bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro and In Vivo Analysis of the Role of PrrA in
Rhodobacter sphaeroides
2.4.1
hemA
Gene Expression
Authors: Ranson-Olson Britton , Jones Denise F. , Donohue Timothy J. , Zeilstra-Ryalls Jill H. 
Published: April 2006

ABSTRACT

The
hemA
gene codes for one of two synthases in
Rhodobacter sphaeroides
2.4.1 which catalyze the formation of 5-aminolevulinic acid. We have examined the role of PrrA, a DNA binding protein that is associated with the metabolic switch between aerobic growth and anoxygenic photosynthetic growth, in
hemA
expression and found that
hemA
transcription is directly activated by PrrA. Using electrophoretic mobility shift assays and DNase I protection assays, we have mapped two binding sites for PrrA within the
hemA
upstream sequences, each of which contains an identical 9-bp motif. Using
lacZ
transcription reporter plasmids in wild-type strain 2.4.1 and PrrA
−
mutant strain PRRA2, we showed that PrrA was required for maximal expression. We also found that the relative impacts of altering DNA sequences within the two binding sites are different depending on whether cells are growing aerobically or anaerobically. This reveals a greater level of complexity associated with PrrA-mediated regulation of transcription than has been heretofore described. Our findings are of particular importance with respect to those genes regulated by PrrA having more than one upstream binding site. In the case of the
hemA
gene, we discuss possibilities as to how these new insights can be accommodated within the context of what has already been established for
hemA
transcription regulation in
R. sphaeroides
.
Pyoverdine-Mediated Iron Uptake in
Pseudomonas aeruginosa
: the Tat System Is Required for PvdN but Not for FpvA Transport
Authors: Voulhoux Romé , Filloux Alain , Schalk Isabelle J. 
Published: April 2006

ABSTRACT

Under iron-limiting conditions,
Pseudomonas aeruginosa
PAO1 secretes a fluorescent siderophore called pyoverdine (Pvd). After chelating iron, this ferric siderophore is transported back into the cells via the outer membrane receptor FpvA. The Pvd-dependent iron uptake pathway requires several essential genes involved in both the synthesis of Pvd and the uptake of ferric Pvd inside the cell. A previous study describing the global phenotype of a
tat
-deficient
P. aeruginosa
strain showed that the defect in Pvd-mediated iron uptake was due to the Tat-dependent export of proteins involved in Pvd biogenesis and ferric Pvd uptake (U. Ochsner, A. Snyder, A. I. Vasil, and M. L. Vasil, Proc. Natl. Acad. Sci. USA 99:8312-8317, 2002). Using biochemical and biophysical tools, we showed that despite its predicted Tat signal sequence, FpvA is correctly located in the outer membrane of a
tat
mutant and is fully functional for all steps of the iron uptake process (ferric Pvd uptake and recycling of Pvd on FpvA after iron release). However, in the
tat
mutant, no Pvd was produced. This suggested that a key element in the Pvd biogenesis pathway must be exported to the periplasm by the Tat pathway. We located PvdN, a still unknown but essential component in Pvd biogenesis, at the periplasmic side of the cytoplasmic membrane and showed that its export is Tat dependent. Our results further support the idea that a critical step of the Pvd biogenesis pathway involving PvdN occurs at the periplasmic side of the cytoplasmic membrane.
The Hydantoin Transport Protein from
Microbacterium liquefaciens
Authors: Suzuki Shun'ichi , Henderson Peter J. F. 
Published: April 2006

ABSTRACT

The gene
hyuP
from
Microbacterium liquefaciens
AJ 3912 with an added His
6
tag was cloned into the expression plasmid pTTQ18 in an
Escherichia coli
host strain. The transformed
E. coli
showed transport of radioisotope-labeled 5-substituted hydantoins with apparent

