bluuebunny/crossref_metadata_2025_split huggingface dataset:
DsdX Is the Second
d
-Serine Transporter in Uropathogenic
Escherichia coli
Clinical Isolate CFT073
Authors: Anfora Andrew T. , Welch Rodney A. 
Published: September 2006

ABSTRACT

d
-Serine is an amino acid present in mammalian urine that is inhibitory to
Escherichia coli
strains lacking a functional
dsdA
gene. Counterintuitively, a
dsdA
strain of
E. coli
clinical isolate CFT073 hypercolonizes the bladder and kidneys of mice relative to wild type during a coinfection in the murine model of urinary tract infection. We are interested in the mechanisms for uptake of
d
-serine in CFT073.
d
-Serine enters
E. coli
K-12 via CycA, the
d
-alanine transporter and
d
-cycloserine sensitivity locus. CFT073
cycA
can grow on minimal medium with
d
-serine as a sole carbon source. The
dsdX
gene of the
dsdCXA
locus is a likely candidate for an additional
d
-serine transporter based on its predicted amino acid sequence similarity to gluconate transporters. In minimal medium, CFT073
dsdX
can grow on
d
-serine as a sole carbon source; however, CFT073
dsdX cycA
cannot. Additionally, CFT073
dsdXA cycA
is not sensitive to inhibitory concentrations of
d
-serine during growth on glycerol and
d
-serine minimal medium.
d
-[
14
C]serine uptake experiments with CFT073
dsdX cycA
harboring
dsdX
or
cycA
recombinant plasmids confirm that
d
-serine is able to enter
E. coli
cells via CycA or DsdX. In whole-cell
d
-[
14
C]serine uptake experiments, DsdX has an apparent

K
m

of 58.75 μM and a
V
max
of 75.96 nmol/min/mg, and CycA has an apparent

K
m

of 82.40 μM and a

V
max

of 58.90 nmol/min/mg. Only
d
-threonine marginally inhibits DsdX-mediated
d
-serine transport, whereas
d
-alanine, glycine, and
d
-cycloserine inhibit CycA-mediated
d
-serine transport. DsdX or CycA is sufficient to transport physiological quantities of
d
-serine, but DsdX is a
d
-serine-specific permease.
The AlgT-Dependent Transcriptional Regulator AmrZ (AlgZ) Inhibits Flagellum Biosynthesis in Mucoid, Nonmotile
Pseudomonas aeruginosa
Cystic Fibrosis Isolates
Authors: Tart Anne H. , Blanks Michael J. , Wozniak Daniel J. 
Published: September 2006

ABSTRACT

Pseudomonas aeruginosa
is a microorganism associated with the disease cystic fibrosis. While environmental
P. aeruginosa
strains are generally nonmucoid and motile, isolates recovered from the cystic fibrosis lung frequently display a mucoid, nonmotile phenotype. This phenotypic conversion is mediated by the alternative sigma factor AlgT. Previous work has shown that repression of
fleQ
by AlgT accounts for the loss of flagellum biosynthesis in these strains. Here, we elucidate the mechanism involved in the AlgT-mediated control of
fleQ.
Electrophoretic mobility shift assays using purified AlgT and extracts derived from isogenic AlgT
+
and AlgT
−
strains revealed that AlgT inhibits
fleQ
indirectly. We observed that the AlgT-dependent transcriptional regulator AmrZ interacts directly with the
fleQ
promoter. To determine whether AmrZ functions as a repressor of
fleQ
, we mutated
amrZ
in the mucoid, nonmotile
P. aeruginosa
strain FRD1. Unlike the parental strain, the
amrZ
mutant was nonmucoid and motile. Complementation of the mutant with
amrZ
restored the mucoid, nonmotile phenotype. Thus, our data show that AlgT inhibits flagellum biosynthesis in mucoid, nonmotile
P. aeruginosa
cystic fibrosis isolates by promoting expression of AmrZ, which subsequently represses
fleQ
. Since
fleQ
directly or indirectly controls the expression of almost all flagellar genes, its repression ultimately leads to the loss of flagellum biosynthesis.
Thiamine Is Synthesized by a Salvage Pathway in
Rhizobium leguminosarum
bv. viciae Strain 3841
Authors: Karunakaran R. , Ebert K. , Harvey S. , Leonard M. E. , Ramachandran V. , Poole P. S. 
Published: September 2006

