bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Mechanism of c‐jun Antisense Gene Transfection in Alleviating Injury of Cardiomyocytes Treated with Burn Serum and Hypoxia
Authors: Huang Yuesheng , Hu Angeng 
Published: October 2004

AbstractTo explore the molecular mechanism of c‐jun antisense gene transfection in alleviating injury of cardiomyocytes treated with burn serum and hypoxia, burn serum was collected from Wistar rats inflicted with 30% third‐degree burn of the total body surface area. The cardiomyocytes of neonatal Wistar rats were cultured and then treated with burn serum and hypoxia (a gas mixture containing 1% O2). The constructed c‐jun antisense gene recombinant was transfected into the cardiomyocytes of neonatal Wistar rats. TdT‐mediated d‐utp nick end labeling (TUNEL) was adopted to examine cardiomyocyte apoptosis. Morphological changes of cardiomyocytes were observed under an optic‐microscope and an electron‐microscope. Expression of troponin T and ß‐tubulin protein, c‐jun protein, protein kinase Ca (PKCa), and c‐jun N‐terminal kinase (JNK) were assayed with Western blot in the transfected and non‐transfected groups. The morphology of cardiomyocytes in the non‐transfected group changed explicitly, but the change was not so obvious in the transfected cardiomyocytes. The expression of ß‐tubulin and troponin increased significantly in the transfected group as compared with the non‐transfected group. In the non‐transfected group, numbers of apoptotic cardiomyocytes were significantly higher than in the transfected group. The c‐jun protein, PKCa, and JNK were significantly expressed in the non‐transfected group, and they reached a maximum at the 24th hour after cardiomyocytes were treated with burn serum and hypoxia. In the transfected group, however, expressions of c‐jun protein, PKCa, and JNK decreased significantly compared with the non‐transfected group. The c‐jun antisense gene recombinant transfection alleviates injury to cardiomyocytes treated with burn serum and hypoxia, probably through low expression of PKCa and JNK.
Medicine’s Greatest Gifts to Surgery
Authors: Perrier Nancy D. , Boger Michael S. 
Published: October 2004

AbstractDr. Robert Graves and Dr. Henry Plummer are immortalized by the thyroid diseases bearing their names. Dr. Graves’ clinical lectures and Dr. Plummer’s “goiter lunches” were considered medical masterpieces; they introduced novel concepts in physical diagnosis that helped surgeons determine when to operate on patients with thyrotoxicosis. Dr. Plummer’s observations with perioperative iodine administration helped lower the mortality associated with thyroidectomy—at that time a treacherous operation—to make it one of the safest operations in history. Their fascinating discoveries laid foundations for thyroid surgery today. They truly are among medicine’s greatest gifts to surgery.
Jan Mikulicz‐Radecki (1850–1905): Pioneer of Endoscopy and Surgery of the Sinuses, Throat, and Digestive Tract
Authors: Kuczkowski Jerzy , Stankiewicz Czeslaw , Kopacz Andrzej , Narozny Waldemar , Mikaszewski Boguslaw , Drucis Kamil 
Published: October 2004

AbstractThe authors described the medical achievements of Jan Antoni Mikulicz‐Radecki—–a famous surgeon and laryngologist of Polish origin, belonging to the Viennese surgical school of Prof. Theodor Billroth at the turn of the 20th century. His scientific and clinical activity in Vienna, Cracow, Königsberg, and Wroclaw resulted in 232 publications and several new surgical methods. He changed the opinion on scleroma and described benign lymphoepithelial lesions. He was one of the authors of modern aseptics, antisepsis in surgery, and is regarded as a pioneer of endoscopic procedures. He was interested mainly in thoracic surgery, surgery of the abdomen, orthopedics, and laryngology. Mikulicz was the first to describe the method of surgical treatment of the maxillary sinus, osteoplastic surgery of the nose, esophagoscopy, and lateral pharyngotomy in tonsil carcinoma. Prof. Mikulicz was the first to perform thoracic surgery; he performed the first pyloroplasty, the first partial esophagectomy and gave rise to antiseptic procedures and general surgical management. He described many modifications of surgical operations and he constructed the esophagoscope, scoliozymeter, and many other useful surgical devices.
Delayed gadolinium‐enhanced MRI of cartilage (dGEMRIC): intra‐ and interobserver variability in standardized drawing of regions of interest
Authors: Tiderius C. J. , Tjörnstrand J. , Åkeson P. , Södersten K. , Dahlberg L. , Leander P. 
Published: October 2004