K
m

values in the micromolar range. This activity exhibited a pH optimum of 6.6 and was inhibited by dinitrophenol, indicating the requirement of energy for the transport system. 5-Indolyl methyl hydantoin and 5-benzyl hydantoin were the preferred substrates, with selectivity for a hydrophobic substituent in position 5 of hydantoin and for the
l
isomer over the
d
isomer. Hydantoins with less hydrophobic substituents, cytosine, thiamine, uracil, allantoin, adenine, and guanine, were not effective ligands. The His-tagged hydantoin transport protein was located in the inner membrane fraction, from which it was solubilized and purified and its identity was authenticated.
Heme and a Five-Amino-Acid Hemophore Region Form the Bipartite Stimulus Triggering the
has
Signaling Cascade
Authors: Cwerman Hélène , Wandersman Cécile , Biville Francis 
Published: April 2006

ABSTRACT

Bacterial cells sense the extracellular environment and adapt to that environment by activating gene regulation circuits, often by means of signaling molecules. The
Serratia marcescens
hemophore is a signaling molecule that acts as an extracellular heme-scavenging protein. The heme-loaded hemophore interacts with its cognate receptor (HasR), triggering transmembrane signaling and turning on transcription of hemophore-dependent heme uptake genes. We investigated the features of the holo-hemophore, the only HasR ligand known to act as an inducer. We used a hemophore mutant that does not deliver its heme and a HasR mutant that does not bind heme, and we showed that heme transfer from the hemophore to the receptor is necessary for induction. Using a hemophore mutant that does not bind heme and that blocks heme transport, we demonstrated that two molecules that do not interact (heme and the mutant hemophore) may nonetheless induce this system. These findings suggest that hemophore-mediated induction and heme transport involve different mechanisms. The hemophore region important for induction was precisely localized to amino acids 50 to 55, which lie in one of the two HasR-binding hemophore regions. This bipartite stimulus probably corresponds to a physiological process because heme is transferred to the receptor before apo-hemophore release. This bipartite regulation mechanism may allow the bacterium to adjust its heme transport mechanism to the perceived environmental heme concentration.
Positive Selection Acting on a Surface Membrane Protein of the Plant-Pathogenic Phytoplasmas
Authors: Kakizawa Shigeyuki , Oshima Kenro , Jung Hee-Young , Suzuki Shiho , Nishigawa Hisashi , Arashida Ryo , Miyata Shin-ichi , Ugaki Masashi , Kishino Hirohisa , Namba Shigetou 
Published: April 2006

ABSTRACT
Phytoplasmas are plant-pathogenic bacteria that cause numerous diseases. This study shows a strong positive selection on the phytoplasma antigenic membrane protein (Amp). The ratio of nonsynonymous to synonymous substitutions was >1 with all the methods we tested. The clear positive selections imply an important biological role for Amp in host-bacterium interactions.
The role of mechanosensory input in flower handling efficiency and learning byManduca sexta
Authors: Goyret Joaquín , Raguso Robert A. 
Published: April 2006

SUMMARYNectar-foraging animals are known to utilize nectar guides – patterns of visual contrast in flowers – to find hidden nectar. However, few studies have explored the potential for mechanosensory cues to function as nectar guides, particularly for nocturnal pollinators such as the tobacco hornworm moth, Manduca sexta. We used arrays of artificial flowers to investigate the flower handling behavior (the ability to locate and drink from floral nectaries) of naïve moths, looking specifically at: (1) how the shape and size of flat (two-dimensional) artificial corollas affect nectar discovery and (2) whether three-dimensional features of the corolla can be used to facilitate nectar discovery. In these experiments, we decoupled visual from tactile flower features to explore the role of mechanosensory input,putatively attained via the extended proboscides of hovering moths. In addition, we examined changes in nectar discovery times within single foraging bouts to test whether moths can learn to handle different kinds of artificial flowers. We found that corolla surface area negatively affects flower handling efficiency, and that reliable mechanosensory input is crucial for the moths' performance. We also found that three-dimensional features of the corolla, such as grooves, can significantly affect the foraging behavior,both positively (when grooves converge to the nectary) and negatively (when grooves are unnaturally oriented). Lastly, we observed that moths can decrease nectar discovery time during a single foraging bout. This apparent learning ability seems to be possible only when reliable mechanosensory input is available.
Constraints of tolerance: why are desiccation-tolerant organisms so small or rare?
Authors: Alpert Peter 
Published: April 2006

