bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a Genesis Potential Index to Diagnose ENSO Effects on Tropical Cyclone Genesis
Authors: Camargo Suzana J. , Emanuel Kerry A. , Sobel Adam H. 
Published: October 2007

AbstractENSO (El Niño–Southern Oscillation) has a large influence on tropical cyclone activity. The authors examine how different environmental factors contribute to this influence, using a genesis potential index developed by Emanuel and Nolan. Four factors contribute to the genesis potential index: low-level vorticity (850 hPa), relative humidity at 600 hPa, the magnitude of vertical wind shear from 850 to 200 hPa, and potential intensity (PI). Using monthly NCEP Reanalysis data in the period of 1950–2005, the genesis potential index is calculated on a latitude strip from 60°S to 60°N. Composite anomalies of the genesis potential index are produced for El Niño and La Niña years separately. These composites qualitatively replicate the observed interannual variations of the observed frequency and location of genesis in several different basins. This justifies producing composites of modified indices in which only one of the contributing factors varies, with the others set to climatology, to determine which among the factors are most important in causing interannual variations in genesis frequency. Specific factors that have more influence than others in different regions can be identified. For example, in El Niño years, relative humidity and vertical shear are important for the reduction in genesis seen in the Atlantic basin, and relative humidity and vorticity are important for the eastward shift in the mean genesis location in the western North Pacific.
Influence of El Niño on the Upper-Ocean Circulation in the Tropical Atlantic Ocean
Authors: Lohmann Katja , Latif Mojib 
Published: October 2007

Abstract
This study investigates the influence of El Niño on the upper-ocean circulation in the tropical Atlantic Ocean (via changes in the Atlantic trade winds) by analyzing observed sea surface temperature (SST) together with an ocean general circulation model integration forced by the NCEP–NCAR reanalysis. During periods with anomalously warm (cold) eastern equatorial Pacific SST, the southern Atlantic tropical cell is strengthened (weakened). The difference of the cell strength between El Niño and La Niña years is about 20% of the mean cell strength. However, the variability of the cell is not dominated by the remote forcing from the eastern equatorial Pacific but seems to be caused by intrinsic tropical Atlantic variability. A strengthening (weakening) for periods with anomalously warm (cold) eastern equatorial Pacific SST is also found for the zonal surface and subsurface currents. TOPEX/Poseidon altimetry data are used to validate the results based on the OGCM integration.
Tropical Air–Sea Interactions Accelerate the Recovery of the Atlantic Meridional Overturning Circulation after a Major Shutdown
Authors: Krebs Uta , Timmermann A. 
Published: October 2007

Abstract
Using a coupled ocean–sea ice–atmosphere model of intermediate complexity, the authors study the influence of air–sea interactions on the stability of the Atlantic Meridional Overturning Circulation (AMOC). Mimicking glacial Heinrich events, a complete shutdown of the AMOC is triggered by the delivery of anomalous freshwater forcing to the northern North Atlantic. Analysis of fully and partially coupled freshwater perturbation experiments under glacial conditions shows that associated changes of the heat transport in the North Atlantic lead to a cooling north of the thermal equator and an associated strengthening of the northeasterly trade winds. Because of advection of cold air and an intensification of the trade winds, the intertropical convergence zone (ITCZ) is shifted southward. Changes of the accumulated precipitation lead to the generation of a positive salinity anomaly in the northern tropical Atlantic and a negative anomaly in the southern tropical Atlantic. During the shutdown phase of the AMOC, cross-equatorial oceanic surface flow is halted, preventing dilution of the positive salinity anomaly in the North Atlantic. Advected northward by the wind-driven ocean circulation, the positive salinity anomaly increases the upper-ocean density in the deep-water formation regions, thereby accelerating the recovery of the AMOC considerably. Partially coupled experiments that neglect tropical air–sea coupling reveal that the recovery time of the AMOC is almost twice as long as in the fully coupled case.
The impact of a shutdown of the AMOC on the Indian and Pacific Oceans can be decomposed into atmospheric and oceanic contributions. Temperature anomalies in the Northern Hemisphere are largely controlled by atmospheric circulation anomalies, whereas those in the Southern Hemisphere are strongly determined by ocean dynamical changes and exhibit a time lag of several decades. An intensification of the Pacific meridional overturning cell in the northern North Pacific during the AMOC shutdown can be explained in terms of wind-driven ocean circulation changes acting in concert with global ocean adjustment processes.
Mineralogy, chemistry and physical properties of bentonites from Başören, Kütahya, W Anatolia, Turkey
Authors: Yildiz A. , Kuşcu M. 
Published: October 2007