Purpose: To establish the reproducibility of a standardized region of interest (ROI) drawing procedure in delayed gadolinium‐enhanced magnetic resonance imaging (MRI) of cartilage (dGEMRIC). Material and Methods: A large ROI in lateral and medial femoral weight‐bearing cartilage was drawn in images of 12 healthy male volunteers by 6 investigators with different skills in MRI. The procedure was done twice, with a 1‐week interval. Calculated T1‐values were evaluated for intra‐ and interobserver variability. Results: The mean interobserver variability for both compartments ranged between 1.3% and 2.3% for the 6 different investigators without correlation to their experience in MRI. Post‐contrast intra‐observer variability was low in both the lateral and the medial femoral cartilage, 2.6% and 1.5%, respectively. The larger variability in lateral than in medial cartilage was related to slightly longer and thinner ROIs. Conclusion: Intra‐observer variability and interobserver variability are both low when a large standardized ROI is used in dGEMRIC. The experience of the investigator does not affect the variability, which further supports a clinical applicability of the method.
Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
Authors: Zheng Xiangqun H. , Lu Fu , Wang Zhen-Yuan , Zhong Fei , Hoover Jeffrey , Mural Richard 
Published: October 2004

Abstract
Motivation: The identification of orthologous gene pairs is generally based on sequence similarity. Gene pairs that are mutually ‘best hits’ between the genomes being compared are asserted to be orthologs. Although this method identifies most orthologous gene pairs with high confidence, it will miss a fraction of them, especially genes in duplicated gene families. In addition, the approach depends heavily on the completeness and quality of gene annotation. When the gene sequences are not correctly represented the approach is unlikely to find the correct ortholog. To overcome these limitations, we have developed an approach to identify orthologous gene pairs using shared chromosomal synteny and the annotation of protein function.
Results: Assembled mouse and human genomes were used to identify the regions of conserved synteny between these genomes. ‘Syntenic anchors’ are conserved non-repetitive locations between mouse and human genomes. Using these anchors, we identified blocks of sequences that contain consistently ordered anchors between the two genomes (syntenic blocks). The synteny information has been used to help us identify orthologous gene pairs between mouse and human genomes. The approach combines the mutual selection of the best tBlastX hits between human and mouse transcripts, and inferring gene orthologous relationships based on sharing syntenic anchors, collocating in the same syntenic blocks and sharing the same annotated protein function. Using this approach, we were able to find 19 357 orthologous gene pairs between human and mouse genomes, a 20% increase in the number of orthologs identified by conventional approaches.
Contact: richard.mural@celera.com
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version
Authors: da Fontoura Costa Luciano 
Published: October 2004

AbstractMotivation: The necessity to characterize the spatial uniformity (or lack of it) of symbols in biological sequences, given its implications for identification of the properties of the structures associated with the sequences.Methods: A one-dimensional version of a recently introduced percolation-based approach is presented, which allows the accurate quantification of symbol distributions even in the presence of co-existing densities. An enhanced version of this methodology, which uses an agglomerative process to organize hierarchically the sequence into subsequences, is also proposed and illustrated.3. Results: The potential of the proposed methodology is illustrated with respect to synthetic and real data (1881 zebrafish and 1200 Xenopus proteins) and compared to two alternative multiscale methodologies, with encouraging results including the possibility to identify particularly remarkable amino acid arrangements in proteins.4. Contact: luciano@if.sc.usp.br
Repeated Evolution of the Pyrrolizidine Alkaloid–Mediated Defense System in Separate Angiosperm Lineages w⃞
Authors: Reimann Andreas , Nurhayati Niknik , Backenköhler Anita , Ober Dietrich 
Published: October 2004

