bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gzf3p, a fourth GATA factor involved in nitrogen‐regulated transcription in Saccharomyces cerevisiae
Authors: Soussi‐Boudekou Saïd , Vissers Stephan , Urrestarazu Antonio , Jauniaux Jean‐Claude , André Bruno 
Published: November 2003

SummaryIn Saccharomyces cerevisiae, two positive transcription factors of the GATA family, Gln3p and NiMp/ Gatlp, upregulate the expression of multiple nitrogen pathway genes via upstream 5‐GATA‐3′ sequences. Another GATA factor, Uga43p/Da180p, downregulates to varying degrees the expression of some nitrogen‐regulated genes. Here, we report the functional analysis of a fourth GATA factor, Gzf 3p/Ni12p, whose gene was discovered by systematic sequencing of chromosome X. The Gzf3 protein most closely resembles Uga43p. Similar to Uga43p, Gzf3p has the properties of a negative GATA factor. While Uga43p is active specifically under nitrogen‐derepression conditions, Gzf 3p exerts its negative regulatory function specifically on preferred nitrogen sources: it is involved in nitrogen repression of NiMp‐dependent transcription. At least one positive GATA factor is required for the UGA43 and GZF3 genes to be expressed. The Uga43p factor negatively regulates GZF3 expression and vice versa. In addition, both Uga43p and Gzf3p moderately regulate expression of their own genes. These two proteins seem to be parts of a complex network of GATA factors which probably play a determining role in nitrogen‐regulated transcription.
Temperature‐regulated mRNA accumulation and stabilization for fatty acid desaturase genes in the cyanobacterium Synechococcus sp. strain PCC 7002
Authors: Sakamoto Toshio , Bryant Donald A. 
Published: November 2003

SummaryCyanobacteria acclimate to low‐temperature conditions by desaturating their membrane lipids. The desB (ω3 desaturase) and desC (A9 desaturase) genes of Synechococcus sp. strain PCC 7002 were cloned and characterized, and the expression of the desA (Δ12 desaturase), desB and desC genes was studied as a function of temperature. The steady‐state mRNA abundance for the desA gene was threefold higher in cells grown at 22 C than in cells grown at 38°C. des B transcripts were not detected at 38°C, but were abundant in cells grown at 22°C. Levels of desC mRNA were similar at both growth temperatures. The mRNA levels of each desaturase gene increased within 15min of a temperature shift‐down to 22°C, and mRNA levels recovered within 15min after a shift‐up to 38°C. The cold‐induced accumulation of transcripts from the desA and desB genes was suppressed by the addition of chloramphenicol, but the transient elevation of the desC transcript levels at 22°C was not affected by chloramphenicol. The half‐lives of the desA and desB mRNAs were significantly longer in cells grown at 22°C than in cells grown at 38°C, but the desC mRNA had a similar half‐life at both temperatures. These studies reveal three patterns of temperature regulation for the desaturase genes, whose expression is tightly controlled by a combination of mRNA synthesis and stabilization. These studies demonstrate that elevation of desaturase mRNA levels is not the rate‐limiting event during the low‐temperature acclimation of cyanobacteria.
Cell‐type specificity of the Anabaena fdxN‐element rearrangement requires xisH and xisl
Authors: Ramaswamy K. S. , Carrasco Claudio D. , Fatma Tasneem , Golden James W. 
Published: November 2003

Summary The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in Anabaena sp. strain PCC 7120. Previous work showed that rearrangement of the fdxN element requires the xisF gene, which encodes a site‐specific recombinase, and suggested that at least one other heterocyst‐specific factor is involved. Here we report that the xisH and xisl genes are necessary for the heterocyst‐specific excision of the fdxN element. Deletion of a 3.2 kb region downstream of the xisF gene blocked the fdxN‐element rearrangement in hetero‐cysts. The 3.2 kb deletion was complemented by the two overlapping genes xisH and xisl. Interestingly, extra copies of xlsHI on a replicating plasmid resulted in the xisF‐dependent excision of the fdxN element in vegetative cells. Therefore, xisHI are involved in the control of cell‐type specificity of the fdxN rearrangement. The xisHI genes had no effect on the two other DNA rearrangements. The xisHl‐induced excision of the fdxN element produced strains lacking the element and demonstrates that the 55 kb element contains no essential genes. xisH and xisl do not show similarity to any known genes.
Autoregulation of the Escherichia coli replication initiator protein, DnaA, is indirect
Authors: Smith R. W. P. , McAteer Sean , Masters Millicent 
Published: November 2003

