bluuebunny/crossref_metadata_2025_split huggingface dataset:
How are nitrogen fixation rates regulated in legumes?
Authors: Schulze Joachim 
Published: March 2004

AbstractSymbiotic nitrogen fixation by the legume‐Rhizobium symbiosis is a finely regulated process that involves significant carbon and energy metabolism by the plant. At present, there are three competing theories as to how the regulation of the process is achieved at the whole plant level. Theory one (carbon supply regulation) states that nitrogen fixation rates are regulated by either current nodule assimilate supply or through metabolism of assimilates into compounds that can be used by the bacteroids. A second theory (oxygen supply regulation) assumes that oxygen diffusion into the nodules is tightly regulated and is the principal regulatory factor for nitrogen fixation rates. A third theory (N‐feedback regulation) suggests that a product of nitrogen fixation or assimilation exerts a feedback regulatory impact. The paper summarizes experimental data which support or reject the mentioned theories. Moreover, implications of nitrogen fixation under P stress and of phenomena connected with the argon or acetylene induced decline in nitrogenase activity for the understanding of nitrogen fixation regulation are discussed. It is concluded that we currently have no theory that explains all aspects and experimental results concerning the regulation of nitrogen fixation in legumes. With our growing ability to impact the process, e.g., by genetic engineering, this understanding of nitrogen fixation regulation has potential to be translated into agronomically sustainable benefits.
Effect of biosolid amendment on enzyme activities in earthworm (Lumbricus terrestris) casts
Authors: Kızılkaya Rıdvan , Heps̨en S̨üheda 
Published: March 2004

AbstractWe studied the effect of amendment of sewage sludge biosolids on enzyme activity in soil and earthworm (Lumbricus terrestris) casts. Enzyme activities and contents of nutrients and organic matter of surrounding soil were compared with the corresponding properties of earthworm casts. This short time experiment was conducted at 20 ± 0.5 °C in the laboratory, simulating field conditions of biosolid treatments. In general, all of doses of biosolid treatments influenced the enzyme activity and contents of nutrients and organic matter of earthworm casts and surrounding soil. Enzyme activity such as urease (UA), alkaline phosphatase (APA), and arylsulfatase (ASA) and the contents of organic matter and nutrients N and P in earthworm casts and surrounding soil increased with increasing biosolid application. Without biosolid additions, enzyme activities in cast of L. terrestris exceeded those in the soil. In contrast, when biosolid was added, DHA in casts was lower than the soil. Activities of UA and APA were consistently higher in L. terrestris casts than in soil of all biosolid treatments. Biosolid amendments generally increased ASA at low doses, but at higher doses, ASA decreased. In general, organic matter and contents of N and P were higher in surface casts of L. terrestris and soils than in the control soil. Activities of UA, APA, the contents of organic carbon and nutrients N and P in soil and casts showed positive correlations. On the contrary, ASA and DHA were negatively correlated with the contents of organic matter and nutrients.
Solution chemistry in acid forest soils: Are the BC : Al ratios as critical as expected in Switzerland?
Authors: Graf Pannatier Elisabeth , Walthert Lorenz , Blaser Peter 
Published: March 2004

AbstractThe molar ratio of base nutrient cations to total dissolved aluminum (BC : Altot) in the soil solution was measured at six forest sites in Switzerland in acid mineral soils to determine whether the ratio measured in the field was lower than the critical value of 1, as predicted by the mapping of exceedances of critical loads of acidity. The soil chemistry was then related to the soil solution composition to characterize the typical effective base saturation (BS) and BC : Al ratio in soil leading to critical BC : Altot in the soil solution. The median BC : Altot ratio in the soil solution never reached the critical value in the root zone at any sites for the whole observation period (1999–2002), suggesting that the BC : Altot ratios measured in the field might be higher than those modeled for the determination of critical loads of acidity. The gibbsite model usually applied for the calculation of critical loads was a poor predictor of the Al3+ activity at the study sites. A curvilinear pH‐pAl3+ relationship was found over the whole range of pH (3.8–6.5). Above a pH of 5.5, the slope of the pH‐pAl3+ relation was close to 3, suggesting equilibrium with Al(OH)3. It decreased to values smaller than 1.3 below a pH of 5.5, indicating complexation reactions with soil organic matter. The BS and the BC : Al ratios in the soils were significantly correlated to the BC : Altot ratios in the soil solution. The soil solutions with the lowest BC : Altot ratios (≤ 2) were typically found in mineral soils with a BS below 10 % and a BC : Al ratio in the soil lower than 0.2. In acid pseudogleyed horizons overlying a calcareous substrate, the soil solution chemistry was strongly influenced by the composition of the underlying soil layers. The soil solutions at 80 cm had pH values and BC : Altot ratios much higher than expected. This situation should be taken into account for the calculations of critical loads of acidity.
Long‐term effects of leguminous cover crops on microbial indices and their relationships in soils of a coconut plantation of a humid tropical region
Authors: Dinesh R. 
Published: March 2004

