bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence Polymorphism in the Glycosylation Island and Flagellins of
Pseudomonas aeruginosa
Authors: Arora Shiwani K. , Wolfgang Matthew C. , Lory Stephen , Ramphal Reuben 
Published: March 2004

ABSTRACT

A genomic island consisting of 14 open reading frames,
orfA
to
orfN
was previously identified in
Pseudomonas aeruginosa
strain PAK and shown to be essential for glycosylation of flagellin. DNA microarray hybridization analysis of a number of
P. aeruginosa
strains from diverse origins showed that this island is polymorphic. PCR and sequence analysis confirmed that many
P. aeruginosa
strains carry an abbreviated version of the island (short island) in which
orfD
, -
E
and -
H
are polymorphic and
orfI
, -
J
, -
K
, -
L
, and -
M
are absent. To ascertain whether there was a relationship between the inheritance of the short island and specific flagellin sequence variants, complete or partial nucleotide sequences of flagellin genes from 24 a-type
P. aeruginosa
strains were determined. Two distinct flagellin subtypes, designated A1 and A2, were apparent. Strains with the complete 14-gene island (long island) were almost exclusively of the A1 type, whereas strains carrying the short island were associated with both A1- and A2-type flagellins. These findings indicate that
P. aeruginosa
possesses a relatively low number of distinct flagellin types and probably has the capacity to further diversify this antigenic surface protein by glycosylation.
Cell Death in
Escherichia coli dnaE
(Ts) Mutants Incubated at a Nonpermissive Temperature Is Prevented by Mutation in the
cydA
Gene
Authors: Strauss Bernard , Kelly Kemba , Dincman Toros , Ekiert Damian , Biesieda Theresa , Song Richard 
Published: March 2004

ABSTRACT

Cells of the
Escherichia coli dnaE
(Ts)
dnaE74
and
dnaE486
mutants die after 4 h of incubation at 40°C in Luria-Bertani medium. Cell death is preceded by elongation, is inhibited by chloramphenicol, tetracycline, or rifampin, and is dependent on cell density. Cells survive at 40°C when they are incubated at a high population density or at a low density in conditioned medium, but they die when the medium is supplemented with glucose and amino acids. Deletion of
recA
or
sulA
has no effect. We isolated suppressors which survived for long periods at 40°C but did not form colonies. The suppressors protected against hydroxyurea-induced killing. Sequence and complementation analysis indicated that suppression was due to mutation in the
cydA
gene. The DNA content of
dnaE
mutants increased about eightfold in 4 h at 40°C, as did the DNA content of the suppressed strains. The amount of plasmid pBR322 in a
dnaE74
strain increased about fourfold, as measured on gels, and the electrophoretic pattern appeared to be normal even though the viability of the parent cells decreased 2 logs. Transformation activity also increased. 4′,6′-Diamidino-2-phenylindole staining demonstrated that there were nucleoids distributed throughout the
dnaE
filaments formed at 40°C, indicating that there was segregation of the newly formed DNA. We concluded that the DNA synthesized was physiologically competent, particularly since the number of viable cells of the suppressed strain increased during the first few hours of incubation. These observations support the view that
E. coli
senses the rate of DNA synthesis and inhibits septation when the rate of DNA synthesis falls below a critical level relative to the level of RNA and protein synthesis.
Comparative Genomics of Two
Leptospira interrogans
Serovars Reveals Novel Insights into Physiology and Pathogenesis
Authors: Nascimento A. L. T. O. , Ko A. I. , Martins E. A. L. , Monteiro-Vitorello C. B. , Ho P. L. , Haake D. A. , Verjovski-Almeida S. , Hartskeerl R. A. , Marques M. V. , Oliveira M. C. , Menck C. F. M. , Leite L. C. C. , Carrer H. , Coutinho L. L. , Degrave W. M. , Dellagostin O. A. , El-Dorry H. , Ferro E. S. , Ferro M. I. T. , Furlan L. R. , Gamberini M. , Giglioti E. A. , Góes-Neto A. , Goldman G. H. , Goldman M. H. S. , Harakava R. , Jerônimo S. M. B , Junqueira-de-Azevedo I. L. M. , Kimura E. T. , Kuramae E. E. , Lemos E. G. M. , Lemos M. V. F. , Marino C. L. , Nunes L. R. , de Oliveira R. C. , Pereira G. G. , Reis M. S. , Schriefer A. , Siqueira W. J. , Sommer P. , Tsai S. M. , Simpson A. J. G. , Ferro J. A. , Camargo L. E. A. , Kitajima J. P. , Setubal J. C. , Van Sluys M. A. 
Published: March 2004

