bluuebunny/crossref_metadata_2025_split huggingface dataset:
CsrA Inhibits Translation Initiation of
Escherichia coli hfq
by Binding to a Single Site Overlapping the Shine-Dalgarno Sequence
Authors: Baker Carol S. , Eöry Lél A. , Yakhnin Helen , Mercante Jeffrey , Romeo Tony , Babitzke Paul 
Published: May 2007

ABSTRACT

Csr (carbon storage regulation) of
Escherichia coli
is a global regulatory system that consists of CsrA, a homodimeric RNA binding protein, two noncoding small RNAs (sRNAs; CsrB and CsrC) that function as CsrA antagonists by sequestering this protein, and CsrD, a specificity factor that targets CsrB and CsrC for degradation by RNase E. CsrA inhibits translation initiation of
glgC
,
cstA
, and
pgaA
by binding to their leader transcripts and preventing ribosome binding. Translation inhibition is thought to contribute to the observed mRNA destabilization. Each of the previously known target transcripts contains multiple CsrA binding sites. A position-specific weight matrix search program was developed using known CsrA binding sites in mRNA. This search tool identified a potential CsrA binding site that overlaps the Shine-Dalgarno sequence of
hfq
, a gene that encodes an RNA chaperone that mediates sRNA-mRNA interactions. This putative CsrA binding site matched the SELEX-derived binding site consensus sequence in 8 out of 12 positions. Results from gel mobility shift and footprint assays demonstrated that CsrA binds specifically to this site in the
hfq
leader transcript. Toeprint and cell-free translation results indicated that bound CsrA inhibits Hfq synthesis by competitively blocking ribosome binding. Disruption of
csrA
caused elevated expression of an
hfq
′-′
lacZ
translational fusion, while overexpression of
csrA
inhibited expression of this fusion. We also found that
hfq
mRNA is stabilized upon entry into stationary-phase growth by a CsrA-independent mechanism. The interaction of CsrA with
hfq
mRNA is the first example of a CsrA-regulated gene that contains only one CsrA binding site.
AtlA Functions as a Peptidoglycan Lytic Transglycosylase in the
Neisseria gonorrhoeae
Type IV Secretion System
Authors: Kohler Petra L. , Hamilton Holly L. , Cloud-Hansen Karen , Dillard Joseph P. 
Published: May 2007

ABSTRACT

Type IV secretion systems require peptidoglycan lytic transglycosylases for efficient secretion, but the function of these enzymes is not clear. The type IV secretion system gene cluster of
Neisseria gonorrhoeae
encodes two peptidoglycan transglycosylase homologues. One, LtgX, is similar to peptidoglycan transglycosylases from other type IV secretion systems. The other, AtlA, is similar to endolysins from bacteriophages and is not similar to any described type IV secretion component. We characterized the enzymatic function of AtlA in order to examine its role in the type IV secretion system. Purified AtlA was found to degrade macromolecular peptidoglycan and to produce 1,6-anhydro peptidoglycan monomers, characteristic of lytic transglycosylase activity. We found that AtlA can functionally replace the lambda endolysin to lyse
Escherichia coli
. In contrast, a sensitive measure of lysis demonstrated that AtlA does not lyse gonococci expressing it or gonococci cocultured with an AtlA-expressing strain. The gonococcal type IV secretion system secretes DNA during growth. A deletion of
ltgX
or a substitution in the putative active site of AtlA severely decreased DNA secretion. These results indicate that AtlA and LtgX are actively involved in type IV secretion and that AtlA is not involved in lysis of gonococci to release DNA. This is the first demonstration that a type IV secretion peptidoglycanase has lytic transglycosylase activity. These data show that AtlA plays a role in type IV secretion of DNA that requires peptidoglycan breakdown without cell lysis.
Characterization of Biphenyl Dioxygenase of
Pandoraea pnomenusa
B-356 As a Potent Polychlorinated Biphenyl-Degrading Enzyme
Authors: Gómez-Gil Leticia , Kumar Pravindra , Barriault Diane , Bolin Jeffrey T. , Sylvestre Michel , Eltis Lindsay D. 
Published: May 2007

