bluuebunny/crossref_metadata_2025 huggingface dataset:
Fate of Glycosylphosphatidylinositol (GPI)-Less Procyclin and Characterization of Sialylated Non-GPI-Anchored Surface Coat Molecules of Procyclic-Form
Trypanosoma brucei
Authors: Güther Maria Lucia Sampaio , Beattie Kenneth , Lamont Douglas J. , James John , Prescott Alan R. , Ferguson Michael A. J.
Published: July 2009

A
Trypanosoma brucei
TbGPI12 null mutant that is unable to express cell surface procyclins and free glycosylphosphatidylinositols (GPI) revealed that these are not the only surface coat molecules of the procyclic life cycle stage. Here, we show that non-GPI-anchored procyclins are N-glycosylated, accumulate in the lysosome, and appear as proteolytic fragments in the medium. We also show, using lectin agglutination and galactose oxidase-NaB
3
H
4
labeling, that the cell surface of the TbGPI12 null parasites contains glycoconjugates that terminate in sialic acid linked to galactose. Following desialylation, a high-apparent-molecular-weight glycoconjugate fraction was purified by ricin affinity chromatography and gel filtration and shown to contain mannose, galactose,
N
-acetylglucosamine, and fucose. The latter has not been previously reported in
T. brucei
glycoproteins. A proteomic analysis of this fraction revealed a mixture of polytopic transmembrane proteins, including P-type ATPase and vacuolar proton-translocating pyrophosphatase. Immunolocalization studies showed that both could be labeled on the surfaces of wild-type and TbGPI12 null cells. Neither galactose oxidase-NaB
3
H
4
labeling of the non-GPI-anchored surface glycoconjugates nor immunogold labeling of the P-type ATPase was affected by the presence of procyclins in the wild-type cells, suggesting that the procyclins do not, by themselves, form a macromolecular barrier.
Characterization of Novel Alleles of the
Escherichia coli umuDC
Genes Identifies Additional Interaction Sites of UmuC with the Beta Clamp
Authors: Beuning Penny J. , Chan Sarah , Waters Lauren S. , Addepalli Haripriya , Ollivierre Jaylene N. , Walker Graham C.
Published: July 2009

Translesion synthesis is a DNA damage tolerance mechanism by which damaged DNA in a cell can be replicated by specialized DNA polymerases without being repaired. The
Escherichia coli umuDC
gene products, UmuC and the cleaved form of UmuD, UmuD′, comprise a specialized, potentially mutagenic translesion DNA polymerase, polymerase V (UmuD′
2
C). The full-length UmuD protein, together with UmuC, plays a role in a primitive DNA damage checkpoint by decreasing the rate of DNA synthesis. It has been proposed that the checkpoint is manifested as a cold-sensitive phenotype that is observed when the
umuDC
gene products are overexpressed. Elevated levels of the beta processivity clamp along with elevated levels of the
umuDC
gene products, UmuD′C, exacerbate the cold-sensitive phenotype. We used this observation as the basis for genetic selection to identify two alleles of
umuD
′ and seven alleles of
umuC
that do not exacerbate the cold-sensitive phenotype when they are present in cells with elevated levels of the beta clamp. The variants were characterized to determine their abilities to confer the
umuD
′
C
-specific phenotype UV-induced mutagenesis. The
umuD
variants were assayed to determine their proficiencies in UmuD cleavage, and one variant (G129S) rendered UmuD noncleaveable. We found at least two UmuC residues, T243 and L389, that may further define the beta binding region on UmuC. We also identified UmuC S31, which is predicted to bind to the template nucleotide, as a residue that is important for UV-induced mutagenesis.
Molecular Basis of ChvE Function in Sugar Binding, Sugar Utilization, and Virulence in
Agrobacterium tumefaciens
Authors: He Fanglian , Nair Gauri R. , Soto Cinque S. , Chang Yehchung , Hsu Lillian , Ronzone Erik , DeGrado William F. , Binns Andrew N.
Published: July 2009

ChvE is a chromosomally encoded protein in
Agrobacterium tumefaciens
that mediates a sugar-induced increase in virulence (
vir
) gene expression through the activities of the VirA/VirG two-component system and has also been suggested to be involved in sugar utilization. The ChvE protein has homology to several bacterial periplasmic sugar-binding proteins, such as the ribose-binding protein and the galactose/glucose-binding protein of
Escherichia coli
. In this study, we provide direct evidence that ChvE specifically binds the
vir
gene-inducing sugar
d
-glucose with high affinity. Furthermore, ChvE mutations resulting in altered
vir
gene expression phenotypes have been isolated and characterized. Three distinct categories of mutants have been identified. Strains expressing the first class are defective in both virulence and
d
-glucose utilization as a result of mutations to residues lining the sugar-binding cleft. Strains expressing a second class of mutants are not adversely affected in sugar binding but are defective in virulence, presumably due to impaired interactions with the sensor kinase VirA. A subset of this second class of mutants includes variants of ChvE that also result in defective sugar utilization. We propose that these mutations affect not only interactions with VirA but also interactions with a sugar transport system. Examination of a homology model of ChvE shows that the mutated residues associated with the latter two phenotypes lie in two overlapping solvent-exposed sites adjacent to the sugar-binding cleft where conformational changes associated with the binding of sugar might have a maximal effect on ChvE's interactions with its distinct protein partners.
Characterization and Comparative Analysis of the Genes EncodingHaemophilus parasuisOuter Membrane Proteins P2 and P5
Authors: Mullins Michael A. , Register Karen B. , Bayles Darrell O. , Loving Crystal L. , Nicholson Tracy L. , Brockmeier Susan L. , Dyer David W. , Phillips Gregory J.
Published: July 2009