ABSTRACT

In the absence of added thiamine,
Rhizobium leguminosarum
bv. viciae strain 3841 does not grow in liquid medium and forms only “pin” colonies on agar plates, which contrasts with the good growth of
Sinorhizobium meliloti
1021,
Mesorhizobium loti
303099, and
Rhizobium etli
CFN42. These last three organisms have
thiCOGE
genes, which are essential for de novo thiamine synthesis. While
R. leguminosarum
bv. viciae 3841 lacks
thiCOGE
, it does have
thiMED
. Mutation of
thiM
prevented formation of pin colonies on agar plates lacking added thiamine, suggesting thiamine intermediates are normally present. The putative functions of ThiM, ThiE, and ThiD are 4-methyl-5-(β-hydroxyethyl) thiazole (THZ) kinase, thiamine phosphate pyrophosphorylase, and 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) kinase, respectively. This suggests that a salvage pathway operates in
R. leguminosarum
, and addition of HMP and THZ enabled growth at the same rate as that enabled by thiamine in strain 3841 but elicited no growth in the
thiM
mutant (RU2459). There is a putative
thi
box sequence immediately upstream of the
thiM
, and a
gfp-mut3.1
fusion to it revealed the presence of a promoter that is strongly repressed by thiamine. Using fluorescent microscopy and quantitative reverse transcription-PCR, it was shown that
thiM
is expressed in the rhizosphere of vetch and pea plants, indicating limitation for thiamine. Pea plants infected by RU2459 were not impaired in nodulation or nitrogen fixation. However, colonization of the pea rhizosphere by the
thiM
mutant was impaired relative to that of the wild type. Overall, the results show that a thiamine salvage pathway operates to enable growth of
Rhizobium leguminosarum
in the rhizosphere, allowing its survival when thiamine is limiting.
Sequence Analysis of the Lactococcal Plasmid pNP40: a Mobile Replicon for Coping with Environmental Hazards
Authors: O'Driscoll Jonathan , Glynn Frances , Fitzgerald Gerald F. , Sinderen Douwe van 
Published: September 2006

ABSTRACT

The conjugative lactococcal plasmid pNP40, identified in
Lactococcus lactis
subsp.
diacetylactis
DRC3, possesses a potent complement of bacteriophage resistance systems, which has stimulated its application as a fitness-improving, food-grade genetic element for industrial starter cultures. The complete sequence of this plasmid allowed the mapping of previously known functions including replication, conjugation, bacteriocin resistance, heavy metal tolerance, and bacteriophage resistance. In addition, functions for cold shock adaptation and DNA damage repair were identified, further confirming pNP40's contribution to environmental stress protection. A plasmid cointegration event appears to have been part of the evolution of pNP40, resulting in a “stockpiling” of bacteriophage resistance systems.
Transcriptional Response ofEscherichia colito TPEN
Authors: Sigdel Tara K. , Easton J. Allen , Crowder Michael W. 
Published: September 2006

ABSTRACTDNA microarrays were used to probe the transcriptional response ofEscherichia colitoN,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Fifty-five transcripts were significantly up-regulated, including all of the genes that are regulated by Zur and many that are regulated by Fur. In the same TPEN-treated cells, 46 transcripts were significantly down-regulated.
Mlc of
Thermus thermophilus
: a Glucose-Specific Regulator for a Glucose/Mannose ABC Transporter in the Absence of the Phosphotransferase System
Authors: Chevance Fabienne F. V. , Erhardt Marc , Lengsfeld Christina , Lee Sung-Jae , Boos Winfried 
Published: September 2006

ABSTRACT

We report the presence of Mlc in a thermophilic bacterium. Mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting EII
Glc
of the phosphotransferase system (PTS). Since thermophilic bacteria do not possess PTS, Mlc in
Thermus thermophilus
must be differently controlled. DNA sequence alignments between Mlc from
T. thermophilus
(Mlc
Tth
) and Mlc from
E. coli
(Mlc
Eco
) revealed that Mlc
Tth
conserved five residues of the glucose-binding motif of glucokinases. Here we show that Mlc
Tth
is not a glucokinase but is indeed able to bind glucose (

K
D

= 20 μM), unlike Mlc
Eco
. We found that
mlc
of
T. thermophilus
is the first gene within an operon encoding an ABC transporter for glucose and mannose, including a glucose/mannose-binding protein and two permeases.
malK1
, encoding the cognate ATP-hydrolyzing subunit, is located elsewhere on the chromosome. The system transports glucose at 70°C with a

K
m

of 0.15 μM and a
V
max
of 4.22 nmol per min per ml at an optical density (OD) of 1. Mlc
Tth
negatively regulates itself and the entire glucose/mannose ABC transport system operon but not
malK1
, with glucose acting as an inducer. MalK1 is shared with the ABC transporter for trehalose, maltose, sucrose, and palatinose (TMSP). Mutants lacking
malK1
do not transport either glucose or maltose. The TMSP transporter is also able to transport glucose with a