ABSTRACT

Biphenyl dioxygenase (BPDO) catalyzes the aerobic transformation of biphenyl and various polychlorinated biphenyls (PCBs). In three different assays, BPDO
B356
from
Pandoraea pnomenusa
B-356 was a more potent PCB-degrading enzyme than BPDO
LB400
from
Burkholderia xenovorans
LB400 (75% amino acid sequence identity), transforming nine congeners in the following order of preference: 2,3′,4-trichloro ∼ 2,3,4′-trichloro > 3,3′-dichloro > 2,4,4′-trichloro > 4,4′-dichloro ∼ 2,2′-dichloro > 2,6-dichloro > 2,2′,3,3′-tetrachloro ∼ 2,2′,5,5′-tetrachloro. Except for 2,2′,5,5′-tetrachlorobiphenyl, BPDO
B356
transformed each congener at a higher rate than BPDO
LB400
. The assays used either whole cells or purified enzymes and either individual congeners or mixtures of congeners. Product analyses established previously unrecognized BPDO
B356
activities, including the 3,4-dihydroxylation of 2,6-dichlorobiphenyl. BPDO
LB400
had a greater apparent specificity for biphenyl than BPDO
B356
(
k
cat
/
K

m

= 2.4 × 10
6
± 0.7 × 10
6
M
−1
s
−1
versus
k
cat
/
K

m

= 0.21 × 10
6
± 0.04 × 10
6
M
−1
s
−1
). However, the latter transformed biphenyl at a higher maximal rate (
k
cat
= 4.1 ± 0.2 s
−1
versus
k
cat
= 0.4 ± 0.1 s
−1
). A variant of BPDO
LB400
containing four active site residues of BPDO
B356
transformed
para
-substituted congeners better than BPDO
LB400
. Interestingly, a substitution remote from the active site, A267S, increased the enzyme's preference for
meta
-substituted congeners. Moreover, this substitution had a greater effect on the kinetics of biphenyl utilization than substitutions in the substrate-binding pocket. In all variants, the degree of coupling between congener depletion and O
2
consumption was approximately proportional to congener depletion. At 2.4-Å resolution, the crystal structure of the BPDO
B356
-2,6-dichlorobiphenyl complex, the first crystal structure of a BPDO-PCB complex, provided additional insight into the reactivity of this isozyme with this congener, as well as into the differences in congener preferences of the BPDOs.
Crystal Structure of the
Vibrio cholerae
Quorum-Sensing Regulatory Protein HapR
Authors: De Silva Rukman S. , Kovacikova Gabriela , Lin Wei , Taylor Ronald K. , Skorupski Karen , Kull F. Jon 
Published: May 2007

ABSTRACT

Quorum sensing in
Vibrio cholerae
involves signaling between two-component sensor protein kinases and the response regulator LuxO to control the expression of the master regulator HapR. HapR, in turn, plays a central role in regulating a number of important processes, such as virulence gene expression and biofilm formation. We have determined the crystal structure of HapR to 2.2-Å resolution. Its structure reveals a dimeric, two-domain molecule with an all-helical structure that is strongly conserved with members of the TetR family of transcriptional regulators. The N-terminal DNA-binding domain contains a helix-turn-helix DNA-binding motif and alteration of certain residues in this domain completely abolishes the ability of HapR to bind to DNA, alleviating repression of both virulence gene expression and biofilm formation. The C-terminal dimerization domain contains a unique solvent accessible tunnel connected to an amphipathic cavity, which by analogy with other TetR regulators, may serve as a binding pocket for an as-yet-unidentified ligand.
Human Body Temperature (37°C) Increases the Expression of Iron, Carbohydrate, and Amino Acid Utilization Genes in
Escherichia coli
K-12
Authors: White-Ziegler Christine A. , Malhowski Amy J. , Young Sarah 
Published: May 2007

ABSTRACT

Using DNA microarrays, we identified 126 genes in
Escherichia coli
K-12 whose expression is increased at human body temperature (37°C) compared to growth at 23°C. Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. Using quantitative real-time PCR, we investigated the thermoregulatory response for representative genes in each of these three categories (
hisJ
,
cysP
,
srlE
,
garP
,
fes
, and
cirA
), along with the fimbrial gene
papB
. Increased expression at 37°C compared to 23°C was retained in both exponential and stationary phases for all of the genes and in most of the various media tested, supporting the relative importance of this cue in adapting to changing environments. Because iron acquisition is important for both growth and virulence, we analyzed the regulation of the iron utilization genes
cirA
and
fes
and found that growth in iron-depleted medium abrogated the thermoregulatory effect, with high-level expression at both temperatures, contrasting with
papB
thermoregulation, which was not greatly altered by limiting iron levels. A positive role for the environmental regulator H-NS was found for
fes
,
cirA
,
hisJ
, and
srlE
transcription, whereas it had a primarily negative effect on
cysP
and
garP
expression. Together, these studies indicate that temperature is a broadly used cue for regulating gene expression in
E. coli
and that H-NS regulates iron, carbohydrate, and amino acid utilization gene expression.
Rule change incidence on physiological characteristics of elite basketball players: a 10-year-period investigation
Authors: Cormery B , Marcil M , Bouvard M 
Published: May 2007