ABSTRACT

Leptospira
species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of
Leptospira interrogans
serovar Copenhageni and comparative analysis with the available
Leptospira interrogans
serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.
Reconstruction of the Central Carbohydrate Metabolism of
Thermoproteus tenax
by Use of Genomic and Biochemical Data
Authors: Siebers Bettina , Tjaden Britta , Michalke Klaus , Dörr Christine , Ahmed Hatim , Zaparty Melanie , Gordon Paul , Sensen Christoph W. , Zibat Arne , Klenk Hans-Peter , Schuster Stephan C. , Hensel Reinhard 
Published: March 2004

ABSTRACT

The hyperthermophilic, facultatively heterotrophic crenarchaeum
Thermoproteus tenax
was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total genome), with an average gap size of 100 bp and 5.3-fold coverage, are reported, giving insights into the genome of
T. tenax
. Genome analysis and biochemical studies enabled us to reconstruct its central carbohydrate metabolism.
T. tenax
uses a variant of the reversible Embden-Meyerhof-Parnas (EMP) pathway and two different variants of the Entner-Doudoroff (ED) pathway (a nonphosphorylative variant and a semiphosphorylative variant) for carbohydrate catabolism. For the EMP pathway some new, unexpected enzymes were identified. The semiphosphorylative ED pathway, hitherto supposed to be active only in halophiles, is found in
T. tenax
. No evidence for a functional pentose phosphate pathway, which is essential for the generation of pentoses and NADPH for anabolic purposes in bacteria and eucarya, is found in
T. tenax
. Most genes involved in the reversible citric acid cycle were identified, suggesting the presence of a functional oxidative cycle under heterotrophic growth conditions and a reductive cycle for CO
2
fixation under autotrophic growth conditions. Almost all genes necessary for glycogen and trehalose metabolism were identified in the
T. tenax
genome.
Bacillus anthracisandBacillus cereusPcrA Helicases Can Support DNA Unwinding and In Vitro Rolling-Circle Replication of Plasmid pT181 ofStaphylococcus aureus
Authors: Anand Syam P. , Mitra Poulami , Naqvi Asma , Khan Saleem A. 
Published: March 2004

ABSTRACTReplication of rolling-circle replicating (RCR) plasmids in gram-positive bacteria requires the unwinding of initiator protein-nicked plasmid DNA by the PcrA helicase. In this report, we demonstrate that heterologous PcrA helicases fromBacillus anthracisandBacillus cereusare capable of unwindingStaphylococcus aureusplasmid pT181 from the initiator-generated nick and promoting in vitro replication of the plasmid. These helicases also physically interact with the RepC initiator protein of pT181. The ability of PcrA helicases to unwind noncognate RCR plasmids may contribute to the broad-host-range replication and dissemination of RCR plasmids in gram-positive bacteria.
The PaaX Repressor, a Link between Penicillin G Acylase and the Phenylacetyl-Coenzyme A Catabolon of
Escherichia coli
W
Authors: Galán Beatriz , García José L. , Prieto María A. 
Published: March 2004