K
m

of 1.4 μM and a
V
max
of 7.6 nmol per min per ml at an OD of 1, but it does not transport mannose.
ThehmuQandhmuDGenes fromBradyrhizobium japonicumEncode Heme-Degrading Enzymes
Authors: Puri Sumant , O'Brian Mark R. 
Published: September 2006

ABSTRACTUtilization of heme by bacteria as a nutritional iron source involves the transport of exogenous heme, followed by cleavage of the heme macrocycle to release iron.Bradyrhizobium japonicumcan use heme as an iron source, but no heme-degrading oxygenase has been described. Here, bioinformatics analyses of theB. japonicumgenome identified two paralogous genes renamedhmuQ(bll7075) andhmuD(bll7423) that encode proteins with weak similarity to the heme-degrading monooxygenase IsdG fromStaphylococcus aureus. ThehmuQgene is clustered with known heme transport genes in the genome. Recombinant HmuQ bound heme with aKdvalue of 0.8 μM and showed spectral properties consistent with a heme oxygenase. In the presence of a reductant, HmuQ catalyzed the degradation of heme and the formation of biliverdin. ThehmuQandhmuDgenes complemented aCorynebacterium ulceransheme oxygenase mutant intransfor utilization of heme as the sole iron source for growth. Furthermore, homologs ofhmuQandhmuDwere identified in many bacterial genera, and the recombinant homolog fromBrucella melitensisbound heme and catalyzed its degradation. The findings show thathmuQandhmuDencode heme oxygenases and indicate that the IsdG family of heme-degrading monooxygenases is not restricted to gram-positive pathogenic bacteria.
Gliding Motility of
Mycoplasma mobile
Can Occur by Repeated Binding to
N
-Acetylneuraminyllactose (Sialyllactose) Fixed on Solid Surfaces
Authors: Nagai Ryoichiro , Miyata Makoto 
Published: September 2006

ABSTRACT

Mycoplasma mobile
relies on an unknown mechanism to glide across solid surfaces including glass, animal cells, and plastics. To identify the direct binding target, we examined the factors that affect the binding of
Mycoplasma pneumoniae
to solid surfaces and concluded that
N
-acetylneuraminyllactose (sialyllactose) attached to a protein can mediate glass binding on the basis of the following four lines of evidence: (i) glass binding was inhibited by
N
-acetylneuraminidase, (ii) glass binding was inhibited by
N
-acetylneuraminyllactose in a structure-dependent manner, (iii) binding occurred on glass pretreated with bovine serum albumin attached to
N
-acetylneuraminyllactose, and (iv) gliding speed depended on the density of
N
-acetylneuraminyllactose on glass.
Characteristic Features in the Structure and Collagen-Binding Ability of a Thermophilic Collagenolytic Protease from the Thermophile
Geobacillus collagenovorans
MO-1
Authors: Itoi Yuichi , Horinaka Mano , Tsujimoto Yoshiyuki , Matsui Hiroshi , Watanabe Kunihiko 
Published: September 2006

ABSTRACT

A collagen-degrading thermophile,
Geobacillus collagenovorans
MO-1, extracellularly produces a collagenolytic protease with a large molecular mass. Complete nucleotide sequencing of this gene after gene cloning revealed that the collagenolytic protease is a member of the subtilisin family of serine proteases and consists of a signal sequence for secretion, a prosequence for maturation, a catalytic region, 14 direct repeats of 20 amino acids at the C terminus, and a region with unknown function intervening between the catalytic region and the numerous repeats. Since the unusual repeats are most likely to be cleaved in the secreted form of the enzyme, the intervening region was investigated to determine whether it participates in collagen binding to facilitate collagen degradation. It was found that the mature collagenolytic protease containing the intervening region at the C terminus bound collagen but not the other insoluble proteins, elastin and keratin. Furthermore, the intervening region fused with glutathione
S
-transferase showed a collagen-binding ability comparable to that of the mature collagenolytic protease. The collagen-binding ability was finally attributed to two-thirds of the intervening region which is rich in β-strands and is approximately 35 kDa in molecular mass. In the collagenolytic protease from strain MO-1, hydrogen bonds most likely predominate over the hydrophobic interaction for collagen binding, since a higher concentration of NaCl released collagen from the enzyme surface but a nonionic detergent could not. To the best of our knowledge, this is the first report of a thermophilic collagenolytic protease containing the collagen-binding segment.
Identification of an Essential Gene ofListeria monocytogenesInvolved in Teichoic Acid Biogenesis
Authors: Dubail Iharilalao , Bigot Armelle , Lazarevic Vladimir , Soldo Blazenka , Euphrasie Daniel , Dupuis Marion , Charbit Alain 
Published: September 2006