AbstractSpecies of several unrelated families within the angiosperms are able to constitutively produce pyrrolizidine alkaloids as a defense against herbivores. In pyrrolizidine alkaloid (PA) biosynthesis, homospermidine synthase (HSS) catalyzes the first specific step. HSS was recruited during angiosperm evolution from deoxyhypusine synthase (DHS), an enzyme involved in the posttranslational activation of eukaryotic initiation factor 5A. Phylogenetic analysis of 23 cDNA sequences coding for HSS and DHS of various angiosperm species revealed at least four independent recruitments of HSS from DHS: one within the Boraginaceae, one within the monocots, and two within the Asteraceae family. Furthermore, sequence analyses indicated elevated substitution rates within HSS-coding sequences after each gene duplication, with an increased level of nonsynonymous mutations. However, the contradiction between the polyphyletic origin of the first enzyme in PA biosynthesis and the structural identity of the final biosynthetic PA products needs clarification.
Phytochrome Phosphorylation Modulates Light Signaling by Influencing the Protein–Protein Interaction[W]
Authors: Kim Jeong-Il , Shen Yu , Han Yun-Jeong , Park Joung-Eun , Kirchenbauer Daniel , Soh Moon-Soo , Nagy Ferenc , Schäfer Eberhard , Song Pill-Soon 
Published: October 2004

AbstractPlant photoreceptor phytochromes are phosphoproteins, but the question as to the functional role of phytochrome phosphorylation has remained to be elucidated. We investigated the functional role of phytochrome phosphorylation in plant light signaling using a Pfr-specific phosphorylation site mutant, Ser598Ala of oat (Avena sativa) phytochrome A (phyA). The transgenic Arabidopsis thaliana (phyA-201 background) plants with this mutant phyA showed hypersensitivity to light, suggesting that phytochrome phosphorylation at Serine-598 (Ser598) in the hinge region is involved in an inhibitory mechanism. The phosphorylation at Ser598 prevented its interaction with putative signal transducers, Nucleoside Diphosphate Kinase-2 and Phytochrome-Interacting Factor-3. These results suggest that phosphorylation in the hinge region of phytochromes serves as a signal-modulating site through the protein–protein interaction between phytochrome and its putative signal transducer proteins.
A Patch of Surface-Exposed Residues Mediates Negative Regulation of Immune Signaling by Tomato Pto Kinase[W]
Authors: Wu Ai-Jiuan , Andriotis Vasilios M.E. , Durrant Marcus C. , Rathjen John P. 
Published: October 2004

AbstractTomato (Lycopersicon esculentum) Pto kinase specifically recognizes the Pseudomonas effector proteins AvrPto and AvrPtoB, leading to induction of defense responses and hypersensitive cell death. Structural modeling of Pto combined with site-directed mutagenesis identified a patch of surface-exposed residues required for native regulation of signaling. Mutations in this area resulted in constitutive gain-of-function (CGF) forms of Pto that activated AvrPto-independent cell death via the cognate signaling pathway. The patch overlaps the peptide binding region of the kinase catalytic cleft and is part of a broader region required for interaction with bacterial effectors. We propose that the negative regulatory patch is normally occupied by a peptide that represses Pto signaling. Furthermore, we found that Pto kinase activity was required for Avr-dependent activation but dispensable for signaling by CGF forms of Pto. This suggests that Pto signals by a conformational change rather than phosphorylation of downstream substrates in the defense signaling pathway.
Stimulus-Dependent, Promoter-Specific Binding of Transcription Factor WRKY1 to Its Native Promoter and the Defense-Related GenePcPR1-1in Parsley[W]
Authors: Turck Franziska , Zhou Aifen , Somssich Imre E. 
Published: October 2004

AbstractWRKY transcription factors form a large family that plays a role in plant responses to biotic stress and during senescence. Defining in vivo relevant WRKY/promoter relationships has been hampered by the factors' indiscriminate binding to known W box DNA elements and their possible genetic redundance. Employing chromatin immunoprecipitations (ChIP) of cultured cells, we show that parsley (Petroselinum crispum) WRKY1 protein binds to the W boxes of its native promoter as well as to that of PcWRKY3 and the defense-related PR10-class marker gene Pathogenesis-Related1-1 (PcPR1-1). Although present at low concentrations in resting cells, WRKY1 does not appear to play a role in the immediate early gene response upon elicitation because it does not bind to the promoter at this time. Paradoxically, in vivo binding at the PcWRKY1 promoter correlates more with downregulation of gene expression, whereas previous overexpression studies suggested an activating function of WRKY1 on PcWRKY1 expression. By contrast, PcPR1-1 expression remains strong when its promoter is occupied in vivo by WRKY1. Unexpectedly, ChIP revealed that W boxes at promoter sites are constitutively occupied by other WRKY transcription factors, indicating that site recruitment does not seem to play a major role in their regulation. Rather, WRKY proteins very likely act in a network of mutually competing participants with temporal displacement occurring at defined preoccupied sites by other family members in a stimulus-dependent manner.
HANABA TARANU Is a GATA Transcription Factor That Regulates Shoot Apical Meristem and Flower Development in Arabidopsis[W]
Authors: Zhao Yuanxiang , Medrano Leonard , Ohashi Kazuaki , Fletcher Jennifer C. , Yu Hao , Sakai Hajime , Meyerowitz Elliot M. 
Published: October 2004

