, and the relaxation of cross-shore velocities after northeast storm events. This contribution provides a first interpretation of the inner-shelf dynamics in the Catalan Sea.

Magnetothermal Convection of Water with the Presence or Absence of a Magnetic Force Acting on the Susceptibility Gradient

PubMed Central

Maki, Syou

2016-01-01

Heat transfer of magnetothermal convection with the presence or absence of the magnetic force acting on the susceptibility gradient (fsc) was examined by three-dimensional numerical computations. Thermal convection of water enclosed in a shallow cylindrical vessel (diameter over vessel height = 6.0) with the Rayleigh-Benard model was adopted as the model, under the conditions of Prandtl number 6.0 and Ra number 7000, respectively. The momentum equations of convection were nondimensionalized, which involved the term of fsc and the term of magnetic force acting on the magnetic field gradient (fb). All the computations resulted in axisymmetric steady rolls. The values of the averaged Nu, the averaged velocity components U, V, and W, and the isothermal distributions and flow patterns were almost completely the same, regardless of the presence or absence of the term of fsc. As a result, we found that the effect of fsc was extremely small, although much previous research emphasized the effect with paramagnetic solutions under an unsteady state. The magnitude of fsc depends not only on magnetic conditions (magnitudes of magnetic susceptibility and magnetic flux density), but also on the thermal properties of the solution (thermal conductivity, thermal diffusivity, and viscosity). Therefore the effect of fb becomes dominant on the magnetothermal convection. Active control over the density gradient with temperature will be required to advance heat transfer with the effect of fsc. PMID:27606823

Modeling the nitrogen cycle one gene at a time

NASA Astrophysics Data System (ADS)

Coles, V.; Stukel, M. R.; Hood, R. R.; Moran, M. A.; Paul, J. H.; Satinsky, B.; Zielinski, B.; Yager, P. L.

2016-02-01

Marine ecosystem models are lagging the revolution in microbial oceanography. As a result, modeling of the nitrogen cycle has largely failed to leverage new genomic information on nitrogen cycling pathways and the organisms that mediate them. We developed a nitrogen based ecosystem model whose community is determined by randomly assigning functional genes to build each organism's "DNA". Microbes are assigned a size that sets their baseline environmental responses using allometric response curves. These responses are modified by the costs and benefits conferred by each gene in an organism's genome. The microbes are embedded in a general circulation model where environmental conditions shape the emergent population. This model is used to explore whether organisms constructed from randomized combinations of metabolic capability alone can self-organize to create realistic oceanic biogeochemical gradients. Community size spectra and chlorophyll-a concentrations emerge in the model with reasonable fidelity to observations. The model is run repeatedly with randomly-generated microbial communities and each time realistic gradients in community size spectra, chlorophyll-a, and forms of nitrogen develop. This supports the hypothesis that the metabolic potential of a community rather than the realized species composition is the primary factor setting vertical and horizontal environmental gradients. Vertical distributions of nitrogen and transcripts for genes involved in nitrification are broadly consistent with observations. Modeled gene and transcript abundance for nitrogen cycling and processing of land-derived organic material match observations along the extreme gradients in the Amazon River plume, and they help to explain the factors controlling observed variability.

Evaluation of the accuracy of the Rotating Parallel Ray Omnidirectional Integration for instantaneous pressure reconstruction from the measured pressure gradient

NASA Astrophysics Data System (ADS)

Moreto, Jose; Liu, Xiaofeng

2017-11-01

The accuracy of the Rotating Parallel Ray omnidirectional integration for pressure reconstruction from the measured pressure gradient (Liu et al., AIAA paper 2016-1049) is evaluated against both the Circular Virtual Boundary omnidirectional integration (Liu and Katz, 2006 and 2013) and the conventional Poisson equation approach. Dirichlet condition at one boundary point and Neumann condition at all other boundary points are applied to the Poisson solver. A direct numerical simulation database of isotropic turbulence flow (JHTDB), with a homogeneously distributed random noise added to the entire field of DNS pressure gradient, is used to assess the performance of the methods. The random noise, generated by the Matlab function Rand, has a magnitude varying randomly within the range of +/-40% of the maximum DNS pressure gradient. To account for the effect of the noise distribution pattern on the reconstructed pressure accuracy, a total of 1000 different noise distributions achieved by using different random number seeds are involved in the evaluation. Final results after averaging the 1000 realizations show that the error of the reconstructed pressure normalized by the DNS pressure variation range is 0.15 +/-0.07 for the Poisson equation approach, 0.028 +/-0.003 for the Circular Virtual Boundary method and 0.027 +/-0.003 for the Rotating Parallel Ray method, indicating the robustness of the Rotating Parallel Ray method in pressure reconstruction. Sponsor: The San Diego State University UGP program.

Experiments and models of MHD jets and their relevance to astrophysics and solar physics

NASA Astrophysics Data System (ADS)

Bellan, Paul M.

2018-05-01

Magnetohydrodynamic (MHD)-driven jets involve poloidal and toroidal magnetic fields, finite pressure gradients, and unbalanced forces. The mechanism driving these jets is first discussed qualitatively by decomposing the magnetic force into a curvature and a gradient component. The mechanism is then considered quantitatively by consideration of all terms in the three components of the MHD equation of motion and in addition, the implications of Ampere's law, Faraday's law, the ideal Ohm's law, and the equation of continuity. The analysis shows that jets are self-collimating with the tip of the jet moving more slowly than the main column of the jet so there is a continuous stagnation near the tip in the jet frame. Experiments supporting these conclusions are discussed and it is shown how this mechanism relates to jets in astrophysical and solar corona contexts.

Hybrid Quantum-Classical Approach to Quantum Optimal Control.

PubMed

Li, Jun; Yang, Xiaodong; Peng, Xinhua; Sun, Chang-Pu

2017-04-14

A central challenge in quantum computing is to identify more computational problems for which utilization of quantum resources can offer significant speedup. Here, we propose a hybrid quantum-classical scheme to tackle the quantum optimal control problem. We show that the most computationally demanding part of gradient-based algorithms, namely, computing the fitness function and its gradient for a control input, can be accomplished by the process of evolution and measurement on a quantum simulator. By posing queries to and receiving answers from the quantum simulator, classical computing devices update the control parameters until an optimal control solution is found. To demonstrate the quantum-classical scheme in experiment, we use a seven-qubit nuclear magnetic resonance system, on which we have succeeded in optimizing state preparation without involving classical computation of the large Hilbert space evolution.

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

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

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

Single-vesicle imaging reveals different transport mechanisms between glutamatergic and GABAergic vesicles.

PubMed

Farsi, Zohreh; Preobraschenski, Julia; van den Bogaart, Geert; Riedel, Dietmar; Jahn, Reinhard; Woehler, Andrew

2016-02-26

Synaptic transmission is mediated by the release of neurotransmitters, which involves exo-endocytotic cycling of synaptic vesicles. To maintain synaptic function, synaptic vesicles are refilled with thousands of neurotransmitter molecules within seconds after endocytosis, using the energy provided by an electrochemical proton gradient. However, it is unclear how transmitter molecules carrying different net charges can be efficiently sequestered while maintaining charge neutrality and osmotic balance. We used single-vesicle imaging to monitor pH and electrical gradients and directly showed different uptake mechanisms for glutamate and γ-aminobutyric acid (GABA) operating in parallel. In contrast to glutamate, GABA was exchanged for protons, with no other ions participating in the transport cycle. Thus, only a few components are needed to guarantee reliable vesicle filling with different neurotransmitters. Copyright © 2016, American Association for the Advancement of Science.

The Role of Endocytosis during Morphogenetic Signaling

PubMed Central

Gonzalez-Gaitan, Marcos; Jülicher, Frank

2014-01-01

Morphogens are signaling molecules that are secreted by a localized source and spread in a target tissue where they are involved in the regulation of growth and patterning. Both the activity of morphogenetic signaling and the kinetics of ligand spreading in a tissue depend on endocytosis and intracellular trafficking. Here, we review quantitative approaches to study how large-scale morphogen profiles and signals emerge in a tissue from cellular trafficking processes and endocytic pathways. Starting from the kinetics of endosomal networks, we discuss the role of cellular trafficking and receptor dynamics in the formation of morphogen gradients. These morphogen gradients scale during growth, which implies that overall tissue size influences cellular trafficking kinetics. Finally, we discuss how such morphogen profiles can be used to control tissue growth. We emphasize the role of theory in efforts to bridge between scales. PMID:24984777

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

DOE PAGES

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

2016-04-07

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

Intraspecific Adaptations to Thermal Gradients in a Cosmopolitan Coccolithophore

NASA Astrophysics Data System (ADS)

Matson, P. G.; Ladd, T. M.; Iglesias-Rodriguez, D.

2016-02-01

The species concept in marine phytoplankton has enormous biological complexity. Differences in genomic, morphological, physiological, biogeochemical, and ecological/biogeographic properties between strains of the same species can be comparable or even exceed those between species. This complexity is particularly pronounced in the cosmopolitan coccolithophore species Emiliania huxleyi. This bloom-forming species is found at nearly every latitude in a variety of environments including upwelling regions, and exposed to large temperature gradients. We present results from experiments using two strains of E. huxleyi isolated from different latitudes and environmental conditions. Tests involved semi-continuous culturing in lab manipulation experiments to determine how carbon fixation, growth, and morphology respond to temperature-driven alterations in physico-chemical conditions. This talk will discuss the observed differences in physiology within an ecological context and the implications of these biogeochemical differences in modeling carbon fluxes driven by phytoplankton.

NDR proteins: lessons learned from Arabidopsis and animal cells prompt a testable hypothesis.

PubMed

Mudgil, Yashwanti; Jones, Alan M

2010-08-01

N-myc Down Regulated (NDR) genes were discovered more than fifteen years ago. Indirect evidence support a role in tumor progression and cellular differentiation, but their biochemical function is still unknown. Our detailed analyses on Arabidopsis NDL proteins show their involvement in altering auxin transport, local auxin gradients and expression level of auxin transport proteins. Animal NDL proteins may be involved in membrane recycling of E-cadherin and effector for the small GTPase. In light of these findings, we hypothesize that NDL proteins regulate vesicular trafficking of auxin transport facilitator PIN proteins by biochemically alterating the local lipid environment of PIN proteins.

Correlation-based regularization and gradient operators for (joint) inversion on unstructured meshes

NASA Astrophysics Data System (ADS)

Jordi, Claudio; Doetsch, Joseph; Günther, Thomas; Schmelzbach, Cedric; Robertsson, Johan

2017-04-01

When working with unstructured meshes for geophysical inversions, special attention should be paid to the design of the operators that are used for regularizing the inverse problem and coupling of different property models in joint inversions. Regularization constraints for inversions on unstructured meshes are often defined in a rather ad-hoc manner and usually only involve the cell to which the operator is applied and its direct neighbours. Similarly, most structural coupling operators for joint inversion, such as the popular cross-gradients operator, are only defined in the direct neighbourhood of a cell. As a result, the regularization and coupling length scales and strength of these operators depend on the discretization as well as cell sizes and shape. Especially for unstructured meshes, where the cell sizes vary throughout the model domain, the dependency of the operator on the discretization may lead to artefacts. Designing operators that are based on a spatial correlation model allows to define correlation length scales over which an operator acts (called footprint), reducing the dependency on the discretization and the effects of variable cell sizes. Moreover, correlation-based operators can accommodate for expected anisotropy by using different length scales in horizontal and vertical directions. Correlation-based regularization operators also known as stochastic regularization operators have already been successfully applied to inversions on regular grids. Here, we formulate stochastic operators for unstructured meshes and apply them in 2D surface and 3D cross-well electrical resistivity tomography data inversion examples of layered media. Especially for the synthetic cross-well example, improved inversion results are achieved when stochastic regularization is used instead of a classical smoothness constraint. For the case of cross-gradients operators for joint inversion, the correlation model is used to define the footprint of the operator and weigh the contributions of the property values that are used to calculate the cross-gradients. In a first series of synthetic-data tests, we examined the mesh dependency of the cross-gradients operators. Compared to operators that are only defined in the direct neighbourhood of a cell, the dependency on the cell size of the cross-gradients calculation is markedly reduced when using operators with larger footprints. A second test with synthetic models focussed on the effect of small-scale variabilities of the parameter value on the cross-gradients calculation. Small-scale variabilities that are superimposed on a global trend of the property value can potentially degrade the cross-gradients calculation and destabilize joint inversion. We observe that the cross-gradients from operators with footprints larger than the length scale of the variabilities are less affected compared to operators with a small footprint. In joint inversions on unstructured meshes, we thus expect the correlation-based coupling operators to ensure robust coupling on a physically meaningful scale.

MODELING TRANSPORT IN THE DOWN GRADIENT PORTION OF THE 200-PO-1 OPERABLE UNIT AT THE HANFORD SITE

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

MEHTA S; ALY AH; MILLER CW

2009-12-03

Remedial Investigations are underway for the 200-PO-l Operable Unit (OU) at the U.S. Department of Energy's Hanford Site in Washington State. To support the baseline risk assessment and evaluation of remedial alternatives, fate and transport modeling is being conducted to predict the future concentration of contaminants of potential concern in the 200-PO-1 OU. This study focuses on modeling the 'down gradient' transport of those contaminants that migrate beyond the 3-D model domain selected for performing detailed 'source area' modeling within the 200-PO-1 OU. The down gradient portion is defined as that region of the 200-PO-1 OU that is generally outsidemore » the 200 Area (considered 'source area') of the Hanford Site. A 1-D transport model is developed for performing down gradient contaminant fate and transport modeling. The 1-D transport model is deemed adequate based on the inferred transport pathway of tritium in the past and the observation that most of the contaminant mass remains at or near the water table within the unconfined aquifer of the Hanford Formation and the Cold-Creek/Pre-Missoula Gravel unit. The Pipe Pathway feature of the GoldSim software is used to perform the calculations. The Pipe Pathway uses a Laplace transform approach to provide analytical solutions to a broad range of advection-dominated mass transport systems involving one-dimensional advection, longitudinal dispersion, retardation, decay and ingrowth, and exchanges with immobile storage zones. Based on the historical concentration distribution data for the extensive tritium plume in this area, three Pipe Pathways are deemed adequate for modeling transport of contaminants. Each of these three Pipe Pathways is discretized into several zones, based on the saturated thickness variation in the unconfined aquifer and the location of monitoring wells used for risk assessment calculation. The mass fluxes of contaminants predicted to exit the source area model domain are used as an input to the down gradient model, while the flow velocities applied are based on the present-day hydraulic gradients and estimation of hydraulic conductivity in the unconfined aquifer. The results of the calculation indicate that the future concentrations of contaminants of potential concern in the down gradient portion of the 200-PO-1 OU declines with time and distance.« less

On Nonconvex Decentralized Gradient Descent

DTIC Science & Technology

2016-08-01

and J. Bolte, On the convergence of the proximal algorithm for nonsmooth functions involving analytic features, Math . Program., 116: 5-16, 2009. [2] H...splitting, and regularized Gauss-Seidel methods, Math . Pro- gram., Ser. A, 137: 91-129, 2013. [3] P. Bianchi and J. Jakubowicz, Convergence of a multi-agent...subgradient method under random communication topologies , IEEE J. Sel. Top. Signal Process., 5:754-771, 2011. [11] A. Nedic and A. Ozdaglar, Distributed

System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

DOEpatents

Craig, George D.; Glass, Robert; Rupp, Bernhard

1997-01-01

A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

Supercritical Fluid Chromatography of Drugs: Parallel Factor Analysis for Column Testing in a Wide Range of Operational Conditions

PubMed Central

Al-Degs, Yahya; Andri, Bertyl; Thiébaut, Didier; Vial, Jérôme

2017-01-01

Retention mechanisms involved in supercritical fluid chromatography (SFC) are influenced by interdependent parameters (temperature, pressure, chemistry of the mobile phase, and nature of the stationary phase), a complexity which makes the selection of a proper stationary phase for a given separation a challenging step. For the first time in SFC studies, Parallel Factor Analysis (PARAFAC) was employed to evaluate the chromatographic behavior of eight different stationary phases in a wide range of chromatographic conditions (temperature, pressure, and gradient elution composition). Design of Experiment was used to optimize experiments involving 14 pharmaceutical compounds present in biological and/or environmental samples and with dissimilar physicochemical properties. The results showed the superiority of PARAFAC for the analysis of the three-way (column × drug × condition) data array over unfolding the multiway array to matrices and performing several classical principal component analyses. Thanks to the PARAFAC components, similarity in columns' function, chromatographic trend of drugs, and correlation between separation conditions could be simply depicted: columns were grouped according to their H-bonding forces, while gradient composition was dominating for condition classification. Also, the number of drugs could be efficiently reduced for columns classification as some of them exhibited a similar behavior, as shown by hierarchical clustering based on PARAFAC components. PMID:28695040

The performance of monotonic and new non-monotonic gradient ascent reconstruction algorithms for high-resolution neuroreceptor PET imaging.

PubMed

Angelis, G I; Reader, A J; Kotasidis, F A; Lionheart, W R; Matthews, J C

2011-07-07

Iterative expectation maximization (EM) techniques have been extensively used to solve maximum likelihood (ML) problems in positron emission tomography (PET) image reconstruction. Although EM methods offer a robust approach to solving ML problems, they usually suffer from slow convergence rates. The ordered subsets EM (OSEM) algorithm provides significant improvements in the convergence rate, but it can cycle between estimates converging towards the ML solution of each subset. In contrast, gradient-based methods, such as the recently proposed non-monotonic maximum likelihood (NMML) and the more established preconditioned conjugate gradient (PCG), offer a globally convergent, yet equally fast, alternative to OSEM. Reported results showed that NMML provides faster convergence compared to OSEM; however, it has never been compared to other fast gradient-based methods, like PCG. Therefore, in this work we evaluate the performance of two gradient-based methods (NMML and PCG) and investigate their potential as an alternative to the fast and widely used OSEM. All algorithms were evaluated using 2D simulations, as well as a single [(11)C]DASB clinical brain dataset. Results on simulated 2D data show that both PCG and NMML achieve orders of magnitude faster convergence to the ML solution compared to MLEM and exhibit comparable performance to OSEM. Equally fast performance is observed between OSEM and PCG for clinical 3D data, but NMML seems to perform poorly. However, with the addition of a preconditioner term to the gradient direction, the convergence behaviour of NMML can be substantially improved. Although PCG is a fast convergent algorithm, the use of a (bent) line search increases the complexity of the implementation, as well as the computational time involved per iteration. Contrary to previous reports, NMML offers no clear advantage over OSEM or PCG, for noisy PET data. Therefore, we conclude that there is little evidence to replace OSEM as the algorithm of choice for many applications, especially given that in practice convergence is often not desired for algorithms seeking ML estimates.

On a concurrent element-by-element preconditioned conjugate gradient algorithm for multiple load cases

NASA Technical Reports Server (NTRS)

Watson, Brian; Kamat, M. P.

1990-01-01

Element-by-element preconditioned conjugate gradient (EBE-PCG) algorithms have been advocated for use in parallel/vector processing environments as being superior to the conventional LDL(exp T) decomposition algorithm for single load cases. Although there may be some advantages in using such algorithms for a single load case, when it comes to situations involving multiple load cases, the LDL(exp T) decomposition algorithm would appear to be decidedly more cost-effective. The authors have outlined an EBE-PCG algorithm suitable for multiple load cases and compared its effectiveness to the highly efficient LDL(exp T) decomposition scheme. The proposed algorithm offers almost no advantages over the LDL(exp T) algorithm for the linear problems investigated on the Alliant FX/8. However, there may be some merit in the algorithm in solving nonlinear problems with load incrementation, but that remains to be investigated.

Microfluidic Devices for Analysis of Spatial Orientation Behaviors in Semi-Restrained Caenorhabditis elegans

PubMed Central

McCormick, Kathryn E.; Gaertner, Bryn E.; Sottile, Matthew; Phillips, Patrick C.; Lockery, Shawn R.