SummaryThe expression of dnaA is autoregulated, in that transcription of the gene increases when DnaA is inactivated (and initiation of replication prevented) and decreases when DnaA is supplied in excess. However, the inactivation of DnaA does not necessarily lead to increased DnaA production, as dnaA(7s; temperature sensitive) strains which are integratively suppressed by derivatives of the plasmid R1 do not show temperature‐induced derepression. Several possible explanations for this unanticipated behaviour were considered and ruled out. We suggest here that the completion of a critical step in initiation may prevent dnaA derepression: although DnaA would be required to complete this step at oriC, DnaA(Ts) would be sufficient at the R1 origin. Autoregulation of dnaA has been attributed to the binding of DnaA at a consensus binding site in the dnaA promoter region. We show here, using reporter systems, that this DnaA‐binding site is not required for the autoregu‐latory response. We find, further, that replacement of the chromosomal dnaA gene with one containing a mutated binding site causes no demonstrable pheno‐typic change: cells with the mutant gene show no disadvantage in competition with dnaA+ cells.
Gastric emptying patterns of a liquid meal in newborn infants measured by epigastric impedance
Authors: Lange A. , Funch‐Jensen P. , Thommesen P. , Schiøtz P. O. 
Published: November 2003

Epigastric impedance was used to measure the gastric emptying patterns of a liquid non‐caloric meal (5 mL water kg−1) in 30 healthy newborn infants. Twenty‐six mature infants were examined in the first eight days of life, and four preterm infants were examined within 6 weeks after birth. The recordings consisted of two components: the emptying signal (the DC component), and a phasic 3 cycles per minutes (CPM) signal (the AC component). In some of the infants the phasic 3 CPM signal was also seen during the fasting state. For mature infants the median half emptying time (T50) was 6.9 min. For a second meal given within one hour after the first meal the half emptying time was 5.5 min (P < 0.01). In preterm infants the emptying times were not significantly different from mature infants. Day‐to‐day variation was low with a coefficient of variation of 17% in nine infants. A periodic change of the impedance signal, the phasic 3 CPM signal, was observed after a meal in 24 of the infants. The median frequency was 3.0 CPM in 20 mature and 2.9 CPM in four preterm infants. In nine infants a phasic 3 CPM signal was also observed during the fasting state, with a median frequency of 2.9 CPM. Measurement of gastric emptying pattern with epigastric impedance is a simple investigation for the evaluation of gastric emptying time and phasic activity in mature and preterm infants. However, the method is sensitive to spontaneous movements of the children, resulting in non‐valid measurements in around one fourth of the infants.
Use of echo planar imaging to demonstrate the effect of posture on the intragastric distribution and emptying of an oil/water meal
Authors: Boulby P. , Gowland P. , Adams V. , Spiller R. C. 
Published: November 2003

Intragastric distribution of solids and liquids is far from uniform but until recently technical limitations have prevented detailed study. Echo planar imaging (EPI), which can provide high‐quality images of intragastric contents, has been used in this study to assess the intragastric distribution of oil and water and gastric emptying in subjects lying on either their left or right side. Eight healthy volunteers underwent four gastric emptying studies after consuming either an aqueous meal (400 mL beef consomme soup + 100 mL water) or a fat/aqueous meal (400 mL soup + 100 mL olive oil) lying on either their left or right side. Using a water suppressed imaging mode the lipid phase was clearly seen layering above the aqueous phase with little evidence of mixing. Gastric emptying of the aqueous meal (A) was not significantly different when lying on the left compared to the right side. However, gastric emptying of the aqueous phase of the fat/aqueous meal (B) was considerably slower when lying on the left compared to the right side, gastric volumes actually increasing over the 90 min of the study P ≤ 0.05. When lying on the right side the aqueous phase of meal B emptied significantly slower than meal A. Oil was clearly observed to layer above the water and fill the duodenal cap when subjects lay on their left and the fundus when they lay on their right side. EPI clearly demonstrates the intragastric layering of oil which causes posture to strongly influence gastric emptying. EPI is a tool with great potential to describe the intragastric events following ingestion of complex multiphase meals.
Stress‐induced visceral hypersensitivity to rectal distension in rats: role of CRF and mast cells
Authors: GUÉ M. , DEL RIO‐LACHEZE C. , EUTAMENE H. , THÉODOROU V. , FIORAMONTI J. , BUÉNO L. 
Published: November 2003