ABSTRACTListeria monocytogenesis a facultative intracellular gram-positive bacterium responsible for severe opportunistic infections in humans and animals. We had previously identified a gene encoding a putative UDP-N-acetylglucosamine 2-epimerase, a precursor of the teichoic acid linkage unit, in the genome ofL monocytogenesstrain EGD-e. This gene, now designated lmo2537, encodes a protein that shares 62% identity with the cognate epimerase MnaA ofBacillus subtilisand 55% identity with Cap5P ofStaphylococcus aureus. Here, we addressed the role of lmo2537 inL. monocytogenespathogenesis by constructing a conditional knockout mutant. The data presented here demonstrate that lmo2537 is an essential gene ofL. monocytogenesthat is involved in teichoic acid biogenesis. In vivo, the conditional mutant is very rapidly eliminated from the target organs of infected mice and thus is totally avirulent.
3-Hydroxy-3-Methylglutaryl-Coenzyme A (CoA) Synthase Is Involved in Biosynthesis of Isovaleryl-CoA in the Myxobacterium
Myxococcus xanthus
during Fruiting Body Formation
Authors: Bode Helge B. , Ring Michael W. , Schwär Gertrud , Kroppenstedt Reiner M. , Kaiser Dale , Müller Rolf 
Published: September 2006

ABSTRACT

Isovaleryl-coenzyme A (IV-CoA) is the starting unit for some secondary metabolites and iso-odd fatty acids in several bacteria. According to textbook biochemistry, IV-CoA is derived from leucine degradation, but recently an alternative pathway that branches from the well-known mevalonate-dependent isoprenoid biosynthesis has been described for myxobacteria. A double mutant was constructed in
Myxococcus xanthus
by deletion of genes involved in leucine degradation and disruption of
mvaS
encoding the 3-hydroxy-3-methylglutaryl-coenzyme A synthase. A dramatic decrease of IV-CoA-derived iso-odd fatty acids was observed for the mutant, confirming
mvaS
to be involved in the alternative pathway. Additional quantitative real-time reverse transcription-PCR experiments indicated that
mvaS
is transcriptionally regulated by isovalerate. Furthermore, feeding studies employing an intermediate specific for the alternative pathway revealed that this pathway is induced during fruiting body formation, which presumably increases the amount of IV-CoA available when leucine is limited.
Hodgkin lymphoma cells express TACI and BCMA receptors and generate survival and proliferation signals in response to BAFF and APRIL
Authors: Chiu April , Xu Weifeng , He Bing , Dillon Stacey R. , Gross Jane A. , Sievers Eric , Qiao Xugang , Santini Paul , Hyjek Elizabeth , Lee Joong-won , Cesarman Ethel , Chadburn Amy , Knowles Daniel M. , Cerutti Andrea 
Published: September 2006

Abstract
Hodgkin lymphoma (HL) originates from the clonal expansion of malignant Hodgkin and Reed-Sternberg (HRS) cells. These B-cell–derived elements constitute less than 10% of the tumoral mass. The remaining tissue is comprised of an inflammatory infiltrate that includes myeloid cells. Myeloid cells activate B cells by producing BAFF and APRIL, which engage TACI, BCMA, and BAFF-R receptors on the B cells. Here, we studied the role of BAFF and APRIL in HL. Inflammatory and HRS cells from HL tumors expressed BAFF and APRIL. Unlike their putative germinal center B-cell precursors, HRS cells lacked BAFF-R, but expressed TACI and BCMA, a phenotype similar to that of plasmacytoid B cells. BAFF and APRIL enhanced HRS cell survival and proliferation by delivering nonredundant signals via TACI and BCMA receptors through both autocrine and paracrine pathways. These signals caused NF-κB activation; Bcl-2, Bcl-xL, and c-Myc up-regulation; and Bax down-regulation, and were amplified by APRIL-binding proteoglycans on HRS cells. Interruption of BAFF and APRIL signaling by TACI-Ig decoy receptor, which binds to and neutralizes BAFF and APRIL, or by small-interfering RNAs targeting BAFF, APRIL, TACI, and BCMA inhibited HRS cell accumulation in vitro and might attenuate HL expansion in vivo.
Use of a Volumetric Target for Image-guided Surgery
Authors: Gildenberg Philip L. , Labuz Jeffrey 
Published: September 2006