2011-01-01

This article describes the fabrication and use of microfluidic devices for investigating spatial orientation behaviors in nematode worms (Caenorhabditis elegans). Until now, spatial orientation has been studied in freely moving nematodes in which the frequency and nature of encounters with the gradient are uncontrolled experimental variables. In the new devices, the nematode is held in place by a restraint that aligns the longitudinal axis of the body with the border between two laminar fluid streams, leaving the animal's head and tail free to move. The content of the fluid streams can be manipulated to deliver step gradients in space or time. We demonstrate the utility of the device by identifying previously uncharacterized aspects of the behavioral mechanisms underlying chemotaxis, osmotic avoidance, and thermotaxis in this organism. The new devices are readily adaptable to behavioral and imaging studies involving fluid borne stimuli in a wide range of sensory modalities. PMID:22022437

Evolutionarily conserved coupling of adaptive and excitable networks mediates eukaryotic chemotaxis

NASA Astrophysics Data System (ADS)

Tang, Ming; Wang, Mingjie; Shi, Changji; Iglesias, Pablo A.; Devreotes, Peter N.; Huang, Chuan-Hsiang

2014-10-01

Numerous models explain how cells sense and migrate towards shallow chemoattractant gradients. Studies show that an excitable signal transduction network acts as a pacemaker that controls the cytoskeleton to drive motility. Here we show that this network is required to link stimuli to actin polymerization and chemotactic motility and we distinguish the various models of chemotaxis. First, signalling activity is suppressed towards the low side in a gradient or following removal of uniform chemoattractant. Second, signalling activities display a rapid shut off and a slower adaptation during which responsiveness to subsequent test stimuli decline. Simulations of various models indicate that these properties require coupled adaptive and excitable networks. Adaptation involves a G-protein-independent inhibitor, as stimulation of cells lacking G-protein function suppresses basal activities. The salient features of the coupled networks were observed for different chemoattractants in Dictyostelium and in human neutrophils, suggesting an evolutionarily conserved mechanism for eukaryotic chemotaxis.

Mechanosensing is critical for axon growth in the developing brain

PubMed Central

Pillai, Eva K.; Sheridan, Graham K.; Svoboda, Hanno; Viana, Matheus; da F. Costa, Luciano; Guck, Jochen; Holt, Christine E.; Franze, Kristian

2016-01-01

During nervous system development, neurons extend axons along well-defined pathways. The current understanding of axon pathfinding is based mainly on chemical signalling. However, growing neurons interact not only chemically but also mechanically with their environment. Here we identify mechanical signals as important regulators of axon pathfinding. In vitro, substrate stiffness determined growth patterns of Xenopus retinal ganglion cell (RGC) axons. In vivo atomic force microscopy revealed striking stiffness gradient patterns in the embryonic brain. RGC axons grew towards the tissue’s softer side, which was reproduced in vitro in the absence of chemical gradients. To test the importance of mechanical signals for axon growth in vivo, we altered brain stiffness, blocked mechanotransduction pharmacologically, and knocked down the mechanosensitive ion channel Piezo1. All treatments resulted in aberrant axonal growth and pathfinding errors, suggesting that local tissue stiffness–read out by mechanosensitive ion channels–is critically involved in instructing neuronal growth in vivo. PMID:27643431

Geophysical, geochemical, and geological investigations of the Dunes geothermal system, Imperial Valley, California

NASA Technical Reports Server (NTRS)

Elders, W. A.; Combs, J.; Coplen, T. B.; Kolesar, P.; Bird, D. K.

1974-01-01

The Dunes anomaly is a water-dominated geothermal system in the alluvium of the Salton Trough, lacking any surface expression. It was discovered by shallow-temperature gradient measurements. A 612-meter-deep test well encountered several temperature-gradient reversals, with a maximum of 105 C at 114 meters. The program involves surface geophysics, including electrical, gravity, and seismic methods, down-hole geophysics and petrophysics of core samples, isotopic and chemical studies of water samples, and petrological and geochemical studies of the cores and cuttings. The aim is (1) to determine the source and temperature history of the brines, (2) to understand the interaction between the brines and rocks, and (3) to determine the areal extent, nature, origin, and history of the geothermal system. These studies are designed to provide better definition of exploration targets for hidden geothermal anomalies and to contribute to improved techniques of exploration and resource assessment.

Nonlinear responses of chiral fluids from kinetic theory

NASA Astrophysics Data System (ADS)

Hidaka, Yoshimasa; Pu, Shi; Yang, Di-Lun

2018-01-01

The second-order nonlinear responses of inviscid chiral fluids near local equilibrium are investigated by applying the chiral kinetic theory (CKT) incorporating side-jump effects. It is shown that the local equilibrium distribution function can be nontrivially introduced in a comoving frame with respect to the fluid velocity when the quantum corrections in collisions are involved. For the study of anomalous transport, contributions from both quantum corrections in anomalous hydrodynamic equations of motion and those from the CKT and Wigner functions are considered under the relaxation-time (RT) approximation, which result in anomalous charge Hall currents propagating along the cross product of the background electric field and the temperature (or chemical-potential) gradient and of the temperature and chemical-potential gradients. On the other hand, the nonlinear quantum correction on the charge density vanishes in the classical RT approximation, which in fact satisfies the matching condition given by the anomalous equation obtained from the CKT.

Hygrothermal wave propagation in viscoelastic graphene under in-plane magnetic field based on nonlocal strain gradient theory

NASA Astrophysics Data System (ADS)

Karami, Behrouz; Shahsavari, Davood; Li, Li

2018-03-01

A size-dependent model is developed for the hygrothermal wave propagation analysis of an embedded viscoelastic single layer graphene sheet (SLGS) under the influence of in-plane magnetic field. The bi-Helmholtz nonlocal strain gradient theory involving three small scale parameters is introduced to account for the size-dependent effects. The size-dependent model is deduced based on Hamilton's principle. The closed-form solution of eigenfrequency relation between wave number and phase velocity is achieved. By studying the size-dependent effects on the flexural wave of SLGS, the dispersion relation predicted by the developed size-dependent model can show a good match with experimental data. The influence of in-plane magnetic field, temperature and moisture of environs, structural damping, damped substrate, lower and higher order nonlocal parameters and the material characteristic parameter on the phase velocity of SLGS is explored.

Geodesic regression on orientation distribution functions with its application to an aging study.

PubMed

Du, Jia; Goh, Alvina; Kushnarev, Sergey; Qiu, Anqi

2014-02-15

In this paper, we treat orientation distribution functions (ODFs) derived from high angular resolution diffusion imaging (HARDI) as elements of a Riemannian manifold and present a method for geodesic regression on this manifold. In order to find the optimal regression model, we pose this as a least-squares problem involving the sum-of-squared geodesic distances between observed ODFs and their model fitted data. We derive the appropriate gradient terms and employ gradient descent to find the minimizer of this least-squares optimization problem. In addition, we show how to perform statistical testing for determining the significance of the relationship between the manifold-valued regressors and the real-valued regressands. Experiments on both synthetic and real human data are presented. In particular, we examine aging effects on HARDI via geodesic regression of ODFs in normal adults aged 22 years old and above. © 2013 Elsevier Inc. All rights reserved.

Proline transport in Leishmania donovani amastigotes: dependence on pH gradients and membrane potential.

PubMed

Glaser, T A; Mukkada, A J

1992-03-01

Amastigotes of Leishmania donovani develop and multiply within the acidic phagolysosomes of mammalian macrophages. Isolated amastigotes are acidophilic; they catabolize substrates and synthesize macromolecules optimally at pH 5.5. Substrate transport in amastigotes has not been characterized. Here we show that amastigotes exhibit an uphill transport of proline (active transport) with an acid pH optimum (pH 5.5). It is dependent upon metabolic energy and is driven by proton motive force. Agents which selectively disturb the component forces of proton motive force, such as carbonyl cyanide chlorophenylhydrazone, nigericin and valinomycin, inhibit proline transport. Transport is sensitive to dicyclohexylcarbodiimide and insensitive to ouabain, demonstrating the involvement of a proton ATPase in the maintenance of proton motive force. It is suggested that the plasma membrane pH gradient probably makes the greatest contribution to proton motive force that drives substrate transport in the amastigote stage.

Western blot (immunoblot) assay of small, round-structured virus associated with an acute gastroenteritis outbreak in Tokyo.

PubMed

Hayashi, Y; Ando, T; Utagawa, E; Sekine, S; Okada, S; Yabuuchi, K; Miki, T; Ohashi, M

1989-08-01

Small, round-structured virus (SRSV) was detected in a stool specimen of a patient during an acute gastroenteritis outbreak in Tokyo and was tentatively named SRSV-9. SRSV-9 was purified by sucrose velocity gradient centrifugation after CsCl density gradient centrifugation. The buoyant density of SRSV-9 appeared to be 1.36 g/ml in CsCl. A Western blot (immunoblot) assay using the biotin-avidin system revealed that SRSV-9 was antigenically related to the Hawaii agent but distinct from the Norwalk agent and contained a single major structural protein with a molecular size of 63.0 +/- 0.6 kilodaltons. The prevalence of SRSV-9 infection in Tokyo was surveyed by the Western blot antibody assay by using a crude virus preparation as the antigen. Seroconversion was observed in 56.5% of the patients involved in the outbreaks from which SRSV was detected by electron microscopy.

D-Optimal Experimental Design for Contaminant Source Identification

NASA Astrophysics Data System (ADS)

Sai Baba, A. K.; Alexanderian, A.

2016-12-01

Contaminant source identification seeks to estimate the release history of a conservative solute given point concentration measurements at some time after the release. This can be mathematically expressed as an inverse problem, with a linear observation operator or a parameter-to-observation map, which we tackle using a Bayesian approach. Acquisition of experimental data can be laborious and expensive. The goal is to control the experimental parameters - in our case, the sparsity of the sensors, to maximize the information gain subject to some physical or budget constraints. This is known as optimal experimental design (OED). D-optimal experimental design seeks to maximize the expected information gain, and has long been considered the gold standard in the statistics community. Our goal is to develop scalable methods for D-optimal experimental designs involving large-scale PDE constrained problems with high-dimensional parameter fields. A major challenge for the OED, is that a nonlinear optimization algorithm for the D-optimality criterion requires repeated evaluation of objective function and gradient involving the determinant of large and dense matrices - this cost can be prohibitively expensive for applications of interest. We propose novel randomized matrix techniques that bring down the computational costs of the objective function and gradient evaluations by several orders of magnitude compared to the naive approach. The effect of randomized estimators on the accuracy and the convergence of the optimization solver will be discussed. The features and benefits of our new approach will be demonstrated on a challenging model problem from contaminant source identification involving the inference of the initial condition from spatio-temporal observations in a time-dependent advection-diffusion problem.

Expression patterns of Eph genes in the "dual visual development" of the lamprey and their significance in the evolution of vision in vertebrates.

PubMed

Suzuki, Daichi G; Murakami, Yasunori; Yamazaki, Yuji; Wada, Hiroshi

2015-01-01

Image-forming vision is crucial to animals for recognizing objects in their environment. In vertebrates, this type of vision is achieved with paired camera eyes and topographic projection of the optic nerve. Topographic projection is established by an orthogonal gradient of axon guidance molecules, such as Ephs. To explore the evolution of image-forming vision in vertebrates, lampreys, which belong to the basal lineage of vertebrates, are key animals because they show unique "dual visual development." In the embryonic and pre-ammocoete larval stage (the "primary" phase), photoreceptive "ocellus-like" eyes develop, but there is no retinotectal optic nerve projection. In the late ammocoete larval stage (the "secondary" phase), the eyes grow and form into camera eyes, and retinotectal projection is newly formed. After metamorphosis, this retinotectal projection in adult lampreys is topographic, similar to that of gnathostomes. In this study, we explored the involvement of Ephs in lamprey "dual visual development" and establishment of the image-form vision. We found that gnathostome-like orthogonal gradient expression was present in the retina during the "secondary" phase; i.e., EphB showed a gradient of expression along the dorsoventral axis, while EphC was expressed along the anteroposterior axis. However, no orthogonal gradient expression was observed during the "primary" phase. These observations suggest that Ephs are likely recruited de novo for the guidance of topographical "second" optic nerve projection. Transformations during lamprey "dual visual development" may represent "recapitulation" from a protochordate-like ancestor to a gnathostome-like vertebrate ancestor. © 2015 Wiley Periodicals, Inc.

Demonstration of a strategy for product purification by high-gradient magnetic fishing: recovery of superoxide dismutase from unconditioned whey.

PubMed

Meyer, Andrea; Hansen, Dennis B; Gomes, Cláudia S G; Hobley, Timothy J; Thomas, Owen R T; Franzreb, Matthias

2005-01-01

A systematic approach for the design of a bioproduct recovery process employing magnetic supports and the technique of high-gradient magnetic fishing (HGMF) is described. The approach is illustrated for the separation of superoxide dismutase (SOD), an antioxidant protein present in low concentrations (ca. 0.15-0.6 mg L(-1)) in whey. The first part of the process design consisted of ligand screening in which metal chelate supports charged with copper(II) ions were found to be the most suitable. The second stage involved systematic and sequential optimization of conditions for the following steps: product adsorption, support washing, and product elution. Next, the capacity of a novel high-gradient magnetic separator (designed for biotechnological applications) for trapping and holding magnetic supports was determined. Finally, all of the above elements were assembled to deliver a HGMF process for the isolation of SOD from crude sweet whey, which consisted of (i) binding SOD using Cu2+ -charged magnetic metal chelator particles in a batch reactor with whey; (ii) recovery of the "SOD-loaded" supports by high-gradient magnetic separation (HGMS); (iii) washing out loosely bound and entrained proteins and solids; (iv) elution of the target protein; and (v) recovery of the eluted supports from the HGMF rig. Efficient recovery of SOD was demonstrated at approximately 50-fold increased scale (cf magnetic rack studies) in three separate HGMF experiments, and in the best of these (run 3) an SOD yield of >85% and purification factor of approximately 21 were obtained.

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

Regularized magnetotelluric inversion based on a minimum support gradient stabilizing functional

NASA Astrophysics Data System (ADS)

Xiang, Yang; Yu, Peng; Zhang, Luolei; Feng, Shaokong; Utada, Hisashi

2017-11-01

Regularization is used to solve the ill-posed problem of magnetotelluric inversion usually by adding a stabilizing functional to the objective functional that allows us to obtain a stable solution. Among a number of possible stabilizing functionals, smoothing constraints are most commonly used, which produce spatially smooth inversion results. However, in some cases, the focused imaging of a sharp electrical boundary is necessary. Although past works have proposed functionals that may be suitable for the imaging of a sharp boundary, such as minimum support and minimum gradient support (MGS) functionals, they involve some difficulties and limitations in practice. In this paper, we propose a minimum support gradient (MSG) stabilizing functional as another possible choice of focusing stabilizer. In this approach, we calculate the gradient of the model stabilizing functional of the minimum support, which affects both the stability and the sharp boundary focus of the inversion. We then apply the discrete weighted matrix form of each stabilizing functional to build a unified form of the objective functional, allowing us to perform a regularized inversion with variety of stabilizing functionals in the same framework. By comparing the one-dimensional and two-dimensional synthetic inversion results obtained using the MSG stabilizing functional and those obtained using other stabilizing functionals, we demonstrate that the MSG results are not only capable of clearly imaging a sharp geoelectrical interface but also quite stable and robust. Overall good performance in terms of both data fitting and model recovery suggests that this stabilizing functional is effective and useful in practical applications.[Figure not available: see fulltext.

Membrane Transport in Isolated Vesicles from Sugarbeet Taproot 1

PubMed Central

Briskin, Donald P.; Thornley, W. Robert; Wyse, Roger E.

1985-01-01

Sealed membrane vesicles were isolated from homogenates of sugarbeet (Beta vulgaris L.) taproot by a combination of differential centrifugation, extraction with KI, and dextran gradient centrifugation. Relative to the KI-extracted microsomes, the content of plasma membranes, mitochondrial membranes, and Golgi membranes was much reduced in the final vesicle fraction. A component of ATPase activity that was inhibited by nitrate co-enriched with the capacity of the vesicles to form a steady state pH gradient during the purification procedure. This suggests that the nitrate-sensitive ATPase may be involved in driving H+-transport, and this is consistent with the observation that H+-transport, in the final vesicle fraction was inhibited by nitrate. Proton transport in the sugarbeet vesicles was substrate specific for ATP, insensitive to sodium vanadate and oligomycin but was inhibited by diethylstilbestrol and N,N′-dicyclohexylcarbodiimide. The formation of a pH gradient in the vesicles was enhanced by halide ions in the sequence I− > Br− > Cl− while F− was inhibitory. These stimulatory effects occur from both a direct stimulation of the ATPase by anions and a reduction in the vesicle membrane potential. In the presence of Cl−, alkali cations reduce the pH gradient relative to that observed with bis-tris-propane, possibly by H+/alkali cation exchange. Based upon the properties of the H+-transporting vesicles, it is proposed that they are most likely derived from the tonoplast so that this vesicle preparation would represent a convenient system for studying the mechanism of transport at this membrane boundary. PMID:16664342

Trouble with diffusion: Reassessing hillslope erosion laws with a particle-based model

NASA Astrophysics Data System (ADS)

Tucker, Gregory E.; Bradley, D. Nathan

2010-03-01

Many geomorphic systems involve a broad distribution of grain motion length scales, ranging from a few particle diameters to the length of an entire hillslope or stream. Studies of analogous physical systems have revealed that such broad motion distributions can have a significant impact on macroscale dynamics and can violate the assumptions behind standard, local gradient flux laws. Here, a simple particle-based model of sediment transport on a hillslope is used to study the relationship between grain motion statistics and macroscopic landform evolution. Surface grains are dislodged by random disturbance events with probabilities and distances that depend on local microtopography. Despite its simplicity, the particle model reproduces a surprisingly broad range of slope forms, including asymmetric degrading scarps and cinder cone profiles. At low slope angles the dynamics are diffusion like, with a short-range, thin-tailed hop length distribution, a parabolic, convex upward equilibrium slope form, and a linear relationship between transport rate and gradient. As slope angle steepens, the characteristic grain motion length scale begins to approach the length of the slope, leading to planar equilibrium forms that show a strongly nonlinear correlation between transport rate and gradient. These high-probability, long-distance motions violate the locality assumption embedded in many common gradient-based geomorphic transport laws. The example of a degrading scarp illustrates the potential for grain motion dynamics to vary in space and time as topography evolves. This characteristic renders models based on independent, stationary statistics inapplicable. An accompanying analytical framework based on treating grain motion as a survival process is briefly outlined.

Simple method for RF pulse measurement using gradient reversal.

PubMed

Landes, Vanessa L; Nayak, Krishna S

2018-05-01

To develop and evaluate a simple method for measuring the envelope of small-tip radiofrequency (RF) excitation waveforms in MRI, without extra hardware or synchronization. Gradient reversal approach to evaluate RF (GRATER) involves RF excitation with a constant gradient and reversal of that gradient during signal reception to acquire the time-reversed version of an RF envelope. An outer-volume suppression prepulse is used optionally to preselect a uniform volume. GRATER was evaluated in phantom and in vivo experiments. It was compared with the programmed waveform and the traditional pick-up coil method. In uniform phantom experiments, pick-up coil, GRATER, and outer-volume suppression + GRATER matched the programmed waveforms to less than 2.1%, less than 6.1%, and less than 2.4% normalized root mean square error, respectively, for real RF pulses with flip angle less than or equal to 30°, time-bandwidth product 2 to 8, and two to five excitation bands. For flip angles greater than 30°, GRATER measurement error increased as predicted by Bloch simulation. Fat-water phantom and in vivo experiments with outer-volume suppression + GRATER demonstrated less than 6.4% normalized root mean square error. The GRATER sequence measures small-tip RF envelopes without extra hardware or synchronization in just over two times the RF duration. The sequence may be useful in prescan calibration and for measurement and precompensation of RF amplifier nonlinearity. Magn Reson Med 79:2642-2651, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient.

PubMed

Nunes, Vera L; Beaumont, Mark A; Butlin, Roger K; Paulo, Octávio S

2011-01-01

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3-4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life-history variation of L. lepida subspecies along the environmental gradient. © 2010 Blackwell Publishing Ltd.

The role of time and risk preferences in smoking inequalities: a population-based study.

PubMed

Jusot, Florence; Khlat, Myriam

2013-05-01

Heterogeneity in time and risk preferences has been proposed as one of the mechanisms involved in the educational gradient in smoking, but this mechanism has scarcely been explored empirically. Subjective scales were introduced in the 2008 French National Health, Health Care and Insurance Survey in order to elicit measures of time and risk preferences for a representative sample of 5188 men and 5684 women. Men and women were treated separately. First, logistic regressions were used to test the associations between preferences and education and between preferences and smoking. Second, nested logistic models were built to investigate the mediating role of preferences in the educational gradient in smoking, with an econometric treatment of the rescaling problem. Preference for the present and risk loving were found to be: inversely related to educational level; strongly related to each other, and; strongly associated to current smoking, even after adjustment for educational level. There was a weakening of the educational gradient after the control for preferences, which supports the role of these two preferences as partial mediators in the educational gradient in smoking. Among men, time preference was more strongly associated with smoking than risk aversion, while the reverse was found for women. We provide convincing evidence in favour of the mediating role of time preference and risk aversion in educational inequalities in smoking and highlight the connection between those two dimensions. Gender patterns are discussed and potential implications in terms of designing targeted anti-tobacco programmes are delineated. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison of microbial taxonomic and functional shift pattern along contamination gradient.