Background: psychological factors have long been implicated in the aetiology of irritable bowel syndrome often associated with abdominal pain. This work was designed to study, in rats, the influence of partial restraint stress on the abdominal cramps induced by rectal distension and to determine the role of corticotropin releasing factor (CRF) and mast cells degranulation in this response. Methods: abdominal contractions were electromyographically recorded. Thirty minutes after stress or intracerebroventricular CRF, rectal distension was performed by inflation of a balloon (0.4–1.2 mL). α‐helical CRF9–41 or doxantrazole were administered centrally (15 min) and intraperitoneally (30 min), respectively, before stress. Histamine release and the number of mast cells were determined in colonic pieces from stressed and control rats. Results: stress and CRF enhanced the number of abdominal cramps evoked by rectal distension without affecting rectal compliance. α‐helical CRF9–41 and doxantrazole antagonized the stress and CRF‐induced enhancement of abdominal cramps. Stress increased the colonic histamine content whereas the number of colonic mast cells was unchanged. Conclusions: stress enhances abdominal contractions in response to rectal distension in rats via pathways involving central CRF and intestinal mast cells.
Phytochrome degradation
Authors: CLOUGH R. C. , VIERSTRA R. D. 
Published: November 2003

ABSTRACTPlants actively modulate the levels of the various phyto‐chrome isoforms during their life cycle to optimize light absorption and perception. For phytochrome A (phyA), one of the most influential methods of control is selective turnover of the photoreceptor upon photoconversion from the red‐absorbing form (Pr) to the far‐red‐absorbing form (Pfr). Whereas the Pr form has a half‐life of approximately 1 week, the Pfr form is rapidly degraded with a half‐life of 1–2 h. The ubiquitin/26S proteasome pathway has been implicated in phyA breakdown. In this proteolytic pathway, multiple ubiquitins are covalently attached to proteins committed for degradation; these ubiquitin‐protein conjugates then serve as intermediates in the breakdown of the target protein by the 26S proteasome, a multi‐subunit proteolytic complex. In several plant species, ubiquitin‐phyA conjugates have been detected in vivo following Pfr formation that show accumulation and decay kinetics expected for Pfr degradation intermediates. Analyses of phyA mutants and phyA/phyB chimeras expressed in transgenic plants have been particularly useful in mapping domains within the chromoprotein that are necessary for Pfr degradation. Several domains have been identified within both the N‐ and C‐terminal portions of the photoreceptor that presumably serve as recognition and/or acceptor sites for ubiquitination
An emerging molecular map of the phytochromes
Authors: QUAIL P. H. 
Published: November 2003

ABSTRACTMolecular mapping studies and sequence comparisons are providing provocative new insights into regions of the phytochrome polypeptide important to the functional activities of the photoreceptor. The NH2‐terminal structural domain contains the determinants for photoperception, and for the differences in photosensory specificity and photolability between phyA and phyB. However, a contiguous COOH‐terminal domain is also required for the transfer of perceived informational signals downstream to transduction pathway components and for PfrA‐specific degradation to proceed. The COOH‐terminal domains of phyA and phyB are functionally interchangeable in these processes and a core sequence at the proximal end of this domain contains determinants necessary for signal transfer from both phyA and phyB, suggesting a common biochemical mechanism of signal transfer for the two photoreceptors. Striking sequence similarity between the NH2‐terminal domain of aSynechocystisprotein, ORF SLR0473, and the phytochromes indicates that the cyanobacteria contain phytochrome‐related photoreceptors. The COOH‐terminal domains of ORF SLR0473 and the phytochromes are also related to one another and both show sequence similarities to the sensor histidine kinases. These data raise the possibility that the cyanobacteria have a functional photoregulated histidine kinase signalling system and that the plant phytochromes represent remnants of that system.
Photoreceptors and signals in the photoperiodic control of development
Authors: JACKSON S. , THOMAS B. 
Published: November 2003