ABSTRACT

The
pac
gene, encoding the penicillin G acylase from
Escherichia coli
W, is regulated by the PaaX repressor of the phenylacetate catabolic pathway.
pac
expression depends on the synthesis of phenylacetyl-coenzyme A. PaaX and the cyclic AMP receptor protein (CRP) bind in vitro to the
Ppac
promoter region. A palindromic sequence proposed as the PaaX operator is located upstream of the −35 box overlapping a CRP binding site, an unusual position that suggests a novel regulatory mechanism.
Compartmentalization of Gene Expression during Sporulation of
Bacillus subtilis
Is Compromised in Mutants Blocked at Stage III of Sporulation
Authors: Li Zusheng , Di Donato Francis , Piggot Patrick J. 
Published: March 2004

ABSTRACT

Mutations in the
spoIIIA
and
spoIIIJ
loci disrupt the compartmentalization of gene expression during sporulation of
Bacillus subtilis
. The breakdown in compartmentalization is not the cause of their being blocked in spore formation. Rather, it appears to be a consequence of the engulfed prespore's being unstable.
Temporal and spatial opportunities for polygamy in a monogamous seahorse, Hippocampus whitei
Authors: Evans Karl , Sadler Laila , Vincent Amanda , Marsden A. Dale 
Published: March 2004

AbstractThe sex with the higher potential reproductive rate is expected to mate polygamously unless there are temporal or spatial constraints on mate availability. We investigated whether such constraints were evident in a population of the monogamous seahorse Hippocampus whitei (family Syngnathidae). Across the whole study site, breeding was more asynchronous than expected by chance. Our findings are thus compatible with the hypothesis that asynchronous breeding may promote and/or maintain monogamy. Asynchrony per se was unlikely to explain monogamy entirely, however, as temporal opportunities for polygamy remained and the males that were nearest one another had the lowest level of asynchrony. Moreover, each animal's home range overlapped with home ranges of potential mates other than their partner, implying a lack of spatial constraints on polygamy. We suggest that H. whitei mated monogamously because the benefits of polygamy were reduced by (1) only small differences in the potential reproductive rates of males and females and/or (2) a mate familiarity effect that increased reproductive success in successive matings. Further research could investigate relationships between mating pattern and varying intersexual differences in potential reproductive rates across syngnathid species.
Ultrasonic responses of CBA pups to the odour of genetically different mice
Authors: Szentgyörgyi Hajnalka , Kapusta Joanna 
Published: March 2004

AbstractMouse pups that are separated from the nest and exposed to cold temperature emit ultrasonic calls. These signals are perceived by conspecifics and play an important communicative role in mother-offspring interaction. Newborn mice are able to modify ultrasonic calls in response to different olfactory cues. Three-day-old CBA-strain mouse pups produced fewer sounds in contact with bedding of adult CBA mice than when exposed to genetically unrelated cues of C57BL and DBA adult animals. The pulses were also significantly shorter in the presence of odour of CBA mice than when exposed to another strain. Newborns emitted the shortest signals when in contact with urine of CBA virgin females, but there were no differences in vocalizations in response to odours from intact, castrated, and testosterone-treated castrated CBA males. These results confirm that CBA pups can distinguish the odour of their genotype. The paper also presents the first evidence that CBA pups discriminate the sex of adult animals and that the chemosignals recognized by pups are secreted with urine but are not testosterone-dependent.
Social dynamics of captive western lowland gorillas living in all-male groups
Authors: Lukas K.E. , Maple T.L. , Stoinski T.S. , Kuhar C.W. 
Published: March 2004

