bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐pollen Movement and Deviation of Random Mating in a Low‐density Continuous Population of a Tropical Tree Hymenaea courbaril in the Brazilian Amazon
Authors: Eduardo André , De Lacerda Biscaia , Kanashiro Milton , Sebbenn Alexandre Magno 
Published: February 2008

ABSTRACTMating system and pollen flow are two key elements to understand the genetic structure of tree species. Mating and pollen‐dispersal patterns of a low‐density population of bat pollinated Hymanea courbaril were examined before logging in a 546‐ha plot in the Brazilian Amazon. The multilocus genotypes of nine microsatellite loci were determined for 130 adult‐trees and 367 seeds collected from 20 seed‐trees. Mating system analysis, using mixed‐mating model and paternity analysis showed that the studied population is perfectly outcrossed (tm= 1.002), and probably self‐incompatible. However, significant deviations from random mating were detected for mating among relatives (tm−ts= 0.096, P < 0.05) and correlated matings (rp= 0.289, P < 0.05), indicating inbreeding in the population and that part of offspring are full‐sibs (28.9%). Inbreeding was reflected in the positive and significant fixation index observed in adult trees (F= 0.137, P < 0.05), although no significant inbreeding was detected in offspring (F= 0.074, P > 0.05). The effective number of pollen donors mating with each seed‐tree was determined to be low (Nep≈ 4). The average of pollen flow distance was measured inside of the plot by both paternity (827 ± 429 m) and TwoGener analysis (115–363 m). However, this underestimated pollen dispersal distance, since the detected rate of pollen immigration inside of the plot was high (55%). The observed long‐pollen dispersal distance is probably related to pollination by bats and the low density of reproductive trees in the site.
Establishment of Epiphytic Bromeliads in Successional Tropical Premontane Forests in Costa Rica
Authors: Marín Alfredo Cascante , Wolf Jan H. D. , Oostermeijer J. Gerard B. , Den Nijs Joannes C. M. 
Published: February 2008

ABSTRACTPlant community composition is the combined result of species‐specific competitive abilities and the availability of propagules. For epiphytic plants, current hypotheses consider that dispersal‐related factors are most important. By controlling seed dispersal constraints, we experimentally examined whether the community composition of epiphytic bromeliads in a tropical premontane area is determined during early phases of seedling recruitment. Also, we tested whether establishment success was related to eco‐physiological traits of the species. A total of 7200 seeds were artificially affixed on several host trees in two secondary forest patches and in a mature forest stand. Four bromeliad species with differing physiological characteristics (CAM, C3‐CAM, and C3) and habitat preference (secondary vs. primary forest) were selected. We found that differences in seed germination probability among habitats and species were not likely to influence community assembly. After 2 yr, seedling survival and plant development were relatively higher in the early‐successional forest. Seedling establishment success was not associated with specific physiological and morphological adaptations or habitat preference of the studied species. Our results were not consistent with the described community composition and rates of population recruitment of the studied species in the same successional habitats. The results support the hypothesis that chance and historic events related to seed dispersal have an important influence on community assembly of epiphytic plants. In addition, differences in growth rates and reproductive turnover among species are expected to influence the relative abundance and recruitment rates in a particular habitat.
Changes in the contractile properties of motor units in the rat medial gastrocnemius muscle after one month of treadmill training
Authors: Pogrzebna M. , Celichowski J. 
Published: February 2008

AbstractAim: The influence of 4 weeks treadmill training on the contractile properties of motor units (MUs) in the rat medial gastrocnemius muscle was investigated.Methods: A population of 18 Wistar rats was divided into two groups: trained on a treadmill (n = 7, locomotion speed 27 cm s−1, 1 km daily, 5 days a week, for 4 weeks) and control (n = 11). The contractile properties of isolated MUs were studied. Functional isolation of units was achieved by electrical stimulation of filaments of the ventral roots. A total of 299 MUs were investigated (142 in the control group and 157 in the trained group). They were divided into fast fatigable (FF), fast resistant to fatigue (FR) and slow (S). Their proportions and parameters of contractions were analysed.Results: Following training, the number of FF units decreased and the number of FR units increased. The distribution of the fatigue index changed within these two types of fast units. The twitch and tetanus forces increased considerably in fast MUs, mainly in those of the FF type. The contraction and relaxation times shortened in the FR and S MUs. The steep part of the force–frequency curves shifted towards higher stimulation frequencies in FR and S units, while in FF units the shift was in the opposite direction.Conclusion: The significant change in the proportions of fast MUs following training indicates FF to FR transformation. The various effects of training seen in the different MU types help explain the rationale behind mixed training.
Species-Specific Identification of Campylobacters by PCR-Restriction Fragment Length Polymorphism and PCR Targeting of the Gyrase B Gene
Authors: Kawasaki Susumu , Fratamico Pina M. , Wesley Irene V. , Kawamoto Shinichi 
Published: February 2008