AbstractWe have isolated a new mutant, hanaba taranu (han), which affects both flower and shoot apical meristem (SAM) development in Arabidopsis thaliana. Mutants have fused sepals and reduced organ numbers in all four whorls, especially in the 2nd (petal) and 3rd (stamen) whorls. han meristems can become flatter or smaller than in the wild type. HAN encodes a GATA-3–like transcription factor with a single zinc finger domain. HAN is transcribed at the boundaries between the meristem and its newly initiated organ primordia and at the boundaries between different floral whorls. It is also expressed in vascular tissues, developing ovules and stamens, and in the embryo. han interacts strongly with clavata (clv) mutations (clv1, clv2, and clv3), resulting in highly fasciated SAMs, and we find that WUS expression is altered in han mutants from early embryogenesis. In addition, HAN is ectopically expressed both in clv1 and clv3 mutants. We propose that HAN is normally required for establishing organ boundaries in shoots and flowers and for controlling the number and position of WUS-expressing cells. Ectopic HAN expression causes growth retardation, aberrant cell division patterns, and loss of meristem activity, suggesting that HAN is involved in controlling cell proliferation and differentiation.
Spotted leaf11, a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activityw⃞
Authors: Zeng Li-Rong , Qu Shaohong , Bordeos Alicia , Yang Chengwei , Baraoidan Marietta , Yan Hongyan , Xie Qi , Nahm Baek Hie , Leung Hei , Wang Guo-Liang 
Published: October 2004

Abstract
The rice (Oryza sativa) spotted leaf11 (spl11) mutant was identified from an ethyl methanesulfonate–mutagenized indica cultivar IR68 population and was previously shown to display a spontaneous cell death phenotype and enhanced resistance to rice fungal and bacterial pathogens. Here, we have isolated Spl11 via a map-based cloning strategy. The isolation of the Spl11 gene was facilitated by the identification of three additional spl11 alleles from an IR64 mutant collection. The predicted SPL11 protein contains both a U-box domain and an armadillo (ARM) repeat domain, which were demonstrated in yeast and mammalian systems to be involved in ubiquitination and protein–protein interactions, respectively. Amino acid sequence comparison indicated that the similarity between SPL11 and other plant U-box-ARM proteins is mostly restricted to the U-box and ARM repeat regions. A single base substitution was detected in spl11, which results in a premature stop codon in the SPL11 protein. Expression analysis indicated that Spl11 is induced in both incompatible and compatible rice–blast interactions. In vitro ubiquitination assay indicated that the SPL11 protein possesses E3 ubiquitin ligase activity that is dependent on an intact U-box domain, suggesting a role of the ubiquitination system in the control of plant cell death and defense.
Biosynthesis of Very-Long-Chain Polyunsaturated Fatty Acids in Transgenic Oilseeds: Constraints on Their Accumulationw⃞
Authors: Abbadi Amine , Domergue Freéderic , Bauer Jörg , Napier Johnathan A. , Welti Ruth , Zähringer Ulrich , Cirpus Petra , Heinz Ernst 
Published: October 2004

Abstractω6- and ω3-polyunsaturated C20 fatty acids represent important components of the human diet. A more regular consumption and an accordingly sustainable source of these compounds are highly desirable. In contrast with the very high levels to which industrial fatty acids have to be enriched in plant oils for competitive use as chemical feedstocks, much lower percentages of very-long-chain polyunsaturated fatty acids (VLCPUFA) in edible plant oils would satisfy nutritional requirements. Seed-specific expression in transgenic tobacco (Nicotiana tabacum) and linseed (Linum usitatissimum) of cDNAs encoding fatty acyl-desaturases and elongases, absent from all agronomically important plants, resulted in the very high accumulation of Δ6-desaturated C18 fatty acids and up to 5% of C20 polyunsaturated fatty acids, including arachidonic and eicosapentaenoic acid. Detailed lipid analyses of developing seeds from transgenic plants were interpretated as indicating that, after desaturation on phosphatidylcholine, Δ6-desaturated products are immediately channeled to the triacylglycerols and effectively bypass the acyl-CoA pool. Thus, the lack of available Δ6-desaturated acyl-CoA substrates in the acyl-CoA pool limits the synthesis of elongated C20 fatty acids and disrupts the alternating sequence of lipid-linked desaturations and acyl-CoA dependent elongations. As well as the successful production of VLCPUFA in transgenic oilseeds and the identification of constraints on their accumulation, our results indicate alternative strategies to circumvent this bottleneck.
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8
Authors: Kukimoto‐Niino Mutsuko , Murayama Kazutaka , Kato‐Murayama Miyuki , Idaka Miki , Bessho Yoshitaka , Tatsuguchi Ayako , Ushikoshi‐Nakayama Ryoko , Terada Takaho , Kuramitsu Seiki , Shirouzu Mikako , Yokoyama Shigeyuki 
Published: October 2004