AbstractMale mammals show considerable variation in their association (e.g. single-male, multi-male, all-male groups) and relationship (e.g. affiliative versus intolerant) patterns. Although a number of primates have been observed to form all-male groups, studies of the social dynamics of these groups are limited. This study examined the social interactions of 25 male western lowland gorillas living in nine captive all-male groups. Over 1,300 hours of data were collected using group scan and all-occurrence sampling methodologies. Groups were cohesive, with males spending approximately one-third of their time within 5 meters of another individual. Although complete linear dominance hierarchies within a group were not observed, dominance relationships between individuals were evident for the majority (66%) of dyads. Social interactions varied as a function of age, with subadults engaging in more affiliative behavior and less non-contact aggression than either blackbacks or silverbacks. Visual/olfactory access to females increased non-contact aggression between males. Such results are similar to those found for all-male groups of mountain gorillas in the wild and demonstrate that all-male groups can be a cohesive social unit in this species. They also raise the questions of why all-male groups have rarely been observed in wild populations and how social, ecological and anthropogenic factors influence male sociality.
Factors mediating inter-group encounters in savannah baboons (Papio cynocephalus ursinus)
Authors: Kitchen Dawn , Seyfarth Robert , Cheney Dorothy 
Published: March 2004

AbstractInter-group encounters among baboons range from peaceful to aggressive. During 23 months we observed 110 inter-group interactions involving four groups of chacma baboons in the Okavango Delta, Botswana. Results supported the hypothesis that male behavior functions to prevent extra-group males from gaining access to sexually receptive females. Males were more likely to chase females in their own group when estrous females were present, and their chases targeted estrous females more often than expected. Males also chased members of the opposing group more when estrous females were present. When estrous females were absent, male displays were shorter in duration, involved fewer participants, were less intense, and were more likely to result in peaceful mingling between groups. The alpha male was the individual most actively involved in inter-group chases and displays, but males of all ranks participated, especially when they were in consort with a female. However, males did not cooperate in group defense. While behavior during encounters was affected by the presence of estrous females, the outcome of encounters was affected by location and rival group identity. Groups were more likely to approach and displace opponents in the core of their range and more likely to retreat in the periphery. Correcting for location, we also found some evidence for an inter-group dominance hierarchy based on the relative number of males.
Food stress, fluctuating asymmetry and reproductive performance in the gryllid crickets Gryllus bimaculatus and Gryllodes sigillatus
Authors: Mallard Samantha , Barnard C.J. 
Published: March 2004

AbstractWhile associations between sexual selection, developmental stress and fluctuating asymmetry (FA) remain controversial, this does not necessarily undermine the more general hypothesis that FA reflects developmental instability and functional competence. This applies as much to reproductive processes as to any other. If this is the case, however, we should expect FA and measures of performance to covary under conditions of developmental stress. Using an established association between morphometric FA and reproductive performance in the gryllid crickets Gryllus bimaculatus and Gryllodes sigillatus, we looked at the effect of food stress on covariation between FA and measures of performance (vigour of locomotion and interaction, mating speed, sperm transfer, egg production and offspring weight). The results showed a clear effect of food treatment in males and females of both species, with composite measures reflecting greater FA and reduced performance being greatest when crickets were reared on impoverished food. Inspection of independent means suggested FA may have been most influenced by a relaxation of food stress under high quality feeding conditions, while reproductive performance was more susceptible to the reduction in food quality under low quality conditions.
Foraging behaviour of Armadillidium vulgare (Isopoda: Oniscidea) in heterogeneous environments
Authors: Tuck Joanne , Hassall Mark 
Published: March 2004