PubMed

Ren, Youhua; Niu, Jiaojiao; Huang, Wenkun; Peng, Deliang; Xiao, Yunhua; Zhang, Xian; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-06-14

The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.

Novel determinants of the neuronal Cl− concentration

PubMed Central

Delpire, Eric; Staley, Kevin J

2014-01-01

It is now a well-accepted view that cation-driven Cl− transporters in neurons are involved in determining the intracellular Cl− concentration. In the present review, we propose that additional factors, which are often overlooked, contribute substantially to the Cl− gradient across neuronal membranes. After briefly discussing the data supporting and opposing the role of cation–chloride cotransporters in regulating Cl−, we examine the participation of the following factors in the formation of the transmembrane Cl− gradient: (i) fixed ‘Donnan’ charges inside and outside the cell; (ii) the properties of water (free vs. bound); and (iii) water transport through the cotransporters. We demonstrate a steep relationship between intracellular Cl− and the concentration of fixed negative charges on macromolecules. We show that in the absence of water transport through the K+–Cl− cotransporter, a large osmotic gradient builds at concentrations below or above a set value of ‘Donnan’ charges, and show that at any value of these fixed charges, the reversal potential for Cl− equates that of K+. When the movement of water across the membrane is a source of free energy, it is sufficient to modify the movement of Cl− through the cotransporter. In this scenario, the reversal potential for Cl− does not closely follow that of K+. Furthermore, our simulations demonstrate that small differences in the availability of freely diffusible water between inside and outside the cell greatly affect the Cl− reversal potential, particularly when osmolar transmembrane gradients are minimized, for example by idiogenic osmoles. We also establish that the presence of extracellular charges has little effect on the chloride reversal potential, but greatly affects the effective inhibitory conductance for Cl−. In conclusion, our theoretical analysis of the presence of fixed anionic charges and water bound on macromolecules inside and outside the cell greatly impacts both Cl− gradient and Cl− conductance across neuronal membranes. PMID:25107928

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

PubMed Central

Verd, Berta; Crombach, Anton

2017-01-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory processes in development. PMID:28158178

The relationship between maternal education and reported childhood conditions.

PubMed

Berchick, Edward R

2016-12-01

Children of more-educated mothers tend to be healthier than children of less-educated mothers. However, in the United States, evidence for this relationship largely focuses on summary measures of health, such as subjective health status, birth weight, and height. Few studies have examined the relationship between mothers' education and children's reported conditions, the health metric that underlies many policy decisions concerning population health. Contrary to stylized facts about socioeconomic gradients in health, higher detection and reporting rates may lead to higher reporting rates among children of more-educated mothers, despite their better underlying health. This reporting pattern that might not mirror gradients for summary health measures. To examine this possibility, I investigate the association between maternal education and nine health conditions in the 1998-2014 National Health Interview Surveys (n = 176,097). I consider variation in the maternal education gradient across the specific reported conditions that children experience, paying particular attention to how patterns differ across children's ages. Results suggest that, unlike for the income gradient in child health, the relationship between maternal education and reported conditions varies in magnitude and direction across conditions. With some exceptions, the probability of reporting a diagnosed condition increases with maternal schooling. For some diagnoses, like asthma, this relationship is curvilinear, with an inverse gradient for children of the most educated mothers. However, the probability of reporting conditions that require neither diagnosis nor substantial parent-child involvement for detection tends to be flat across maternal education. Contrary to expectations, these relationships tend to be more pronounced for children who are 6 years of age or older than for younger children. These results expand understanding of the production and reporting of early-life health inequalities and illustrate limitations of an oft-used health metric. Reported conditions may underestimate socioeconomic inequalities in children's health. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression.

PubMed

Verd, Berta; Crombach, Anton; Jaeger, Johannes

2017-02-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory processes in development.

Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

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

Yu, Haoyu S.; Zhang, Wenjing; Verma, Pragya

2015-01-01

The goal of this work is to develop a gradient approximation to the exchange–correlation functional of Kohn–Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange–correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newlymore » extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange–correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy for all the key properties needed for molecular catalysis make the GAM functional very promising for future applications.« less

Spatial and temporal differences in traffic-related air pollution in three urban neighborhoods near an interstate highway.

PubMed

Patton, Allison P; Perkins, Jessica; Zamore, Wig; Levy, Jonathan I; Brugge, Doug; Durant, John L

2014-12-01

Relatively few studies have characterized differences in intra- and inter-neighborhood traffic-related air pollutant (TRAP) concentrations and distance-decay gradients in along an urban highway for the purposes of exposure assessment. The goal of this work was to determine the extent to which intra- and inter-neighborhood differences in TRAP concentrations can be explained by traffic and meteorology in three pairs of neighborhoods along Interstate 93 (I-93) in the metropolitan Boston area (USA). We measured distance-decay gradients of seven TRAPs (PNC, pPAH, NO, NO X , BC, CO, PM 2.5 ) in near-highway (<400 m) and background areas (>1 km) in Somerville, Dorchester/South Boston, Chinatown and Malden to determine whether (1) spatial patterns in concentrations and inter-pollutant correlations differ between neighborhoods, and (2) variation within and between neighborhoods can be explained by traffic and meteorology. The neighborhoods ranged in area from 0.5 to 2.3 km 2 . Mobile monitoring was performed over the course of one year in each pair of neighborhoods (one pair of neighborhoods per year in three successive years; 35-47 days of monitoring in each neighborhood). Pollutant levels generally increased with highway proximity, consistent with I-93 being a major source of TRAP; however, the slope and extent of the distance-decay gradients varied by neighborhood as well as by pollutant, season and time of day. Correlations among pollutants differed between neighborhoods (e.g., ρ = 0.35-0.80 between PNC and NO X and ρ = 0.11-0.60 between PNC and BC) and were generally lower in Dorchester/South Boston than in the other neighborhoods. We found that the generalizability of near-road gradients and near-highway/urban background contrasts was limited for near-highway neighborhoods in a metropolitan area with substantial local street traffic. Our findings illustrate the importance of measuring gradients of multiple pollutants under different ambient conditions in individual near-highway neighborhoods for health studies involving inter-neighborhood comparisons.

Spatial and temporal differences in traffic-related air pollution in three urban neighborhoods near an interstate highway

PubMed Central

Patton, Allison P.; Perkins, Jessica; Zamore, Wig; Levy, Jonathan I.; Brugge, Doug; Durant, John L.

2014-01-01

Relatively few studies have characterized differences in intra- and inter-neighborhood traffic-related air pollutant (TRAP) concentrations and distance-decay gradients in along an urban highway for the purposes of exposure assessment. The goal of this work was to determine the extent to which intra- and inter-neighborhood differences in TRAP concentrations can be explained by traffic and meteorology in three pairs of neighborhoods along Interstate 93 (I-93) in the metropolitan Boston area (USA). We measured distance-decay gradients of seven TRAPs (PNC, pPAH, NO, NOX, BC, CO, PM2.5) in near-highway (<400 m) and background areas (>1 km) in Somerville, Dorchester/South Boston, Chinatown and Malden to determine whether (1) spatial patterns in concentrations and inter-pollutant correlations differ between neighborhoods, and (2) variation within and between neighborhoods can be explained by traffic and meteorology. The neighborhoods ranged in area from 0.5 to 2.3 km2. Mobile monitoring was performed over the course of one year in each pair of neighborhoods (one pair of neighborhoods per year in three successive years; 35-47 days of monitoring in each neighborhood). Pollutant levels generally increased with highway proximity, consistent with I-93 being a major source of TRAP; however, the slope and extent of the distance-decay gradients varied by neighborhood as well as by pollutant, season and time of day. Correlations among pollutants differed between neighborhoods (e.g., ρ = 0.35-0.80 between PNC and NOX and ρ = 0.11-0.60 between PNC and BC) and were generally lower in Dorchester/South Boston than in the other neighborhoods. We found that the generalizability of near-road gradients and near-highway/urban background contrasts was limited for near-highway neighborhoods in a metropolitan area with substantial local street traffic. Our findings illustrate the importance of measuring gradients of multiple pollutants under different ambient conditions in individual near-highway neighborhoods for health studies involving inter-neighborhood comparisons. PMID:25364295

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

USGS Publications Warehouse

Baillie, Shauna M.; Muir, Andrew M.; Hansen, Michael J.; Krueger, Charles C.; Bentzen, Paul

2016-01-01

BackgroundAdaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycushthat considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.ResultsFour putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.ConclusionWe provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake in the world for a species that recently lost considerable genetic diversity and is now in recovery. Unknown is whether observed patterns are a result of an early stage of incipient speciation, gene flow-selection equilibrium, or reverse speciation causing formerly divergent ecotypes to collapse into a single gene pool.

PDC-SGB: Prediction of effective drug combinations using a stochastic gradient boosting algorithm.

PubMed

Xu, Qian; Xiong, Yi; Dai, Hao; Kumari, Kotni Meena; Xu, Qin; Ou, Hong-Yu; Wei, Dong-Qing

2017-03-21

Combinatorial therapy is a promising strategy for combating complex diseases by improving the efficacy and reducing the side effects. To facilitate the identification of drug combinations in pharmacology, we proposed a new computational model, termed PDC-SGB, to predict effective drug combinations by integrating biological, chemical and pharmacological information based on a stochastic gradient boosting algorithm. To begin with, a set of 352 golden positive samples were collected from the public drug combination database. Then, a set of 732 dimensional feature vector involving biological, chemical and pharmaceutical information was constructed for each drug combination to describe its properties. To avoid overfitting, the maximum relevance & minimum redundancy (mRMR) method was performed to extract useful ones by removing redundant subsets. Based on the selected features, the three different type of classification algorithms were employed to build the drug combination prediction models. Our results demonstrated that the model based on the stochastic gradient boosting algorithm yield out the best performance. Furthermore, it is indicated that the feature patterns of therapy had powerful ability to discriminate effective drug combinations from non-effective ones. By analyzing various features, it is shown that the enriched features occurred frequently in golden positive samples can help predict novel drug combinations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spatial temperature gradients guide axonal outgrowth

PubMed Central

Black, Bryan; Vishwakarma, Vivek; Dhakal, Kamal; Bhattarai, Samik; Pradhan, Prabhakar; Jain, Ankur; Kim, Young-tae; Mohanty, Samarendra

2016-01-01

Formation of neural networks during development and regeneration after injury depends on accuracy of axonal pathfinding, which is primarily believed to be influenced by chemical cues. Recently, there is growing evidence that physical cues can play crucial role in axonal guidance. However, detailed mechanism involved in such guidance cues is lacking. By using weakly-focused near-infrared continuous wave (CW) laser microbeam in the path of an advancing axon, we discovered that the beam acts as a repulsive guidance cue. Here, we report that this highly-effective at-a-distance guidance is the result of a temperature field produced by the near-infrared laser light absorption. Since light absorption by extracellular medium increases when the laser wavelength was red shifted, the threshold laser power for reliable guidance was significantly lower in the near-infrared as compared to the visible spectrum. The spatial temperature gradient caused by the near-infrared laser beam at-a-distance was found to activate temperature-sensitive membrane receptors, resulting in an influx of calcium. The repulsive guidance effect was significantly reduced when extracellular calcium was depleted or in the presence of TRPV1-antagonist. Further, direct heating using micro-heater confirmed that the axonal guidance is caused by shallow temperature-gradient, eliminating the role of any non-photothermal effects. PMID:27460512

Demographic compensation among populations: what is it, how does it arise and what are its implications?

PubMed

Villellas, Jesús; Doak, Daniel F; García, María B; Morris, William F

2015-09-10

Most species are exposed to significant environmental gradients across their ranges, but vital rates (survival, growth, reproduction and recruitment) need not respond in the same direction to those gradients. Opposing vital rate trends across environments, a phenomenon that has been loosely called 'demographic compensation', may allow species to occupy larger geographical ranges and alter their responses to climate change. Yet the term has never been precisely defined, nor has its existence or strength been assessed for multiple species. Here, we provide a rigorous definition, and use it to develop a strong test for demographic compensation. By applying the test to data from 26 published, multi-population demographic studies of plants, we show that demographic compensation commonly occurs. We also investigate the mechanisms by which this phenomenon arises by assessing which demographic processes and life stages are most often involved. In addition, we quantify the effect of demographic compensation on variation in population growth rates across environmental gradients, a potentially important determinant of the size of a species' geographical range. Finally, we discuss the implications of demographic compensation for the responses of single populations and species' ranges to temporal environmental variation and to ongoing environmental trends, e.g. due to climate change. © 2015 John Wiley & Sons Ltd/CNRS.

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

PubMed

Mandakovic, Dinka; Rojas, Claudia; Maldonado, Jonathan; Latorre, Mauricio; Travisany, Dante; Delage, Erwan; Bihouée, Audrey; Jean, Géraldine; Díaz, Francisca P; Fernández-Gómez, Beatriz; Cabrera, Pablo; Gaete, Alexis; Latorre, Claudio; Gutiérrez, Rodrigo A; Maass, Alejandro; Cambiazo, Verónica; Navarrete, Sergio A; Eveillard, Damien; González, Mauricio

2018-04-12

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.

Spatial temperature gradients guide axonal outgrowth

NASA Astrophysics Data System (ADS)

Black, Bryan; Vishwakarma, Vivek; Dhakal, Kamal; Bhattarai, Samik; Pradhan, Prabhakar; Jain, Ankur; Kim, Young-Tae; Mohanty, Samarendra

2016-07-01

Formation of neural networks during development and regeneration after injury depends on accuracy of axonal pathfinding, which is primarily believed to be influenced by chemical cues. Recently, there is growing evidence that physical cues can play crucial role in axonal guidance. However, detailed mechanism involved in such guidance cues is lacking. By using weakly-focused near-infrared continuous wave (CW) laser microbeam in the path of an advancing axon, we discovered that the beam acts as a repulsive guidance cue. Here, we report that this highly-effective at-a-distance guidance is the result of a temperature field produced by the near-infrared laser light absorption. Since light absorption by extracellular medium increases when the laser wavelength was red shifted, the threshold laser power for reliable guidance was significantly lower in the near-infrared as compared to the visible spectrum. The spatial temperature gradient caused by the near-infrared laser beam at-a-distance was found to activate temperature-sensitive membrane receptors, resulting in an influx of calcium. The repulsive guidance effect was significantly reduced when extracellular calcium was depleted or in the presence of TRPV1-antagonist. Further, direct heating using micro-heater confirmed that the axonal guidance is caused by shallow temperature-gradient, eliminating the role of any non-photothermal effects.

Control of Internal Transport Barriers in Magnetically Confined Fusion Plasmas

NASA Astrophysics Data System (ADS)

Panta, Soma; Newman, David; Sanchez, Raul; Terry, Paul

2016-10-01

In magnetic confinement fusion devices the best performance often involves some sort of transport barriers to reduce the energy and particle flow from core to edge. Those barriers create gradients in the temperature and density profiles. If gradients in the profiles are too steep that can lead to instabilities and the system collapses. Control of these barriers is therefore an important challenge for fusion devices (burning plasmas). In this work we focus on the dynamics of internal transport barriers. Using a simple 7 field transport model, extensively used for barrier dynamics and control studies, we explore the use of RF heating to control the local gradients and therefore the growth rates and shearing rates for barrier initiation and control in self-heated fusion plasmas. Ion channel barriers can be formed in self-heated plasmas with some NBI heating but electron channel barriers are very sensitive. They can be formed in self-heated plasmas with additional auxiliary heating i.e. NBI and radio-frequency(RF). Using RF heating on both electrons and ions at proper locations, electron channel barriers along with ion channel barriers can be formed and removed demonstrating a control technique. Investigating the role of pellet injection in controlling the barriers is our next goal. Work supported by DOE Grant DE-FG02-04ER54741.

Predicting the chromatographic retention of polymers: application of the polymer model to poly(styrene/ethylacrylate)copolymers.

PubMed

Bashir, Mubasher A; Radke, Wolfgang

2012-02-17

The retention behavior of a range of statistical poly(styrene/ethylacrylate) copolymers is investigated, in order to determine the possibility to predict retention volumes of these copolymers based on a suitable chromatographic retention model. It was found that the composition of elution in gradient chromatography of the copolymers is closely related to the eluent composition at which, in isocratic chromatography, the transition from elution in adsorption to exclusion mode occurs. For homopolymers this transition takes place at a critical eluent composition at which the molar mass dependence of elution volume vanishes. Thus, similar critical eluent compositions can be defined for statistical copolymers. The existence of a critical eluent composition is further supported by the narrower peak width, indicating that the broad molar mass distribution of the samples does not contribute to the retention volume. It is shown that the existing retention model for homopolymers allows for correct quantitative predictions of retention volumes based on only three appropriate initial experiments. The selection of these initial experiments involves a gradient run and two isocratic experiments, one at the composition of elution calculated from first gradient run and second at a slightly higher eluent strength. Copyright © 2011 Elsevier B.V. All rights reserved.

Improving a maximum horizontal gradient algorithm to determine geological body boundaries and fault systems based on gravity data

NASA Astrophysics Data System (ADS)

Van Kha, Tran; Van Vuong, Hoang; Thanh, Do Duc; Hung, Duong Quoc; Anh, Le Duc

2018-05-01

The maximum horizontal gradient method was first proposed by Blakely and Simpson (1986) for determining the boundaries between geological bodies with different densities. The method involves the comparison of a center point with its eight nearest neighbors in four directions within each 3 × 3 calculation grid. The horizontal location and magnitude of the maximum values are found by interpolating a second-order polynomial through the trio of points provided that the magnitude of the middle point is greater than its two nearest neighbors in one direction. In theoretical models of multiple sources, however, the above condition does not allow the maximum horizontal locations to be fully located, and it could be difficult to correlate the edges of complicated sources. In this paper, the authors propose an additional condition to identify more maximum horizontal locations within the calculation grid. This additional condition will improve the method algorithm for interpreting the boundaries of magnetic and/or gravity sources. The improved algorithm was tested on gravity models and applied to gravity data for the Phu Khanh basin on the continental shelf of the East Vietnam Sea. The results show that the additional locations of the maximum horizontal gradient could be helpful for connecting the edges of complicated source bodies.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

PubMed

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of cochlear ablation on choline acetyltransferase activity in the rat cochlear nucleus and superior olive.

PubMed

Jin, Yong-Ming; Godfrey, Donald A; Sun, Yizhe

2005-07-01

Using microdissection and quantitative microassay, choline acetyltransferase (ChAT) activity was mapped in the cochlear nucleus (CN) and in the source nuclei of the olivocochlear bundle, the lateral superior olive and ventral nucleus of the trapezoid body. In control rats, gradients of ChAT activity were found within the major subdivisions of the CN and in the lateral superior olive. These gradients correlated with the known tonotopic organizations, with higher activities corresponding to locations representing higher sound frequencies. No gradient was found in the ventral nucleus of the trapezoid body. In rats surviving 7 days or 1 or 2 months after cochlear ablation, ChAT activity was increased 1 month after ablation in the anteroventral CN by 30-50% in most parts of the lesion-side and by 40% in the contralateral ventromedial part. ChAT activity in the lesion-side posteroventral CN was increased by approximately 40-50% at all survival times. Little change was found in the dorsal CN. Decreases of ChAT activity were also found ipsilaterally in the lateral superior olive and bilaterally in the ventral nucleus of the trapezoid body. Our results suggest that cholinergic neurons are involved in plasticity within the CN and superior olive following cochlear lesions. Copyright 2005 Wiley-Liss, Inc.

Substrate and metabolite diffusion within model medium for soft cheese in relation to growth of Penicillium camembertii.

PubMed

Aldarf, Mazen; Fourcade, Florence; Amrane, Abdeltif; Prigent, Yves

2006-08-01

Penicillium camembertii was cultivated on a jellified peptone-lactate based medium to simulate the composition of Camembert cheese. Diffusional limitations due to substrate consumption were not involved in the linear growth recorded during culture, while nitrogen (peptone) limitation accounted for growth cessation. Examination of gradients confirmed that medium neutralization was the consequence of lactate consumption and ammonium production. The diffusion of the lactate assimilated from the core to the rind and that of the ammonium produced from the rind to the core was described by means of a diffusion/reaction model involving a partial linking of consumption or production to growth. The model matched experimental data throughout growth.

Systems of Inhomogeneous Linear Equations

NASA Astrophysics Data System (ADS)

Scherer, Philipp O. J.

Many problems in physics and especially computational physics involve systems of linear equations which arise e.g. from linearization of a general nonlinear problem or from discretization of differential equations. If the dimension of the system is not too large standard methods like Gaussian elimination or QR decomposition are sufficient. Systems with a tridiagonal matrix are important for cubic spline interpolation and numerical second derivatives. They can be solved very efficiently with a specialized Gaussian elimination method. Practical applications often involve very large dimensions and require iterative methods. Convergence of Jacobi and Gauss-Seidel methods is slow and can be improved by relaxation or over-relaxation. An alternative for large systems is the method of conjugate gradients.