ABSTRACTMany plant species are sensitive to changes in the seasons, especially with regard to their reproductive behaviour. Sexual or vegetative reproductive structures are often only formed at times of the year when days are sufficiently long, or short. Plants perceive daylength in the leaves, but reproductive changes occur in shoot apices in response to the movement of signals throughout the plant. There is good evidence that phytochrome A is an essential component of the daylength‐sensing mechanism in long‐day plants, and preliminary evidence suggests a potential interaction between phytochrome C and daylength sensitivity in short‐day plants. The sensitivity of reproductive processes to photoperiodic control is directly altered by photoreceptor action, particularly in the case of phytochrome B, which has a major influence on whether flowering or tuberization occurs under non‐inductive conditions in both long‐ and short‐day plants, but is not involved in daylength measurement. The signals which move from leaves to the sites of reproductive development are not known, but there is good evidence that gibberellins may be important and some preliminary indication that brassinosteroids might also be involved in photoperiodic signalling.
The function of phytochrome A
Authors: CASAL J. J. , SANCHEZ R. A. , YANOVSKY M. J. 
Published: November 2003

ABSTRACTKnowledge of the photoperceptive function of phytochrome A has improved substantially thanks to the availability of mutants lacking phytochrome A and transgenic plants transformed with the PHYA gene in sense or anti‐sense orientation. In imbibed seeds, phytochrome A mediates very‐low‐fluence responses. In etiolated seedlings, phytochrome A mediates very‐low‐fluence responses, high‐irradiance responses under continuous far‐red light, responsivity amplification to phytochrome B and red‐light enhancement of the phototropic response to blue light. In light‐grown seedings, phytochrome A modulates the extent of response to reductions in red/far‐red ratio perceived by phytochrome B, perceives daylength extensions and night interruptions affecting flowering, and perceives light treatments resetting endogenous rhythms. Under natural radiation these abilities are manifested during seed germination and seedling de‐etiolation under dense canopies or extremely low light fluences, and during early neighbour detection, but other processes await experimental evaluation. Phytochrome A affects growth and development throughout the whole life cycle of angiosperms.
Cryptogam phytochromes
Authors: WADA M. , KANEGAE T. , NOZUE K. , FUKUDA S. 
Published: November 2003

ABSTRACTPhytochrome responses in cryptogams are well characterized. However, the properties of cryptogam phytochromes are not well understood, because of the difficulty in obtaining suitable material. Recent advances in molecular biology offer the possibility of studying cryptogam phytochromes at the molecular level. The functional domains in cryptogam phytochromes have been predicted from the homology of the deduced amino acid sequences to known sequences of different functional proteins. Cryptogam phytochrome gene families are highly variable in size and composition. The most structurally unusual cryptogam phytochrome, found in the moss Ceratodon and the fern Adiantum, has a protein kinase catalytic domain in the C‐terminal half, although the N‐terminal half is homologous to conventional phytochromes. In conventional phytochrome, modules homologous to the bacterial two‐component (transmitter) protein kinase have also been found in the C‐terminal ends. While phytochromes lack membrane‐spanning sequences, some types may have microtubule attachment sequences. The relationship of these to dichroic phytochrome is discussed. Phytochrome mRNA and proteins are also discussed, as well as the use of mutants in elucidating signal transduction pathways.
Transpiration does not control growth and nutrient supply in the amphibious plant Mentha aquatica
Authors: PEDERSEN O. , SAND‐JENSEN K. 
Published: November 2003