Objective:To evaluate, by examining data collected on professional basketball players during a 10-year period, the differences in aerobic capacity in function of the playing position and the impact on these parameters of the change in time regulation of 2000, which shortened the time allowed to attempt a field goal by 6 s and divided the duration of play in four quarters.Methods:Twice a year between 1994 and 2004, professional basketball players (n = 68) were studied for anthropometric characteristics and were submitted to an incremental exercise test on a cycle ergometer. Statistical analyses were carried out to determine the interaction between the playing position and the effect of the change in time regulation on the physiological characteristics of the players.Results:Anthropometric measurements were different in function of the playing position, the centres being taller and heavier than the forwards and the guards. Guards exhibited the highest V̇o2max (54.0 (SE 1.6) ml/min/kg) and were the most affected by the change in time regulation of 2000 with a 19.5% increase. Significant main effects of “before” versus “after” rule changes were found for maximal and submaximal O2consumption, which were increased by 12.8% at ventilatory threshold, 7.3% at respiratory compensation point and 7.8% at V̇o2max.Conclusion:While anthropometric characteristics remained constant during the last decade, the change in rule of 2000 may have contributed in modifying the physiological profile of basketball players, by generally increasing their level of fitness.
Reference intervals for serum creatine kinase in athletes
Authors: Mougios Vassilis 
Published: May 2007

Background:The serum concentration of creatine kinase (CK) is used widely as an index of skeletal muscle fibre damage in sport and exercise. Since athletes have higher CK values than non-athletes, comparing the values of athletes to the normal values established in non-athletes is pointless. The purpose of this study was to introduce reference intervals for CK in athletes.Method:CK was assayed in serum samples from 483 male athletes and 245 female athletes, aged 7–44. Samples had been obtained throughout the training and competition period. For comparison, CK was also assayed in a smaller number of non-athletes. Reference intervals (2.5th to 97.5th percentile) were calculated by the non-parametric method.Results:The reference intervals were 82–1083 U/L (37°C) in male and 47–513 U/L in female athletes. The upper reference limits were twice the limits reported for moderately active non-athletes in the literature or calculated in the non-athletes in this study. The upper limits were up to six times higher than the limits reported for inactive individuals in the literature. When reference intervals were calculated specifically in male football (soccer) players and swimmers, a threefold difference in the upper reference limit was found (1492 vs 523 U/L, respectively), probably resulting from the different training and competition demands of the two sports.Conclusion:Sport training and competition have profound effects on the reference intervals for serum CK. Introducing sport-specific reference intervals may help to avoid misinterpretation of high values and to optimise training.
Heart rate variability modifications following exercise training in type 2 diabetic patients with definite cardiac autonomic neuropathy
Authors: Pagkalos M , Koutlianos N , Kouidi E , Pagkalos E , Mandroukas K , Deligiannis A 
Published: May 2007