System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

DOEpatents

Craig, G.D.; Glass, R.; Rupp, B.

1997-01-28

A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

Topological disposition of the sequences -QRKIVE- and -KETYY in native (Na sup + + K sup + )-ATPase

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

Bayer, R.

1990-03-06

The dispositions with respect to the plane of the membrane of lysine-905 in the internal sequence -EQRKIVE- and of lysine-1012 in the carboxy-terminal sequence -RRPGGWVEKETYY of the {alpha}-polypeptide of sodium and potassium ion activated adenosinetriphosphatase have been determined. These lysines are found in peptides released from the intact {alpha}-polypeptide by the extracellular protease from Staphylococcus aureus strain V8 and by trypsin, respectively. Synthetic peptides containing terminal sequences of these were used to prepare polyclonal antibodies, which were then used to prepare immunoadsorbents directed against the respective peptides. Sealed, right-side-out membrane vesicles containing native (Na{sup +} + K{sup +})-ATPase were labeledmore » with pyridoxal phosphate and sodium ({sup 3}H)borohydride in the absence or presence of saponin. The labeled {alpha}-polypeptide was isolated from these vesicles and digested with appropriate proteases. The incorporation of radioactivity into the peptides binding to the immunoadsorbent directed against the sequence pyrERXIVE increased 3-fold int the presence of saponin as a result of the increased accessibility of this portion of the protein to the reagent when the vesicles were breached by saponin; hence, this sequence is located on the cytoplasmic face of the membrane. It was inferred that the carboxy-terminal sequence -KETYY is on the extracytoplasmic face since the incorporation of radioactivity into peptides binding to the immunoadsorbent directed against the sequence -ETYY did not change when the vesicles were breached with saponin.« less

Anionic lipids and the cytoskeletal proteins MreB and RodZ define the spatio-temporal distribution and function of membrane stress controller PspA in Escherichia coli.

PubMed

Jovanovic, Goran; Mehta, Parul; Ying, Liming; Buck, Martin

2014-11-01

All cell types must maintain the integrity of their membranes. The conserved bacterial membrane-associated protein PspA is a major effector acting upon extracytoplasmic stress and is implicated in protection of the inner membrane of pathogens, formation of biofilms and multi-drug-resistant persister cells. PspA and its homologues in Gram-positive bacteria and archaea protect the cell envelope whilst also supporting thylakoid biogenesis in cyanobacteria and higher plants. In enterobacteria, PspA is a dual function protein negatively regulating the Psp system in the absence of stress and acting as an effector of membrane integrity upon stress. We show that in Escherichia coli the low-order oligomeric PspA regulatory complex associates with cardiolipin-rich, curved polar inner membrane regions. There, cardiolipin and the flotillin 1 homologue YqiK support the PspBC sensors in transducing a membrane stress signal to the PspA-PspF inhibitory complex. After stress perception, PspA high-order oligomeric effector complexes initially assemble in polar membrane regions. Subsequently, the discrete spatial distribution and dynamics of PspA effector(s) in lateral membrane regions depend on the actin homologue MreB and the peptidoglycan machinery protein RodZ. The consequences of loss of cytoplasmic membrane anionic lipids, MreB, RodZ and/or YqiK suggest that the mode of action of the PspA effector is closely associated with cell envelope organization. © 2014 The Authors.

Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida.

PubMed

Sánchez-Hevia, Dione L; Yuste, Luis; Moreno, Renata; Rojo, Fernando

2018-04-30

Metabolically versatile bacteria use catabolite repression control to select their preferred carbon sources, thus optimizing carbon metabolism. In pseudomonads, this occurs through the combined action of the proteins Hfq and Crc, which form stable tripartite complexes at target mRNAs, inhibiting their translation. The activity of Hfq/Crc is antagonised by small RNAs of the CrcZ family, the amounts of which vary according to carbon availability. The present work examines the role of Pseudomonas putida Hfq protein under conditions of low-level catabolite repression, in which Crc protein would have a minor role since it is sequestered by CrcZ/CrcY. The results suggest that, under these conditions, Hfq remains operative and plays an important role in iron homeostasis. In this scenario, Crc appears to participate indirectly by helping CrcZ/CrcY to control the amount of free Hfq in the cell. Iron homeostasis in pseudomonads relies on regulatory elements such as the Fur protein, the PrrF1-F2 sRNAs, and several extracytoplasmic sigma factors. Our results show that the absence of Hfq is paralleled by a reduction in PrrF1-F2 small RNAs. Hfq thus provides a regulatory link between iron and carbon metabolism, coordinating the iron supply to meet the needs of the enzymes operational under particular nutritional regimes. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.

PubMed

Sittka, Alexandra; Sharma, Cynthia M; Rolle, Katarzyna; Vogel, Jörg

2009-01-01

The bacterial Sm-like protein, Hfq, is a key factor for the stability and function of small non-coding RNAs (sRNAs) in Escherichia coli. Homologues of this protein have been predicted in many distantly related organisms yet their functional conservation as sRNA-binding proteins has not entirely been clear. To address this, we expressed in Salmonella the Hfq proteins of two eubacteria (Neisseria meningitides, Aquifex aeolicus) and an archaeon (Methanocaldococcus jannaschii), and analyzed the associated RNA by deep sequencing. This in vivo approach identified endogenous Salmonella sRNAs as a major target of the foreign Hfq proteins. New Salmonella sRNA species were also identified, and some of these accumulated specifically in the presence of a foreign Hfq protein. In addition, we observed specific RNA processing defects, e.g., suppression of precursor processing of SraH sRNA by Methanocaldococcus Hfq, or aberrant accumulation of extracytoplasmic target mRNAs of the Salmonella GcvB, MicA or RybB sRNAs. Taken together, our study provides evidence of a conserved inherent sRNA-binding property of Hfq, which may facilitate the lateral transmission of regulatory sRNAs among distantly related species. It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo.

Refractory hypoglycaemia in a dog infected with Trypanosoma congolense

PubMed Central

Deschamps, Jack-Yves; Desquesnes, Marc; Dorso, Laetitia; Ravel, Sophie; Bossard, Géraldine; Charbonneau, Morgane; Garand, Annabelle; Roux, Françoise A.

2016-01-01

A 20 kg German shepherd dog was presented to a French veterinary teaching hospital for seizures and hyperthermia. The dog had returned 1 month previously from a six-month stay in Senegal and sub-Saharan Africa. Biochemistry and haematology showed severe hypoglycaemia (0.12 g/L), anaemia and thrombocytopenia. Despite administration of large amounts of glucose (30 mL of 30% glucose IV and 10 mL of 70% sucrose by gavage tube hourly), 26 consecutive blood glucose measurements were below 0.25 g/L (except one). Routine cytological examination of blood smears revealed numerous free extracytoplasmic protozoa consistent with Trypanosoma congolense. PCR confirmed a Trypanosoma congolense forest-type infection. Treatment consisted of six injections of pentamidine at 48-hour intervals. Trypanosomes had disappeared from the blood smears four days following the first injection. Clinical improvement was correlated with the normalization of laboratory values. The infection relapsed twice and the dog was treated again; clinical signs and parasites disappeared and the dog was considered cured; however, 6 years after this incident, serological examination by ELISA T. congolense was positive. The status of this dog (infected or non-infected) remains unclear. Hypoglycaemia was the most notable clinical feature in this case. It was spectacular in its severity and in its refractory nature; glucose administration seemed only to feed the trypanosomes, indicating that treatment of hypoglycaemia may in fact have been detrimental. PMID:26795063

Molecular evidence that rough endoplasmic reticulum is the site of calreticulin translation in Petunia pollen tubes growing in vitro.

PubMed

Suwińska, Anna; Lenartowski, Robert; Smoliński, Dariusz Jan; Lenartowska, Marta

2015-07-01

In germinating pollen grains and growing pollen tubes, CRT is translated on ER membrane-bound ribosomes in the regions where its activity is required for stabilization of tip-focused Ca (2+) gradient. Pollen tube growth requires coordination of signaling, exocytosis, and actin cytoskeletal organization. Many of these processes are thought to be controlled by finely tuned regulation of cytoplasmic Ca(2+) in discrete regions of the tube cytoplasm. Most notably, a mechanism must function to maintain a steep gradient of Ca(2+) that exists at the tip of growing pollen tube. Several pieces of evidence point to calreticulin (CRT) as a key Ca(2+)-binding/-buffering protein involved in pollen germination and pollen tube growth. We previously hypothesized that in germinating pollen and growing tubes, CRT is translated on the ribosomes associated with endoplasmic reticulum (ER) in the regions where its activity might be required. In this report, we have addressed this idea by identifying the sites where CRT mRNA, CRT protein, 18S rRNA, and rough ER are localized in Petunia pollen tubes. We observed all four components in the germinal aperture of pollen grains and in subapical regions of elongating tubes. These results seem to support our idea that CRT is translated on ER membrane-bound ribosomes during pollen germination and pollen tube growth. In elongated pollen tubes, we found CRT mainly localized in the subapical zone, where ER and Golgi stacks are abundant. In eukaryotic cells, these organelles serve as mobile intracellular stores of easily releasable Ca(2+), which can be buffered by proteins such as CRT. Therefore, we postulate that subapical-localized CRT is involved in pollen tube growth by maintaining the stable tip-focused Ca(2+) gradient and thus modulating local Ca(2+) concentration within the tube cytoplasm.

Shock-induced flow separation and the orbiter thermal protection system

NASA Astrophysics Data System (ADS)

Waiter, S.-A.

The Space Shuttle orbiter's thermal protection system (TPS) is composed of reusable tiles separated by narrow gaps that accommodate the contraction and expansion of the aluminum structure that the tiles protect. When local pressure gradients exist, air flows through the tile gaps and releases heat energy by convection. The gaps represent a heat short to the structure, strain isolator pad (SIP), and filler bar. A typical problem is the pressure gradient created during entry by body flap deflection. After a brief description of how this problem affects the Space Shuttle orbiter, a theoretical and experimental review of the major parameters involved in gap heating are analyzed. Then, a review of well-known classical methods to resolve the gap aeroheating problem in the presence of a pressure gradient is presented, and a few solutions are illustrated to assess the sensitivity of each one. The following section starts with a basic relationship (called "eyeball" because of its simplicity) and follows the results up through the most modern engineering approach available in the literature. It shows that in all cases calculated significant areas of overtemperature were predicted. However, none of these methods could be correlated by experimental data. Lastly, the paper presents the solution obtained by using the most sophisticated method, based upon the Navier-Stokes equations. This approach shows excellent correlation with wind tunnel data. The application to four trajectory time points shows less severe results than the other methods. This can be explained by the introduction of a certain amount of conservatism to account for uncertainties inherent in the previous analyses. No correlation of this "exact solution" with the simple preestablished relationships has been found, indicating that more parameters than expected could be involved. However, an after-the-fact, semi-empirical engineering solution that fits the Navier-Stokes solution with good agreement was established.

A theoretical study of thorium titanium-based alloys

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Chetty, N.

2013-09-01

Using theoretical quantum chemical methods, we investigate the dearth of ordered alloys involving thorium and titanium. Whereas both these elements are known to alloy very readily with various other elements, for example with oxygen, current experimental data suggests that Th and Ti do not alloy very readily with each other. In this work, we consider a variety of ordered alloys at varying stoichiometries involving these elements within the framework of density functional theory using the generalized gradient approximation for the exchange and correlation functional. By probing the energetics, electronic, phonon and elastic properties of these systems, we confirm the scarcity of ordered alloys involving Th and Ti, since for a variety of reasons many of the systems that we considered were found to be unfavorable. However, our investigations resulted in one plausible ordered structure: We propose ThTi3 in the Cr3Si structure as a metastable ordered alloy.

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

Sueyoshi, Eijun, E-mail: EijunSueyoshi@aol.com; Sakamoto, Ichiro; Okimoto, Tomoaki

Amyloidosis is a rare systemic disease. However, involvement of the heart is a common finding and is the most frequent cause of death in amyloidosis. We report the sonographic, scintigraphic, and MRI features of a pathologically proven case of cardiac amyloidosis. Delayed contrast-enhanced MR images, using an inversion recovery prepped gradient-echo sequence, revealed diffuse enhancement in the wall of both left and right ventricles. This enhancement suggested expansion of the extracellular space of the myocardium caused by diffuse myocardial necrosis secondary to deposition of amyloid.

Optimal startup control of a jacketed tubular reactor.

NASA Technical Reports Server (NTRS)

Hahn, D. R.; Fan, L. T.; Hwang, C. L.

1971-01-01

The optimal startup policy of a jacketed tubular reactor, in which a first-order, reversible, exothermic reaction takes place, is presented. A distributed maximum principle is presented for determining weak necessary conditions for optimality of a diffusional distributed parameter system. A numerical technique is developed for practical implementation of the distributed maximum principle. This involves the sequential solution of the state and adjoint equations, in conjunction with a functional gradient technique for iteratively improving the control function.

Heat Pipe Thermal Conditioning Panel

NASA Technical Reports Server (NTRS)

Saaski, E. W.

1973-01-01

The technology involved in designing and fabricating a heat pipe thermal conditioning panel to satisfy a broad range of thermal control system requirements on NASA spacecraft is discussed. The design specifications were developed for a 30 by 30 inch heat pipe panel. The fundamental constraint was a maximum of 15 gradient from source to sink at 300 watts input and a flux density of 2 watts per square inch. The results of the performance tests conducted on the panel are analyzed.

Gas Diffusion in Fluids Containing Bubbles

NASA Technical Reports Server (NTRS)

Zak, M.; Weinberg, M. C.

1982-01-01

Mathematical model describes movement of gases in fluid containing many bubbles. Model makes it possible to predict growth and shrink age of bubbles as function of time. New model overcomes complexities involved in analysis of varying conditions by making two simplifying assumptions. It treats bubbles as point sources, and it employs approximate expression for gas concentration gradient at liquid/bubble interface. In particular, it is expected to help in developing processes for production of high-quality optical glasses in space.

Studying neuronal biomechanics and its role in CNS development

NASA Astrophysics Data System (ADS)

Franze, Kristian; Svoboda, Hanno; da F. Costa, Luciano; Guck, Jochen; Holt, Christine

2013-03-01

During the development of the nervous system, neurons migrate and grow over great distances. Currently, our understanding of nervous tissue development is, in large part, based on studies of biochemical signaling. Despite the fact that forces are involved in any kind of cell motion, mechanical aspects have so far rarely been considered. Here we used deformable cell culture substrates, traction force microscopy and calcium imaging to investigate how neurons probe and respond to their mechanical environment. While the growth rate of retinal ganglion cell axons was increased on stiffer substrates, their tendency to grow in bundles, which they show in vivo, was significantly enhanced on more compliant substrates. Moreover, if grown on substrates incorporating linear stiffness gradients, neuronal axons were repelled by stiff substrates. Mechanosensing involved the application of forces driven by the interaction of actin and myosin II, and the activation of stretch-activated ion channels leading to calcium influxes into the cells. Applying a modified atomic force microscopy techniquein vivo, we found mechanical gradients in developing brain tissue along which neurons grow. The application of chondroitin sulfate, which is a major extracellular matrix component in the developing brain, changed tissue mechanics and disrupted axonal pathfinding. Hence, our data suggest that neuronal growth is not only guided by chemical signals - as it is currently assumed - but also by the nervous tissue's mechanical properties.

Comparative expression profiling of AtRAD5B and AtNDL1: Hints towards a role in G protein mediated signaling.

PubMed

Khatri, Nisha; Singh, Swati; Hakim, Nasmeen; Mudgil, Yashwanti

2017-11-01

Arabidopsis AtRAD5B encodes for a putative helicase of the class SWItch/Sucrose Non-Fermentable (SWI/SNF) ATPases. We identified AtRAD5B as an interactor of N-MYC DOWNREGULATED-LIKE1 (AtNDL1) in a yeast two-hybrid screen. AtNDL1 is a G protein signaling component which regulates auxin transport and gradients together with GTP binding protein beta 1 (AGB1). Auxin gradients are known to recruit SWI/SNF remodeling complexes to the chromatin and regulate expression of genes involved in flower and leaf formation. In current study, a comparative spatial and temporal co-expression/localization analysis of AtNDL1, AGB1 with AtRAD5B was carried out in order to explore the possibility of their coexistence in a common signaling network. Translational fusion (GUS) of AtNDL1 and AtRAD5B in seedlings and reproductive organs revealed that both shared similar expression patterns with the highest expression observed in male reproductive organs. Moreover, they shared similar domains of localization in roots, suggesting their potential functioning together in reproductive and root development processes. This study predicts the existence of a signaling network involving AtNDL1, AGB1 with AtRAD5B. Copyright © 2017 Elsevier B.V. All rights reserved.

N-WASP and cortactin are involved in invadopodium-dependent chemotaxis to EGF in breast tumor cells

PubMed Central

DesMarais, Vera; Yamaguchi, Hideki; Oser, Matthew; Soon, Lilian; Mouneimne, Ghassan; Sarmiento, Corina; Eddy, Robert; Condeelis, John

2009-01-01

Metastatic mammary carcinoma cells, which have previously been observed to form mature, matrix degrading invadopodia on a thick ECM matrix, are able to form invadopodia with similar characteristics on glass without previously applied matrix. They form in response to EGF, and contain the usual invadopodium core proteins N-WASP, Arp2/3, cortactin, cofilin, and F-actin. The study of invadopodia on glass allows for higher resolution analysis including the use of total internal reflection microscopy and analysis of their relationship to other cell motility events, in particular, lamellipodium extension and chemotaxis toward an EGF gradient. Invadopodium formation on glass requires N-WASP and cortactin but not microtubules. In a gradient of EGF more invadopodia form on the side of the cells facing the source of EGF. In addition, depletion of N-WASP or cortactin, which blocks invadopodium fromation, inhibits chemotaxis of cells towards EGF. This appears to be a localized defect in chemotaxis since depletion of N-WASP or cortactin via siRNA had no effect on lamellipodium protrusion or barbed end generation at the lamellipodium's leading edge. Since chemotaxis to EGF by breast tumor cells is involved in metastasis, inhibiting N-WASP activity in breast tumor cells might prevent metastasis of tumor cells while not affecting chemotaxis-dependent innate immunity which depends on WASp function in macrophages. PMID:19373774

Neoclassical, semi-collisional tearing mode theory in an axisymmetric torus

NASA Astrophysics Data System (ADS)

Connor, J. W.; Hastie, R. J.; Helander, P.

2017-12-01

A set of layer equations for determining the stability of semi-collisional tearing modes in an axisymmetric torus, incorporating neoclassical physics, in the small ion Larmor radius limit, is provided. These can be used as an inner layer module for inclusion in numerical codes that asymptotically match the layer to toroidal calculations of the tearing mode stability index, \\prime $ . They are more complete than in earlier work and comprise equations for the perturbed electron density and temperature, the ion temperature, Ampère's law and the vorticity equation, amounting to a twelvth-order set of radial differential equations. While the toroidal geometry is kept quite general when treating the classical and Pfirsch-Schlüter transport, parallel bootstrap current and semi-collisional physics, it is assumed that the fraction of trapped particles is small for the banana regime contribution. This is to justify the use of a model collision term when acting on the localised (in velocity space) solutions that remain after the Spitzer solutions have been exploited to account for the bulk of the passing distributions. In this respect, unlike standard neoclassical transport theory, the calculation involves the second Spitzer solution connected with a parallel temperature gradient, because this stability problem involves parallel temperature gradients that cannot occur in equilibrium toroidal transport theory. Furthermore, a calculation of the linearised neoclassical radial transport of toroidal momentum for general geometry is required to complete the vorticity equation. The solutions of the resulting set of equations do not match properly to the ideal magnetohydrodynamic (MHD) equations at large distances from the layer, and a further, intermediate layer involving ion corrections to the electrical conductivity and ion parallel thermal transport is invoked to achieve this matching and allow one to correctly calculate the layer \\prime $ .

Recognition of mite-infested brood by honeybee (Apis mellifera) workers may involve thermal sensing.