AbstractIn this study, leguminous crops likeAtylosia scarabaeoides, Centrosema pubescens, Calopogonium mucunoides, andPueraria phaseoloides.grown as soil cover individually in the interspaces of a 19‐yr‐old coconut plantation in S. Andaman (India) were assessed for their influence on various microbial indices (microbial biomass C, biomass N, basal respiration, ergosterol, levels of ATP, AMP, ADP) in soils (0–50 cm) collected from these plots after 10 years. The effects of these cover crops on.CO2(metabolic quotient), adenylate energy charge (AEC), and the ratios of various soil microbial propertiesviz., biomass C : soil organic C, biomass C : N, biomass N : total N, ergosterol : biomass C, and ATP : biomass C were also examined.Cover cropping markedly enhanced the levels of organic matter and microbial activity in soils after the 10‐yr‐period. Microbial biomass C and N, basal respiration,.CO2, ergosterol and levels of ATP, AMP, ADP in the cover‐cropped plots significantly exceeded the corresponding values in the control plot. While the biomass C : N ratio tended to decrease, the ratios of biomass N : total N, ergosterol : biomass C, and ATP : biomass C increased significantly due to cover cropping. Greater ergosterol : biomass C ratio in the cover‐cropped plots indicated a decomposition pathway dominated by fungi, and high.CO2levels in these plots indicated a decrease in substrate use efficiency probably due to the dominance of fungi. The AEC levels ranged from 0.80 to 0.83 in the cover‐cropped plots, thereby reflecting greater microbial proliferation and activity. The ratios of various microbial and chemical properties could be assigned to three different factors by principal components analysis. The first factor (PC1) with strong loadings of ATP : biomass C ratio, AEC, and.CO2reflected the specific metabolic activity of soil microbes. The ratios of ergosterol : biomass C, soil organic C : total N, and biomass N : total N formed the second factor (PC2) indicating a decomposition pathway dominated by fungi. The biomass C : N and biomass C : soil organic C ratios formed the third principal component (PC3), reflecting soil organic matter availability in relation to nutrient availability. Overall, the study suggested thatPueraria phaseoloides.orAtylosia scarabaeoideswere better suited as cover crops for the humid tropics due to their positive contribution to soil organic C, N, and microbial activity.
Proteome analysis of apoptotic cells
Authors: Thiede Bernd , Rudel Thomas 
Published: March 2004

