bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced Glycation in Health and Disease: Role of the Modern Environment
Authors: VLASSARA HELEN
Published: July 2005

Abstract: It is believed that intracellular and extracellular advanced glycation (AGEs) or lipoxidation end products (ALEs), together with dysregulated glucose and lipid metabolism, are important contributors to oxidant or carbonyl stress, enhanced cellular redox‐sensitive transcription factor activity, and impaired innate immune defense, causing over time inappropriate inflammatory responses. However, neither the magnitude nor the persistent nature of this increased prooxidant state are completely understood. A significant correlation has been found between ingested and circulating AGEs in humans in recent years. Based on animal studies, the injurious impact of diet‐derived AGEs to vascular and kidney tissues is estimated to rival or even exceed that caused by hyperglycemia or hyperlipidemia. Consistent with this view, dietary AGE restriction has been associated with suppression of several immune defects, insulin resistance, and diabetic complications, whether genetically or diet induced, despite persistent diabetes. These findings are in support of clinical evidence from subjects with diabetes or vascular or kidney disease. Most recently, evidence from animal studies points to AGE restriction as an effective means for extending median life span, similar to that previously shown by marked caloric restriction. We conclude that excessive AGE consumption, in the current dietary/social structure, represents an independent factor for inappropriate oxidant stress responses, which may promote the premature expression of complex diseases associated with adult life, such as diabetes and cardiovascular disease.
Diet‐Derived Advanced Glycation End Products Are Major Contributors to the Body's AGE Pool and Induce Inflammation in Healthy Subjects
Authors: URIBARRI JAIME , CAI WEIJING , SANDU OANA , PEPPA MELPOMENI , GOLDBERG TERESIA , VLASSARA HELEN
Published: July 2005

Abstract: Advanced glycation end products (AGEs) are a heterogeneous group of compounds that form continuously in the body. Their rate of endogenous formation is markedly increased in diabetes mellitus, a condition in which AGEs play a major pathological role. It is also known, however, that AGEs form during the cooking of foods, primarily as the result of the application of heat. This review focuses on the generation of AGEs during the cooking of food, the gastrointestinal absorption of these compounds, and their biological effects in vitro and in vivo. We also present preliminary evidence of a direct association between dietary AGE intake and markers of systemic inflammation such as C‐reactive protein in a large group of healthy subjects. Together with previous evidence from diabetics and renal failure patients, these data suggest that dietary AGEs may play an important role in the causation of chronic diseases associated with underlying inflammation.
Plasma Low‐Molecular Weight Fluorescence in Type 1 Diabetes Mellitus
Authors: JANUSZEWSKI A S , THOMAS M C , CHUNG S J , KARSCHIMKUS C S , ROWLEY K G , NELSON C , O'NEAL D , WANG Z , BEST J D , JENKINS A J
Published: July 2005

Abstract: Characteristic tissue fluorescence is associated with advanced glycation end product (AGE) accumulation in experimental diabetes models, but its utility in patients with type 1 diabetes remains to be established. We studied 148 patients with type 1 diabetes and 77 healthy age‐matched control subjects. Low‐molecular weight (LMW) fluorophore levels were estimated in plasma samples obtained after an overnight fast. Intra‐ and interassay coefficients of variation were 4.7% and 6.4%, respectively. LMW fluorophore levels were significantly higher in patients with diabetes than in control subjects (6.3 ± 0.6 AU/mL vs. 4.1 ± 0.3; P= 0.007). However, all of this difference came from patients with microvascular complications (n= 67, 7.5 ± 1.3). There was no significant difference in LMW fluorescence between complication‐free patients (4.4 ± 0.2) and control subjects (P > 0.05). On multivariate analysis, LMW fluorophores correlated with measures of renal function (P < 0.05) but not with diabetes per se. In addition, there was no correlation between LMW fluorophores and the markers of oxidative stress or systemic inflammation. Longitudinal and interventional studies are required to determine whether the association between LMW fluorophores and nephropathy is cause or effect.
Advanced Glycation End Product Receptor‐Mediated Cellular Dysfunction
Authors: BIERHAUS ANGELIKA , HUMPERT PER M. , STERN DAVID M. , ARNOLD BERND , NAWROTH PETER P.
Published: July 2005