PubMed

Bauer, Daniel; Wegener, Jakob; Bienefeld, Kaspar

2018-05-01

Hygienic behavior, i.e. the removal of diseased or damaged brood by worker honey bees (Apis mellifera), is seen as one of the principal behavioral elements of this species' social immunity. Identification of the stimuli that trigger it would be helpful in searching for biochemical and molecular markers of this important breeding trait. While many studies at the genomic, transcriptomic, and behavioral level have pointed to the implication of chemical cues, we here hypothesized that thermal cues are alternatively/additionally involved. To test this hypothesis, we first measured whether infestation by the mite Varroa destructor (a condition known to induce hygienic behavior) leads to a thermal gradient between affected and unaffected brood. We found that infested brood cells were between 0.03 and 0.19 °C warmer than uninfested controls. Next, we tested whether artificially heating an area of a brood comb would increase the removal of infested or uninfested brood as compared to an unheated control area, and found that this was not the case. Finally, we investigated whether the heating of individual brood cells, as opposed to comb areas, would influence brood removal from cells adjacent to the heated one. This was the case for uninfested, though not for infested cells. We conclude that infestation by V. destructor leads to a heating of brood cells that should be perceivable by bees, and that small-scale temperature gradients can influence brood removal. This makes it appear possible that thermal cues play a role in triggering hygienic behavior of honey bees directed at varroa-infested larvae/pupae, although our results are insufficient to prove such an involvement. Copyright © 2018. Published by Elsevier Ltd.

Gradient-based multiconfiguration Shepard interpolation for generating potential energy surfaces for polyatomic reactions.

PubMed

Tishchenko, Oksana; Truhlar, Donald G

2010-02-28

This paper describes and illustrates a way to construct multidimensional representations of reactive potential energy surfaces (PESs) by a multiconfiguration Shepard interpolation (MCSI) method based only on gradient information, that is, without using any Hessian information from electronic structure calculations. MCSI, which is called multiconfiguration molecular mechanics (MCMM) in previous articles, is a semiautomated method designed for constructing full-dimensional PESs for subsequent dynamics calculations (classical trajectories, full quantum dynamics, or variational transition state theory with multidimensional tunneling). The MCSI method is based on Shepard interpolation of Taylor series expansions of the coupling term of a 2 x 2 electronically diabatic Hamiltonian matrix with the diagonal elements representing nonreactive analytical PESs for reactants and products. In contrast to the previously developed method, these expansions are truncated in the present version at the first order, and, therefore, no input of electronic structure Hessians is required. The accuracy of the interpolated energies is evaluated for two test reactions, namely, the reaction OH+H(2)-->H(2)O+H and the hydrogen atom abstraction from a model of alpha-tocopherol by methyl radical. The latter reaction involves 38 atoms and a 108-dimensional PES. The mean unsigned errors averaged over a wide range of representative nuclear configurations (corresponding to an energy range of 19.5 kcal/mol in the former case and 32 kcal/mol in the latter) are found to be within 1 kcal/mol for both reactions, based on 13 gradients in one case and 11 in the other. The gradient-based MCMM method can be applied for efficient representations of multidimensional PESs in cases where analytical electronic structure Hessians are too expensive or unavailable, and it provides new opportunities to employ high-level electronic structure calculations for dynamics at an affordable cost.

Finite-frequency tomography using adjoint methods-Methodology and examples using membrane surface waves

NASA Astrophysics Data System (ADS)

Tape, Carl; Liu, Qinya; Tromp, Jeroen

2007-03-01

We employ adjoint methods in a series of synthetic seismic tomography experiments to recover surface wave phase-speed models of southern California. Our approach involves computing the Fréchet derivative for tomographic inversions via the interaction between a forward wavefield, propagating from the source to the receivers, and an `adjoint' wavefield, propagating from the receivers back to the source. The forward wavefield is computed using a 2-D spectral-element method (SEM) and a phase-speed model for southern California. A `target' phase-speed model is used to generate the `data' at the receivers. We specify an objective or misfit function that defines a measure of misfit between data and synthetics. For a given receiver, the remaining differences between data and synthetics are time-reversed and used as the source of the adjoint wavefield. For each earthquake, the interaction between the regular and adjoint wavefields is used to construct finite-frequency sensitivity kernels, which we call event kernels. An event kernel may be thought of as a weighted sum of phase-specific (e.g. P) banana-doughnut kernels, with weights determined by the measurements. The overall sensitivity is simply the sum of event kernels, which defines the misfit kernel. The misfit kernel is multiplied by convenient orthonormal basis functions that are embedded in the SEM code, resulting in the gradient of the misfit function, that is, the Fréchet derivative. A non-linear conjugate gradient algorithm is used to iteratively improve the model while reducing the misfit function. We illustrate the construction of the gradient and the minimization algorithm, and consider various tomographic experiments, including source inversions, structural inversions and joint source-structure inversions. Finally, we draw connections between classical Hessian-based tomography and gradient-based adjoint tomography.

Electrically controlled lens and prism using nanoscale polymer-dispersed and polymer-networked liquid crystals

NASA Astrophysics Data System (ADS)

Fan, Yun Hsing; Ren, Hongwen; Wu, Shin Tson

2004-05-01

Inhomogeneous nanoscale polymer-dispersed liquid crystal (PDLC) devices having gradient nanoscale droplet distribution were fabricated. This gradient refractive index nanoscale (GRIN) PDLC film was obtained by exposing the LC/ monomer with a uniform ultraviolet (UV) light through a patterned photomask. The monomer and LC were mixed at 70: 30 wt% ratio. The area exposed to a weaker UV intensity would produce a larger droplet size, and vice versa. Owing to the nanoscale LC droplets involved, the GRIN PDLC devices are highly transparent in the whole visible region. The gradient refractive index profile can be used as switchable prism gratings, Fresnel lens, and positive and negative lenses with tunable focal lengths. Such a GRIN PDLC device is a broadband device and independent of light polarization. The diffraction efficiency of the lens is controllable by the applied voltage. The major advantages of the GRIN PDLC devices are in simple fabrication process, polarization-independent, and fast switching speed, although the required driving voltage is higher than 100 Vrms. To lower the driving voltage, the technique of polymer-networked liquid crystal (PNLC) has been developed. The PNLC was also produced by exposing the LC/monomer mixture with a uniform UV light through a patterned photomask. However, the monomer concentration in PNLC is only around 2-5 wt%. The formed PNLC structure exhibits a gradient polymer network distribution. The LC in the regions stabilized by a higher polymer concentration exhibits a higher threshold voltage. By using this technique, prism grating, tunable electronic lens and Fresnel lens have been demonstrated. The driving voltage is around 10 Vrms. A drawback of this kind of device is polarization dependence. To overcome the polarization dependence, stacking two orthogonal homogeneous PNLC lens is considered.

A New Kind of Single-Well Tracer Test for Assessing Subsurface Heterogeneity

NASA Astrophysics Data System (ADS)

Hansen, S. K.; Vesselinov, V. V.; Lu, Z.; Reimus, P. W.; Katzman, D.

2017-12-01

Single-well injection-withdrawal (SWIW) tracer tests have historically been interpreted using the idealized assumption of tracer path reversibility (i.e., negligible background flow), with background flow due to natural hydraulic gradient being an un-modeled confounding factor. However, we have recently discovered that it is possible to use background flow to our advantage to extract additional information about the subsurface. To wit: we have developed a new kind of single-well tracer test that exploits flow due to natural gradient to estimate the variance of the log hydraulic conductivity field of a heterogeneous aquifer. The test methodology involves injection under forced gradient and withdrawal under natural gradient, and makes use of a relationship, discovered using a large-scale Monte Carlo study and machine learning techniques, between power law breakthrough curve tail exponent and log-hydraulic conductivity variance. We will discuss how we performed the computational study and derived this relationship and then show an application example in which our new single-well tracer test interpretation scheme was applied to estimation of heterogeneity of a formation at the chromium contamination site at Los Alamos National Laboratory. Detailed core hole records exist at the same site, from which it was possible to estimate the log hydraulic conductivity variance using a Kozeny-Carman relation. The variances estimated using our new tracer test methodology and estimated by direct inspection of core were nearly identical, corroborating the new methodology. Assessment of aquifer heterogeneity is of critical importance to deployment of amendments associated with in-situ remediation strategies, since permeability contrasts potentially reduce the interaction between amendment and contaminant. Our new tracer test provides an easy way to obtain this information.

Calreticulin is required for calcium homeostasis and proper pollen tube tip growth in Petunia.

PubMed

Suwińska, Anna; Wasąg, Piotr; Zakrzewski, Przemysław; Lenartowska, Marta; Lenartowski, Robert

2017-05-01

Calreticulin is involved in stabilization of the tip-focused Ca 2+ gradient and the actin cytoskeleton arrangement and function that is required for several key processes driving Petunia pollen tube tip growth. Although the precise mechanism is unclear, stabilization of a tip-focused calcium (Ca 2+ ) gradient seems to be critical for pollen germination and pollen tube growth. We hypothesize that calreticulin (CRT), a Ca 2+ -binding/buffering chaperone typically residing in the lumen of the endoplasmic reticulum (ER) of eukaryotic cells, is an excellent candidate to fulfill this role. We previously showed that in Petunia pollen tubes growing in vitro, CRT is translated on ER membrane-bound ribosomes that are abundant in the subapical zone of the tube, where CRT's Ca 2+ -buffering and chaperone activities might be particularly required. Here, we sought to determine the function of CRT using small interfering RNA (siRNA) to, for the first time in pollen tubes growing in vitro, knockdown expression of a gene. We demonstrate that siRNA-mediated post-transcriptional silencing of Petunia hybrida CRT gene (PhCRT) expression strongly impairs pollen tube growth, cytoplasmic zonation, actin cytoskeleton organization, and the tip-focused Ca 2+ gradient. Moreover, reduction of CRT alters the localization and disturbs the structure of the ER in abnormally elongating pollen tubes. Finally, cytoplasmic streaming is inhibited, and most of the pollen tubes rupture. Our data clearly show an interplay between CRT, Ca 2+ gradient, actin-dependent cytoplasmic streaming, organelle positioning, and vesicle trafficking during pollen tube elongation. Thus, we suggest that CRT functions in Petunia pollen tube growth by stabilizing Ca 2+ homeostasis and acting as a chaperone to assure quality control of glycoproteins passing through the ER.

The Grism Lens-amplified Survey from Space (GLASS). X. Sub-kiloparsec Resolution Gas-phase Metallicity Maps at Cosmic Noon behind the Hubble Frontier Fields Cluster MACS1149.6+2223

NASA Astrophysics Data System (ADS)

Wang, Xin; Jones, Tucker A.; Treu, Tommaso; Morishita, Takahiro; Abramson, Louis E.; Brammer, Gabriel B.; Huang, Kuang-Han; Malkan, Matthew A.; Schmidt, Kasper B.; Fontana, Adriano; Grillo, Claudio; Henry, Alaina L.; Karman, Wouter; Kelly, Patrick L.; Mason, Charlotte A.; Mercurio, Amata; Rosati, Piero; Sharon, Keren; Trenti, Michele; Vulcani, Benedetta

2017-03-01

We combine deep Hubble Space Telescope grism spectroscopy with a new Bayesian method to derive maps of gas-phase metallicity for 10 star-forming galaxies at high redshift (1.2≲ z≲ 2.3). Exploiting lensing magnification by the foreground cluster MACS1149.6+2223, we reach sub-kiloparsec spatial resolution and push the limit of stellar mass associated with such high-z spatially resolved measurements below {10}8 {M}⊙ for the first time. Our maps exhibit diverse morphologies, indicative of various effects such as efficient radial mixing from tidal torques, rapid accretion of low-metallicity gas, and other physical processes that can affect the gas and metallicity distributions in individual galaxies. Based upon an exhaustive sample of all existing sub-kiloparesec resolution metallicity gradient measurements at high z, we find that predictions given by analytical chemical evolution models assuming a relatively extended star-formation profile in the early disk-formation phase can explain the majority of observed metallicity gradients, without involving galactic feedback or radial outflows. We observe a tentative correlation between stellar mass and metallicity gradients, consistent with the “downsizing” galaxy formation picture that more massive galaxies are more evolved into a later phase of disk growth, where they experience more coherent mass assembly at all radii and thus show shallower metallicity gradients. In addition to the spatially resolved analysis, we compile a sample of homogeneously cross-calibrated integrated metallicity measurements spanning three orders of magnitude in stellar mass at z ˜ 1.8. We use this sample to study the mass-metallicity relation (MZR) and find that the slope of the observed MZR can rule out the momentum-driven wind model at a 3σ confidence level.

The effect of temperature, gradient, and load carriage on oxygen consumption, posture, and gait characteristics.

PubMed

Hinde, Katrina; Lloyd, Ray; Low, Chris; Cooke, Carlton

2017-03-01

The purpose of this experiment was to evaluate the effect of load carriage in a range of temperatures to establish the interaction between cold exposure, the magnitude of change from unloaded to loaded walking and gradient. Eleven participants (19-27 years) provided written informed consent before performing six randomly ordered walking trials in six temperatures (20, 10, 5, 0, -5, and -10 °C). Trials involved two unloaded walking bouts before and after loaded walking (18.2 kg) at 4 km · h -1 , on 0 and 10% gradients in 4 min bouts. The change in absolute oxygen consumption (V̇O 2 ) from the first unloaded bout to loaded walking was similar across all six temperatures. When repeating the second unloaded bout, V̇O 2 at both -5 and -10 °C was greater compared to the first. At -10 °C, V̇O 2 was increased from 1.60 ± 0.30 to 1.89 ± 0.51 L · min -1 . Regardless of temperature, gradient had a greater effect on V̇O 2 and heart rate (HR) than backpack load. HR was unaffected by temperature. Stride length (SL) decreased with decreasing temperature, but trunk forward lean was greater during cold exposure. Decreased ambient temperature did not influence the magnitude of change in V̇O 2 from unloaded to loaded walking. However, in cold temperatures, V̇O 2 was significantly higher than in warm conditions. The increased V̇O 2 in colder temperatures at the same exercise intensity is predicted to ultimately lead to earlier onset of fatigue and cessation of exercise. These results highlight the need to consider both appropriate clothing and fitness during cold exposure.

Establishment of spatial pattern.

PubMed

Slack, Jonathan

2014-01-01

An overview and perspective are presented of mechanisms for the development of spatial pattern in animal embryos. It is intended both for new entrants to developmental biology and for specialists in other fields, with only a basic knowledge of animal life cycles being required. The first event of pattern formation is normally the localization of a cytoplasmic determinant in the egg, either during oogenesis or post-fertilization. Following cleavage to a multicellular stage, some cells contain the determinant and others do not. The determinant confers a specific developmental pathway on the cells that contain it, often making them the source of the first extracellular signal, or inducing factor. Inducing factors often form concentration gradients to which cells respond by up or downregulating genes at various concentration thresholds. This enables an initial situation consisting of two cell states (with or without the determinant) to generate a multistate pattern. Multiple rounds of gradient signaling, interspersed with phases of morphogenetic movements, can generate a complex pattern using a small number of signals and responding genes. Development proceeds in a hierarchical manner, with broad body subdivisions being specified initially, and becoming successively subdivided to give individual organs and tissues composed of multiple cell types in a characteristic arrangement. Double gradient models can account for embryonic regulation, whereby a similarly proportioned body pattern is formed following removal of material. Processes that are involved at the later stages include the formation of repeating structures by the combination of an oscillator with a gradient, and the formation of tissues with one cell type scattered in a background of another through a process called lateral inhibition. This set of processes make up a 'developmental toolkit' which can be deployed in various sequences and combinations to generate a very wide variety of structures and cell types. © 2014 Wiley Periodicals, Inc.

Generation of dark solitons and their instability dynamics in two-dimensional condensates

NASA Astrophysics Data System (ADS)

Verma, Gunjan; Rapol, Umakant D.; Nath, Rejish

2017-04-01

We analyze numerically the formation and the subsequent dynamics of two-dimensional matter wave dark solitons in a Thomas-Fermi rubidium condensate using various techniques. An initially imprinted sharp phase gradient leads to the dynamical formation of a stationary soliton as well as very shallow gray solitons, whereas a smooth gradient only creates gray solitons. The depth and hence, the velocity of the soliton is provided by the spatial width of the phase gradient, and it also strongly influences the snake-instability dynamics of the two-dimensional solitons. The vortex dipoles stemming from the unstable soliton exhibit rich dynamics. Notably, the annihilation of a vortex dipole via a transient dark lump or a vortexonium state, the exchange of vortices between either a pair of vortex dipoles or a vortex dipole and a single vortex, and so on. For sufficiently large width of the initial phase gradient, the solitons may decay directly into vortexoniums instead of vortex pairs, and also the decay rate is augmented. Later, we discuss alternative techniques to generate dark solitons, which involve a Gaussian potential barrier and time-dependent interactions, both linear and periodic. The properties of the solitons can be controlled by tuning the amplitude or the width of the potential barrier. In the linear case, the number of solitons and their depths are determined by the quench time of the interactions. For the periodic modulation, a transient soliton lattice emerges with its periodicity depending on the modulation frequency, through a wave number selection governed by the local Bogoliubov spectrum. Interestingly, for sufficiently low barrier potential, both Faraday pattern and soliton lattice coexist. The snake instability dynamics of the soliton lattice is characteristically modified if the Faraday pattern is present.

Nonadiabatic excited-state molecular dynamics: modeling photophysics in organic conjugated materials.

PubMed

Nelson, Tammie; Fernandez-Alberti, Sebastian; Roitberg, Adrian E; Tretiak, Sergei

2014-04-15

To design functional photoactive materials for a variety of technological applications, researchers need to understand their electronic properties in detail and have ways to control their photoinduced pathways. When excited by photons of light, organic conjugated materials (OCMs) show dynamics that are often characterized by large nonadiabatic (NA) couplings between multiple excited states through a breakdown of the Born-Oppenheimer (BO) approximation. Following photoexcitation, various nonradiative intraband relaxation pathways can lead to a number of complex processes. Therefore, computational simulation of nonadiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons. Over the years, we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework that efficiently and accurately describes photoinduced phenomena in extended conjugated molecular systems. We use the fewest-switches surface hopping (FSSH) algorithm to treat quantum transitions among multiple adiabatic excited state potential energy surfaces (PESs). Extended molecular systems often contain hundreds of atoms and involve large densities of excited states that participate in the photoinduced dynamics. We can achieve an accurate description of the multiple excited states using the configuration interaction single (CIS) formalism with a semiempirical model Hamiltonian. Analytical techniques allow the trajectory to be propagated "on the fly" using the complete set of NA coupling terms and remove computational bottlenecks in the evaluation of excited-state gradients and NA couplings. Furthermore, the use of state-specific gradients for propagation of nuclei on the native excited-state PES eliminates the need for simplifications such as the classical path approximation (CPA), which only uses ground-state gradients. Thus, the NA-ESMD methodology offers a computationally tractable route for simulating hundreds of atoms on ~10 ps time scales where multiple coupled excited states are involved. In this Account, we review recent developments in the NA-ESMD modeling of photoinduced dynamics in extended conjugated molecules involving multiple coupled electronic states. We have successfully applied the outlined NA-ESMD framework to study ultrafast conformational planarization in polyfluorenes where the rate of torsional relaxation can be controlled based on the initial excitation. With the addition of the state reassignment algorithm to identify instances of unavoided crossings between noninteracting PESs, NA-ESMD can now be used to study systems in which these so-called trivial unavoided crossings are expected to predominate. We employ this technique to analyze the energy transfer between poly(phenylene vinylene) (PPV) segments where conformational fluctuations give rise to numerous instances of unavoided crossings leading to multiple pathways and complex energy transfer dynamics that cannot be described using a simple Förster model. In addition, we have investigated the mechanism of ultrafast unidirectional energy transfer in dendrimers composed of poly(phenylene ethynylene) (PPE) chromophores and have demonstrated that differential nuclear motion favors downhill energy transfer in dendrimers. The use of native excited-state gradients allows us to observe this feature.

Superelliptical insert gradient coil with a field-modifying layer for breast imaging.

PubMed

Moon, Sung M; Goodrich, K Craig; Hadley, J Rock; Kim, Seong-Eun; Zeng, Gengsheng L; Morrell, Glen R; McAlpine, Matthew A; Chronik, Blaine A; Parker, Dennis L

2011-03-01

Many MRI applications such as dynamic contrast-enhanced MRI of the breast require high spatial and temporal resolution and can benefit from improved gradient performance, e.g., increased gradient strength and reduced gradient rise time. The improved gradient performance required to achieve high spatial and temporal resolution for this application may be achieved by using local insert gradients specifically designed for a target anatomy. Current flat gradient systems cannot create an imaging volume large enough to accommodate both breasts; further, their gradient fields are not homogeneous, dropping off rapidly with distance from the gradient coil surface. To attain an imaging volume adequate for bilateral breast MRI, a planar local gradient system design has been modified into a superellipse shape, creating homogeneous gradient volumes that are 182% (Gx), 57% (Gy), and 75% (Gz) wider (left/right direction) than those of the corresponding standard planar gradient. Adding an additional field-modifying gradient winding results in an additional improvement of the homogeneous gradient field near the gradient coil surface over the already enlarged homogeneous gradient volumes of the superelliptical gradients (67%, 89%, and 214% for Gx, Gy, and Gz respectively). A prototype y-gradient insert has been built to demonstrate imaging and implementation characteristics of the superellipse gradient in a 3 T MRI system. Copyright © 2010 Wiley-Liss, Inc.