AbstractThe bentonite deposits in Başören Kütahya, W Anatolia, Turkey were formed by alteration of Pliocene perlite and pyroclastic rocks. Two types of bentonites are distinguished in this area on the basis of their physical properties, chemistry and occurrence. Bentonites were examined to determine their mineralogical, chemical and physical properties. Analytical methods include X-ray diffraction (XRD), scanning electron microscopy (SEM), chemical analysis and measurement of cation exchange capacity (CEC), swelling volume, water adsorption, bleaching capacity, and firing shrinkage. Bentonites consist mainly of dioctahedral smectite. They also contain zeolite, opal-CT, cristobalite, quartz, feldspar, dolomite and calcite. The ‘Type 2’ bentonites had greater CEC, swelling volume, water adsorption and bleaching capacity than ‘Type 1’. The variation in the physical properties of the two bentonites is attributed to the differences in the non-clay mineralogy and to the chemical composition and nature of interlayer cation.
Identification of genes differentially expressed during prenatal development of skeletal muscle in two pig breeds differing in muscularity
Authors: Muráni Eduard , Murániová Mária , Ponsuksili Siriluck , Schellander Karl , Wimmers Klaus 
Published: October 2007

Abstract

Background
Postnatal muscle growth is largely depending on the number and size of muscle fibers. The number of myofibers and to a large extent their metabolic and contractile properties, which also influence their size, are determined prenatally during the process of myogenesis. Hence identification of genes and their networks governing prenatal development of skeletal muscles will provide insight into the control of muscle growth and facilitate finding the source of its variation. So far most of the genes involved in myogenesis were identified by in vitro studies using gene targeting and transgenesis. Profiling of transcriptome changes during the myogenesis in vivo promises to obtain a more complete picture. In order to address this, we performed transcriptome profiling of prenatal skeletal muscle using differential display RT-PCR as on open system with the potential to detect novel transcripts. Seven key stages of myogenesis (days 14, 21, 35, 49, 63, 77 and 91 post conception) were studied in two breeds, Pietrain and Duroc, differing markedly in muscularity and muscle structure.

Results
Eighty prominent cDNA fragments were sequenced, 43 showing stage-associated and 37 showing breed-associated differences in the expression, respectively. Out of the resulting 85 unique expressed sequence tags, EST, 52 could be assigned to known genes. The most frequent functional categories represented genes encoding myofibrillar proteins (8), genes involved in cell adhesion, cell-cell signaling and extracellular matrix synthesis/remodeling (8), genes regulating gene expression (8), and metabolism genes (8). Some of the EST that showed no identity to any known transcripts in the databases are located in introns of known genes and most likely represent novel exons (e.g. HMGA2). Expression of thirteen transcripts along with five reference genes was further analyzed by means of real-time quantitative PCR. Nine of the target transcripts showed higher than twofold differences in the expression between the two breeds (GATA3, HMGA2, NRAP, SMC6L1, SPP1, RAB6IP2, TJP1 and two EST).

Conclusion
The present study revealed several genes and novel transcripts not previously associated with myogenesis and expands our knowledge of genetic factors operating during myogenesis. Genes that exhibited differences between the divergent breeds represent candidate genes for muscle growth and structure.
Ptf1a triggers GABAergic neuronal cell fates in the retina
Authors: Dullin Jean-Philippe , Locker Morgane , Robach Mélodie , Henningfeld Kristine A , Parain Karine , Afelik Solomon , Pieler Tomas , Perron Muriel 
Published: October 2007