AbstractTT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of TT1887 and TT1465 at 1.8 Å and 2.2 Å resolutions, respectively, as determined by the multiwavelength anomalous dispersion (MAD) method. TT1887 is a homotetramer, while TT1465 is a homohexamer in the crystal and in solution. The structures of the TT1887 and TT1465 monomers contain single domains with the Rossmann fold, comprising six α helices and seven β strands, and are quite similar to each other. The major structural differences exist in the N terminus of TT1465, where there are two additional α helices. A comparison of the structures revealed the elements that are responsible for the different oligomerization modes. The distributions of the electrostatic potential on the solvent‐accessible surfaces suggested putative active sites.
Protein self‐association in crowded protein solutions: A time‐resolved fluorescence polarization study
Authors: Zorrilla Silvia , Rivas Germán , Acuña A. Ulises , Lillo M. Pilar 
Published: October 2004

AbstractThe self‐association equilibrium of a tracer protein, apomyoglobin (apoMb), in highly concentrated crowded solutions of ribonuclease A (RNase A) and human serum albumin (HSA), has been studied as a model system of protein interactions that occur in crowded macromolecular environments. The rotational diffusion of the tracer protein labeled with two different fluorescent dyes, 8‐anilinonaphthalene‐1‐sulfonate and fluorescein isothiocyanate, was successfully recorded as a function of the two crowder concentrations in the 50–200 mg/mL range, using picosecond‐resolved fluorescence anisotropy methods. It was found that apoMb molecules self‐associate at high RNase A concentration to yield a flexible dimer. The apparent dimerization constant, which increases with RNase A concentration, could also be estimated from the fractional contribution of monomeric and dimeric species to the total fluorescence anisotropy of the samples. In contrast, an equivalent mass concentration of HSA does not result in tracer dimerization. This different effect of RNase A and HSA is much larger than that predicted from simple models based only on the free volume available to apoMb, indicating that additional, nonspecific interactions between tracer and crowder should come into play. The time‐resolved fluorescence polarization methods described here are expected to be of general applicability to the detection and quantification of crowding effects in a variety of macromolecules of biological relevance.
Effect of sodium dodecyl sulfate on folding and thermal stability of acid‐denatured cytochrome c: A spectroscopic approach
Authors: Xu Qi , Keiderling Timothy A. 
Published: October 2004

AbstractThe molten globule (MG) state can be an intermediate in the protein folding pathway; thus, its detailed description can help understanding protein folding. Sodium dodecyl sulfate (SDS), an anionic surfactant that is commonly used to mimic hydrophobic binding environments such as cell membranes, is known to denature some native state proteins, including horse cytochrome c (cyt c). In this article, refolding of acid denatured cyt c is studied under the influence of SDS to form MG‐like states at both low concentration and above the critical micelle concentration using Fourier transform Infrared (FTIR) and ultraviolet and visible absorption as well as fluorescence and circular dichroism (CD). Thermal denaturation monitored with FTIR and CD shows distinct final high temperature states starting from MG‐like states formed with different SDS/protein ratios. The results suggest that the SDS/protein ratio as well as the actual SDS (or protein) concentration affects structure and its thermal stability. Thermal denaturation monitored with CD and FTIR for cyt c at neutral pH but denatured with SDS showed that at a high SDS/protein ratio, the thermal behavior of MG‐like states formed at low and neutral pH are quite similar. Based on the results obtained, the merits of two models of the protein–surfactant structure are discussed for different SDS concentrations.