ABSTRACT

PCR-restriction fragment length polymorphism (RFLP) analysis of a 960-bp fragment of the
Campylobacter gyrB
gene with either DdeI or XspI restriction enzymes generated unique digestion patterns for 12 different
Campylobacter
species. In addition, PCR assays using species-specific primer sets targeting
gyrB
were specific for the respective
Campylobacter
species. Therefore, PCR-RFLP analysis and species-specific PCR assays based on the
gyrB
gene provide valuable tools for rapid and unambiguous identification of the majority of
Campylobacter
species.
Removal of Free Extracellular DNA from Environmental Samples by Ethidium Monoazide and Propidium Monoazide
Authors: Wagner Andreas O. , Malin Cornelia , Knapp Brigitte A. , Illmer Paul 
Published: February 2008

ABSTRACT
Recently, new DNA extraction techniques (using ethidium monoazide and propidium monoazide) have been developed to discriminate between alive and dead bacterial cells. Nevertheless, for complex environmental samples, no data are available yet. In the present study, these new methods were applied to anaerobic-fermentor sludge and the results were compared to a conventional microbiological approach.
Role of Ureolytic Activity in
Bacillus cereus
Nitrogen Metabolism and Acid Survival
Authors: Mols Maarten , Abee Tjakko 
Published: February 2008

ABSTRACT

The presence and activities of urease genes were investigated in 49 clinical, food, and environmental
Bacillus cereus
isolates. Ten strains were shown to have urease genes, with eight of these strains showing growth on urea as the sole nitrogen source. Two of the urease-positive strains, including the sequenced strain ATCC 10987, could not use urea for growth, despite their capacities to produce active urease. These observations can be explained by the inability of the two strains to use ammonium as a nitrogen source. The impact of urea hydrolysis on acid stress resistance was subsequently assessed among the ureolytic
B. cereus
strains. However, none of the strains displayed increased fitness under acidic conditions or showed enhanced acid shock survival in the presence of urea. Expression analysis of urease genes in
B. cereus
ATCC 10987 revealed a low level of expression of these genes and a lack of pH-, nitrogen-, urea-, oxygen-, and growth phase-dependent modulation of mRNA transcription. This is in agreement with the low urease activity observed in strain ATCC 10987 and the other nine strains tested. Although a role for
B. cereus
ureolytic activity in acid survival cannot be excluded, its main role appears to be in nitrogen metabolism, where ammonium may be provided to the cells in nitrogen-limited, urea-containing environments.
Promoter Activation by Repositioning of RNA Polymerase
Authors: Kumar Amrita , Moran Charles P. 
Published: February 2008

ABSTRACT

Spo0A, a classical two-component-type response regulator in
Bacillus subtilis
, binds to a specific DNA sequence found in many promoters to repress or activate the transcription of over 100 genes. On the
spoIIG
promoter, one of the Spo0A binding sites, centered at position −40, overlaps a consensus −35 element that may also interact with region 4 of the sigma A (σ
A
) subunit of RNA polymerase. Molecular modeling corroborated by genetic evidence led us to propose that the binding of Spo0A to this site repositions σ
A
region 4 on the promoter. Therefore, we used a chemical nuclease,
p
-bromoacetamidobenzyl-EDTA-Fe, that was covalently tethered to a single cysteine in region 4 of σ
A
to map the position of σ
A
on the promoter. The results indicated that in the absence of Spo0A, σ
A
region 4 of the RNA polymerase was located near the −35 element sequence centered at position −40. However, in the presence of Spo0A, σ
A
region 4 was displaced downstream from the −35 element by 4 bp. These and other results support the model in which the binding of Spo0A to the
spoIIG
promoter stimulates promoter utilization by repositioning prebound RNA polymerase and stabilizing the repositioned RNA polymerase-promoter complex at a new position that aligns σ
A
region 2 with the −10 region sequences of the promoter, thus facilitating open complex formation.
Two RecA Protein Types That Mediate Different Modes of Hyperrecombination
Authors: Baitin Dmitry M. , Bakhlanova Irina V. , Chervyakova Darya V. , Kil Yury V. , Lanzov Vladislav A. , Cox Michael M. 
Published: February 2008