AbstractBackgroundIn recent years, considerable knowledge has been gained on the molecular mechanisms underlying retinal cell fate specification. However, hitherto studies focused primarily on the six major retinal cell classes (five types of neurons of one type of glial cell), and paid little attention to the specification of different neuronal subtypes within the same cell class. In particular, the molecular machinery governing the specification of the two most abundant neurotransmitter phenotypes in the retina, GABAergic and glutamatergic, is largely unknown. In the spinal cord and cerebellum, the transcription factor Ptf1a is essential for GABAergic neuron production. In the mouse retina, Ptf1a has been shown to be involved in horizontal and most amacrine neurons differentiation.ResultsIn this study, we examined the distribution of neurotransmitter subtypes followingPtf1again and loss of function in the Xenopus retina. We found cell-autonomous dramatic switches between GABAergic and glutamatergic neuron production, concomitant with profound defects in the genesis of amacrine and horizontal cells, which are mainly GABAergic. Therefore, we investigated whether Ptf1a promotes the fate of these two cell types or acts directly as a GABAergic subtype determination factor. In ectodermal explant assays, Ptf1a was found to be a potent inducer of the GABAergic subtype. Moreover, clonal analysis in the retina revealed thatPtf1aoverexpression leads to an increased ratio of GABAergic subtypes among the whole amacrine and horizontal cell population, highlighting its instructive capacity to promote this specific subtype of inhibitory neurons. Finally, we also found that within bipolar cells, which are typically glutamatergic interneurons, Ptf1a is able to trigger a GABAergic fate.ConclusionAltogether, our results reveal for the first time in the retina a major player in the GABAergicversusglutamatergic cell specification genetic pathway.
Recurrent adenylation domain replacement in the microcystin synthetase gene cluster
Authors: Fewer David P , Rouhiainen Leo , Jokela Jouni , Wahlsten Matti , Laakso Kati , Wang Hao , Sivonen Kaarina 
Published: October 2007

Abstract

Background
Microcystins are small cyclic heptapeptide toxins produced by a range of distantly related cyanobacteria. Microcystins are synthesized on large NRPS-PKS enzyme complexes. Many structural variants of microcystins are produced simulatenously. A recombination event between the first module of mcyB (mcyB1) and mcyC in the microcystin synthetase gene cluster is linked to the simultaneous production of microcystin variants in strains of the genus Microcystis.

Results
Here we undertook a phylogenetic study to investigate the order and timing of recombination between the mcyB1 and mcyC genes in a diverse selection of microcystin producing cyanobacteria. Our results provide support for complex evolutionary processes taking place at the mcyB1 and mcyC adenylation domains which recognize and activate the amino acids found at X and Z positions. We find evidence for recent recombination between mcyB1 and mcyC in strains of the genera Anabaena, Microcystis, and Hapalosiphon. We also find clear evidence for independent adenylation domain conversion of mcyB1 by unrelated peptide synthetase modules in strains of the genera Nostoc and Microcystis. The recombination events replace only the adenylation domain in each case and the condensation domains of mcyB1 and mcyC are not transferred together with the adenylation domain. Our findings demonstrate that the mcyB1 and mcyC adenylation domains are recombination hotspots in the microcystin synthetase gene cluster.

Conclusion
Recombination is thought to be one of the main mechanisms driving the diversification of NRPSs. However, there is very little information on how recombination takes place in nature. This study demonstrates that functional peptide synthetases are created in nature through transfer of adenylation domains without the concomitant transfer of condensation domains.
The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement
Authors: Park Shin-Ju , Lee Yong-Seok , Hwang Ui Wook 
Published: October 2007

Abstract

Background
The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.

Results
The complete mitochondrial genome (15,474 bp) of a sea spider (Achelia bituberculata) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile) may be closely related to the clade of Acari and Araneae.

Conclusion
The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae) and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like), but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory – that the pycnogonids are a sister group of all other arthropods – should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.
RBM6-RBM5 transcription-induced chimeras are differentially expressed in tumours
Authors: Wang Ke , Ubriaco Gino , Sutherland Leslie C 
Published: October 2007

Abstract

Background
Transcription-induced chimerism, a mechanism involving the transcription and intergenic splicing of two consecutive genes, has recently been estimated to account for ~5% of the human transcriptome. Despite this prevalence, the regulation and function of these fused transcripts remains largely uncharacterised.