Haemophilus parasuisis a swine pathogen of significant industry concern, but little is known about how the organism causes disease. A related human pathogen,Haemophilus influenzae, has been better studied, and many of its virulence factors have been identified. Two of these, outer membrane proteins P2 and P5, are known to have important virulence properties. The goals of this study were to identify, analyze, and compare the genetic relatedness of orthologous genes encoding P2 and P5 proteins in a diverse group of 35H. parasuisstrains. Genes encoding P2 and P5 proteins were detected in allH. parasuisstrains evaluated. The predicted amino acid sequences for both P2 and P5 proteins exhibit considerable heterogeneity, particularly in regions corresponding to predicted extracellular loops. Twenty-five variants of P2 and 17 variants of P5 were identified. The P2 proteins of seven strains were predicted to contain a highly conserved additional extracellular loop compared to the remaining strains and toH. influenzaeP2. Antigenic-site predictions coincided with predicted extracellular loop regions of both P2 and P5. Neighbor-joining trees constructed using P2 and P5 sequences predicted divergent evolutionary histories distinct from those predicted by a multilocus sequence typing phylogeny based on partial sequencing of seven housekeeping genes. Real-time reverse transcription-PCR indicated that both genes are expressed in all of the strains.
Feedback Control of DnaA-Mediated Replication Initiation by Replisome-Associated HdaA Protein inCaulobacter
Authors: Collier Justine , Shapiro Lucy
Published: July 2009

Chromosome replication inCaulobacter crescentusis tightly regulated to ensure that initiation occurs at the right time and only once during the cell cycle. The timing of replication initiation is controlled by both CtrA and DnaA. CtrA binds to and silences the origin. Upon the clearance of CtrA from the cell, the DnaA protein accumulates and allows loading of the replisome at the origin. Here, we identify an additional layer of replication initiation control that is mediated by the HdaA protein. InEscherichia coli, the Hda protein inactivates DnaA after replication initiation. We show that theCaulobacterHdaA homologue is necessary to restrict the initiation of DNA replication to only once per cell cycle and that it dynamically colocalizes with the replisome throughout the cell cycle. Moreover, the transcription ofhdaAis directly activated by DnaA, providing a robust feedback regulatory mechanism that adjusts the levels of HdaA to inactivate DnaA.
Isolation of a Variant of Subtilosin A with Hemolytic Activity
Authors: Huang Tai , Geng Hao , Miyyapuram Venugopal R. , Sit Clarissa S. , Vederas John C. , Nakano Michiko M.
Published: July 2009

Bacillus subtilis
produces an anionic bacteriocin called subtilosin A that possesses antibacterial activity against certain gram-positive bacteria. In this study, we uncovered a hemolytic mutant of
B. subtilis
that produces an altered form of subtilosin A. The mutant bacteriocin, named subtilosin A1, has a replacement of threonine at position 6 with isoleucine. In addition to the hemolytic activity, subtilosin A1 was found to exhibit enhanced antimicrobial activity against specific bacterial strains. The
B. subtilis albB
mutant that does not produce a putative immunity peptide was more sensitive to both subtilosin A and subtilosin A1. A spontaneous suppressor mutation of
albB
that restored resistance to subtilosin A and subtilosin A1 was obtained. The
sbr
(
s
u
b
tilosin
r
esistance) mutation conferring the resistance is not linked to the
sboA-alb
locus. The
sbr
mutation does not increase the resistance of
B. subtilis
to other cell envelope-targeted antimicrobial agents, indicating that the mutation specifically confers the resistance to subtilosins. The findings suggest possible bioengineering approaches for obtaining anionic bacteriocins with enhanced and/or altered bactericidal activity. Furthermore, future identification of the subtilosin-resistant mutation could provide insights into the mechanism of subtilosin A activity.
Role of the Twin-Arginine Translocation Pathway in
Staphylococcus
Authors: Biswas Lalitha , Biswas Raja , Nerz Christiane , Ohlsen Knut , Schlag Martin , Schäfer Tina , Lamkemeyer Tobias , Ziebandt Anne-Kathrin , Hantke Klaus , Rosenstein Ralf , Götz Friedrich
Published: July 2009

In
Staphylococcus
, the twin-arginine translocation (Tat) pathway is present only in some species and is composed of TatA and TatC. The
tatAC
operon is associated with the
fepABC
operon, which encodes homologs to an iron-binding lipoprotein, an iron-dependent peroxidase (FepB), and a high-affinity iron permease. The FepB protein has a typical twin-arginine (RR) signal peptide. The
tat
and
fep
operons constitute an entity that is not present in all staphylococcal species. Our analysis was focused on
Staphylococcus aureus
and
S. carnosus
strains. Tat deletion mutants (
ΔtatAC
) were unable to export active FepB, indicating that this enzyme is a Tat substrate. When the RR signal sequence from FepB was fused to prolipase and protein A, their export became Tat dependent. Since no other protein with a Tat signal could be detected, the
fepABC
-
tatAC
genes comprise not only a genetic but also a functional unit. We demonstrated that FepABC drives iron import, and in a mouse kidney abscess model, the bacterial loads of Δ
tatAC
and Δ
tat
-
fep
mutants were decreased. For the first time, we show that the Tat pathway in
S. aureus
is functional and serves to translocate the iron-dependent peroxidase FepB.
The
pgaABCD
Locus of
Acinetobacter baumannii
Encodes the Production of Poly-β-1-6-
N
-Acetylglucosamine, Which Is Critical for Biofilm Formation
Authors: Choi Alexis H. K. , Slamti Leyla , Avci Fikri Y. , Pier Gerald B. , Maira-Litrán Tomás
Published: July 2009