Abstract: Advanced glycation end products (AGEs), S100/calgranulins, and HMGB1 proteins supposedly play a pivotal role in diabetes mellitus and other chronic inflammatory diseases by promoting cellular dysfunction via binding to cellular surface receptors. Particularly, engagement of the receptor for AGEs (RAGE) has gained major attention because it converts short‐lasting cellular activation in sustained cellular dysfunction. Consistently, blockade of ligand‐RAGE interaction with soluble RAGE (sRAGE) suppresses chronic cellular activation and dysfunction in animal models of chronic diseases. RAGE−/− mice, however, demonstrate that the protection conferred by RAGE deficiency is lower than that mediated by sRAGE. Furthermore, RAGE−/− mice can be protected by sRAGE in certain settings of the adaptive immune response. This finding implies that abounding RAGE ligands overworking the RAGE pathway might also activate other receptors.
Advanced Glycation End Products in Diabetes‐Associated Atherosclerosis and Renal Disease: Interventional Studies
Authors: JANDELEIT‐DAHM KARIN A. , LASSILA MARKUS , ALLEN TERRI J.
Published: July 2005

Abstract: There is increasing evidence that advanced glycation end products (AGEs) and their interactions with various receptors (in particular, the receptor RAGE) play a pivotal role in the development and progression of diabetic macro‐ and microvascular complications. Several approaches have been used to inhibit tissue accumulation of AGEs in diabetes, including inhibitors of AGE formation such as aminoguanidine, ALT 946, and pyridoxamine—or putative cross‐link breakers such as ALT 711. Alternative interventions have also included the administration of a soluble receptor for RAGE, sRAGE, thus capturing circulating AGEs and preventing them from binding to the cell‐bound full‐length receptor RAGE, thereby inhibiting the proinflammatory and profibrotic response following AGE‐RAGE binding. In this review we summarize the evidence for such antiglycation therapies in retarding or delaying the development and progression of diabetes‐associated atherosclerosis and renal disease while focusing on interventional strategies inhibiting AGE accumulation. In summary, all approaches have been shown to confer some degree of antiatherosclerotic and renoprotective effects, albeit to different degrees and by different mechanisms.
Renoprotective and Lipid‐Lowering Effects of LR Compounds, Novel Advanced Glycation End Product Inhibitors, in Streptozotocin‐Induced Diabetic Rats
Authors: FIGAROLA JAMES LESTER , SCOTT STEVEN , LOERA SOFIA , XI BIXIN , SYNOLD TIMOTHY , RAHBAR SAMUEL
Published: July 2005

Abstract: The accelerated formation of advanced glycation/lipoxidation end products (AGEs/ALEs) has been implicated in the pathogenesis of various diabetic complications. Several natural and synthetic compounds have been proposed and advanced as inhibitors of AGE/ALE formation. We examined the effects of two new AGE/ALE inhibitors, LR‐9 and LR‐74, on the prevention of early renal disease and dyslipidemia in streptozotocin (STZ)‐induced diabetic rats. Diabetic rats were treated with either LR‐9 or LR‐74 for 32 weeks. Progression of renal disease was evaluated by measurements of urinary albumin and plasma creatinine concentrations. AGE‐induced chemical modification of the tail tendon collagen and levels of Nε‐(carboxymethyl)‐ and (carboxyethyl)‐ lysines (CML and CEL) in skin collagen were measured. AGE/ALE levels in kidneys were determined by immunohistochemistry. Plasma lipids and their lipid hydroperoxide concentrations were also determined. Treatment of either LR‐9 or LR‐74 significantly inhibited the increase in albuminuria, plasma creatinine, hyperlipidemia, and plasma lipid peroxidation in diabetic rats without any effects on hyperglycemia. Both compounds also reduced CML‐AGE accumulation in kidney glomeruli and tubules, AGE‐linked fluorescence and cross‐linking of tail collagen, and levels of CML and CEL in skin collagen. These results suggest that both LR compounds can inhibit the progression of renal disease and also prevent dyslipidemia in experimental diabetes. These compounds may have an additional beneficial effect as an antioxidant against lipid peroxidation, and thus may provide alternative therapeutic options for the treatment of various diabetic macrovascular complications.
Inhibitors of Advanced Glycation End Product Formation and Neurovascular Dysfunction in Experimental Diabetes
Authors: CAMERON NORMAN E. , GIBSON T MICHAEL , NANGLE MATTHEW R. , COTTER MARY A.
Published: July 2005