Results
We identified three novel transcription-induced chimeras resulting from the intergenic splicing of a single RNA transcript incorporating the two neighbouring 3p21.3 tumour suppressor locus genes, RBM6 and RBM5, which encode the RNA Binding Motif protein 6 and RNA Binding Motif protein 5, respectively. Each of the three novel chimeric transcripts lacked exons 3, 6, 20 and 21 of RBM6 and exon 1 of RBM5. Differences between the transcripts were associated with the presence or absence of exon 4, exon 5 and a 17 nucleotide (nt) sequence from intron 10 of RBM6. All three chimeric transcripts incorporated the canonical splice sites from both genes (excluding the 17 nt intron 10 insertion). Differential expression was observed in tumour tissue compared to non-tumour tissue, and amongst tumour types. In breast tumour tissue, chimeric expression was associated with elevated levels of RBM6 and RBM5 mRNA, and increased tumour size. No protein expression was detected by in vitro transcription/translation.

Conclusion
These results suggest that RBM6 mRNA experiences altered co-transcriptional gene regulation in certain cancers. The results also suggest that RBM6-RBM5 transcription-induced chimerism might be a process that is linked to the tumour-associated increased transcriptional activity of the RBM6 gene. It appears that none of the transcription-induced chimeras generates a protein product; however, the novel alternative splicing, which affects putative functional domains within exons 3, 6 and 11 of RBM6, does suggest that the generation of these chimeric transcripts has functional relevance. Finally, the association of chimeric expression with breast tumour size suggests that RBM6-RBM5 chimeric expression may be a potential tumour differentiation marker.
Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator
Authors: Houot Laetitia , Floutier Martin , Marteyn Benoit , Michaut Magali , Picciocchi Antoine , Legrain Pierre , Aude Jean-Christophe , Cassier-Chauvat Corinne , Chauvat Franck 
Published: October 2007

AbstractBackgroundCadmium is a persistent pollutant that threatens most biological organisms, including cyanobacteria that support a large part of the biosphere. Using a multifaceted approach, we have investigated the global responses to Cd and other relevant stresses (H2O2and Fe) in the model cyanobacteriumSynechocystisPCC6803.ResultsWe found that cells respond to the Cd stress in a two main temporal phases process. In the "early" phase cells mainly limit Cd entry through the negative and positive regulation of numerous genes operating in metal uptake and export, respectively. As time proceeds, the number of responsive genes increases. In this "massive" phase, Cd downregulates most genes operating in (i) photosynthesis (PS) that normally provides ATP and NADPH; (ii) assimilation of carbon, nitrogen and sulfur that requires ATP and NAD(P)H; and (iii) translation machinery, a major consumer of ATP and nutrients. Simultaneously, many genes are upregulated, such as those involved in Fe acquisition, stress tolerance, and protein degradation (crucial to nutrients recycling). The most striking common effect of Cd and H2O2is the disturbance of both light tolerance and Fe homeostasis, which appeared to be interdependent. Our results indicate that cells challenged with H2O2or Cd use different strategies for the same purpose of supplying Fe atoms to Fe-requiring metalloenzymes and the SUF machinery, which synthesizes or repairs Fe-S centers. Cd-stressed cells preferentially breakdown their Fe-rich PS machinery, whereas H2O2-challenged cells preferentially accelerate the intake of Fe atoms from the medium.ConclusionWe view the responses to Cd as an integrated "Yin Yang" reprogramming of the whole metabolism, we found to be controlled by the Slr1738 regulator. As the Yin process, the ATP- and nutrients-sparing downregulation of anabolism limits the poisoning incorporation of Cd into metalloenzymes. As the compensatory Yang process, the PS breakdown liberates nutrient assimilates for the synthesis of Cd-tolerance proteins, among which we found the Slr0946 arsenate reductase enzyme.
Production of L-carnitine by secondary metabolism of bacteria
Authors: Bernal Vicente , Sevilla Ángel , Cánovas Manuel , Iborra José L 
Published: October 2007

AbstractThe increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such asEscherichia coliandProteus sp., which can be used to produce L-carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. Furthermore, the profiles of key central metabolic activities such as the TCA cycle, the glyoxylate shunt and the acetate metabolism are seen to be closely interrelated and affect the biotransformation efficiency. Although genetically modified strains have been obtained, new strain improvement strategies are still needed, especially inEscherichia colias a model organism for molecular biology studies. This review aims to summarize and update the state of the art in L-carnitine production usingE. coliandProteus sp, emphasizing the importance of proper reactor design and operation strategies, together with metabolic engineering aspects and the need for feed-back betweenwetandin silicowork to optimize this biotransformation.