We found that
Acinetobacter baumannii
contains a
pgaABCD
locus that encodes proteins that synthesize cell-associated poly-β-(1-6)-
N
-acetylglucosamine (PNAG). Both a mutant with an in-frame deletion of the
pga
locus (S1Δ
pga
) and a transcomplemented strain (S1Δ
pga
-c) of
A. baumannii
were constructed, and the PNAG production by these strains was compared using an immunoblot assay. Deleting the
pga
locus resulted in an
A. baumannii
strain without PNAG, and transcomplementation of the S1Δ
pga
strain with the
pgaABCD
genes fully restored the wild-type PNAG phenotype. Heterologous expression of the
A. baumannii pga
locus in
Escherichia coli
led to synthesis of significant amounts of PNAG, while no polysaccharide was detected in
E. coli
cells harboring an empty vector. Nuclear magnetic resonance analysis of the extracellular polysaccharide material isolated from
A. baumannii
confirmed that it was PNAG, but notably only 60% of the glucosamine amino groups were acetylated. PCR analysis indicated that all 30 clinical
A. baumannii
isolates examined had the
pga
genes, and immunoblot assays indicated that 14 of the 30 strains strongly produced PNAG, 14 of the strains moderately to weakly produced PNAG, and 2 strains appeared to not produce PNAG. Deletion of the
pga
locus led to loss of the strong biofilm phenotype, which was restored by complementation. Confocal laser scanning microscopy studies combined with COMSTAT analysis demonstrated that the biovolume, mean thickness, and maximum thickness of 16-h and 48-h-old biofilms formed by wild-type and
pga
-complemented
A. baumannii
strains were significantly greater than the biovolume, mean thickness, and maximum thickness of 16-h and 48-h-old biofilms formed by the S1Δ
pga
mutant strain. Biofilm-dependent production of PNAG could be an important virulence factor for this emerging pathogen that has few known virulence factors.
Participation of Regulator AscG of the β-Glucoside Utilization Operon in Regulation of the Propionate Catabolism Operon
Authors: Ishida Yuji , Kori Ayako , Ishihama Akira
Published: July 2009

The
asc
operon of
Escherichia coli
is one of the cryptic genetic systems for β-
d
-galactoside utilization as a carbon source. The
ascFB
genes for β-
d
-galactoside transport and catabolism are repressed by the AscG regulator. After genomic SELEX screening, AscG was found to recognize and bind the consensus palindromic sequence TGAAACC-GGTTTCA. AscG binding was detected at two sites upstream of the
ascFB
promoter and at three sites upstream of the
prpBC
operon for propionate catabolism. In an
ascG
-disrupted mutant, transcription of
ascFB
was enhanced, in agreement with the repressor model of AscG. This repression was indicated to be due to interference of binding of cyclic AMP-CRP to the CRP box, which overlaps with the AscG-binding site 1, as well as binding of RNA polymerase to the promoter. Under conditions of steady-state
E. coli
growth in a rich medium, the intracellular level of AscG stayed constant at a level supposedly leading to tight repression of the
ascFB
operon. The level of
prpR
, encoding the activator of
prpBCDE
, was also increased in the absence of AscG, indicating the involvement of AscG in repression of
prpR
. Taken together, these data suggest a metabolic link through interplay between the
asc
and
prp
operons.
Downregulation of the
Escherichia coli guaB
Promoter by Upstream-Bound Cyclic AMP Receptor Protein
Authors: Husnain Seyyed I. , Busby Stephen J. W. , Thomas Mark S.
Published: July 2009

The
Escherichia coli guaB
promoter (P

guaB

) is responsible for directing transcription of the
guaB
and
guaA
genes, which specify the biosynthesis of the nucleotide GMP. P

guaB

is subject to growth rate-dependent control (GRDC) and possesses an UP element that is required for this regulation. In addition, P

guaB

contains a discriminator, three binding sites for the nucleoid-associated protein FIS, and putative binding sites for the regulatory proteins DnaA, PurR, and cyclic AMP receptor protein (CRP). Here we show that the CRP-cyclic AMP (cAMP) complex binds to a site located over 100 bp upstream of the
guaB
transcription start site, where it serves to downregulate P

guaB

. The CRP-mediated repression of P

guaB

activity increases in media that support lower growth rates. Inactivation of the
crp
or
cyaA
gene or ablation/translocation of the CRP site relieves repression by CRP and results in a loss of GRDC of P

guaB

. Thus, GRDC of P

guaB

involves a progressive increase in CRP-mediated repression of the promoter as the growth rate decreases. Our results also suggest that the CRP-cAMP complex does not direct GRDC at P

guaB

and that at least one other regulatory factor is required for conferring GRDC on this promoter. However, PurR and DnaA are not required for this regulatory mechanism.
Potential Role of Group IIC-attCIntrons in Integron Cassette Formation
Authors: Léon Grégory , Roy Paul H.
Published: July 2009