Objectives:Cardiac autonomic neuropathy (CAN) as a result of diabetic autonomic neuropathy is positively related to a poor prognosis in diabetic patients. The measurement of heart rate variability (HRV) is a remarkable index of cardiac autonomic dysfunction. The aim of this study was to examine the effects of long-term exercise training on HRV in type 2 diabetic patients with definite CAN.Methods:Seventeen type 2 diabetic patients with definite CAN (group A: 56.2 years (SD 5.8)) and 15 without CAN (group B: 55.8 years (SD 5.6)) participated in the study. All patients followed an aerobic exercise training programme three times a week for 6 months; the intensity of the session was 70% to 85% of heart rate reserve. At the beginning and end of the study all subjects underwent graded maximal exercise testing with spiroergometry for the evaluation of their aerobic capacity (VO2peak). Moreover, time and frequency domain indices of HRV were obtained from 24 h ambulatory continuous ECG Holter recordings.Results:At baseline, all measurements of HRV indices were significantly reduced in group A compared with group B (p<0.05). Moreover, group A reached a significantly lower VO2peakby 14.8% compared with group B (p<0.05). Following the exercise training programme, the SD of all normal-to-normal RR intervals in the entire recording (SDNN) was increased by 18.8% (p<0.05) and 13.8% (p<0.05), the square root of the average of sum of squares of difference between adjacent filtered RR intervals (rMSSd) was increased by 35% (p<0.05) and 15.2% (p<0.05), and the percentage of differences between adjacent filtered RR intervals which was greater than 50 ms for the entire analysis (pNN50) was increased by 400% (p<0.05) and 67.9% (p<0.05) in groups A and B, respectively. Regarding the frequency domain indices, only the high frequency power (HF) was found to be significantly increased in group A. At the end of the exercise training programme, SDNN, rMSSd and low frequency power (LF) were significantly lower (24.3% (p<0.05), 20.3% (p<0.05) and 40% (p<0.05), respectively) in group A compared with group B. Also, VO2peakincreased by 17.8% (p<0.05) in group A and by 11% (p<0.05) in group B. Furthermore, the exercise training programme had significant effects on blood lipid and glucose levels and glycosylated haemoglobin (HbA1c) in both groups.Conclusions:The results indicate that 6-month aerobic exercise training improves the cardiac autonomic nervous system function in type 2 diabetic patients. However, more favourable effects are found in type 2 diabetic patients with definite CAN.
Effect of plyometric training on sand versus grass on muscle soreness and jumping and sprinting ability in soccer players
Authors: Impellizzeri F M , Rampinini E , Castagna C , Martino F , Fiorini S , Wisloff U 
Published: May 2007

Objective:The lower impact on the musculoskeletal system induced by plyometric exercise on sand compared to a firm surface might be useful to reduce the stress of intensified training periods or during rehabilitation from injury. The aim of this study was to compare the effects of plyometric training on sand versus a grass surface on muscle soreness, vertical jump height and sprinting ability.Design:Parallel two-group, randomised, longitudinal (pretest−post-test) study.Methods:After random allocation, 18 soccer players completed 4 weeks of plyometric training on grass (grass group) and 19 players on sand (sand group). Before and after plyometric training, 10 m and 20 m sprint time, squat jump (SJ), countermovement jump (CMJ), and eccentric utilization ratio (CMJ/SJ) were determined. Muscle soreness was measured using a Likert scale.Results:No training surface × time interactions were found for sprint time (p>0.87), whereas a trend was found for SJ (p = 0.08), with both groups showing similar improvements (p<0.001). On the other hand, the grass group improved their CMJ (p = 0.033) and CMJ/SJ (p = 0.005) significantly (p<0.001) more than players in the sand group. In contrast, players in the sand group experienced less muscle soreness than those in the grass group (p<0.001).Conclusions:Plyometric training on sand improved both jumping and sprinting ability and induced less muscle soreness. A grass surface seems to be superior in enhancing CMJ performance while the sand surface showed a greater improvement in SJ. Therefore, plyometric training on different surfaces may be associated with different training-induced effects on some neuromuscular factors related to the efficiency of the stretch-shortening cycle.
Bone marrow trephine combined with immunohistochemistry is superior to bone marrow aspirate in follow-up of myeloma patients
Authors: Joshi R , Horncastle D , Elderfield K , Lampert I , Rahemtulla A , Naresh K N 
Published: May 2007

Aims:Multiple myeloma (MM) guidelines in the UK do not advocate performing bone marrow trephine biopsy (BMTB) during follow-up. In a recent study, it was found that the plasma cell per cent (PC%) in BMTB performed at the time of autologous stem cell transplant strongly correlated with survival. The current study addresses whether BMTB is superior to bone marrow aspiration (BMA) in documenting presence of disease and its volume at follow-up.Methods:The study involved 106 samples. A conventional 500-cell differential count was performed on the BMAs to document the PC%. The PC% on BMTBs had been estimated on CD138 immunostain. Furthermore, BMTBs had also been immunostained for CD56, cyclin D1 and light chains.Results:The mean (2SEM) PC% values in BMAs and BMTBs were 13.1 (2.6)% and 31.8 (5.8)% respectively. Based on BMA, BMTB and serum/urine paraprotein or light chain estimation, on 92 occasions (89%) there was detectable disease. The positive predictive value of both BMA and BMTB was 100%, and the negative predictive values for BMTB and BMA were 57% and 22% respectively. Among 98 secretory MM cases, the BMTB-PC% showed significant correlation with paraprotein levels, whereas BMA-PC% did not.Conclusions:It is strongly recommended that BMTB is performed and adequately investigated with immunohistochemistry during follow-up of MM.
Treatment of severe aplastic anemia with antithymocyte globulin and cyclosporin A with or without G-CSF in adults: a multicenter randomized study in Japan
Authors: Teramura Masanao , Kimura Akiro , Iwase Satsuki , Yonemura Yuji , Nakao Shinji , Urabe Akio , Omine Mitsuhiro , Mizoguchi Hideaki 
Published: May 2007