A Strategy to Validate the Role of Callose-mediated Plasmodesmal Gating in the Tropic Response.

PubMed

Kumar, Ritesh; Wu, Shu Wei; Iswanto, Arya Bagus Boedi; Kumar, Dhinesh; Han, Xiao; Kim, Jae-Yean

2016-04-17

The plant hormone auxin plays an important role in many growth and developmental processes, including tropic responses to light and gravity. The establishment of an auxin gradient is a key event leading to phototropism and gravitropism. Previously, polar auxin transport (PAT) was shown to establish an auxin gradient in different cellular domains of plants. However, Han et al. recently demonstrated that for proper auxin gradient formation, plasmodesmal callose-mediated symplasmic connectivity between the adjacent cells is also a critical factor. In this manuscript, the strategy to elucidate the role of particular genes, which can affect phototropism and gravitropism by altering the symplasmic connectivity through modulating plasmodesmal callose synthesis, is discussed. The first step is to screen aberrant tropic responses from 3-day-old etiolated seedlings of mutants or over-expression lines of a gene along with the wild type. This preliminary screening can lead to the identification of a range of genes functioning in PAT or controlling symplasmic connectivity. The second screening involves the sorting of candidates that show altered tropic responses by affecting symplasmic connectivity. To address such candidates, the movement of a symplasmic tracer and the deposition of plasmodesmal callose were examined. This strategy would be useful to explore new candidate genes that can regulate symplasmic connectivity directly or indirectly during tropic responses and other developmental processes.

Segmentation of knee MRI using structure enhanced local phase filtering

NASA Astrophysics Data System (ADS)

Lim, Mikhiel; Hacihaliloglu, Ilker

2016-03-01

The segmentation of bone surfaces from magnetic resonance imaging (MRI) data has applications in the quanti- tative measurement of knee osteoarthritis, surgery planning for patient specific total knee arthroplasty and its subsequent fabrication of artificial implants. However, due to the problems associated with MRI imaging such as low contrast between bone and surrounding tissues, noise, bias fields, and the partial volume effect, segmentation of bone surfaces continues to be a challenging operation. In this paper, a new framework is presented for the enhancement of knee MRI scans prior to segmentation in order to obtain high contrast bone images. During the first stage, a new contrast enhanced relative total variation (RTV) regularization method is used in order to remove textural noise from the bone structures and surrounding soft tissue interface. This salient bone edge information is further enhanced using a sparse gradient counting method based on L0 gradient minimization, which globally controls how many non-zero gradients are resulted in order to approximate prominent bone structures in a structure-sparsity-management manner. The last stage of the framework involves incorporation of local phase bone boundary information in order to provide an intensity invariant enhancement of contrast between the bone and surrounding soft tissue. The enhanced images are segmented using a fast random walker algorithm. Validation against expert segmentation was performed on 10 clinical knee MRI images, and achieved a mean dice similarity coefficient (DSC) of 0.975.

Design and Construction of a Dual Anti-Helmholtz Magnet System for a Side-by-Side MOT

NASA Astrophysics Data System (ADS)

Narducci, Frank; Prasher, Rebecca; Adler, Charles

2012-06-01

The design of a cold-atom interferometric gradient magnetometer [1] requires two side-by-side identical atom clouds separated by approximately 1 cm for noise reduction purposes. The first step in building this system is a side-by-side MOT to capture the atoms; however, the design of a coil system to provide two zero field crossings with high field gradients separated by a small distance with low power consumption can be challenging. These three requirements are not easy to satisfy simultaneously, but there is a large ``state space'' in which we can evolve different designs. In this poster we analyze the requirements for such a system and discuss our design consisting of coils with wires wrapped on a truncated cone; this type of design has been made possible by recent advances in 3D printers, and we will go over the issues involved in printing the coil supports, building the coils and comparison of our measurements of the magnetic field to theory. We also discuss the possibility of optimizing coil design using state space searches like the Metropolis algorithm, and how these designs can be realized using 3D printing technology. [4pt] [1] Davis, J. P. and Narducci, F. A.(2008) ``A proposal for a gradient magnetometer atom interferometer,'' Journal of Modern Optics,55:19,3173 --- 3185

The lagRST Model: A Turbulence Model for Non-Equilibrium Flows

NASA Technical Reports Server (NTRS)

Lillard, Randolph P.; Oliver, A. Brandon; Olsen, Michael E.; Blaisdell, Gregory A.; Lyrintzis, Anastasios S.

2011-01-01

This study presents a new class of turbulence model designed for wall bounded, high Reynolds number flows with separation. The model addresses deficiencies seen in the modeling of nonequilibrium turbulent flows. These flows generally have variable adverse pressure gradients which cause the turbulent quantities to react at a finite rate to changes in the mean flow quantities. This "lag" in the response of the turbulent quantities can t be modeled by most standard turbulence models, which are designed to model equilibrium turbulent boundary layers. The model presented uses a standard 2-equation model as the baseline for turbulent equilibrium calculations, but adds transport equations to account directly for non-equilibrium effects in the Reynolds Stress Tensor (RST) that are seen in large pressure gradients involving shock waves and separation. Comparisons are made to several standard turbulence modeling validation cases, including an incompressible boundary layer (both neutral and adverse pressure gradients), an incompressible mixing layer and a transonic bump flow. In addition, a hypersonic Shock Wave Turbulent Boundary Layer Interaction with separation is assessed along with a transonic capsule flow. Results show a substantial improvement over the baseline models for transonic separated flows. The results are mixed for the SWTBLI flows assessed. Separation predictions are not as good as the baseline models, but the over prediction of the peak heat flux downstream of the reattachment shock that plagues many models is reduced.

Adaptive root foraging strategies along a boreal-temperate forest gradient.

PubMed

Ostonen, Ivika; Truu, Marika; Helmisaari, Heljä-Sisko; Lukac, Martin; Borken, Werner; Vanguelova, Elena; Godbold, Douglas L; Lõhmus, Krista; Zang, Ulrich; Tedersoo, Leho; Preem, Jens-Konrad; Rosenvald, Katrin; Aosaar, Jürgen; Armolaitis, Kęstutis; Frey, Jane; Kabral, Naima; Kukumägi, Mai; Leppälammi-Kujansuu, Jaana; Lindroos, Antti-Jussi; Merilä, Päivi; Napa, Ülle; Nöjd, Pekka; Parts, Kaarin; Uri, Veiko; Varik, Mats; Truu, Jaak

2017-08-01

The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

EFFECTS OF NON-CIRCULAR MOTIONS ON AZIMUTHAL COLOR GRADIENTS

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

Martinez-Garcia, Eric E.; Gonzalez-Lopezlira, Rosa A.; Gomez, Gilberto C., E-mail: emartinez@cida.v, E-mail: r.gonzalez@crya.unam.m, E-mail: g.gomez@crya.unam.m

2009-12-20

Assuming that density waves trigger star formation, and that young stars preserve the velocity components of the molecular gas where they are born, we analyze the effects that non-circular gas orbits have on color gradients across spiral arms. We try two approaches, one involving semianalytical solutions for spiral shocks, and another with magnetohydrodynamic (MHD) numerical simulation data. We find that, if non-circular motions are ignored, the comparison between observed color gradients and stellar population synthesis models would in principle yield pattern speed values that are systematically too high for regions inside corotation, with the difference between the real and themore » measured pattern speeds increasing with decreasing radius. On the other hand, image processing and pixel averaging result in systematically lower measured spiral pattern speed values, regardless of the kinematics of stellar orbits. The net effect is that roughly the correct pattern speeds are recovered, although the trend of higher measured OMEGA{sub p} at lower radii (as expected when non-circular motions exist but are neglected) should still be observed. We examine the MartInez-GarcIa et al. photometric data and confirm that this is indeed the case. The comparison of the size of the systematic pattern speed offset in the data with the predictions of the semianalytical and MHD models corroborates that spirals are more likely to end at outer Lindblad resonance, as these authors had already found.« less

Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

PubMed

Shrot, Yoav; Frydman, Lucio

2011-04-01

A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. Copyright © 2011 Elsevier Inc. All rights reserved.

Three-dimensional full waveform inversion of short-period teleseismic wavefields based upon the SEM-DSM hybrid method

NASA Astrophysics Data System (ADS)

Monteiller, Vadim; Chevrot, Sébastien; Komatitsch, Dimitri; Wang, Yi

2015-08-01

We present a method for high-resolution imaging of lithospheric structures based on full waveform inversion of teleseismic waveforms. We model the propagation of seismic waves using our recently developed direct solution method/spectral-element method hybrid technique, which allows us to simulate the propagation of short-period teleseismic waves through a regional 3-D model. We implement an iterative quasi-Newton method based upon the L-BFGS algorithm, where the gradient of the misfit function is computed using the adjoint-state method. Compared to gradient or conjugate-gradient methods, the L-BFGS algorithm has a much faster convergence rate. We illustrate the potential of this method on a synthetic test case that consists of a crustal model with a crustal discontinuity at 25 km depth and a sharp Moho jump. This model contains short- and long-wavelength heterogeneities along the lateral and vertical directions. The iterative inversion starts from a smooth 1-D model derived from the IASP91 reference Earth model. We invert both radial and vertical component waveforms, starting from long-period signals filtered at 10 s and gradually decreasing the cut-off period down to 1.25 s. This multiscale algorithm quickly converges towards a model that is very close to the true model, in contrast to inversions involving short-period waveforms only, which always get trapped into a local minimum of the cost function.

Microstructural and Mechanical Study of Press Hardening of Thick Boron Steel Sheet

NASA Astrophysics Data System (ADS)

Pujante, J.; Garcia-Llamas, E.; Golling, S.; Casellas, D.

2017-09-01

Press hardening has become a staple in the production of automotive safety components, due to the combination of high mechanical properties and form complexity it offers. However, the use of press hardened components has not spread to the truck industry despite the advantages it confers, namely affordable weight reduction without the use of exotic materials, would be extremely attractive for this sector. The main reason for this is that application of press hardened components in trucks implies adapting the process to the manufacture of thick sheet metal. This introduces an additional layer of complexity, mainly due to the thermal gradients inside the material resulting in though-thickness differences in austenitization and cooling, potentially resulting in complex microstructure and gradient of mechanical properties. This work presents a preliminary study on the press hardening of thick boron steel sheet. First of all, the evolution of the sheet metal during austenitization is studied by means of dilatometry tests and by analysing the effect of furnace dwell time on grain size. Afterwards, material cooled using different cooling strategies, and therefore different effective cooling rates, is studied in terms of microstructure and mechanical properties. Initial results from finite element simulation are compared to experimental results, focusing on the phase composition in through thickness direction. Results show that industrial-equivalent cooling conditions do not lead to gradient microstructures, even in extreme scenarios involving asymmetrical cooling.

Temperature-dependent MR signals in cortical bone: potential for monitoring temperature changes during high-intensity focused ultrasound treatment in bone.

PubMed

Ramsay, Elizabeth; Mougenot, Charles; Kazem, Mohammad; Laetsch, Theodore W; Chopra, Rajiv

2015-10-01

Because existing magnetic resonance thermometry techniques do not provide temperature information within bone, high-intensity focused ultrasound (HIFU) exposures in bone are monitored using temperature changes in adjacent soft tissues. In this study, the potential to monitor temperature changes in cortical bone using a short TE gradient echo sequence is evaluated. The feasibility of this proposed method was initially evaluated by measuring the temperature dependence of the gradient echo signal during cooling of cortical bone samples implanted with fiber-optic temperature sensors. A subsequent experiment involved heating a cortical bone sample using a clinical MR-HIFU system. A consistent relationship between temperature change and the change in magnitude signal was observed within and between cortical bone samples. For the two-dimensional gradient echo sequence implemented in this study, a least-squares linear fit determined the percentage change in signal to be (0.90 ± 0.01)%/°C. This relationship was used to estimate temperature changes observed in the HIFU experiment and these temperatures agreed well with those measured from an implanted fiber-optic sensor. This method appears capable of displaying changes related to temperature in cortical bone and could improve the safety of MR-HIFU treatments. Further investigations into the sensitivity of the technique in vivo are warranted. © 2014 Wiley Periodicals, Inc.

Spatial pattern formation of coastal vegetation in response to external gradients and positive feedbacks affecting soil porewater salinity: A model study

USGS Publications Warehouse

Jiang, J.; DeAngelis, D.L.; Smith, T. J.; Teh, S.Y.; Koh, H. L.

2012-01-01

Coastal vegetation of South Florida typically comprises salinity-tolerant mangroves bordering salinity-intolerant hardwood hammocks and fresh water marshes. Two primary ecological factors appear to influence the maintenance of mangrove/hammock ecotones against changes that might occur due to disturbances. One of these is a gradient in one or more environmental factors. The other is the action of positive feedback mechanisms, in which each vegetation community influences its local environment to favor itself, reinforcing the boundary between communities. The relative contributions of these two factors, however, can be hard to discern. A spatially explicit individual-based model of vegetation, coupled with a model of soil hydrology and salinity dynamics is presented here to simulate mangrove/hammock ecotones in the coastal margin habitats of South Florida. The model simulation results indicate that an environmental gradient of salinity, caused by tidal flux, is the key factor separating vegetation communities, while positive feedback involving the different interaction of each vegetation type with the vadose zone salinity increases the sharpness of boundaries, and maintains the ecological resilience of mangrove/hammock ecotones against small disturbances. Investigation of effects of precipitation on positive feedback indicates that the dry season, with its low precipitation, is the period of strongest positive feedback. ?? 2011 Springer Science+Business Media B.V. (outside the USA).

Distinguishing graded and ultrasensitive signalling cascade kinetics by the shape of morphogen gradients in Drosophila.

PubMed

MacNamara, Shev; Baker, Ruth E; Maini, Philip K

2011-09-21

Recently, signalling gradients in cascades of two-state reaction-diffusion systems were described as a model for understanding key biochemical mechanisms that underlie development and differentiation processes in the Drosophila embryo. Diffusion-trapping at the exterior of the cell membrane triggers the mitogen-activated protein kinase (MAPK) cascade to relay an appropriate signal from the membrane to the inner part of the cytosol, whereupon another diffusion-trapping mechanism involving the nucleus reads out this signal to trigger appropriate changes in gene expression. Proposed mathematical models exhibit equilibrium distributions consistent with experimental measurements of key spatial gradients in these processes. A significant property of the formulation is that the signal is assumed to be relayed from one system to the next in a linear fashion. However, the MAPK cascade often exhibits nonlinear dose-response properties and the final remark of Berezhkovskii et al. (2009) is that this assumption remains an important property to be tested experimentally, perhaps via a new quantitative assay across multiple genetic backgrounds. In anticipation of the need to be able to sensibly interpret data from such experiments, here we provide a complementary analysis that recovers existing formulae as a special case but is also capable of handling nonlinear functional forms. Predictions of linear and nonlinear signal relays and, in particular, graded and ultrasensitive MAPK kinetics, are compared. Copyright © 2011 Elsevier Ltd. All rights reserved.

Changes in scleractinian coral Seriatopora hystrix morphology and its endocellular Symbiodinium characteristics along a bathymetric gradient from shallow to mesophotic reef

NASA Astrophysics Data System (ADS)

Nir, O.; Gruber, D. F.; Einbinder, S.; Kark, S.; Tchernov, D.

2011-12-01

The algae living endosymbiotically within coral are thought to increase algal pigmentation with increasing depth to capture the diminishing light. Here, we follow distribution of the hermatypic coral Seriatopora hystrix along a 60-m bathymetric gradient in the Gulf of Eilat, Red Sea, to study coral ecophysiology and response to light regimes. Combining work on coral morphology, pigment content and genotyping of the photosymbiont, we found that total chlorophyll concentration per zooxanthellae cell and the dark- and light-acclimated quantum yield of photosystem II did not vary significantly along the 60-m gradient. However, the chlorophyll a/c ratio increased with depth. This suggests that the symbiotic algae in S. hystrix possess a mechanism for acclimatization or adaptation that differs from previously described pathways. The accepted photoacclimatory process involves an increase in chlorophyll content per alga as light intensity decreases. Based on corallite and branch morphology, this research suggests that S. hystrix has two depth-dependent ecophenotypes. Above 10 m depth, S. hystrix exhibits sturdier colony configurations with thick branches, while below 30 m depth, colonies are characterized by thin branches and the presence of a larger polyp area. Between 10 and 30 m depth, both ecophenotypes are present, suggesting that corallite morphology may act as another axis of photoacclimation with depth.

Calf pump activity influencing venous hemodynamics in the lower extremity.

PubMed

Recek, Cestmir

2013-03-01

Calf muscle pump is the motive force enhancing return of venous blood from the lower extremity to the heart. It causes displacement of venous blood in both vertical and horizontal directions, generates ambulatory pressure gradient between thigh and lower leg veins, and bidirectional streaming within calf perforators. Ambulatory pressure gradient triggers venous reflux in incompetent veins, which induces ambulatory venous hypertension in the lower leg and foot. Bidirectional flow in calf perforators enables quick pressure equalization between deep and superficial veins of the lower leg; the outward (into the superficial veins) oriented component of the bidirectional flow taking place during calf muscle contraction is no pathological reflux but a physiological centripetal flow streaming via great saphenous vein into the femoral vein. Calf perforators are communicating channels between both systems making them conjoined vessels; they are not involved in the generation of pathological hemodynamic situations, nor do they cause ambulatory venous hypertension. The real cause why recurrences develop has not as yet been cleared. Pressure gradient arising during calf pump activity between the femoral vein and the saphenous remnant after abolition of saphenous reflux triggers biophysical and biochemical events, which might induce recurrence. Thus, abolition of saphenous reflux removes the hemodynamic disturbance, but at the same time it generates precondition for reflux recurrence and for the comeback of the previous pathological situation; this chain of events has been called hemodynamic paradox.

Multigrid one shot methods for optimal control problems: Infinite dimensional control

NASA Technical Reports Server (NTRS)

Arian, Eyal; Taasan, Shlomo

1994-01-01

The multigrid one shot method for optimal control problems, governed by elliptic systems, is introduced for the infinite dimensional control space. ln this case, the control variable is a function whose discrete representation involves_an increasing number of variables with grid refinement. The minimization algorithm uses Lagrange multipliers to calculate sensitivity gradients. A preconditioned gradient descent algorithm is accelerated by a set of coarse grids. It optimizes for different scales in the representation of the control variable on different discretization levels. An analysis which reduces the problem to the boundary is introduced. It is used to approximate the two level asymptotic convergence rate, to determine the amplitude of the minimization steps, and the choice of a high pass filter to be used when necessary. The effectiveness of the method is demonstrated on a series of test problems. The new method enables the solutions of optimal control problems at the same cost of solving the corresponding analysis problems just a few times.

In vitro maturation of Drosophila melanogaster Spätzle protein with refolded Easter reveals a novel cleavage site within the prodomain.

PubMed

Ursel, Christian; Fandrich, Uwe; Hoffmann, Anita; Sieg, Torsten; Ihling, Christian; Stubbs, Milton T

2013-08-01

Dorsoventral patterning during Drosophila melanogaster embryogenesis is mediated by a well-defined gradient of the mature NGF-like ligand Spätzle. Easter, the ultimate protease of a ventrally-restricted serine protease cascade, plays a key role in the regulation of the morphogenic gradient, catalyzing the activation cleavage of proSpätzle. As a result of alternative splicing, proSpätzle exists in multiple isoforms, almost all of which differ only in their prodomain. Although this domain is unstructured in isolation, it has a stabilizing influence on the mature cystine knot domain and is involved in the binding to the Toll receptor. Here, we report the expression and refolding of Easter, and show that the renatured enzyme performs the activation cleavage of two Spätzle isoforms. We determine the affinity of the prodomain for the cystine knot domain, and show that Easter performs a previously unknown secondary cleavage in each prodomain.

A density-adaptive SPH method with kernel gradient correction for modeling explosive welding

NASA Astrophysics Data System (ADS)

Liu, M. B.; Zhang, Z. L.; Feng, D. L.

2017-09-01

Explosive welding involves processes like the detonation of explosive, impact of metal structures and strong fluid-structure interaction, while the whole process of explosive welding has not been well modeled before. In this paper, a novel smoothed particle hydrodynamics (SPH) model is developed to simulate explosive welding. In the SPH model, a kernel gradient correction algorithm is used to achieve better computational accuracy. A density adapting technique which can effectively treat large density ratio is also proposed. The developed SPH model is firstly validated by simulating a benchmark problem of one-dimensional TNT detonation and an impact welding problem. The SPH model is then successfully applied to simulate the whole process of explosive welding. It is demonstrated that the presented SPH method can capture typical physics in explosive welding including explosion wave, welding surface morphology, jet flow and acceleration of the flyer plate. The welding angle obtained from the SPH simulation agrees well with that from a kinematic analysis.