Abstract: Advanced glycation and lipoxidation end products (AGEs/ALEs) have been implicated in the pathogenesis of the major microvascular complications of diabetes mellitus: nephropathy, neuropathy, and retinopathy. This article reviews the evidence regarding the peripheral nerve and its vascular supply. Most investigations done to assess the role of AGEs/ALEs in animal models of diabetic neuropathy have used aminoguanidine as a prototypic inhibitor. Preventive or intervention experiments have shown treatment benefits for motor and sensory nerve conduction velocity, autonomic nitrergic neurotransmission, nerve morphometry, and nerve blood flow. The latter depends on improvements in nitric oxide‐mediated endothelium‐dependent vasodilation and is responsible for conduction velocity improvements. A mechanistic interpretation of aminoguanidine's action in terms of AGE/ALE inhibition is made problematic by the relative lack of specificity. However, other unrelated compounds, such as pyridoxamine and pyridoxamine analogues, have recently been shown to have beneficial effects similar to aminoguanidine, as well as to improve pain‐related measures of thermal hyperalgesia and tactile allodynia. These data also stress the importance of redox metal ion‐catalyzed AGE/ALE formation. A further approach is to decrease substrate availability by reducing the elevated levels of hexose and triose phosphates found in diabetes. Benfotiamine is a transketolase activator that directs these substrates to the pentose phosphate pathway, thus reducing tissue AGEs. A similar spectrum of improvements in nerve and vascular function were noted when using benfotiamine in diabetic rats. Taken together, the data provide strong support for an important role for AGEs/ALEs in the etiology of diabetic neuropathy.
Receptor for Advanced Glycation End Products and Its Ligands: A Journey from the Complications of Diabetes to Its Pathogenesis
Authors: KIM WILLIAM , HUDSON BARRY I. , MOSER BERNHARD , GUO JIANCHENG , RONG LING LING , LU YAN , QU WU , LALLA EVANTHIA , LERNER SHULAMIT , CHEN YALI , YAN SHIRLEY SHI DU , D'AGATI VIVETTE , NAKA YOSHIFUMI , RAMASAMY RAVICHANDRAN , HEROLD KEVAN , YAN SHI FANG , SCHMIDT ANN MARIE
Published: July 2005

Abstract: Many studies have suggested that the expression of RAGE (receptor for advanced glycation end products) is upregulated in human tissues susceptible to the long‐term complications of diabetes. From the kidneys to the macrovessels of the aorta, RAGE expression is upregulated in a diverse array of cell types, from glomerular epithelial cells (podocytes) to endothelial cells, vascular smooth muscle cells, and inflammatory mononuclear phagocytes and lymphocytes. Although RAGE was first described as a receptor for advanced glycation end products (AGEs), the key finding that RAGE was also a signaling receptor for proinflammatory S100/calgranulins and amphoterin, led to the premise that even in euglycemia, ligand‐RAGE interaction propagated inflammatory mechanisms linked to chronic cellular perturbation and tissue injury. Indeed, such considerations suggested that RAGE might even participate in the pathogenesis of type 1 diabetes. Our studies have shown that pharmacological and/or genetic deletion/mutation of the receptor attenuates the development of hyperglycemia in NOD mice; in mice with myriad complications of diabetes, interruption of ligand‐RAGE interaction prevents or delays the chronic complications of the disease in both macro‐ and microvessel structures. Taken together, these findings suggest that RAGE is “at the right place and time” to contribute to the pathogenesis of diabetes and it complications. Studies are in progress to test the premise that antagonism of this interaction is a logical strategy for the prevention and treatment of diabetes.
Role of Advanced Glycation End Products and Their Receptors in Development of Diabetic Neuropathy
Authors: WADA RYUICHI , YAGIHASHI SOROKU
Published: July 2005

Abstract: Diabetic neuropathy is a life‐threatening complication involving both peripheral and autonomic nerves. The hyperglycemia‐induced polyol pathway as well as enhanced oxidative stress are among the factors implicated in the pathogenesis of diabetic neuropathy. Their effects are possibly exerted by direct nerve tissue damage or mediated by endothelial injury or vascular dysfunction. Formation of advanced glycation end product (AGE) is another important candidate for the cause of peripheral neuropathy. Indeed, the levels of AGEs were increased in the serum and also in the peripheral nerves obtained from diabetic patients. Structural and functional proteins of those nerves are also glycated, resulting in impaired nerve function and characteristic pathologic alterations. In addition, interaction between AGEs and their receptors induce biological effects on the target tissues for diabetic complications. In the peripheral nerve, the receptor for AGE (RAGE) is expressed in endothelial and Schwann cells. It is thus anticipated that interactions between AGEs and RAGE facilitate endoneural vascular dysfunction, leading to microangiopathy in the peripheral nerve. The roles of these mechanisms, in particular on the molecular mechanisms of AGE‐RAGE interactions in the development of diabetic neuropathy are largely still speculative and yet to be explored.
Synergistic Contributions of Carbonyl Stress and Megsin in Diabetic Nephropathy
Authors: INAGI REIKO , NANGAKU MASAOMI , MIYATA TOSHIO
Published: July 2005