Abstract

I.
Introduction
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II.
Global Analyses of Apoptosis by 2DGE and MS
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A.  General Experimental Design
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B.  Identification of Protein Degradation
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C.  Identification of Other Protein Modifications
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D.  Identification of Protein Translocation
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E.  Identification of Protein Synthesis
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F.  Survey of Identified Proteins
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G.  Impact of Experimental Design
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III.
Analysis of Mitochondrial Releasing Factors by LC/MS
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IV.
Analysis of the Death‐Inducing Signaling Complex (DISC)
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V.
Analysis of IAP‐Interacting Proteins
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VI.
Chemical Proteomics of Caspases
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VII.
Conclusions and Outlook
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VIII.
Abbreviations
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Acknowledgments
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References
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Apoptosis, a genetically determined form of cell death, is a central and complex process involved in the development of multicellular organisms in the maintenance of cell homeostasis. During apoptosis, a large number of proteins involved in transducing signals are posttranslationally modified. Classical proteomics, the combination of protein separation by two‐dimensional gel electrophoresis (2DGE) and protein identification by mass spectrometry (MS), enabled the discovery of more than 100 proteins altered during apoptosis. Functional data about protein degradation, modification, translocation, and synthesis were obtained. In addition to classical proteomics, some specifically designed proteome studies were carried out to analyze specific apoptotic components such as the mitochondrial releasing factors, death‐inducing signaling complex (DISC), inhibitor of apoptosis (IAP) interacting proteins, and caspases. The identification of main regulators significantly influenced the elucidation of the concept underlying apoptosis signaling. Thus, the application of detailed protein analytical methods in the young field of apoptosis research was particularly fruitful. © 2004 Wiley Periodicals, Inc., Mass Spec Rev
Investigation of intact protein complexes by mass spectrometry
Authors: Heck Albert J. R. , van den Heuvel Robert H. H. 
Published: March 2004

Abstract

I.
Introduction
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II.
Electrospray Ionization of Biomacromolecules
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III.
Mass Analyzers for Biomacromolecular Mass Spectrometry
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A.  Collisional Cooling and/or Focusing
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B.  Alternative Mass Analyzers
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IV.
Solution‐Phase Properties of Proteins Complexes
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A.  Protein–Protein Interactions
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B.  Cooperativity and Cofactors
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C.  Dynamics of Assembly
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V.
Gas‐Phase Properties of Protein Complexes
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A.  Tandem Mass Spectrometry
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B.  Charge Separation in Protein Dissociation
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VI.
Future Outlook
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Acknowledgments
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References
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Mass spectrometry has grown in recent years to a well‐accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non‐covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non‐covalent protein–protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights. © 2004 Wiley Periodicals, Inc., Mass Spec Rev
Metabolomics applications of FT‐ICR mass spectrometry
Authors: Brown Stephen C. , Kruppa Gary , Dasseux Jean‐Louis 
Published: March 2004

AbstractMetabolomics, also known as Metabolic Profiling, is an emerging discipline under the umbrella concept of systems biology. The goal of metabolomics is to know and understand the concentrations and fluxes of endogenous metabolites within a living biological system under study. General tools are being developed for the rapid measurement of many metabolites in a single experiment, most of which are mass spectrometric methods. FT‐ICR has unique advantages, as a mass spectrometric method, in this regard. Applications of FT‐ICR to metabolomics analyses will be discussed and reviewed in the context of the single publication currently available. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:223–231, 2005
The results of aneuploidy screening in 276 couples undergoing assisted reproductive techniques
Authors: Kahraman S. , Benkhalifa M. , Donmez E. , Biricik A. , Sertyel S. , Findikli N. , Berkil H. 
Published: March 2004

AbstractPreimplantation genetic diagnosis for aneuploidy screening (PGD‐AS) using sequential in situ hybridization was applied for aneuploidy testing in 276 couples with 282 ART cycles. Patients with advanced maternal age (AMA, n = 147), recurrent implantation failure (RIF, n = 48), repeated early spontaneous abortion (RSA, n = 32) and abnormal gamete cell morphology (AGCM, n = 55) including macrocephal sperm forms or cytoplasmic granular oocytes were included. Embryo biopsy was performed on day 3 in a calcium–magnesium–free medium by using a noncontact diode laser system. After fixation and enzymatic treatment, fluorescent in situ hybridization (FISH) was carried out on 1147 blastomeres with specific probes for chromosomes 13, 16, 18, 21 and 22 for AMA group, 13, 18, 21, X and Y for AGCM group and 13, 16, 18, 21, 22, X and Y for RIF and RSA groups respectively. The overall chromosomal abnormality rate in analyzed embryos was 40.9%, with no significant difference between AMA, RIF and RSA groups (p > 0.05). However, AGCM group presented a higher rate of chromosomal aneuploidies (57.4%) than the other three groups (p < 0.01). A total of 84% biopsied embryos presented cleavage in 24 h and embryo transfer was realized in 278 cycles. In four cycles, no chromosomally normal embryo was found for embryo transfer. A total of 88 pregnancies (31.6%) were achieved, 19.3% resulted in abortion and 63 healthy births were obtained, with a total of 93 babies born. Aneuploidy testing in couples with poor prognosis undergoing ART cycles is a useful tool to increase the chance of ART success. Furthermore, abnormal gamete cell morphology should be considered one of the major indications for PGD in ART programs as high aneuploidy rates were observed in this group. Copyright © 2004 John Wiley & Sons, Ltd.
The prenatal presentation of congenital erythropoietic porphyria: report of two siblings with elevated maternal serum alpha‐fetoprotein
Authors: Lazebnik Noam , Lazebnik Roee S. 
Published: March 2004