Abstract
A VIRTUAL REALITY system has been devised to superimpose a computer-generated rendering of a volumetric target to be surgically approached or resected on a real-time video image of the surgical field. A stereotactic frame is used to register the image from the video camera with the image of the target volume for accurate localization. The volumetric target is obtained from preoperative imaging studies and can be modified to adjust the intended line of resection or to avoid eloquent vascular or neural tissue. The computer-generated image is updated throughout surgery to visualize only that part of the tumor under resection so the surgeon may guide the resection along the border of the mass or intended preplanned line of resection. To date, 74 intracranial tumor resections have been performed under video virtual reality guidance. Postoperative scanning corresponds in every case with preoperative planning. This system is also designed to be adapted to frameless guidance, which can be further enhanced by the incorporation of an audible tone to signal the relationship of the tip of the resection instrument to the line of resection.
Outcomes of Surgery for Resection of Regions of Symptomatic Radiation Injury After Stereotactic Radiosurgery for Arteriovenous Malformations
Authors: Massengale Justin L. , Levy Richard P. , Marcellus Mary , Moes Gregory , Marks Michael P. , Steinberg Gary K. 
Published: September 2006

Abstract

OBJECTIVE:
Although radiation injury after stereotactic radiosurgery (SRS), including radiation necrosis (RN), is often treated with surgical resection, detailed outcome data are lacking after resection of symptomatic radiation-injured regions with imaging characteristics suspicious for RN after SRS for arteriovenous malformations (AVM). We present outcomes in seven such patients.

METHODS:
We conducted a retrospective chart review of seven patients with AVMs of Spetzler-Martin Grades II (n = 1), III (n = 2), and IV (n = 4) who underwent helium ion, proton beam, or gamma knife SRS and required resection of RN-suspicious tissue 1 to 24 months after post-SRS symptom onset. Postoperative outcomes included Karnofsky Performance Scale (KPS) score and time to symptomatic improvement.

RESULTS:
Symptomatic improvement required at least 9 months in the three patients with large regions suspicious for RN (≥4 cm), whereas of four patients with smaller regions (&lt;4 cm), three showed improvement within 2 months (P &lt; 0.05). The remaining patient, who showed no benefit, underwent resection 2 years after the onset of RN symptoms (compared with ≤ 8 mo for the other six patients). Surgery improved KPS scores in four patients with a preoperative KPS score of 50 or lower, but not in three patients with preoperative KPS scores greater than 70 (P &lt; 0.05). Outcomes were not consistently associated with AVM size or location, SRS treatment volume or dose, associated aneurysm, or residual AVM.

CONCLUSION:
After SRS for AVMs, resection of symptomatic RN-suspicious tissue areas is beneficial in reversing neurological deficits and improving KPS scores in selected patients. Times to improvement were longer when larger areas were resected. Delaying such surgery after symptom onset may negatively affect improvement.
Cervical Catheter Tip Placement for Intrathecal Baclofen Administration
Authors: McCall Todd D. , MacDonald Joel D. 
Published: September 2006

Abstract

OBJECTIVE:
Intrathecal baclofen can reduce congenital and posttraumatic spasticity. Traditionally, the catheter tip for baclofen delivery is placed in a low thoracic position, which can result in a lumbar-to-cisternal cerebrospinal fluid baclofen concentration gradient. We investigated whether more rostral catheter placement was technically feasible, safe, and able to control upper extremity spasticity.

METHODS:
The records of 48 patients with a baclofen pump were reviewed retrospectively to evaluate the safety and efficacy of cervically placed intrathecal catheters for baclofen administration. Twenty-three patients had a catheter located in a cervical position and 25 had a catheter in a thoracic position (control group). Complications, including baclofen overdose, mechanical failures, and infections, were noted. Pre- and postoperative Ashworth scores were determined by a physical therapist using a standardized protocol.

RESULTS:
The mean duration of the follow-up period was 10 months. The groups were not significantly different in patient age, baclofen dose, or duration of follow-up, but differed somewhat in the causes of spasticity. For patients with a cervical catheter tip position, upper extremity Ashworth scores decreased significantly from 4.0 ± 0.8 (standard deviation) preoperatively to 3.0 ± 0.9 postoperatively (P = 0.003). In both groups, lower extremity spasticity was significantly reduced. Postoperatively, one patient with a cervical catheter developed aspiration pneumonia, possibly because of sedation. Other complications included hardware infections, mechanical malfunctions, and pseudomeningoceles.

CONCLUSION:
In this series, placement of intrathecal baclofen catheters in the cervical region resulted in equal control of spasticity in the upper and lower extremities and did not increase complications related to the catheter position.