Abstract: Diabetic nephropathy is the most common cause of end‐stage renal failure. The primary glomerular changes in diabetic nephropathy are diffuse and nodular glomerulosclerosis, manifested by an increase in mesangial matrix. Research has demonstrated that advanced glycation end products (AGEs), oxidative stress, and carbonyl stress might play a crucial role in the pathogenesis of diabetic nephropathy via multiple mechanisms. AGEs augment extracellular matrix synthesis, contribute to the release of proinflammatory cytokines and expression of growth factors and adhesion molecules, and interact with the renin‐angiotensin system. Megsin is a novel serine protease inhibitor predominantly expressed in mesanguim. Megsin is upregulated in kidney samples of patients with diabetic nephropathy. Transgenic mice overexpressing megsin spontaneously develop kidney disease characterized by mesangial injury. Megsin is likely to contribute to mesangial injury in the process of diabetic nephropathy. Lack of appropriate animal models has hampered understanding the pathogenesis of diabetic nephropathy and development of effective therapies. Megsin and AGEs are suitable targets for new drugs of diabetic nephropathy and for the development of appropriate animal models of diabetic nephropathy.
Processing Advanced Glycation End Product‐Modified Albumin by the Renal Proximal Tubule and the Early Pathogenesis of Diabetic Nephropathy
Authors: OZDEMIR AYLIN M. , HOPFER ULRICH , ERHARD PENNY , MONNIER VINCENT M. , WEISS MIRIAM F.
Published: July 2005

Abstract: Diabetes is characterized by increased quantities of circulating proteins modified by advanced glycation end products (AGEs). Proteins filtered at the glomerulus and presented to the renal proximal tubule are likely to be highly modified by AGEs. The proximal tubule binds, takes up, and catabolizes AGE‐modified albumin by pathways different from those of unmodified albumin. These differences were examined in polarized, electrically resistant proximal tubular cells grown in monolayer culture. In patients with type 1 diabetes, urinary excretion of a lysosomal enzyme predicted the development of nephropathy.
Mutations in the Epidermal Growth Factor Receptor and in KRAS Are Predictive and Prognostic Indicators in Patients With Non–Small-Cell Lung Cancer Treated With Chemotherapy Alone and in Combination With Erlotinib
Authors: Eberhard David A. , Johnson Bruce E. , Amler Lukas C. , Goddard Audrey D. , Heldens Sherry L. , Herbst Roy S. , Ince William L. , Jänne Pasi A. , Januario Thomas , Johnson David H. , Klein Pam , Miller Vincent A. , Ostland Michael A. , Ramies David A. , Sebisanovic Dragan , Stinson Jeremy A. , Zhang Yu R. , Seshagiri Somasekar , Hillan Kenneth J.
Published: July 2005

Purpose

Epidermal growth factor receptor (EGFR) mutations have been associated with tumor response to treatment with single-agent EGFR inhibitors in patients with relapsed non–small-cell lung cancer (NSCLC). The implications of EGFR mutations in patients treated with EGFR inhibitors plus first-line chemotherapy are unknown. KRAS is frequently activated in NSCLC. The relationship of KRAS mutations to outcome after EGFR inhibitor treatment has not been described.

Patients and Methods

Previously untreated patients with advanced NSCLC in the phase III TRIBUTE study who were randomly assigned to carboplatin and paclitaxel with erlotinib or placebo were assessed for survival, response, and time to progression (TTP). EGFR exons 18 through 21 and KRAS exon 2 were sequenced in tumors from 274 patients. Outcomes were correlated with EGFR and KRAS mutations in retrospective subset analyses.

Results

EGFR mutations were detected in 13% of tumors and were associated with longer survival, irrespective of treatment (P < .001). Among erlotinib-treated patients, EGFR mutations were associated with improved response rate (P < .05) and there was a trend toward an erlotinib benefit on TTP (P = .092), but not improved survival (P = .96). KRAS mutations (21% of tumors) were associated with significantly decreased TTP and survival in erlotinib plus chemotherapy–treated patients.