AbstractCongenital erythropoietic porphyria (CEP), also termed Günther's disease, is extremely rare and is inherited as an autosomal recessive trait. The mutation that causes the most severe deficiency of the enzyme uroporphyrinogen III synthase (URO‐synthase) is C73R. Inheritance of two abnormal alleles results in the accumulation of porphyrins of isomer type I that are biologically useless but cause a wide spectrum of abnormalities in multiple organs. The intrauterine diagnosis of the first affected conceptus within a family is extremely challenging despite abnormal ultrasound findings suggesting severe fetal anemia. We report the abnormal findings in a pair of successive pregnancies in a single Caucasian family that yielded two C73R homozygous affected offspring. The course of the pregnancies, sonographic and laboratory abnormalities, method used for intrauterine diagnosis, therapeutic interventions, and variability of outcome between cases within a single family and the difficulty in managing even prenatally diagnosed cases are reported and discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Complete large bowel duplication with paraduodenal cyst: prenatal sonographic features
Authors: Khanna Paritosh C. , Gawand Vinit , Nawale Ajita J. , Deshmukh Tejaswini , Merchant Suleman A. 
Published: March 2004

AbstractObjectivesTo illustrate diagnostic dilemmas while considering a diagnosis of complete large bowel duplication and duodenal duplication cysts.MethodsA case of large bowel dilatation with a peripancreatic cyst was identified sonographically in a 27‐year‐old gravida 3 at 35 weeks of gestation, suffering from gestational diabetes and pregnancy‐induced hypertension.ResultsOn the basis of sonographic findings of dilated, hyperperistaltic large bowel loops, and a large cyst with echo‐free contents near the pancreas, a diagnosis of large bowel obstruction with a paraduodenal cyst was considered. The findings were confirmed after postnatal ultrasonography. At the time of surgery, it proved to be a completely duplicated large bowel with a paraduodenal cyst.ConclusionPrenatal findings of a hugely dilated, hyperperistaltic large bowel should lead one to suspect/consider large bowel duplication. Associated cysts are likely to be bowel duplication cysts. Timely intervention can thus obviate potentially serious complications. Copyright © 2004 John Wiley & Sons, Ltd.
Biaxial stretching and structure of various LLDPE resins
Authors: Ajji A. , Auger J. , Huang J. , Kale L. 
Published: March 2004

AbstractThe purpose of this study is to investigate the biaxial stretchability, the structure developed, molecular orientation and shrinkage of linear low‐density octene copolymers (LLDPEs) biaxially stretched using a laboratory biaxial stretcher. Seven resins having different molecular characteristics were used in this study. The effect of stretching temperature and rate on stretchability is assessed. Biaxial orientation factors for the crystalline axes as well as that of the amorphous phase were determined using FTIR spectroscopy and shrinkage of oriented films was measured. The results indicate that the high molecular weight tail (Mz) and comonomer content play important roles in orientation of the resins. Higher Mz, MWD and resin content eluting above 90°C (by TREF technique) tends to increase orientation, and finally, some correlation between orientation and Mz, MWD and resin content eluting above 90°C and between shrinkage and amorphous orientation were observed.
RELIC – A bioinformatics server for combinatorial peptide analysis and identification of protein‐ligand interaction sites
Authors: Mandava Suneeta , Makowski Lee , Devarapalli Satish , Uzubell Joseph , Rodi Diane J. 
Published: March 2004