SUMMARYDrying to equilibrium with the air kills nearly all animals and flowering plants, including livestock and crops. This makes drought a key ecological problem for terrestrial life and a major cause of human famine. However, the ability to tolerate complete desiccation is widespread in organisms that are either &lt;5 mm long or found mainly where desiccation-sensitive organisms are scarce. This suggests that there is a trade-off between desiccation tolerance and growth. Recent molecular and biochemical research shows that organisms tolerate desiccation through a set of mechanisms, including sugars that replace water and form glasses, proteins that stabilize macromolecules and membranes, and anti-oxidants that counter damage by reactive oxygen species. These protections are often induced by drying, and some of the genes involved may be homologous in microbes, plants and animals. Understanding how mechanisms of desiccation tolerance may constrain growth might show how to undo the constraint in some economically important macroorganisms and elucidate the much-studied but elusive relationship between tolerance of stress and productivity.
Metabolic, respiratory and cardiovascular responses to acute and chronic hypoxic exposure in tadpole shrimp Triops longicaudatus
Authors: Harper S. L. , Reiber C. L. 
Published: April 2006

SUMMARY
Hypoxic exposure experienced during sensitive developmental periods can shape adult physiological capabilities and define regulatory limits. Tadpole shrimp were reared under normoxic (19–21 kPa O2), moderate(10–13 kPa O2) or severe (1–3 kPa O2)hypoxic conditions to investigate the influence of developmental oxygen partial pressure (PO2) on adult metabolic,respiratory and cardiovascular physiology. Developmental PO2 had no effect on metabolic rate or metabolic response to hypoxic exposure in adults. All rearing groups decreased O2 consumption as water PO2decreased. Heart rate, stroke volume and cardiac output were independent of PO2 down to 5 kPa O2 in all rearing groups. Below this, cardiac output was maintained only in tadpole shrimp reared under severe hypoxic conditions. The enhanced ability to maintain cardiac output was attributed to an increase in hemoglobin concentration and O2-binding affinity in those animals. Oxygen-delivery potential was also significantly higher in the group reared under severe hypoxic conditions(1336 μl O2 min–1) when compared with the group reared under normoxic conditions (274 μl O2min–1). Differences among the rearing groups that were dependent on hemoglobin were not considered developmental effects because hemoglobin concentration could be increased within seven days of hypoxic exposure independent of developmental PO2. Hypoxia-induced hemoglobin synthesis may be a compensatory mechanism that allows tadpole shrimp to regulate O2 uptake and transport in euryoxic (O2 variable) environments. The results of this study indicate that increased hemoglobin concentration, increased O2-binding affinity and transient decreases in metabolic demand may account for tadpole shrimp hypoxic tolerance.
Polarization sensitivity in the red swamp crayfish Procambarus clarkii enhances the detection of moving transparent objects
Authors: Tuthill John C. , Johnsen Sönke 
Published: April 2006

SUMMARY
We tested the hypothesis that polarization sensitivity enhances the detection of moving, transparent objects by examining the escape response of the red swamp crayfish (Procambarus clarkii Girard) from a visual threat. A transparent, birefringent target trans-illuminated by either partially linear polarized or unpolarized light was advanced toward individual crayfish. The optical axis of the target was aligned such that it would be conspicuous to a viewer with polarization sensitivity when trans-illuminated by polarized light. Under polarized light, significantly more crayfish retreated from the target than under unpolarized light of identical intensity(P&lt;0.00005, Fisher's exact test). Whereas the potential for polarization sensitivity has been shown in neurophysiological and structural studies of the visual system of P. clarkii and the signal crayfish Pasifastacus leniusculus (Dana), our results provide the first behavioral evidence for polarization sensitivity among crayfish. The ecological function of this ability is unclear, but it may enhance the detection of fish with silvered scales, transparent zooplankton or macroinvertebrates. Because escape responses are generally more reliably induced than other behaviors, the method employed in this study may prove useful for examining sensory capabilities in other species.
The significance of spiracle conductance and spatial arrangement for flight muscle function and aerodynamic performance in flyingDrosophila
Authors: Heymann Nicole , Lehmann Fritz-Olaf 
Published: April 2006