[Establishment and evaluation of an in vitro method for neutrophil extracellular trap generation and degradation].

PubMed

Li, Jinlong; Zhang, Yidan; Zhou, Xin; Ji, Wenjie; Zhao, Jihong; Wei, Luqing; Li, Yuming

2014-09-01

To evaluate a novel method for in vitro generation and degradation of neutrophil extracellular traps (NETs), which are a newly recognized structure that is involved in the pathogenesis of autoimmune diseases and thrombosis. Neutrophils from peripheral blood of healthy donors were obtained by Ficoll-Histopaque gradient separation. NET release was initiated by phorbol myristate acetate (PMA) and validated by immunofluorescence staining and agarose gel electrophoresis. NETs degraded by DNase I and healthy human plasma were quantified by fluorescence spectrometry after staining with PicoGreen. HE staining showed that the purity of neutrophils was up to 95% after Ficoll-Histopaque gradient separation. NET immunofluorescent staining revealed that the network structure was mainly composed of DNA and histones, with molecular length more than 10 kb as demonstrated by agarose gel electrophoresis. Moreover, both DNase and healthy human plasma could induce the degradation of NETs, in varying degrees. This work established an efficient method for in vitro generation and degradation of human NETs.

Measurement by reversed-phase high-performance liquid chromatography of malondialdehyde in normal human urine following derivatisation with 2,4-dinitrophenylhydrazine.

PubMed

Korchazhkina, Olga; Exley, Christopher; Andrew Spencer, Stephen

2003-09-05

A selective and sensitive method based on derivatisation with 2,4-dinitrophenylhydrazine (DNPH) and consecutive HPLC gradient separation is described for the determination of malondialdehyde (MDA) in urine. Preparation of urine samples involved a one-step derivatisation/extraction procedure. Separation was achieved using a Waters SymmetryC(18) column (3.9 x 150 mm) and linear gradient of acetonitrile in water (from 30% to 70% in 30 min). The overall detection limit of the method was 56 nM of MDA in urine. The recovery of MDA was 94.3+/-8.6%. MDA in urine of healthy volunteers, measured using the method of standard additions, was 0.019+/-0.012 microM/mmol creatinine. MDA in the same samples measured using the 2-thiobarbituric acid (TBA) assay was 0.181+/-0.063 microM/mmol creatinine. We demonstrate that the commonly used TBA assay in conjunction with HPLC may overestimate the MDA concentration in human urine by almost 10-fold.

Return current instability driven by a temperature gradient in ICF plasmas

DOE PAGES

Rozmus, W.; Brantov, A. V.; Sherlock, M.; ...

2017-10-12

Here, hot plasmas with strong temperature gradients in inertial confinement fusion (ICF) experiments are examined for ion acoustic instabilities produced by electron heat flow. The return current instability (RCI) due to a neutralizing current of cold electrons arising in response to a large electron heat flux has been considered. First, the linear threshold and growth rates are derived in the nonlocal regime of thermal transport. They are compared with the results of Vlasov-Fokker-Planck (VFP) simulations in one spatial dimension. Very good agreement has been found between kinetic VFP simulations and the linear theory of the RCI. A quasi-stationary state ofmore » ion acoustic turbulence produced by the RCI is achieved in the VFP simulations. Saturation of the RCI involves heating of ions in the tail of the ion distribution function and convection of the enhanced ion acoustic fluctuations from the unstable region of the plasma. Further evolution of the ion acoustic turbulence and its effects on absorption and transport are also discussed.« less

Thermodynamic Paradigm for Solution Demixing Inspired by Nuclear Transport in Living Cells

NASA Astrophysics Data System (ADS)

Wang, Ching-Hao; Mehta, Pankaj; Elbaum, Michael

2017-04-01

Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not involve traversing a lipid bilayer membrane. Instead, large protein channels known as nuclear pores cross the nuclear envelope and regulate the passage of other proteins and RNA molecules. Beyond simply gating diffusion, the system of nuclear pores and associated transport receptors is able to generate substantial concentration gradients, at the energetic expense of guanosine triphosphate hydrolysis. In contrast to conventional approaches to demixing such as reverse osmosis and dialysis, the biological system operates continuously, without application of cyclic changes in pressure or solvent exchange. Abstracting the biological paradigm, we examine this transport system as a thermodynamic machine of solution demixing. Building on the construct of free energy transduction and biochemical kinetics, we find conditions for the stable operation and optimization of the concentration gradients as a function of dissipation in the form of entropy production.

Analysis of Online Composite Mirror Descent Algorithm.

PubMed

Lei, Yunwen; Zhou, Ding-Xuan

2017-03-01

We study the convergence of the online composite mirror descent algorithm, which involves a mirror map to reflect the geometry of the data and a convex objective function consisting of a loss and a regularizer possibly inducing sparsity. Our error analysis provides convergence rates in terms of properties of the strongly convex differentiable mirror map and the objective function. For a class of objective functions with Hölder continuous gradients, the convergence rates of the excess (regularized) risk under polynomially decaying step sizes have the order [Formula: see text] after [Formula: see text] iterates. Our results improve the existing error analysis for the online composite mirror descent algorithm by avoiding averaging and removing boundedness assumptions, and they sharpen the existing convergence rates of the last iterate for online gradient descent without any boundedness assumptions. Our methodology mainly depends on a novel error decomposition in terms of an excess Bregman distance, refined analysis of self-bounding properties of the objective function, and the resulting one-step progress bounds.

Environment and host as large-scale controls of ectomycorrhizal fungi.

PubMed

van der Linde, Sietse; Suz, Laura M; Orme, C David L; Cox, Filipa; Andreae, Henning; Asi, Endla; Atkinson, Bonnie; Benham, Sue; Carroll, Christopher; Cools, Nathalie; De Vos, Bruno; Dietrich, Hans-Peter; Eichhorn, Johannes; Gehrmann, Joachim; Grebenc, Tine; Gweon, Hyun S; Hansen, Karin; Jacob, Frank; Kristöfel, Ferdinand; Lech, Paweł; Manninger, Miklós; Martin, Jan; Meesenburg, Henning; Merilä, Päivi; Nicolas, Manuel; Pavlenda, Pavel; Rautio, Pasi; Schaub, Marcus; Schröck, Hans-Werner; Seidling, Walter; Šrámek, Vít; Thimonier, Anne; Thomsen, Iben Margrete; Titeux, Hugues; Vanguelova, Elena; Verstraeten, Arne; Vesterdal, Lars; Waldner, Peter; Wijk, Sture; Zhang, Yuxin; Žlindra, Daniel; Bidartondo, Martin I

2018-06-06

Explaining the large-scale diversity of soil organisms that drive biogeochemical processes-and their responses to environmental change-is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is-to our knowledge-unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.

Return current instability driven by a temperature gradient in ICF plasmas

NASA Astrophysics Data System (ADS)

Rozmus, W.; Brantov, A. V.; Sherlock, M.; Bychenkov, V. Yu

2018-01-01

Hot plasmas with strong temperature gradients in inertial confinement fusion experiments are examined for ion acoustic instabilities produced by electron heat flow. The return current instability (RCI) due to a neutralizing current of cold electrons arising in response to a large electron heat flux has been considered. First, the linear threshold and growth rates are derived in the non-local regime of thermal transport. They are compared with the results of Vlasov-Fokker-Planck (VFP) simulations in one spatial dimension. Very good agreement has been found between kinetic VFP simulations and the linear theory of the RCI. A quasi-stationary state of ion acoustic turbulence (IAT) produced by the RCI is achieved in the VFP simulations. Saturation of the RCI involves heating of ions in the tail of the ion distribution function and convection of the enhanced ion acoustic fluctuations from the unstable region of the plasma. Further evolution of the IAT and its effects on absorption and transport are also discussed.

Tumor cell-driven extracellular matrix remodeling drives haptotaxis during metastatic progression

PubMed Central

Oudin, Madeleine J.; Jonas, Oliver; Kosciuk, Tatsiana; Broye, Liliane C.; Guido, Bruna C.; Wyckoff, Jeff; Riquelme, Daisy; Lamar, John M.; Asokan, Sreeja B.; Whittaker, Charlie; Ma, Duanduan; Langer, Robert; Cima, Michael J.; Wisinski, Kari B.; Hynes, Richard O.; Lauffenburger, Douglas A.; Keely, Patricia J.; Bear, James E.; Gertler, Frank B.

2016-01-01

Fibronectin (FN) is a major component of the tumor microenvironment, but its role in promoting metastasis is incompletely understood. Here we show that FN gradients elicit directional movement of breast cancer cells, in vitro and in vivo. Haptotaxis on FN gradients requires direct interaction between α5β1 integrin and Mena, an actin regulator, and involves increases in focal complex signaling and tumor-cell-mediated extracellular matrix (ECM) remodeling. Compared to Mena, higher levels of the pro-metastatic MenaINV isoform associate with α5, which enables 3D haptotaxis of tumor cells towards the high FN concentrations typically present in perivascular space and in the periphery of breast tumor tissue. MenaINV and FN levels were correlated in two breast cancer cohorts, and high levels of MenaINV were significantly associated with increased tumor recurrence as well as decreased patient survival. Our results identify a novel tumor-cell-intrinsic mechanism that promotes metastasis through ECM remodeling and ECM guided directional migration. PMID:26811325

Gravity-regulated differential auxin transport from columella to lateral root cap cells

NASA Technical Reports Server (NTRS)

Ottenschlager, Iris; Wolff, Patricia; Wolverton, Chris; Bhalerao, Rishikesh P.; Sandberg, Goran; Ishikawa, Hideo; Evans, Mike; Palme, Klaus

2003-01-01

Gravity-induced root curvature has long been considered to be regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients, and the transport mechanisms involved, remain to be identified. Here, we describe a GFP-based auxin biosensor to monitor auxin during Arabidopsis root gravitropism at cellular resolution. We identify elevated auxin levels at the root apex in columella cells, the site of gravity perception, and an asymmetric auxin flux from these cells to the lateral root cap (LRC) and toward the elongation zone after gravistimulation. We differentiate between an efflux-dependent lateral auxin transport from columella to LRC cells, and an efflux- and influx-dependent basipetal transport from the LRC to the elongation zone. We further demonstrate that endogenous gravitropic auxin gradients develop even in the presence of an exogenous source of auxin. Live-cell auxin imaging provides unprecedented insights into gravity-regulated auxin flux at cellular resolution, and strongly suggests that this flux is a prerequisite for root gravitropism.

Purification of Torpedo californica post-synaptic membranes and fractionation of their constituent proteins.

PubMed Central

Elliott, J; Blanchard, S G; Wu, W; Miller, J; Strader, C D; Hartig, P; Moore, H P; Racs, J; Raftery, M A

1980-01-01

A rapid methof for preparation of membrane fractions highly enriched in nicotinic acetylcholine receptor from Torpedo californica electroplax is described. The major step in this purification involves sucrose-density-gradient centrifugation in a reorienting rotor. Further purification of these membranes can be achieved by selective extraction of proteins by use of alkaline pH or by treatment with solutions of lithium di-idosalicylate. The alkali-treated membranes retain functional characteristics of the untreated membranes and in addition contain essentially only the four polypeptides (mol.wts. 40000, 50000, 60000 and 65000) characteristic of the receptor purified by affinity chromatography. Dissolution of the purified membranes or of the alkali-treated purified membranes in sodium cholate solution followed by sucrose-density-gradient centrifugation in the same detergent solution yields solubilized receptor preparations comparable with the most highly purified protein obtained by affinity-chromatographic procedures. Images Fig. 1. Fig. 2. Fig. 3. Fig. 5. Fig. 7. PLATE 1 PMID:7387629

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto.

PubMed

Barge, Laura M; Cardoso, Silvana S S; Cartwright, Julyan H E; Doloboff, Ivria J; Flores, Erika; Macías-Sánchez, Elena; Sainz-Díaz, C Ignacio; Sobrón, Pablo

2016-11-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments.

Porous polycarbene-bearing membrane actuator for ultrasensitive weak-acid detection and real-time chemical reaction monitoring.

PubMed

Sun, Jian-Ke; Zhang, Weiyi; Guterman, Ryan; Lin, Hui-Juan; Yuan, Jiayin

2018-04-30

Soft actuators with integration of ultrasensitivity and capability of simultaneous interaction with multiple stimuli through an entire event ask for a high level of structure complexity, adaptability, and/or multi-responsiveness, which is a great challenge. Here, we develop a porous polycarbene-bearing membrane actuator built up from ionic complexation between a poly(ionic liquid) and trimesic acid (TA). The actuator features two concurrent structure gradients, i.e., an electrostatic complexation (EC) degree and a density distribution of a carbene-NH 3 adduct (CNA) along the membrane cross-section. The membrane actuator performs the highest sensitivity among the state-of-the-art soft proton actuators toward acetic acid at 10 -6  mol L -1 (M) level in aqueous media. Through competing actuation of the two gradients, it is capable of monitoring an entire process of proton-involved chemical reactions that comprise multiple stimuli and operational steps. The present achievement constitutes a significant step toward real-life application of soft actuators in chemical sensing and reaction technology.

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto

PubMed Central

Barge, Laura M.; Doloboff, Ivria J.; Flores, Erika; Sobrón, Pablo

2016-01-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments. PMID:27956875

D4Z - a new renumbering for iterative solution of ground-water flow and solute- transport equations

USGS Publications Warehouse

Kipp, K.L.; Russell, T.F.; Otto, J.S.

1992-01-01

D4 zig-zag (D4Z) is a new renumbering scheme for producing a reduced matrix to be solved by an incomplete LU preconditioned, restarted conjugate-gradient iterative solver. By renumbering alternate diagonals in a zig-zag fashion, a very low sensitivity of convergence rate to renumbering direction is obtained. For two demonstration problems involving groundwater flow and solute transport, iteration counts are related to condition numbers and spectra of the reduced matrices.

Coastal Zone Color Scanner studies

NASA Technical Reports Server (NTRS)

Elrod, J.

1988-01-01

Activities over the past year have included cooperative work with a summer faculty fellow using the Coastal Zone Color Scanner (CZCS) imagery to study the effects of gradients in trophic resources on coral reefs in the Caribbean. Other research included characterization of ocean radiances specific to an acid-waste plume. Other activities include involvement in the quality control of imagery produced in the processing of the global CZCS data set, the collection of various other data global sets, and the subsequent data comparison and analysis.

The exponentiated Hencky energy: anisotropic extension and case studies

NASA Astrophysics Data System (ADS)

Schröder, Jörg; von Hoegen, Markus; Neff, Patrizio

2017-10-01

In this paper we propose an anisotropic extension of the isotropic exponentiated Hencky energy, based on logarithmic strain invariants. Unlike other elastic formulations, the isotropic exponentiated Hencky elastic energy has been derived solely on differential geometric grounds, involving the geodesic distance of the deformation gradient \\varvec{F} to the group of rotations. We formally extend this approach towards anisotropy by defining additional anisotropic logarithmic strain invariants with the help of suitable structural tensors and consider our findings for selected case studies.

Electron acceleration in quantum plasma with spin-up and spin-down exchange interaction

NASA Astrophysics Data System (ADS)

Kumar, Punit; Singh, Shiv; Ahmad, Nafees

2018-05-01

Electron acceleration by ponderomotive force of an intense circularly polarized laser pulse in high density magnetized quantum plasma with two different spin states embedded in external static magnetic field. The basic mechanism involves electron acceleration by axial gradient in the ponderomotive potential of laser. The effects of Bohm potential, fermi pressure and intrinsic spin of electron have been taken into account. A simple solution for ponderomotive electron acceleration has been established and effect of spin polarization is analyzed.

Calculation of pressure half-time.

PubMed

Oyama, Mark A; Weidman, Jess A; Cole, Steven G

2008-06-01

Doppler echocardiography is useful in assessing the severity of obstructive cardiac lesions, such as mitral valve stenosis. The Doppler study can be used to calculate pressure half-time (PHT), which is defined as the time required for the pressure gradient across an obstruction to decrease to half of its maximal value. Thus, PHT increases as the severity of stenosis increases. In this report, we describe the methodology involved in measuring PHT in a dog with mitral valve stenosis before and after balloon valvuloplasty.

Nonlinear penetration of whistler pulses into collisional plasmas via conductivity modifications

NASA Technical Reports Server (NTRS)

Urrutia, J. M.; Stenzel, R. L.

1991-01-01

A strong electromagnetic impulse (about 0.2 microsec) with central frequency in the whistler-wave regime is applied to a large laboratory plasma dominated by Coulomb collisions. Local electron heating at the antenna and transport along B0 create a channel of high conductivity along which the whistler pulse penetrates with little damping. Because of its rapid temporal evolution, this new form of modulational instability does not involve ducting by density gradients which require ion time scales to develop.

Clarifying the Conceptualization, Dimensionality, and Structure of Emotion: Response to Barrett and Colleagues

PubMed Central

Cowen, Alan S.; Keltner, Dacher

2018-01-01

We present a mathematically based framework distinguishing the dimensionality, structure, and conceptualization of emotion-related responses. Our recent findings indicate that reported emotional experience is highdimensional, involves gradients between categories traditionally thought of as discrete (e.g., ‘fear’, ‘disgust’), and cannot be reduced to widely used domain-general scales (valence, arousal, etc.). In light of our conceptual framework and findings, we address potential methodological and conceptual confusions in Barrett and colleagues’ commentary on our work. PMID:29477775

Effects of spatial gradients in thermophysical properties on the topology of turbulence in heated channel flow of supercritical fluids

NASA Astrophysics Data System (ADS)

Azih, Chukwudi; Yaras, Metin I.

2018-01-01

The current literature suggests that large spatial gradients of thermophysical properties, which occur in the vicinity of the pseudo-critical thermodynamic state, may result in significant variations in forced-convection heat transfer rates. Specifically, these property gradients induce inertia- and buoyancy-driven phenomena that may enhance or deteriorate the turbulence-dominated heat convection process. Through direct numerical simulations, the present study investigates the role of coherent flow structures in channel geometries for non-buoyant and buoyant flows of supercritical water, with buoyant configurations involving wall-normal oriented gravitational acceleration and downstream-oriented gravitational acceleration. This sequence of simulations enables the evaluation of the relative contributions of inertial and buoyancy phenomena to heat transfer variations. In these simulations, the state of the working fluid is in the vicinity of the pseudo-critical point. The uniform wall heat flux and the channel mass flux are specified such that the heat to mass flux ratio is 3 kJ/kg, with an inflow Reynolds number of 12 000 based on the channel hydraulic diameter, the area-averaged inflow velocity, and fluid properties evaluated at the bulk temperature and pressure of the inflow plane. In the absence of buoyancy forces, notable reductions in the density and viscosity in close proximity of the heated wall are observed to promote generation of small-scale vortices, with resultant breakdown into smaller scales as they interact with preexisting larger near-wall vortices. This interaction results in a reduction in the overall thermal mixing at particular wall-normal regions of the channel. Under the influence of wall-normal gravitational acceleration, the wall-normal density gradients are noted to enhance ejection motions due to baroclinic vorticity generation on the lower wall, thus providing additional wall-normal thermal mixing. Along the upper wall, the same mechanism generates streamwise vorticity of the opposing sense of rotation in the close vicinity to the respective legs of the hairpin vortices causing a net reduction in thermal mixing. Finally, in the case of downstream-oriented gravitational acceleration, baroclinic vorticity generation as per spanwise density gradients causes additional wall-normal thermal mixing by promoting larger-scale ejection and sweep motions.

Adaptive fine root foraging patterns in climate experiments and natural gradients

NASA Astrophysics Data System (ADS)

Ostonen, Ivika; Truu, Marika; Parts, Kaarin; Truu, Jaak

2017-04-01

Site based manipulative experiments and studies along climatic gradients have long been keystones of ecological research. We aimed to compare the response of ectomycorrhizal (EcM) and fine roots in manipulative studies and along climate gradient to describe the universal trends in root traits and to raise hypotheses about general mechanisms in fine root system adaptation of forest trees in global change. The root traits from two climate manipulation experiments - Bangor FACE and FAHM in Estonia, manipulated by CO2 concentration and relative air humidity in silver birch forest ecosystems, respectively and the data for three most ubiquitous tree species - Norway spruce (Picea abies), Scots pine (Pinus sylvestris) and silver birch (Betula pendula) stands along natural gradient encompassing different climate and forest zones in Northern Europe were analysed. There are two main strategies in response of fine root system of trees: A) an extensive increase in absorptive root biomass, surface area and length, or B) a greater reliance on root-associated EcM fungi and bacterial communities with a smaller investment to absorptive root biomass. Trees in all studies tended to increase the EcM root biomass and the proportion of EcM root biomass of total fine root biomass towards harsh (northern boreal forests) or changed conditions (stress created by the increase in CO2 concentration or relative air humidity). We envisage a role of trilateral relation between the morphological traits of absorptive fine roots, exploration types of colonising EcM fungi and rhizosphere and bulk soil bacterial community structure. A significant change in EcM absorptive fine root biomass in all experiments and for all studied tree species coincided with changes in absorptive root morphology, being longer and thinner root tips with higher root tissue density in poor/treated sites. These changes were associated with significant shifts in community structure of dominating EcM fungi as well as soil and rhizosphere bacterial communities. We suggest a multidimensional concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in root-mycorhizosphere along environmental gradients and in climate experiments.