ABSTRACT Mentha aquatica L. was grown at different nutrient availabilities in water and in air at 60% RH. The plants were kept at 600 mmol m−3 free CO2 dissolved in water (40 times air equilibrium) and at 30 mmol m−3 CO2 in air to ensure CO2 saturation of growth in both environments. We quantified the transpiration‐independent water transport from root to shoot in submerged plants relative to the transpiration stream in emergent plants and tested the importance of transpiration in sustaining nutrient flux and shoot growth. The acropetal water flow was substantial in submerged Mentha aquatica, reaching 14% of the transpiration stream in emergent plants. The transpiration‐independent mass flow of water from the roots, measured by means of tritiated water, was diverted to leaves and adventitious shoots in active growth. The plants grew well and at the same rates in water and air, but nutrient fluxes to the shoot were greater in plants grown in air than in those that were submerged when they were rooted in fertile sediments. Restricted O2 supply to the roots of submerged plants may account for the smaller nutrient concentrations, though these exceeded the levels required to saturate growth. In hydroponics, the root medium was aerated and circulated between submerged and emergent plants to minimize differences in medium chemistry, and here the two growth forms behaved similarly and could fully exploit nutrient enrichment. It is concluded that the lack of transpiration from leaf surfaces in a vapour‐saturated atmosphere, or under water, is not likely to constrain the transfer of nutrients from root to shoot in herbaceous plants. Nutrient deficiency under these environmental conditions is more likely to derive from restricted development and function of the roots in waterlogged anoxic soils or from low porewater concentrations of nutrients.
Floral transition mutants in Arabidopsis
Authors: KOORNNEEF M. , PEETERS A. J. M. 
Published: November 2003

ABSTRACTAn inventory of genetic differences in flowering time in Arabidopsis is presented and discussed. Many genes influence the transition to flowering in a quantitative way. Two groups of mutants and natural variants can be distinguished: those that are responsive to environmental factors and those that are less responsive or unresponsive. It is possible that all late/early‐flowering mutants isolated to date carry a mutation with an effect, either promotive or repressive, on a floral repressor. The interaction between light perception and flowering has been studied by analysis of phytochrome‐ and cryptochrome‐deficient mutants, which showed that phyA and probably also cryptochrome have a promotive role in flowering, whereas phyB and other stable phytochromes have an inhibitory role. A circadian rhythm is important in establishing daylength sensitivity, as was shown by the phenotype of the elf 3 mutants.
Phytochrome A, phytochrome B and other phytochrome(s) regulate ATHB‐2 gene expression in etiolated and green Arabidopsis plants
Authors: STEINDLER C. , CARABELLI M. , BORELLO U. , MORELLI G. , RUBERTI I. 
Published: November 2003

ABSTRACTThe expression of the Arabidopsis ATHB‐2 gene is light‐regulated both in seedlings and in adult plants. The gene is expressed at high levels in rapidly elongating etiolated seedlings and is down‐regulated by a pulse of red light (R) through the action of a phytochrome other than phytochrome A or B, or by a pulse of far‐red light (FR) through the action of phytochrome A. In green plants, the expression of the ATHB‐2 gene is rapidly and strongly enhanced by lowering the R:FR ratio perceived by a phytochrome other than A or B. Returning the plant to a high R:FR ratio results in an equally rapid decrease of the ATHB‐2 mRNA. Consistently, plants overproducing ATHB‐2 show developmental phenotypes characteristic of plants grown in low R:FR: elongated petioles, reduced leaf area, early flowering, and reduced number of rosette leaves. Taken together, the data strongly suggest a direct involvement of ATHB‐2 in light‐regulated growth phenomena throughout Arabidopsis development.
A spatially explicit model of patchy stomatal responses to humidity
Authors: HAEFNER J. W. , BUCKLEY T. N. , MOTT K. A. 
Published: November 2003

ABSTRACTStomata of leaves can exhibit either temporally stable, spatially homogeneous behaviour or complex spatial and temporal dynamics, depending on environmental and physiological conditions. To test the ability of accepted physiological mechanisms to describe these patterns, we developed a simple, spatially explicit model of stomatal responses to humidity that incorporated hydraulic interactions among stomata. Model results showed qualitative agreement with experimental evidence for a number of phenomena: (1) at high humidities, whole‐leaf steady‐state conductance is a monotonic function of humidity; (2) the initial stomatal response following a perturbation in humidity is in the direction opposite to the final response, and (3) spatial dynamics include patch formation and self‐organization similar to that observed in actual leaves. These comparisons do not eliminate other explanations, but do suggest that novel mechanisms need not be invoked to explain the diversity of spatial and temporal patterns of stomatal behaviour in leaves.