ABSTRACT

RecAX53 is a chimeric variant of the
Escherichia coli
RecA protein (RecAEc) that contains a part of the central domain of
Pseudomonas aeruginosa
RecA (RecAPa), encompassing a region that differs from RecAEc at 12 amino acid positions. Like RecAPa, this chimera exhibits hyperrecombination activity in
E. coli
cells, increasing the frequency of recombination exchanges per DNA unit length (FRE). RecAX53 confers the largest increase in FRE observed to date. The contrasting properties of RecAX53 and RecAPa are manifested by in vivo differences in the dependence of the FRE value on the integrity of the
mutS
gene and thus in the ratio of conversion and crossover events observed among their hyperrecombination products. In strains expressing the RecAPa or RecAEc protein, crossovers are the main mode of hyperrecombination. In contrast, conversions are the primary result of reactions promoted by RecAX53. The biochemical activities of RecAX53 and its ancestors, RecAEc and RecAPa, have been compared. Whereas RecAPa generates a RecA presynaptic complex (PC) that is more stable than that of RecAEc, RecAX53 produces a more dynamic PC (relative to both RecAEc and RecAPa). The properties of RecAX53 result in a more rapid initiation of the three-strand exchange reaction but an inability to complete the four-strand transfer. This indicates that RecAX53 can form heteroduplexes rapidly but is unable to convert them into crossover configurations. A more dynamic RecA activity thus translates into an increase in conversion events relative to crossovers.
RelA Functionally Suppresses the Growth Defect Caused by a Mutation in the G Domain of the Essential Der Protein
Authors: Hwang Jihwan , Inouye Masayori 
Published: February 2008

ABSTRACTA unique bacterial GTPase, Der, containing two tandem GTP-binding domains, is essential for cell growth and plays a crucial role in a large ribosomal subunit inEscherichia coli. The depletion of Der resulted in accumulation of both large and small ribosomal subunits and also affected the stability of large ribosomal subunits. However, its exact cellular function still remains elusive. Previously, we have shown that two G domain mutants, DerN118D and DerN321D, cannot support cell growth at low temperatures, suggesting that both GTP-binding domains are indispensable. In this study, we show that both Der variants are defective in ribosome biogenesis. Genetic screening of anE. coligenomic library was performed to identify the genes which, when expressed from a multicopy plasmid, can restore the growth defect of the DerN321D mutant at restrictive temperatures. Among seven suppressors isolated, four were located at 62.7 min on theE. coligenomic map, and the gene responsible for the suppression of DerN321D was identified as therelAgene which encodes a ribosome-associated (p)ppGpp synthetase. The synthetic activity of RelA was found to be essential for its DerN321D suppressor activity. Overexpression of RelA in a suppressor strain did not affect the expression of DerN321D but suppressed the polysome defects caused by the DerN321D mutant. This is the first demonstration of suppression of impaired function of Der by a functional enzyme. A possible mechanism of the suppression of DerN321D by RelA overproduction is discussed.
ArnR, a Novel Transcriptional Regulator, Represses Expression of the
narKGHJI
Operon in
Corynebacterium glutamicum
Authors: Nishimura Taku , Teramoto Haruhiko , Vertès Alain A. , Inui Masayuki , Yukawa Hideaki 
Published: February 2008