SUMMARYDuring elevated locomotor activity such as flight, Drosophilasatisfies its increased respiratory demands by increasing the total spiracle opening area of the tracheal gas exchange system. It has been assumed that in a diffusion-based system, each spiracle contributes to oxygen flux into and carbon dioxide flux out of the tracheal system according to the size of its opening. We evaluated this hypothesis by determining how a reduction in size and interference with the spatial distribution of gas exchange areas impair flight muscle function and aerodynamic force production in the small fruit fly Drosophila melanogaster. This was done by selectively blocking thoracic spiracles of tethered flies flying inside a flight simulator. Flow-through respirometry and simultaneous measurements of flight force production and wing kinematics revealed a negligible functional safety margin for respiration. Maximum locomotor performance was only achieved by unmanipulated flies, supporting the general assumption that at the animal's maximum locomotor capacity, maximum spiracle opening area matches respiratory need. The maximum total buffer capacity for carbon dioxide in Drosophila amounts to approximately 33.5 μl g–1body mass, estimated from the temporal integral of carbon dioxide release rate during the resting period after flight. By comparing flight variables in unmanipulated and `spiracle-blocked' flies at comparable flight forces, we found that (i) stroke amplitude, stroke frequency and the chemo-mechanical conversion efficiency of the indirect flight musculature were broadly independent of the arrangement of spiracle conductance, while (ii) muscle mechanical power significantly increased, and (iii) mean lift coefficient and aerodynamic efficiency significantly decreased up to approximately 50% with an increasing number of blocked spiracles. The data suggest that Drosophila apparently maximizes the total efficiency of its locomotor system for flight by allowing oxygen delivery to the flight musculature through multiple spiracles of the thorax.
Beyond the central pattern generator: amine modulation of decision-making neural pathways descending from the brain of the medicinal leech
Authors: Crisp Kevin M. , Mesce Karen A. 
Published: April 2006

SUMMARY
The biological mechanisms of behavioral selection, as it relates to locomotion, are far from understood, even in relatively simple invertebrate animals. In the medicinal leech, Hirudo medicinalis, the decision to swim is distributed across populations of swim-activating and swim-inactivating neurons descending from the subesophageal ganglion of the compound cephalic ganglion, i.e. the brain. In the present study, we demonstrate that the serotonergic LL and Retzius cells in the brain are excited by swim-initiating stimuli and during spontaneous swim episodes. This activity likely influences or resets the neuromodulatory state of neural circuits involved in the activation or subsequent termination of locomotion. When serotonin (5-HT) was perfused over the brain, multi-unit recordings from descending brain neurons revealed rapid and substantial alterations. Subsequent intracellular recordings from identified command-like brain interneurons demonstrated that 5-HT, especially in combination with octopamine, inhibited swim-triggering neuron Tr1, as well as swim-inactivating neurons Tr2 and SIN1. Although 5-HT inhibited elements of the swim-inactivation pathway, rather than promoting them, the indirect and net effect of the amine was a reliable and sustained reduction in the firing of the segmental swim-gating neuron 204. This modulation caused cell 204 to relinquish its excitatory drive to the swim central pattern generator. The activation pattern of serotonergic brain neurons that we observed during swimming and the 5-HT-immunoreactive staining pattern obtained, suggest that within the head brain 5-HT secretion is massive. Over time, 5-HT secretion may provide a homeostatic feedback mechanism to limit swimming activity at the level of the head brain.
Equivariant periodicity for compact group actions
Authors: Weinberger Shmuel , Yan Min 
Published: April 2006

Abstract
For a manifold M, the structure set S (M, rel ∂ )
is the collection of manifolds homotopy equivalent to M relative to the boundary.
Siebenmann [R. C. Kirby, L. C. Siebenmann, Foundational essays on
topological manifolds, smoothings, and triangulations. Princeton Univ.
Press 1977] showed that in the topological category, the structure set is
4-periodic: S (M, rel ∂ ) ≅ S (MｘD 4
, rel ∂ ) up to a copy of ℤ. The periodicity has
been extended to topological manifolds with homotopically stratiﬁed group
actions for various representations in place of D 4, including
twice any complex representation of a compact abelian group. In this paper, we
extend the result to twice any complex representation of a compact Lie group. We
also prove the bundle version of the periodicity.
Category overlap and neutralization: The importance of speakers' classifications in phonology
Authors: Mompeán-González José A. 
Published: April 2006