Abstract
We report the results of a randomized study to elucidate whether addition of granulocyte colony-stimulating factor (G-CSF) to immunosuppressive therapy is valuable for the treatment of severe aplastic anemia (SAA) in adults. A total of 101 previously untreated patients (median age, 54 years; range, 19 to 75 years) were randomized to receive antithymocyte globulin (ATG) and cyclosporin A (CyA) (G-CSF− group) or ATG, CyA, and G-CSF (G-CSF+ group). In the G-CSF+ group, the hematologic response rate at 6 months was higher (77% vs 57%; P = .03) than in the G-CSF− group. No differences were observed between the groups in terms of the incidence of infections and febrile episodes. There were no differences between the G-CSF− group and the G-CSF+ group in terms of survival (88% vs 94% at 4 years), and the development of myelodysplastic syndrome (MDS)/acute leukemia (AL) (1 patient vs 2 patients). However, the relapse rate was lower in the G-CSF+ group compared with the G-CSF− group (42% vs 15% at 4 years; P = .01). Further follow-up is required to elucidate the role of G-CSF in immunosuppressive therapy for adult SAA.
Lymphotoxin a-dependent and -independent signals regulate stromal organizer cell homeostasis during lymph node organogenesis
Authors: White Andrea , Carragher Damian , Parnell Sonia , Msaki Aichi , Perkins Neil , Lane Peter , Jenkinson Eric , Anderson Graham , Caamaño Jorge H. 
Published: May 2007

AbstractLymph nodes provide specialized stromal microenvironments that support the recruitment and organization of T cells and B cells, enabling them to effectively participate in immune responses. While CD4+3− lymphoid tissue inducer cells (LTic's) are known to play a key role in influencing lymph node (LN) development, the mechanisms that regulate the development of stromal organizer cells are unclear. Here, we define an ontogenetic program of lymph node stromal cell maturation in relation to the requirement for LTic's. We also describe a lymph node reaggregation assay to study cell-cell interactions and lymphocyte recruitment to these organs that reproduces the in vivo events during lymph node development. In addition, analysis of the lymph node anlagen in normal and lymphotoxin a (LTa)–deficient embryos shows that LTa-mediated signaling is required to sustain proliferation and survival of stromal cells in vivo. Our data identify LTa-independent and LTa-dependent stages of lymph node development, and provide direct evidence for the role of LTic's during LN organogenesis.
Hematopoietic stem-cell behavior in nonhuman primates
Authors: Shepherd Bryan E. , Kiem Hans-Peter , Lansdorp Peter M. , Dunbar Cynthia E. , Aubert Geraldine , LaRochelle Andre , Seggewiss Ruth , Guttorp Peter , Abkowitz Janis L. 
Published: May 2007

Abstract
Little is known about the behavior of hematopoietic stem cells (HSCs) in primates because direct observations and competitive-repopulation assays are not feasible. Therefore, we used 2 different and independent experimental strategies, the tracking of transgene expression after retroviral-mediated gene transfer (N = 11 baboons; N = 7 rhesus macaques) and quantitation of the average telomere length of granulocytes (N = 132 baboons; N = 14 macaques), together with stochastic methods, to study HSC kinetics in vivo. The average replication rate for baboon HSCs is once per 36 weeks according to gene-marking analyses and once per 23 weeks according to telomere-shortening analyses. Comparable results were derived from the macaque data. These rates are substantially slower than the average replication rates previously reported for HSCs in mice (once per 2.5 weeks) and cats (once per 8.3 weeks). Because baboons and macaques live for 25 to 45 years, much longer than mice (∼2 years) and cats (12-18 years), we can compute that HSCs undergo a relatively constant number (∼80-200) of lifetime replications. Thus, our data suggest that the self-renewal capacity of mammalian stem cells in vivo is defined and evolutionarily conserved.