Integrons are natural expression vectors in which gene cassettes are integrated downstream of a promoter region by a site-specific recombinase. Gene cassettes usually consist of a single gene followed by a recombination site designatedattC. A major unanswered question is how a gene becomes associated with anattCsite. Here, we investigate the potential role of a specific lineage of group IIC introns, named group IIC-attC, in cassette formation. Group IIC-attCintrons preferentially targetattCwhile retaining the ability to target transcriptional terminators. We show using a PCR-based mobility assay withEscherichia colithat theS.ma.I2 intron from the genome of a clinical isolate ofSerratia marcescenscan target bothattCsite and putative terminator motifs of resistance genes. Quantitative results showed thatS.ma.I2 is more efficient in targeting variousattCsequences than three group IIC-attCintrons (54 to 64% sequence identity) from the genomes of environmental isolates. We also show that purified group IIC-attCintron-encoded reverse transcriptases have both RNA-dependent and DNA-dependent DNA polymerase activities in vitro. These data permit us to suggest a new model for gene cassette formation, in which a group IIC-attCintron targets separately a transcriptional terminator adjoining a gene and an isolatedattC, joins the gene and theattCby homologous recombination, and then splices and reverse transcribes a gene-attCRNA template, leading to the formation of a cassette.
Significant Bias against the ACA Triplet in the tmRNA Sequence of
Escherichia coli
K-12
Authors: Baik Sarah , Inoue Koichi , Ouyang Ming , Inouye Masayori
Published: July 2009

The toxin MazF in
Escherichia coli
cleaves single-stranded RNAs specifically at ACA sequences. MazF overexpression virtually eliminates all cellular mRNAs to completely block protein synthesis. However, protein synthesis can continue on an mRNA that is devoid of ACA triplets. The finding that ribosomal RNAs remain intact in the face of complete translation arrest suggested a purpose for such preservation. We therefore examined the sequences of all transcribed RNAs to determine if there was any statistically significant bias against ACA. While ACA motifs are absent from tmRNA, 4.5S RNA, and seven of the eight 5S rRNAs, statistical analysis revealed that only for tmRNA was the absence nonrandom. The introduction of single-strand ACAs makes tmRNA highly susceptible to MazF cleavage. Furthermore, analysis of tmRNA sequences from 442 bacteria showed that the discrimination against ACA in tmRNAs was seen mostly in enterobacteria. We propose that the unusual bias against ACA in tmRNA may have coevolved with the acquisition of MazF.
Mutagenesis and Functional Characterization of the RNA and Protein Components of the
toxIN
Abortive Infection and Toxin-Antitoxin Locus of
Erwinia
Authors: Blower T. R. , Fineran P. C. , Johnson M. J. , Toth I. K. , Humphreys D. P. , Salmond G. P. C.
Published: July 2009

Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multiple adaptive resistance mechanisms. These mechanisms include the abortive infection systems, which promote “altruistic suicide” of an infected cell, protecting the clonal population. A cryptic plasmid of
Erwinia carotovora
subsp.
atroseptica
, pECA1039, has been shown to encode an abortive infection system. This highly effective system is active across multiple genera of gram-negative bacteria and against a spectrum of phages. Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module. ToxIN is the first member of a new type III class of protein-RNA toxin-antitoxin modules, of which there are multiple homologues cross-genera. We characterized in more detail the abortive infection phenotype of ToxIN using a suite of
Erwinia
phages and performed mutagenesis of the ToxI and ToxN components. We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN. Furthermore, site-directed mutagenesis of ToxN revealed key conserved amino acids in this defining member of the new group of toxic proteins. The mechanism of phage activation of the ToxIN system was investigated and was shown to have no effect on the levels of the ToxN protein. Finally, evidence of negative autoregulation of the
toxIN
operon, a common feature of toxin-antitoxin systems, is presented. This work on the components of the ToxIN system suggests that there is very tight toxin regulation prior to suicide activation by incoming phage.
Processing and Stability of Inducibly ExpressedrpsOmRNA Derivatives inBacillus subtilis
Authors: Yao Shiyi , Bechhofer David H.
Published: July 2009

TheBacillus subtilis rpsOgene specifies a small (388-nucleotide), monocistronic mRNA that encodes ribosomal protein S15. We showed earlier thatrpsOmRNA decay intermediates accumulated to a high level in a strain lacking polynucleotide phosphorylase. Here, we used inducibly expressed derivatives ofrpsO, encoding smaller RNAs that had the complex 5′ region deleted, to study aspects of mRNA processing inB. subtilis. An IPTG (isopropyl-β-d-thiogalactopyranoside)-induciblerpsOtranscript that containedlacsequences at the 5′ end, calledlac-rpsORNA, was shown to undergo processing to result in an RNA that was 24 nucleotides shorter than full length. Such processing was dependent on the presence of an accessible 5′ terminus; alac-rpsORNA that contained a strong stem-loop at the 5′ end was not processed and was extremely stable. Interestingly, this stability depended also on ribosome binding to a nearby Shine-Dalgarno sequence but was independent of downstream translation. Either RNase J1 or RNase J2 was capable of processinglac-rpsORNA, demonstrating for the first time a particular in vivo processing event that could be catalyzed by both enzymes. Decay intermediates were detected in thepnpAstrain only for alac-rpsORNA that was untranslated. Analysis of processing of an untranslatedlac-rpsORNA in thepnpAstrain shortly after induction of transcription suggested that endonuclease cleavage at 3′-proximal sites was an early step in turnover of mRNA.
The Novel Genes
emmABC
Are Associated with Exopolysaccharide Production, Motility, Stress Adaptation, and Symbiosis in
Sinorhizobium meliloti
Authors: Morris Jennifer , González Juan E.
Published: July 2009