Abstract
This article briefly reviews categorization models in both cognitive psychology and cognitive phonology in order to set the background for a psycholinguistically plausible account of the classification of the allophones involved in category overlaps (i.e., the overlapping areas between phoneme categories) and in the so-called positions of neutralization. In addition, the traditional proposals of both Bloomfieldian phonemics (i.e., phonetic similarity) and the Prague School (i.e., archiphonemes) are discussed and an alternative proposal is offered. The latter claims that phonological theory should be informed by psycholinguistic evidence obtained by experimental methods. This line of research will progressively make cognitive phonology a functional phonological theory consistent with the way speakers classify the sounds of their language and will contribute to theoretical progress in phonological theory.
The acquisition of auxiliary syntax: BE and HAVE
Authors: Theakston Anna L. , Lieven Elena V. M. , Pine Julian M. , Rowland Caroline F. 
Published: April 2006

Abstract
This study examined patterns of auxiliary provision and omission for the auxiliaries BE and HAVE in a longitudinal data set from 11 children between the ages of two and three years. Four possible explanations for auxiliary omission—a lack of lexical knowledge, performance limitations in production, the Optional Infinitive hypothesis, and patterns of auxiliary use in the input—were examined. The data suggest that although none of these accounts provides a full explanation for the pattern of auxiliary use and nonuse observed in children's early speech, integrating input-based and lexical learning-based accounts of early language acquisition within a constructivist approach appears to provide a possible framework in which to understand the patterns of auxiliary use found in the children's speech. The implications of these findings for models of children's early language acquisition are discussed.
Towards a lexically specific grammar of children’s question constructions
Authors: Dąbrowska Ewa , Lieven Elena 
Published: April 2006

Abstract
This paper examines early syntactic development from a
usage-based perspective, using transcripts of the spontaneous speech of two
Englishspeaking children recorded at relatively dense intervals at ages 2;0 and
3;0. We focus primarily on the children’s question constructions, in an effort
to determine (i) what kinds of units they initially extract from the input
(their size and degree of specificity / abstractness); (ii) what operations they
must perform in order to construct novel utterances using these units; and (iii)
how the units and the operations change between the ages of two and three. In
contrast to nativist theories of language development which suggest that
children are working with abstract syntactic categories from an early point in
development, we suggest that the data are better accounted for by the proposal
that children begin with lexically specific phrases and gradually build up a
repertoire of increasingly abstract constructions.
Converging evidence: Bringing together experimental and corpus data on the association of verbs and constructions
Authors: Gries Stefan Th. , Hampe Beate , Schönefeld Doris 
Published: April 2006

Abstract
Much recent work in Cognitive Linguistics and neighbouring disciplines has
adopted a so-called usage-based perspective in which generalizations are based
on the analysis of authentic usage data provided by computerized corpora.
However, the analysis of such data does not always utilize methodological
findings from other disciplines to avoid analytical pitfalls and, at the same
time, generate robust results. A case in point is the strategy of using corpus
frequencies. In this paper, we take up a recently much debated issue from
construction grammar concerning the association between verbs and
argument-structure constructions, and investigate a construction, the English
as-predicative, in order
to test the predictive power of different kinds of frequency data against that
of a recent, more refined corpus-based approach, the so-called collexeme
analysis. To that end, the results of the application of these corpus-based
approaches to an analysis of the as

predicative are compared
with the results of a sentence-completion experiment. Concerning the topic under
consideration, collexeme analysis is not only shown to be superior on a variety
of theoretical and methodological grounds, it also significantly outperforms
frequency as a predictor of subjects’ production preferences. We conclude by
pointing out some implications for usage-based approaches.
Analyzing scripts in humorous communication
Authors: Brock Alexander 
Published: April 2006

AbstractThe article looks at the assumption of SSTH/GTVH that two fully or partly overlapping semantic scripts in opposition are central to humorous communication. On empirical and technical grounds, it is suggested that the script analysis should be complemented by identifying additional script constellations, i.e. manipulation within one script, the interplay of more than two scripts, and the collision of scripts from different planes of analysis. These suggestions support the idea of multiple incongruities (Attardo et al. 2002: 28), and the category of staggered escalation is put forward for incongruity clusters in addition to Attardo's (2001) strands and stacks.