The relationship between the electrochemical proton gradient and active transport in Escherichia coli membrane vesicles.

PubMed

Ramos, S; Kaback, H R

1977-03-08

In the previous paper [ramos, S., and Kaback, H.R. (1977), Biochemistry 16 (preceding paper in this issue)], it was demonstrated that Escherichia coli membrane vesicles generate a large electrochemical proton gradient (delta-muH+) under appropriate conditions, and some of the properties of delta-muH+ and its component forces [i.e., the membrane potential (delta psi) and the chemical gradient of protons (deltapH)] were described. In this paper, the relationship between delta-muH+, delta psi, and deltapH and the active transport of specific solutes is examined. Addition of lactose or glucose 6-phosphate to membrane vesicles containing the appropriate transport systems results in partial collapse of deltapH, providing direct evidence for the suggestion that respiratory energy can drive active transport via the pH gradient across the membrane. Titration studies with valinomycin and nigericin lead to the conclusion that, at pH 5.5, there are two general classes of transport systems: those that are driven primarily by delta-muH+ (lactose, proline, serine, glycine, tyrosine, glutamate, leucine, lysine, cysteine, and succinate) and those that are driven primarily by deltapH (glucose 6-phosphate, D-lactate, glucuronate, and gluconate). Importantly, however, it is also demonstrated that at pH 7.5, all of these transport systems are driven by delta psi which comprises the only component of delta-muH+ at this external pH. In addition, the effect of external pH on the steady-state levels of accumulation of different solutes is examined, and it is shown that none of the pH profiles correspond to those observed for delta-muH+, delta psi, or deltapH. Moreover, at external pH values above 6.0-6.5, delta-muH+ is insufficient to account for the concentration gradients established for each substrate unless the stoichiometry between protons and accumulated solutes is greater than unity. The results confirm many facets of the chemiosmotic hypothesis, but they also extend the concept in certain important respects and allow explanations for some earlier observations which seemed to preclude the involvement of chemiosmotic phenomena in active transport.

High-pressure nuclear magnetic resonance studies of fuel cell membranes

NASA Astrophysics Data System (ADS)

Mananga, Eugene Stephane

This thesis focuses on the use of high pressure NMR to study transport properties in electrolyte membranes used for fuel cells. The main concern is in studying the self-diffusion coefficients of ions and molecules in membranes and solutions, which can be used to characterize electrolytes in fuel cells. For this purpose, a high-pressure fringe field NMR method to study transport properties in material systems useful for fuel cell and battery electrolytes, was designed, developed, and implemented. In this investigation, pressure is the thermodynamic variable to obtain additional information about the ionic transport process, which could yield the crucial parameter, activation volume. Most of the work involves proton NMR, with additional investigations of others nuclei, such as fluorine, phosphorus and lithium. Using the FFG method, two fuel cell membrane types (NAFION-117, SPTES), and different dilutions of phosphoric acid were investigated, as was LiTf salt in Diglyme solution, which is used as a lithium battery electrolyte. In addition to high-pressure NMR diffusion measurements carried out in the fringe field gradient for the investigation of SPTES, pulse field gradient spin echo NMR was also used to characterize the water diffusion, in addition to measuring diffusion rates as a function of temperature. This second method allows us to measure distinct diffusion coefficients in cases where the different nuclear (proton) environments can be resolved in the NMR spectrum. Polymer electrolyte systems, in which the mobility of both cations and anions is probed by NMR self-diffusion measurements using standard pulsed field gradient methods and static gradient measurements as a function of applied hydrostatic pressure, were also investigated. The material investigated is the low molecular weight liquid diglyme/LiCF3SO3 (LiTf) complexes which can be used as electrolytes in lithium batteries. Finally, high-pressure diffusion coefficient measurements of phosphoric acid in water at different concentrations: proton (1H) and phosphorus (31P) nuclei have been performed using the static field gradient spin-echo nuclear magnetic resonance. This study is expected to be helpful in improving the understanding of phosphoric acid fuel cell technology.

Cause and Cure - Deterioration in Accuracy of CFD Simulations With Use of High-Aspect-Ratio Triangular Tetrahedral Grids

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung; Chang, Chau-Lyan; Venkatachari, Balaji Shankar

2017-01-01

Traditionally high-aspect ratio triangular/tetrahedral meshes are avoided by CFD re-searchers in the vicinity of a solid wall, as it is known to reduce the accuracy of gradient computations in those regions and also cause numerical instability. Although for certain complex geometries, the use of high-aspect ratio triangular/tetrahedral elements in the vicinity of a solid wall can be replaced by quadrilateral/prismatic elements, ability to use triangular/tetrahedral elements in such regions without any degradation in accuracy can be beneficial from a mesh generation point of view. The benefits also carry over to numerical frameworks such as the space-time conservation element and solution element (CESE), where triangular/tetrahedral elements are the mandatory building blocks. With the requirement of the CESE method in mind, a rigorous mathematical framework that clearly identities the reason behind the difficulties in use of such high-aspect ratio triangular/tetrahedral elements is presented here. As will be shown, it turns out that the degree of accuracy deterioration of gradient computation involving a triangular element is hinged on the value of its shape factor Gamma def = sq sin Alpha1 + sq sin Alpha2 + sq sin Alpha3, where Alpha1; Alpha2 and Alpha3 are the internal angles of the element. In fact, it is shown that the degree of accuracy deterioration increases monotonically as the value of Gamma decreases monotonically from its maximal value 9/4 (attained by an equilateral triangle only) to a value much less than 1 (associated with a highly obtuse triangle). By taking advantage of the fact that a high-aspect ratio triangle is not necessarily highly obtuse, and in fact it can have a shape factor whose value is close to the maximal value 9/4, a potential solution to avoid accuracy deterioration of gradient computation associated with a high-aspect ratio triangular grid is given. Also a brief discussion on the extension of the current mathematical framework to the tetrahedral-grid case along with some of the practical results of this extension is also provided. Furthermore, through the use of numerical simulations of practical viscous problems involving high-Reynolds number flows, the effectiveness of the gradient evaluation procedures within the CESE framework (that have their basis on the analysis presented here) to produce accurate and stable results on such high-aspect ratio meshes is also showcased.

Large Eddy Simulation Study for Fluid Disintegration and Mixing

NASA Technical Reports Server (NTRS)

Bellan, Josette; Taskinoglu, Ezgi

2011-01-01

A new modeling approach is based on the concept of large eddy simulation (LES) within which the large scales are computed and the small scales are modeled. The new approach is expected to retain the fidelity of the physics while also being computationally efficient. Typically, only models for the small-scale fluxes of momentum, species, and enthalpy are used to reintroduce in the simulation the physics lost because the computation only resolves the large scales. These models are called subgrid (SGS) models because they operate at a scale smaller than the LES grid. In a previous study of thermodynamically supercritical fluid disintegration and mixing, additional small-scale terms, one in the momentum and one in the energy conservation equations, were identified as requiring modeling. These additional terms were due to the tight coupling between dynamics and real-gas thermodynamics. It was inferred that if these terms would not be modeled, the high density-gradient magnitude regions, experimentally identified as a characteristic feature of these flows, would not be accurately predicted without the additional term in the momentum equation; these high density-gradient magnitude regions were experimentally shown to redistribute turbulence in the flow. And it was also inferred that without the additional term in the energy equation, the heat flux magnitude could not be accurately predicted; the heat flux to the wall of combustion devices is a crucial quantity that determined necessary wall material properties. The present work involves situations where only the term in the momentum equation is important. Without this additional term in the momentum equation, neither the SGS-flux constant-coefficient Smagorinsky model nor the SGS-flux constant-coefficient Gradient model could reproduce in LES the pressure field or the high density-gradient magnitude regions; the SGS-flux constant- coefficient Scale-Similarity model was the most successful in this endeavor although not totally satisfactory. With a model for the additional term in the momentum equation, the predictions of the constant-coefficient Smagorinsky and constant-coefficient Scale-Similarity models were improved to a certain extent; however, most of the improvement was obtained for the Gradient model. The previously derived model and a newly developed model for the additional term in the momentum equation were both tested, with the new model proving even more successful than the previous model at reproducing the high density-gradient magnitude regions. Several dynamic SGS-flux models, in which the SGS-flux model coefficient is computed as part of the simulation, were tested in conjunction with the new model for this additional term in the momentum equation. The most successful dynamic model was a "mixed" model combining the Smagorinsky and Gradient models. This work is directly applicable to simulations of gas turbine engines (aeronautics) and rocket engines (astronautics).

The lateral variation of P n velocity gradient under Eurasia

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

Yang, Xiaoning

We report that mantle lid P wave velocity gradient, or P n velocity gradient, reflects the depth and lateral variations of thermal and rheological state of the uppermost mantle. Mapping the P n velocity gradient and its lateral variation helps us gain insight into the temperature, composition, and dynamics of the uppermost mantle. In addition, because P n velocity gradient has profound influence on P n propagation behavior, an accurate mapping of P n velocity gradient also improves the modeling and prediction of P n travel times and amplitudes. In this study, I used measured P n travel times tomore » derive path-specific P n velocity gradients. I then inverted these velocity gradients for two-dimensional (2-D) P n velocity-gradient models for Eurasia based on the assumption that a path-specific Pn velocity gradient is the mean of laterally varying P n velocity gradients along the P n path. Result from a Monte Carlo simulation indicates that the assumption is appropriate. The 2-D velocity-gradient models show that most of Eurasia has positive velocity gradients. High velocity gradients exist mainly in tectonically active regions. Most tectonically stable regions show low and more uniform velocity gradients. In conclusion, strong velocity-gradient variations occur largely along convergent plate boundaries, particularly under overriding plates.« less

The lateral variation of P n velocity gradient under Eurasia

DOE PAGES

Yang, Xiaoning

2017-05-03

We report that mantle lid P wave velocity gradient, or P n velocity gradient, reflects the depth and lateral variations of thermal and rheological state of the uppermost mantle. Mapping the P n velocity gradient and its lateral variation helps us gain insight into the temperature, composition, and dynamics of the uppermost mantle. In addition, because P n velocity gradient has profound influence on P n propagation behavior, an accurate mapping of P n velocity gradient also improves the modeling and prediction of P n travel times and amplitudes. In this study, I used measured P n travel times tomore » derive path-specific P n velocity gradients. I then inverted these velocity gradients for two-dimensional (2-D) P n velocity-gradient models for Eurasia based on the assumption that a path-specific Pn velocity gradient is the mean of laterally varying P n velocity gradients along the P n path. Result from a Monte Carlo simulation indicates that the assumption is appropriate. The 2-D velocity-gradient models show that most of Eurasia has positive velocity gradients. High velocity gradients exist mainly in tectonically active regions. Most tectonically stable regions show low and more uniform velocity gradients. In conclusion, strong velocity-gradient variations occur largely along convergent plate boundaries, particularly under overriding plates.« less

Regulation of Polycystin-1 Function by Calmodulin Binding

PubMed Central

Doerr, Nicholas; Wang, Yidi; Kipp, Kevin R.; Liu, Guangyi; Benza, Jesse J.; Pletnev, Vladimir; Pavlov, Tengis S.; Staruschenko, Alexander; Mohieldin, Ashraf M.; Takahashi, Maki; Nauli, Surya M.; Weimbs, Thomas

2016-01-01

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a common genetic disease that leads to progressive renal cyst growth and loss of renal function, and is caused by mutations in the genes encoding polycystin-1 (PC1) and polycystin-2 (PC2), respectively. The PC1/PC2 complex localizes to primary cilia and can act as a flow-dependent calcium channel in addition to numerous other signaling functions. The exact functions of the polycystins, their regulation and the purpose of the PC1/PC2 channel are still poorly understood. PC1 is an integral membrane protein with a large extracytoplasmic N-terminal domain and a short, ~200 amino acid C-terminal cytoplasmic tail. Most proteins that interact with PC1 have been found to bind via the cytoplasmic tail. Here we report that the PC1 tail has homology to the regulatory domain of myosin heavy chain including a conserved calmodulin-binding motif. This motif binds to CaM in a calcium-dependent manner. Disruption of the CaM-binding motif in PC1 does not affect PC2 binding, cilia targeting, or signaling via heterotrimeric G-proteins or STAT3. However, disruption of CaM binding inhibits the PC1/PC2 calcium channel activity and the flow-dependent calcium response in kidney epithelial cells. Furthermore, expression of CaM-binding mutant PC1 disrupts cellular energy metabolism. These results suggest that critical functions of PC1 are regulated by its ability to sense cytosolic calcium levels via binding to CaM. PMID:27560828

The negative influence of sperm cryopreservation on the quality and development of the embryo depends on the morphology of the oocyte.

PubMed

Braga, D P A F; Setti, A S; Figueira, R C S; Iaconelli, A; Borges, E

2015-07-01

The present case-control study aimed to identify the effect of sperm cryopreservation on the quality of the embryo and on the probability of blastocyst formation when oocytes free of dimorphisms are injected and when at least one dymorphism is present. The study included 22 186 zygotes, obtained from 2802 patients undergoing intracytoplasmic sperm injection cycles, in a private assisted reproduction center, using either fresh or cryopreserved sperm. The effect of sperm cryopreservation on the embryo quality on cleavage stage and blastocyst formation chance were evaluated when oocytes free of dimorphisms are injected and when at least one dymorphism is present. The quality of the embryo on cleavage stage as well as the chance for blastocyst formation was not influenced by the origin of the spermatozoa when the quality of the oocyte was not considered. When at least one oocyte defect was present, a negative influence of sperm cryopreservation on cleavage stage embryo quality and the chance for blastocyst formation was noted. In oocytes with extra-cytoplasmic dimorphisms, the injection of cryopreserved sperm did not affect the quality of the embryo during the cleavage stage, but did affect the chance for blastocyst formation. Conversely, in oocytes with intracytoplasmic defects, the quality of the embryos on cleavage stage and the chance of blastocyst formation were negatively influenced by the injection of cryopreserved sperm. The results suggest an oocyte quality-dependent negative effect of sperm cryopreservation on embryo quality and on the probability of blastocyst formation. © 2015 American Society of Andrology and European Academy of Andrology.

Novel features of Brassica napus embryogenic microspores revealed by high pressure freezing and freeze substitution: evidence for massive autophagy and excretion-based cytoplasmic cleaning.

PubMed

Corral-Martínez, Patricia; Parra-Vega, Verónica; Seguí-Simarro, Jose M

2013-07-01

Induction of embryogenesis from isolated microspore cultures is a complex experimental system where microspores undergo dramatic changes in developmental fate. After ~40 years of application of electron microscopy to the study of the ultrastructural changes undergone by the induced microspore, there is still room for new discoveries. In this work, high pressure freezing and freeze substitution (HPF/FS), the best procedures known to date for ultrastructural preservation, were used to process Brassica napus microspore cultures covering all the stages of microspore embryogenesis. Analysis of these cultures by electron microscopy revealed massive processes of autophagy exclusively in embryogenic microspores, but not in other microspore-derived structures also present in cultures. However, a significant part of the autophagosomal cargo was not recycled. Instead, it was transported out of the cell, producing numerous deposits of extracytoplasmic fibrillar and membranous material. It was shown that commitment of microspores to embryogenesis is associated with both massive autophagy and excretion of the removed material. It is hypothesized that autophagy would be related to the need for a profound cytoplasmic cleaning, and excretion would be a mechanism to avoid excessive growth of the vacuolar system. Together, the results also demonstrate that the application of HPF/FS to the study of the androgenic switch is the best option currently available to identify the complex and dramatic ultrastructural changes undergone by the induced microspore. In addition, they provide significant insights to understand the cellular basis of induction of microspore embryogenesis, and open a new door for the investigation of this intriguing developmental pathway.

Ba, B, and U element partitioning in magnesian calcite skeletons of Octocorallia corals

NASA Astrophysics Data System (ADS)

Yoshimura, T.; Suzuki, A.; Iwasaki, N.

2015-01-01

Barium, boron and uranium element partitioning and oxygen and carbon isotope fractionation of high-Mg calcite skeletons of Octocorallia corals were investigated. The dissolved Ba concentration in seawater and the coral Ba/Ca ratio showed a clear positive correlation. The empirically derived barium partition coefficient is comparable to previous data for not only calcitic corals but also intermediate- to deep-water-dwelling scleractinian corals whose skeletons are composed of aragonite. Octocorallia corals are geologically important producers of biominerals, and they provide long-term records (up to hundreds of years) of environmental conditions in the deep ocean. Our data suggest that Ba/Ca ratios in Octocorallia corals may be a useful proxy for nutrients in intermediate and deep waters. The Ba/Ca ratio, a possible proxy for pH or carbonate ion concentration in seawater, showed the largest correlation with δ13C among the examined parameters. This result implies that the pH of the extracytoplasmic calcifying fluid (ECF) simultaneously influences δ18O, δ13C, and Ba/Ca by influencing the relative contributions of dissolved carbon sources in the ECF. Positive correlations of Ba/Ca with δ18 and δ13C suggest that δ18 and δ13C are enriched in light isotopes when conditions are less alkaline, suggesting a potential role of biological alkalinity pumping becomes more favorable with decreasing calcifying fluid pH. Substantial inter- and intra-specimen variations in Ba/Ca suggest that physicochemical factors do not exert a dominant systematic control on U incorporation.

Evaluation of differences between dual salt-pH gradient elution and mono gradient elution using a thermodynamic model: Simultaneous separation of six monoclonal antibody charge and size variants on preparative-scale ion exchange chromatographic resin.

PubMed

Lee, Yi Feng; Jöhnck, Matthias; Frech, Christian

2018-02-21

The efficiencies of mono gradient elution and dual salt-pH gradient elution for separation of six mAb charge and size variants on a preparative-scale ion exchange chromatographic resin are compared in this study. Results showed that opposite dual salt-pH gradient elution with increasing pH gradient and simultaneously decreasing salt gradient is best suited for the separation of these mAb charge and size variants on Eshmuno ® CPX. Besides giving high binding capacity, this type of opposite dual salt-pH gradient also provides better resolved mAb variant peaks and lower conductivity in the elution pools compared to single pH or salt gradients. To have a mechanistic understanding of the differences in mAb variants retention behaviors of mono pH gradient, parallel dual salt-pH gradient, and opposite dual salt-pH gradient, a linear gradient elution model was used. After determining the model parameters using the linear gradient elution model, 2D plots were used to show the pH and salt dependencies of the reciprocals of distribution coefficient, equilibrium constant, and effective ionic capacity of the mAb variants in these gradient elution systems. Comparison of the 2D plots indicated that the advantage of opposite dual salt-pH gradient system with increasing pH gradient and simultaneously decreasing salt gradient is the noncontinuous increased acceleration of protein migration. Furthermore, the fitted model parameters can be used for the prediction and optimization of mAb variants separation in dual salt-pH gradient and step elution. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Rarefied-flow pitching moment coefficient measurements of the Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Blanchard, R. C.; Hinson, E. W.

1988-01-01

An overview of the process for obtaining the Shuttle Orbiter rarefied-flow pitching moment from flight gyro data is presented. The extraction technique involves differentiation of the output of the pitch gyro after accounting for nonaerodynamic torques, such as those produced by gravity gradient and the Orbiter's auxiliary power unit and adjusting for drift biases. The overview of the extraction technique includes examples of results from each of the steps involved in the process, using the STS-32 mission as a typical sample case. The total pitching moment and moment coefficient (Cm) for that flight are calculated and compared with preflight predictions. The flight results show the anticipated decrease in Cm with increasing altitude. However, the total moment coefficient is less than predicted using preflight estimates.

Microcompartments and Protein Machines in Prokaryotes

PubMed Central

Saier, Milton H.

2013-01-01

The prokaryotic cell was once thought of as a “bag of enzymes” with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, non-random collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (i) the bacterial cytoskeleton and the apparati allowing DNA segregation during cells division, (ii) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis, (iii) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces, (iv) machines of protein folding, secretion and degradation, (v) metabolasomes carrying out specific chemical reactions, (vi) 24 hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle and (vii) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bounded prokaryotic organelles were considered in a recent JMMB written symposium concerned with membraneous compartmentalization in bacteria [Saier and Bogdanov, 2013]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple non-compartmentalized cell. PMID:23920489