The nitrogen-fixing symbiont
Sinorhizobium meliloti
senses and responds to constantly changing environmental conditions as it makes its way through the soil in search of its leguminous plant host,
Medicago sativa
(alfalfa). As a result, this bacterium regulates various aspects of its physiology in order to respond appropriately to stress, starvation, and competition. For example, exopolysaccharide production, which has been shown to play an important role in the ability of
S. meliloti
to successfully invade its host, also helps the bacterium withstand osmotic changes and other environmental stresses. In an effort to further elucidate the intricate regulation of this important cell component, we set out to identify genetic factors that may affect its production. Here we characterize novel genes that encode a small protein (EmmA) and a putative two-component system (EmmB-EmmC). A mutation in any of these genes leads to increased production of the symbiotically important exopolysaccharide succinoglycan. In addition,
emm
mutants display membrane-associated defects, are nonmotile, and are unable to form an optimal symbiosis with alfalfa, suggesting that these novel genes may play a greater role in the overall fitness of
S. meliloti
both during the free-living stage and in its association with its host.
Comparative Sequence Analysis ofMycobacterium lepraeand the New Leprosy-CausingMycobacterium lepromatosis
Authors: Han Xiang Y. , Sizer Kurt C. , Thompson Erika J. , Kabanja Juma , Li Jun , Hu Peter , Gómez-Valero Laura , Silva Francisco J.
Published: July 2009

Mycobacterium lepromatosisis a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence fromMycobacterium leprae, a well-known cause of leprosy, that justifies the status ofM. lepromatosisas a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences withM. lepraesequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dSvalues) and nonsynonymous substitutions (dNvalues) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placedM. lepromatosisandM. lepraein a tight cluster with long terminal branches, implying that the divergence occurred long ago. ThedSanddNvalues were also much higher than those for other closest pairs of mycobacteria. ThedSvalues were 14 to 28% of thedSvalues forM. lepraeandMycobacterium tuberculosis, a more divergent pair of species. These results thus indicate thatM. lepromatosisandM. lepraediverged ∼10 million years ago. TheM. lepromatosispseudogenes analyzed that were also pseudogenes inM. lepraeshowed nearly neutral evolution, and their relative ages were similar to those ofM. lepraepseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate thatM. lepromatosisandM. lepraediverged from a common ancestor after the massive gene inactivation event described previously forM. leprae.
Cyclic di-GMP Allosterically Inhibits the CRP-Like Protein (Clp) of
Xanthomonas axonopodis
pv. citri
Authors: Leduc Jason L. , Roberts Gary P.
Published: July 2009

The protein Clp from
Xanthomonas axonopodis
pv. citri regulates pathogenesis and is a member of the CRP (cyclic AMP receptor protein) superfamily. We show that unlike the DNA-binding activity of other members of this family, the DNA-binding activity of Clp is allosterically inhibited by its effector and that cyclic di-GMP serves as that effector at physiological concentrations.
Mutual Regulation of
ntcA
and
hetR
during Heterocyst Differentiation Requires Two Similar PP2C-Type Protein Phosphatases, PrpJ1 and PrpJ2, in
Anabaena
sp. Strain PCC 7120
Authors: Jang Jichan , Shi Lei , Tan Hui , Janicki Annick , Zhang Cheng-Cai
Published: July 2009

The filamentous cyanobacterium
Anabaena
sp. strain PCC 7120 can form heterocysts for N
2
fixation. Initiation of heterocyst differentiation depends on mutual regulation of
ntcA
and
hetR
. Control of
hetR
expression by NtcA is partially mediated by
nrrA
, but other factors must be involved in this regulation.
Anabaena
has two closely related PP2C-type protein phosphatases, PrpJ1 (formerly PrpJ) and PrpJ2; PrpJ1 is involved in heterocyst maturation. In this study, we show that PrpJ2, like PrpJ1, has Mn
2+
-dependent phosphatase activity. We further demonstrate that whereas
prpJ2
is dispensable for cell growth under different nitrogen regimens tested, a double mutant with both
prpJ1
and
prpJ2
disrupted did not initiate heterocyst differentiation. Ectopic expression of
hetR
in the double mutant could rescue the failure to initiate heterocyst development, but the heterocysts formed, like those of a
prpJ1
single mutant, were not mature. The expression of
prpJ2
was enhanced during heterocyst development, and the upregulation of the gene was directly under the control of NtcA. Upregulation of both
ntcA
and
hetR
was affected in the double mutant. We propose that PrpJ1 and PrpJ2 together are required for mutual regulation of
ntcA
and
hetR
and are thus involved in regulation of the initiation of heterocyst differentiation.
EXTERNAL SYNCHRONIZATION OF A HYSTERETIC SYSTEM WITH A DUFFING SYSTEM BY FEEDBACK CONTROL STRATEGY
Authors: HAN QINGKAI , SUN XIAOYU , YANG XIAOGUANG , WEN BANGCHUN
Published: July 2009