ABSTRACT

The
narKGHJI
operon that comprises putative nitrate/nitrite transporter (
narK
) and nitrate reductase (
narGHJI
) genes is required for the anaerobic growth of
Corynebacterium glutamicum
with nitrate as a terminal electron acceptor. In this study, we identified a gene,
arnR
, which encodes a transcriptional regulator that represses the expression of the
narKGHJI
operon in
C. glutamicum
cells under aerobic conditions. Disruption of
arnR
induced nitrate reductase activities of
C. glutamicum
cells and increased
narKGHJI
mRNA levels under aerobic growth conditions. DNA microarray analyses revealed that besides the
narKGHJI
operon, the
hmp
gene, which encodes flavohemoglobin, is negatively regulated by ArnR under aerobic conditions. Promoter-reporter assays indicated that
arnR
gene expression was positively autoregulated by its gene product, ArnR, under both aerobic and anaerobic conditions. Electrophoretic mobility shift assay experiments showed that purified hexahistidyl-tagged ArnR protein specifically binds to promoter regions of the
narKGHJI
operon and the
hmp
and
arnR
genes. A consensus sequence, TA(A/T)TTAA(A/T)TA, found in the promoter regions of these genes was demonstrated to be involved in the binding of ArnR. Effects on LacZ activity by deletion of the ArnR binding sites within the promoter regions fused to the reporter gene were consistent with the view that the expression of the
narKGHJI
operon is repressed by the ArnR protein under aerobic conditions, whereas the expression of the
arnR
gene is autoinduced by ArnR.
Microcompartments for B
12
-Dependent 1,2-Propanediol Degradation Provide Protection from DNA and Cellular Damage by a Reactive Metabolic Intermediate
Authors: Sampson Edith M. , Bobik Thomas A. 
Published: February 2008

ABSTRACT

Salmonella enterica
grows on 1,2-propanediol (1,2-PD) in a coenzyme B
12
-dependent fashion. Prior studies showed that a bacterial microcompartment (MCP) is involved in this process and that an MCP-minus mutant undergoes a 20-h period of growth arrest during 1,2-PD degradation. It was previously proposed that growth arrest resulted from propionaldehyde toxicity, but no direct evidence was presented. Here, high-pressure liquid chromatography analyses of culture medium were used to show that the major products of aerobic 1,2-PD degradation are propionaldehyde, propionate, and 1-propanol. A MCP-minus mutant accumulated a level of propionaldehyde 10-fold higher than that of the wild type (1.6 mM compared to 15.7 mM), associating this compound with growth arrest. The addition of propionaldehyde to cultures of
S. enterica
caused growth arrest from 8 to 20 mM, but not at 4 mM, providing direct evidence for propionaldehyde toxicity. Studies also indicated that propionaldehyde was toxic due to the inhibition of respiratory processes, and the growth arrest ended when propionaldehyde was depleted primarily by conversion to propionate and 1-propanol and secondarily due to volatility. The Ames test was used to show that propionaldehyde is a mutagen and that mutation frequencies are increased in MCP-minus mutants during 1,2-PD degradation. We propose that a primary function of the MCPs involved in 1,2-PD degradation is the mitigation of toxicity and DNA damage by propionaldehyde.
DivIVA Is Required for Polar Growth in the MreB-Lacking Rod-Shaped ActinomyceteCorynebacterium glutamicum
Authors: Letek Michal , Ordóñez Efrén , Vaquera José , Margolin William , Flärdh Klas , Mateos Luis M. , Gil José A. 
Published: February 2008

ABSTRACTThe actinomyceteCorynebacterium glutamicumgrows as rod-shaped cells by zonal peptidoglycan synthesis at the cell poles. In this bacterium, experimental depletion of the polar DivIVA protein (DivIVACg) resulted in the inhibition of polar growth; consequently, these cells exhibited a coccoid morphology. This result demonstrated that DivIVA is required for cell elongation and the acquisition of a rod shape. DivIVA fromStreptomycesorMycobacteriumlocalized to the cell poles of DivIVACg-depletedC. glutamicumand restored polar peptidoglycan synthesis, in contrast to DivIVA proteins fromBacillus subtilisorStreptococcus pneumoniae, which localized at the septum ofC. glutamicum. This confirmed that DivIVAs from actinomycetes are involved in polarized cell growth. DivIVACglocalized at the septum after cell wall synthesis had started and the nucleoids had already segregated, suggesting that inC. glutamicumDivIVA is not involved in cell division or chromosome segregation.
Identification of Flotillin-2, a Major Protein on Lipid Rafts, as a Novel Target of p53 Family Members
Authors: Sasaki Yasushi , Oshima Yuichiro , Koyama Ryota , Maruyama Reo , Akashi Hirofumi , Mita Hiroaki , Toyota Minoru , Shinomura Yasuhisa , Imai Kohzoh , Tokino Takashi 
Published: February 2008