AbstractForaging behaviour of Armadillidium vulgare was observed in laboratory arenas in which the spatial distribution of patches of high quality food (powdered dicotyledonous leaf litter) was varied within a background of low quality food (powdered grass leaf litter). The hypotheses that the foraging behaviour and foraging path of A. vulgare would be influenced by food quality and the patchiness of high quality food resources were tested. More time was spent in high quality food patches than in low quality food backgrounds than expected by chance in all heterogeneity treatments, but an increasingly higher percentage of time was spent in low quality food as the high quality food became more clumped in space. More time was spent searching, but less time was spent feeding in low quality food backgrounds than in high quality food patches in all the treatments. Walking speed was found to be lower in high quality food patches than in low quality food backgrounds and this was not affected by treatment. Turning frequency and turning angle were found to be higher in high quality food patches than in low quality backgrounds. Turning frequency in low quality food backgrounds decreased as the high quality food became more clumped in space, whereas turning angle in high quality food patches significantly increased in the patchy, but then decreased again in the clumped treatment. The effects of varying the spatial heterogeneity of high quality foods on the trade-off between costs of searching and intake benefits for saprophages are discussed in relation to predictions from optimal foraging theory for circumstances when intake rate maximisation is affected by the constraint of limited nutrients.
Break-down of arms race between the red-backed shrike (Lanius collurio) and common cuckoo (Cuculus canorus)
Authors: Moskát Csaba , Lovászi Péter 
Published: March 2004

AbstractThe red-backed shrike Lanius collurio once was parasitised by the common cuckoo Cuculus canorus in low frequency until the late 1960s in Hungary, but no case of parasitism is known from the last three or four decades. The cuckoo most probably abandoned this host species because its arms race had defeated, which may be indicated by the high level egg recognition and rejection ability of shrikes. However, mimicry of the cuckoo eggs in the last known cases of parasitism was significantly lower than between cuckoo eggs and host eggs collected from great reed warbler Acrocephalus arundinaceus nests within the same period. This suggests that red-backed shrikes won the arms race leaving no chance for cuckoos to develop better mimicry for their eggs. We tested these findings with experimentally induced parasitism using two types of real eggs: red-backed shrikes rejected 57.6% of the foreign conspecific eggs, but rejected 93.3% of the real cuckoo eggs transferred form nests of great reed warblers. This high level of rejection against real cuckoo eggs shows that there is no chance for presently occurring cuckoos to reparasitise red-backed shrikes in Hungary. Experimental eggs rejected by shrikes had lower mimicry than the eggs which were accepted, but intraclutch variation did not differ between accepters and rejecters. Hosts' aggression was significantly higher against the stuffed cuckoo than against the control species, the collared dove Streptopelia decaocto, and it was the least against female red-backed shrikes. Red-backed shrikes high aggression against cuckoo dummies also showed a highly developed antiparasite adaptation.
Vorticity Balance in Coarse-Resolution Global Ocean Simulations
Authors: Lu Youyu , Stammer Detlef 
Published: March 2004

Abstract
The vorticity budget of the vertically integrated circulation from two global ocean simulations is analyzed using a horizontal spacing of 2° × 2° in longitude/latitude. The two simulations differ in their initial hydrographic conditions and surface wind and buoyancy forcing. The constrained simulation obtains optimal initial condition and surface forcing through assimilating observational data using the model's adjoint, whereas the unconstrained simulation uses Levitus climatological conditions for initialization and is driven by NCEP–NCAR reanalysis forcing, plus restoring to the monthly surface temperature and salinity climatological conditions. The goal is to examine the dynamics that sets the time-mean circulation and to understand the differences between the constrained and unconstrained simulations. It is found that, similar to eddy-permitting simulations, the bottom pressure torque (BPT) in coarse-resolution models plays an important role in the western boundary currents and in the Southern Ocean, and largely balances the difference between wind stress curl and βV for the depth-integrated flow. BPT is a controlling factor of the interior abyssal flow. The geostrophic vorticity relation holds in the interior basins in intermediate and deep layers and breaks down in the upper ocean toward the surface. In the upper layer of the interior basins, the model simulations show statistically significant deviation from the Sverdrup balance. In the subtropical gyre regions, the deviation from Sverdrup balance is confined to zonal bands that are balanced by the curls of lateral friction and nonlinear advection. The differences between the constrained and unconstrained simulations are significant in vorticity terms. The adjustment to Levitus hydrographic climatological data as the model's initial condition causes the most significant changes in BPT, which is the main reason for changes in abyssal flow. The analysis also points to needs for further improvement of models and controlling the influence of data errors in ocean state estimation.