Two or more dynamical systems can achieve external synchronization motions with an especially designed controller, in which one dynamical system is considered as the master, and the other as the slave. In this paper, a general strategy of feedback control to carry out the external synchronization is firstly introduced. The master system consists of a hysteretic device to account for the friction phenomenon, and the slave system comprises a hardening stiffness component that can generate the third order displacement as a Duffing system. The slave system can keep in synchronization with the movements of the master via a feedback control strategy. A stability analysis of the synchronization errors is conducted. Different synchronization motions under different system parameters are simulated, based on which discussions are made for the effects of the controller parameters.
Energy-preserving integrators for fluid animation
Authors: Mullen Patrick , Crane Keenan , Pavlov Dmitry , Tong Yiying , Desbrun Mathieu
Published: July 2009

Numerical viscosity has long been a problem in fluid animation. Existing methods suffer from intrinsic artificial dissipation and often apply complicated computational mechanisms to combat such effects. Consequently, dissipative behavior cannot be controlled or modeled explicitly in a manner independent of time step size, complicating the use of coarse previews and adaptive-time stepping methods. This paper proposes simple, unconditionally stable, fully Eulerian integration schemes with no numerical viscosity that are capable of maintaining the liveliness of fluid motion without recourse to corrective devices. Pressure and fluxes are solved efficiently and simultaneously in a time-reversible manner on simplicial grids, and the energy is preserved exactly over long time scales in the case of inviscid fluids. These integrators can be viewed as an extension of the classical energy-preserving Harlow-Welch / Crank-Nicolson scheme to simplicial grids.
Content-preserving warps for 3D video stabilization
Authors: Liu Feng , Gleicher Michael , Jin Hailin , Agarwala Aseem
Published: July 2009

We describe a technique that transforms a video from a hand-held video camera so that it appears as if it were taken with a directed camera motion. Our method adjusts the video to appear as if it were taken from nearby viewpoints, allowing 3D camera movements to be simulated. By aiming only for perceptual plausibility, rather than accurate reconstruction, we are able to develop algorithms that can effectively recreate dynamic scenes from a single source video. Our technique first recovers the original 3D camera motion and a sparse set of 3D, static scene points using an off-the-shelf structure-from-motion system. Then, a desired camera path is computed either automatically (e.g., by fitting a linear or quadratic path) or interactively. Finally, our technique performs a least-squares optimization that computes a spatially-varying warp from each input video frame into an output frame. The warp is computed to both follow the sparse displacements suggested by the recovered 3D structure,
and
avoid deforming the content in the video frame. Our experiments on stabilizing challenging videos of dynamic scenes demonstrate the effectiveness of our technique.
NURBS with extraordinary points
Authors: Cashman Thomas J. , Augsdörfer Ursula H. , Dodgson Neil A. , Sabin Malcolm A.
Published: July 2009

We present a subdivision framework that adds extraordinary vertices to NURBS of arbitrarily high degree. The surfaces can represent any odd degree NURBS patch exactly. Our rules handle non-uniform knot vectors, and are not restricted to midpoint knot insertion. In the absence of multiple knots at extraordinary points, the limit surfaces have bounded curvature.
Deformable object animation using reduced optimal control
Authors: Barbič Jernej , da Silva Marco , Popović Jovan
Published: July 2009

Keyframe animation is a common technique to generate animations of deformable characters and other soft bodies. With spline interpolation, however, it can be difficult to achieve secondary motion effects such as plausible dynamics when there are thousands of degrees of freedom to animate. Physical methods can provide more realism with less user effort, but it is challenging to apply them to quickly create
specific
animations that closely follow prescribed animator goals. We present a fast space-time optimization method to author physically based deformable object simulations that conform to animator-specified keyframes. We demonstrate our method with FEM deformable objects and mass-spring systems.

Our method minimizes an objective function that penalizes the sum of keyframe deviations plus the deviation of the trajectory from physics. With existing methods, such minimizations operate in high dimensions, are slow, memory consuming, and prone to local minima. We demonstrate that significant computational speedups and robustness improvements can be achieved if the optimization problem is properly solved in a low-dimensional space. Selecting a low-dimensional space so that the intent of the animator is accommodated, and that at the same time space-time optimization is convergent and fast, is difficult. We present a method that generates a quality low-dimensional space using the given keyframes. It is then possible to find quality solutions to difficult space-time optimization problems robustly and in a manner of minutes.
Möbius voting for surface correspondence
Authors: Lipman Yaron , Funkhouser Thomas
Published: July 2009

The goal of our work is to develop an efficient, automatic algorithm for discovering point correspondences between surfaces that are approximately and/or partially isometric.

Our approach is based on three observations. First, isometries are a subset of the Möbius group, which has low-dimensionality -- six degrees of freedom for topological spheres, and three for topological discs. Second, computing the Möbius transformation that interpolates any three points can be computed in closed-form after a mid-edge flattening to the complex plane. Third, deviations from isometry can be modeled by a transportation-type distance between corresponding points in that plane.