Abstractp73 and p63 are members of the p53 gene family and have been shown to play an important role in development and homeostasis mainly by regulating the transcription of a variety of genes. A subset of these genes encodes secreted proteins and receptors that may be involved in the communication between adjacent cells. We report here that flotillin-2, a major hydrophobic protein on biomembrane microdomain lipid rafts, is a direct transcriptional target of the p53 family member genes. It has been suggested that such rafts could play an important role in many cellular processes including signal transduction, membrane trafficking, cytoskeletal organization, and pathogen entry. We found that the expression of flotillin-2 was specifically up-regulated by either TAp73β or TAp63γ, but not significantly by p53. In addition, flotillin-2 transcription is activated in response to cisplatin in a manner dependent on endogenous p73. By using small interference RNA designed to target p73, we showed that silencing endogenous p73 abolishes the induction of flotillin-2 transcription following cisplatin treatment. Furthermore, we identified a p73/p63-binding site located upstream of the flotillin-2 gene that is responsive to the p53 family members. This response element is highly conserved between humans and rodents. We also found that ectopic expression of TAp73 as well as TAp63 enhances signal transduction by assessing the interleukin-6–mediated phosphorylation of signal transducers and activators of transcription 3. Thus, in addition to direct transactivation, p53 family member genes enhance a set of cellular processes via lipid rafts. (Mol Cancer Res 2008;6(3):395–406)
Binding of the Retinoblastoma Protein Is Not the Determinant for Stable Repression of Some E2F-Regulated Promoters in Muscle Cells
Authors: Vandromme Marie , Chailleux Catherine , Escaffit Fabrice , Trouche Didier 
Published: February 2008

Abstract
Permanent silencing of E2F-dependent genes is a hallmark of the irreversible cell cycle exit that characterizes terminally differentiated and senescent cells. The determinant of this silencing during senescence has been proposed to be the binding of the retinoblastoma protein Rb and the consequent methylation of H3K9. During ex vivo skeletal muscle differentiation, while most cells terminally differentiate and form myotubes, a subset of myoblasts remains quiescent and can be reinduced by growth factor stimulation to enter the cell cycle. Thus, differentiating cells are composed of two different populations: one in which E2F-dependent genes are permanently repressed and the other not. We observed that, in a manner reminiscent to senescent cells, permanent silencing of the E2F-dependent cdc6, dhfr, and p107 promoters in myotubes was associated with a specific increase in H3K9 trimethylation. To investigate the role of Rb in this process, we developed a reliable method to detect Rb recruitment by chromatinimmunoprecipitation. Surprisingly, we observed that Rb was recruited to these promoters more efficiently in quiescent cells than in myotubes. Thus, our data indicate that during muscle differentiation, permanent silencing and H3K9 trimethylation of some E2F-dependent genes are not directly specified by Rb binding, in contrast to what is proposed for senescence. (Mol Cancer Res 2008;6(3):418–25)
Elderly Patients as a Vulnerable Category of the Population Requiring Special Legal Protection With Respect to the Provision of Medical Care
Authors: Pishchita  
Published: February 2008

AbstractRussia like other European countries is seeing a growing trend to increased life span of its population. This situation results in an urgent need to address problems not only those related to provision of qualified medical care but a special treatment to protection of rights and legal interests of elderly people. In accordance with effective legislation of the Russian Federation aging and elderly patients enjoy all rights and freedoms of capable citizens, but due to their physical and mental condition they are not always able to exercise their rights. Federal law "Legal basis of health care in the Russian Federation" does not provide for representatives of such group of patients to take part in medical care provision. It is necessary to ensure additional legitimate right protection mechanisms in the legislation for capable elderly patients in the sphere of medical care. The government should act as a guarantor of rights protection for such socially vulnerable group of population.