AbstractPhage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have developed a suite of computational tools for the analysis of peptide populations and made them accessible by integrating fifteen software programs for the analysis of combinatorial peptide sequences into the REceptor LIgand Contacts (RELIC) relational database and web‐server. These programs have been developed for the analysis of statistical properties of peptide populations; identification of weak consensus sequences within these populations; and the comparison of these peptide sequences to those of naturally occurring proteins. RELIC is particularly suited to the analysis of peptide populations affinity selected with a small molecule ligand such as a drug or metabolite. Within this functional context, the ability to identify potential small molecule binding proteins using combinatorial peptide screening will accelerate as more ligands are screened and more genome sequences become available. The broader impact of this work is the addition of a novel means of analyzing peptide populations to the phage display community.
Differential phosphoproteome profiling by affinity capture and tandem matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Metodiev Metodi V. , Timanova Anna , Stone David E. 
Published: March 2004

AbstractProtein phosphorylation is a ubiquitous post‐translational modification that affects a significant subset of the proteome and plays an especially important role in signal transduction and cell cycle control in eukaryotic organisms. Recently developed methods that couple multidimensional liquid chromatography to electrospray mass spectrometers can be used to analyze entire phosphoproteomes. However, they require considerable investments and technical skills that are only available in a few highly specialized laboratories. These methods also appear to be biased. Statistical analyses show that peptides from abundant proteins and multiply phosphorylated peptides are disproportionately identified. We describe an economic alternative that utilizes a phospho‐affinity step to isolate the intact phosphoproteins. These are subsequently characterized by electrophoresis and identified by direct de novo sequencing using tandem mass spectrometry. We applied this technique to probe signal‐induced changes in the phosphoproteome of human U937 cells, and found that the pools of two cancer‐related phosphoproteins implicated in intracellular hormones signaling are dramatically altered in the course of monocyte to macrophage differentiation.
Nondenaturing two‐dimensional electrophoresis enzyme profile involving activity and sequence structure of cytosol proteins from mouse liver
Authors: Shimazaki Youji , Sugawara Yuki , Manabe Takashi 
Published: March 2004

AbstractAfter cytosol proteins in the mouse liver were separated by nondenaturing two‐dimensional electrophoresis (2‐DE), activities of several enzymes, such as fructose bisphosphatase, sorbitol dehydrogenase and malate dehydrogenase, transferase and sorbitol dehydrogenase, or several dehydrogenases, were analyzed on the same 2‐D gel. Further, peptidase (or protease) activity can be examined by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) when peptides such as angiotensin and adenocorticotropic hormone are incubated in the presence of the cytosol protein separated by nondenaturing 2‐DE. Sequence structures of proteins on the 2‐D gel were analyzed by peptide mass fingerprinting using MALDI‐TOF‐MS or by peptide sequencing using electrospray ionization‐tandem mass spectrometry (ESI‐MS/MS). The combination of activity and sequence structure accurately verified the position and activity range of the separated enzymes on the nondenaturing 2‐D gel. From these results, we created a nondenaturing 2‐D enzyme profile involving activities and sequence structure of cytosol proteins from mouse liver. This profile can be used for checking whether activities of enzymes were specifically or nonspecifically inhibited by inhibitors.
Convenient and versatile subcellular extraction procedure, that facilitates classical protein expression profiling and functional protein analysis
Authors: Abdolzade‐Bavil Afsaneh , Hayes Scott , Goretzki Lothar , Kröger Michaela , Anders Jonas , Hendriks Robertus 
Published: March 2004

AbstractStandardized sample preparation to reduce proteome complexity facilitates subsequent proteome analysis. Here we describe a robust sequential extraction method that enables simple fractionation of proteins in their native state according to their subcellular localization, yielding four subproteomes enriched in (a) cytosolic; (b) membrane and membrane organelle‐localized; (c) soluble and DNA‐associated nuclear and (d) cytoskeletal proteins. Efficiency and selectivity is demonstrated by morphological‐, two‐dimensional electrophoresis image‐, immunological‐ as well as enzymatic‐analysis. In pilot studies, subcellular redistribution of regulatory proteins was successfully measured.