Motivated by these observations, we have developed a Möbius Voting algorithm that iteratively: 1) samples a triplet of three random points from each of two point sets, 2) uses the Möbius transformations defined by those triplets to map both point sets into a canonical coordinate frame on the complex plane, and 3) produces "votes" for predicted correspondences between the mutually closest points with magnitude representing their estimated deviation from isometry. The result of this process is a fuzzy correspondence matrix, which is converted to a permutation matrix with simple matrix operations and output as a discrete set of point correspondences with confidence values.

The main advantage of this algorithm is that it can find intrinsic point correspondences in cases of extreme deformation. During experiments with a variety of data sets, we find that it is able to find dozens of point correspondences between different object types in different poses fully automatically.
Deforming meshes that split and merge
Authors: Wojtan Chris , Thürey Nils , Gross Markus , Turk Greg
Published: July 2009

We present a method for accurately tracking the moving surface of deformable materials in a manner that gracefully handles topological changes. We employ a Lagrangian surface tracking method, and we use a triangle mesh for our surface representation so that fine features can be retained. We make topological changes to the mesh by first identifying merging or splitting events at a particular grid resolution, and then locally creating new pieces of the mesh in the affected cells using a standard isosurface creation method. We stitch the new, topologically simplified portion of the mesh to the rest of the mesh at the cell boundaries. Our method detects and treats topological events with an emphasis on the preservation of detailed features, while simultaneously simplifying those portions of the material that are not visible. Our surface tracker is not tied to a particular method for simulating deformable materials. In particular, we show results from two significantly different simulators: a Lagrangian FEM simulator with tetrahedral elements, and an Eulerian grid-based fluid simulator. Although our surface tracking method is generic, it is particularly well-suited for simulations that exhibit fine surface details and numerous topological events. Highlights of our results include merging of viscoplastic materials with complex geometry, a taffy-pulling animation with many fold and merge events, and stretching and slicing of stiff plastic material.
Synchronized multi-character motion editing
Authors: Kim Manmyung , Hyun Kyunglyul , Kim Jongmin , Lee Jehee
Published: July 2009

The ability to interactively edit human motion data is essential for character animation. We present a novel motion editing technique that allows the user to manipulate synchronized multiple character motions interactively. Our Laplacian motion editing method formulates the interaction among multiple characters as a collection of linear constraints and enforces the constraints, while the user directly manipulates the motion of characters in both spatial and temporal domains. Various types of manipulation handles are provided to specify absolute/relative spatial location, direction, time, duration, and synchronization of multiple characters. The capability of non-sequential discrete editing is incorporated into our motion editing interfaces, so continuous and discrete editing is performed simultaneously and seamlessly. We demonstrate that the synchronized multiple character motions are synthesized and manipulated at interactive rates using spatiotemporal constraints.
Linear Bellman combination for control of character animation
Authors: da Silva Marco , Durand Frédo , Popović Jovan
Published: July 2009

Controllers are necessary for physically-based synthesis of character animation. However, creating controllers requires either manual tuning or expensive computer optimization. We introduce linear Bellman combination as a method for reusing existing controllers. Given a set of controllers for related tasks, this combination creates a controller that performs a new task. It naturally weights the contribution of each component controller by its relevance to the current state and goal of the system. We demonstrate that linear Bellman combination outperforms naive combination often succeeding where naive combination fails. Furthermore, this combination is provably optimal for a new task if the component controllers are also optimal for related tasks. We demonstrate the applicability of linear Bellman combination to interactive character control of stepping motions and acrobatic maneuvers.
Rosuvastatin ameliorates the development of pulmonary arterial hypertension in the transgenic (mRen2)27 rat
Authors: DeMarco Vincent G. , Habibi Javad , Whaley-Connell Adam T. , Schneider Rebecca I. , Sowers James R. , Andresen Bradley T. , Gutweiler Alex A. , Ma Lixin , Johnson Megan S. , Ferrario Carlos M. , Dellsperger Kevin C.
Published: July 2009

We have recently reported that transgenic (mRen2)27 rats (Ren2 rats) exhibit pulmonary arterial hypertension (PAH), which is, in part, mediated by oxidative stress. Since 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors (statins) exhibit beneficial vascular effects independent of cholesterol synthesis, we hypothesized that rosuvastatin (RSV) treatment ameliorates PAH and pulmonary vascular remodeling in Ren2 rats, in part, by reducing oxidative stress. Six-week-old male Ren2 and Sprague-Dawley rats received RSV (10 mg·kg−1·day−1 ip) or vehicle for 3 wk. After treatment, right ventricular systolic pressure (RVSP) and mean arterial pressure (MAP) were measured. To evaluate treatment effects on pulmonary arteriole remodeling, morphometric analyses were performed to quantitate medial thickening and cell proliferation, whereas whole lung samples were used to quantitate the levels of 3-nitrotyrosine, superoxide, stable nitric oxide (NO) metabolites [nitrates and nitrites (NOx)], and expression of NO synthase isoforms. In the Ren2 rat, RVSP is normal at 5 wk of age, PAH develops between 5 and 7 wk of age, and the elevated pressure is maintained with little variation through 13 wk. At 8 wk of age, left ventricular function and blood gases were normal in the Ren2 rat. Ren2 rats exhibited elevations in medial hypertrophy due to smooth muscle cell proliferation, 3-nitrotyrosine, NOx, NADPH oxidase activity, and endothelial NO synthase expression compared with Sprague-Dawley rats. RSV significantly blunted the increase in RVSP but did not reduce MAP in the Ren2 rat; additionally, RSV significantly attenuated the elevated parameters examined in the Ren2 rat. These data suggest that statins may be a clinically viable adjunct treatment of PAH through reducing peroxynitrite formation.
Impact of acute exposure to increased hydrostatic pressure and reduced shear rate on conduit artery endothelial function: a limb-specific response
Authors: Padilla Jaume , Sheldon Ryan D. , Sitar Diana M. , Newcomer Sean C.
Published: July 2009

Unlike quadrupeds, humans exhibit a larger hydrostatic pressure in the lower limbs compared with the upper limbs during a major part of the day. It is plausible that repeated episodes of elevated pressure in the legs may negatively impact the endothelium, hence contributing to the greater predisposition of atherosclerosis in the legs. We tested the hypothesis that an acute exposure to increased hydrostatic pressure would induce conduit artery endothelial dysfunction. In protocol 1, to mimic the hemodynamic environment of the leg, we subjected the brachial artery to a hydrostatic pressure gradient (∼15 mmHg) by vertically hanging the arm for 3 h. Brachial artery flow-mediated dilation (FMD) was assessed in both arms before and following the intervention. In protocol 2, we directly evaluated popliteal artery FMD before and after a 3-h upright sitting (pressure gradient ∼48 mmHg) and control (supine position) intervention. Our arm-hanging model effectively resembled the hemodynamic milieu (high pressure and low shear rate) present in the lower limbs during the seated position. Endothelium-dependent vasodilation at the brachial artery was attenuated following arm hanging ( P < 0.05); however, contrary to our hypothesis, upright sitting did not have an impact on popliteal artery endothelial function ( P > 0.05). These data suggest an intriguing vascular-specific response to increased hydrostatic pressure and reduced shear rate. Further efforts are needed to determine if this apparent protection of the leg vasculature against an acute hydrostatic challenge is attributable to posture-induced chronic adaptations.
Myocardial interstitial fluid inhibits proliferation and cardiomyocyte differentiation in pluripotent embryonic stem cells
Authors: Van Orman Jordan R. , Weihrauch Dorothee , Warltier David C. , Lough John
Published: July 2009

Several recent studies have demonstrated that the transplantation of pluripotent murine embryonic stem cells (mESCs) can improve or restore the function of infarcted myocardium. Although the extent of remuscularization and its contribution to the restoration of function are unclear, these outcomes are likely strongly influenced by factors in the infarcted and/or ischemic environment. As an initial step toward understanding how the ischemic environment of host myocardium affects transplanted pluripotent cells, we have taken a reductionist approach wherein mESCs are cultured in medium containing ischemic myocardial interstitial fluid (iMIF). iMIF is generated in canine myocardium during eight hourly episodes of transient ischemia and collected on a daily basis, over a 24-day collection period. iMIF strongly reduced the numbers of pluripotent mESCs after 11 days in culture. This inhibitory effect, which was most pronounced for iMIF pools from early time points of the 24-day collection period, resulted from an inhibition of cell proliferation. iMIF also inhibited the differentiation of pluripotent mESCs into cardiomyocytes. By contrast, the expression of vascular smooth muscle and endothelial cell markers was relatively unaffected, consistent with previous findings that iMIF promotes angiogenesis. Taken together, these results suggest that whereas the ischemic/infarcted environment is favorable to stem cell-mediated angiogenesis, it is hostile to cardiac myogenesis. These findings also imply that observations of mESC-mediated improvement of cardiac function after transplantation of pluripotent cells do not reflect remuscularization.
Impact of age, sex, and exercise on brachial artery flow-mediated dilatation
Authors: Black Mark A. , Cable N. Timothy , Thijssen Dick H. J. , Green Daniel J.
Published: July 2009

Flow-mediated dilatation (%FMD), an index of nitric oxide (NO)-mediated vasodilator function, is regarded as a surrogate marker of cardiovascular disease. Aging is associated with endothelial dysfunction, but underlying sex-related differences may exist and the effects of fitness and exercise on endothelial dysfunction in men (M) and women (W) are poorly understood. We compared %FMD of the brachial artery in 18 young [Y, 26 ± 1 yr; 9 M and 9 W], 12 older fit (OF, 57 ± 2 yr; 6 M and 6 W), and 16 older sedentary (OS, 59 ± 2 yr; 8 M and 8 W) subjects. Glyceryl trinitrate (GTN) administration was used to assess endothelium-independent vasodilatation, and the FMD-to-GTN ratio was calculated to characterize NO dilator function in the context of smooth muscle cell sensitivity. Brachial %FMD in Y (7.1 ± 0.8%) was significantly higher compared with OS (4.8 ± 0.7%, P < 0.05), but not OF (6.4 ± 0.7%). Differences between Y and OS subjects were due primarily to lower FMD in the OS women (4.3 ± 0.6%). OS women exhibited significantly lower FMD-to-GTN ratios compared with Y ( P < 0.05) and OF women ( P < 0.05), whereas these differences were not apparent in men. Exercise training improved brachial artery NO dilator function (FMD-to-GTN ratio) after 24 wk ( P < 0.05) in OS women, but not men. These findings indicate that maintaining a high level of fitness, or undertaking exercise training, prevents the age-related decline in the brachial artery vasodilator function evident in women. In OS men, who had relatively preserved NO dilator function, no training adaptations were observed. This study has potential implications for the prevention of conduit artery endothelial dysfunction in men and women.