Conclusion

EGFR mutations may be a positive prognostic factor for survival in advanced NSCLC patients treated with chemotherapy with or without erlotinib, and may predict greater likelihood of response. Patients with KRAS-mutant NSCLC showed poorer clinical outcomes when treated with erlotinib and chemotherapy. Further studies are needed to confirm the findings of this retrospective subset analysis.
Planarian homologs ofnetrinandnetrin receptorare required for proper regeneration of the central nervous system and the maintenance of nervous system architecture
Authors: Cebrià Francesc , Newmark Phillip A.
Published: July 2005

Conserved axon guidance mechanisms are essential for proper wiring of the nervous system during embryogenesis; however, the functions of these cues in adults and during regeneration remain poorly understood. Because freshwater planarians can regenerate a functional central nervous system (CNS) from almost any portion of their body, they are useful models in which to study the roles of guidance cues during neural regeneration. Here, we characterize two netrin homologs and one netrin receptor family member from Schmidtea mediterranea. RNAi analyses indicate that Smed-netR (netrin receptor) and Smed-netrin2 are required for proper CNS regeneration and that Smed-netR may mediate the response to Smed-netrin2. Remarkably, Smed-netR and Smed-netrin2 are also required in intact planarians to maintain the proper patterning of the CNS. These results suggest a crucial role for guidance cues, not only in CNS regeneration but also in maintenance of neural architecture.
Experimental and numerical study of chip formation during straight turning of hardened AISI 4340 steel
Authors: Belhadi S , Mabrouki T , Rigal J-F , Boulanouar L
Published: July 2005

The present paper is a contribution to the investigation of physical phenomena accompanying sawtooth chip formation in the case of hard turning. The study concerns the machining with coated carbide of tempered AISI 4340 steel with a Rockwell C hardness of 47 HRC. The main idea in this paper deals with the establishment of a direct relationship between serrated-chip morphology simultaneously with force component signals derived from acquisition at high frequency and with the width of facets detected on a workpiece machined surface. This experimental work was supported by a numerical simulation based on Abaqus/ Explicit software. Numerical results dealing with effect of temperature evolution on the chip morphology show that the beginning of the sawtooth chip initiation is due to an adiabatic shear at the tool tip with propagation pathway towards the free surface. In addition, computed results have a good corroboration with those obtained experimentally.
New analytical design of the Smith predictor controller for high-order systems
Authors: Liu Tao , Hu Zhonghui , Yin Rupo , Xu Xiaoming
Published: July 2005

In this paper, a new analytical Smith predictor (SP) controller design method is proposed for industrial and chemical high-order systems. Firstly, by using the integral-squared-error (ISE) performance specification, the ideally optimal SP controller is analytically derived according to the nominal high-order plant model, which inevitably results in the high-order controller. Then the analytical controller reduction formulae based on the mathematical Maclaurin and Padé expansions are proposed to duplicate it in the form of a low-order controller such as the proportional-integral-derivative (PID). Hence, the difficulty of controller implementation in practice is significantly relieved without pitiful system performance degradation in comparison with many existing methods. At the same time, the control system robust stability is analysed. Accordingly, the on-line tuning rule of the single adjustable parameter of the proposed controller is provided to cope with the actual system uncertainties. Finally, several illustrative simulation examples are included to demonstrate the effectiveness of the proposed method.
Control of a servomechanism using non-linear damping
Authors: Garrido R , Soria A
Published: July 2005

A simple non-linear proportional-derivative (PD) controller is proposed to improve the settling time in a servomechanism. Damping depends on the position error; for large errors, damping is small and increases for smaller errors. It is experimentally shown that the proposed algorithm improves the settling time with respect to a linear PD controller.
Transcript selection and the recruitment of mRNA decay factors for NMD in Saccharomyces cerevisiae
Authors: CULBERTSON MICHAEL R. , NEENO-ECKWALL ERIC
Published: July 2005

In Saccharomyces cerevisiae, nonsense-mediated mRNA decay (NMD) requires Upf1p, Upf2p, and Upf3p to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target Cbc-bound or eIF-4E-bound transcripts. Extremely low concentrations of the Upf proteins relative to the total pool of transcripts make it difficult to understand how nonsense transcripts are selectively recruited. To stimulate debate, we propose two alternative mechanisms for selecting nonsense transcripts for NMD and for assembling components of the surveillance complex, one for the first (pioneer) round of translation, called “nuclear marking,” and the other for subsequent rounds, called “reverse assembly.” The model is designed to accommodate (1) the low abundance of NMD factors, (2) the role of nucleocytoplasmic shuttling proteins in NMD, (3) the independent and nonobligate order of assembly of two different subcomplexes of NMD factors, and (4) the ability of NMD to simultaneously reduce or eliminate the synthesis of truncated proteins produced by nonsense transcripts while down-regulating but not completely eliminating functional proteins produced from error-free NMD-sensitive transcripts.
Protein content of minimal and ancestral ribosome
Authors: MUSHEGIAN ARCADY
Published: July 2005

Minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on Earth. A consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. I relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the Last Universal Common Ancestor of Life. Both sets contain between 35 and 40 proteins. There is evidence of protein–protein and protein–RNA displacement in the evolution of both ribosomal subunits.
Evolvability of the mode of peptide binding by an RNA
Authors: IWAZAKI TETSUYA , LI XIANGLAN , HARADA KAZUO
Published: July 2005

The HIV Rev-response element (RRE) RNA binds strongly to two unrelated peptides, the HIV Rev peptide and an RRE-binding aptamer, the RSG-1.2 peptide, at a similar site, but using distinct sets of interactions. In this study, the nucleotide base requirements for the binding of the RRE to the Rev and RSG-1.2 peptides were determined by selection of Rev- and RSG-1.2-binding RRE variants using a bacterial reporter system. As a result, distinct differences in the bases necessary for binding the two peptides were found in the upper stem of the RRE. Strikingly, single nucleotide changes in this region were found to switch the peptide-binding specificity of the RRE from a bifunctional Rev- and RSG-1.2-binding mode to either a Rev-specific or a RSG-1.2- specific mode, demonstrating how an RNA can evolve alternative binding strategies in discrete steps without intermediate loss of function. This evolvability of the mode of peptide binding by an RNA presumably reflects the multidimensionality of conformational space that a given RNA has available for ligand recognition, which may have been utilized in the evolution of RNA–polypeptide complexes.
Lead(II) cleavage analysis of RNase P RNA in vivo
Authors: LINDELL MAGNUS , BRÄNNVALL MATHIAS , WAGNER E. GERHART H. , KIRSEBOM LEIF A.
Published: July 2005

The overall conformation of M1 RNA, the catalytic RNA subunit of RNase P in Escherichia coli, was analyzed in vivo and, in the presence of the C5 protein subunit, in vitro by lead(II) acetate probing. The partial cleavage patterns obtained are congruent with previous structure mapping performed in vitro. Most of the known major and minor cleavages in M1 RNA were supported and could be mapped onto a secondary structure model. The data obtained indicate that C5 has only minor effects on the overall structure of the RNA subunit. The similar cleavage patterns obtained in vitro and in vivo furthermore suggest that the intracellular environment does not greatly alter the overall conformation of M1 RNA within the holoenzyme complex. Moreover, our data indicate that M1 RNA in vivo is present in at least two states—the major fraction is bound to tRNA substrates and a minor fraction is substrate free. Finally, both in this and previous work we found that lead(II) probing data from in vivo experiments conducted on longer RNAs (tmRNA and M1 RNA) generally gives superior resolution compared to parallel in vitro experiments. This may reflect the absence of alternative conformers present in vitro and the more natural state of these RNAs in the cell due to proper, co-transcriptional folding pathways and possibly the presence of RNA chaperones.
Specificity of recognition of mRNA 5′ cap by human nuclear cap-binding complex
Authors: WORCH REMIGIUSZ , NIEDZWIECKA ANNA , STEPINSKI JANUSZ , MAZZA CATHERINE , JANKOWSKA-ANYSZKA MARZENA , DARZYNKIEWICZ EDWARD , CUSACK STEPHEN , STOLARSKI RYSZARD
Published: July 2005

The heterodimeric nuclear cap-binding complex (CBC) binds to the mono-methylated 5′ cap of eukaryotic RNA polymerase II transcripts such as mRNA and U snRNA. The binding is important for nuclear maturation of mRNAs and possibly in the first round of translation and nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans. We report characterization by fluorescence spectroscopy of the recognition of 5′ capped RNA by human CBC. The association constants (Kas) for 17 mono- and dinucleotide cap analogs as well as for the oligomer m7GpppAm2′ pUm2′pAm2′ cover the range from 1.8 × 106 M−1 to 2.3 × 108 M−1. Higher affinity for CBC is observed for the dinucleotide compared with mononucleotide analogs, especially for those containing a purine nucleoside next to m7G. The mRNA tetramer associates with CBC as tightly as the dinucleotide analogs. Replacement of Tyr138 by alanine in the CBP20 subunit of CBC reduces the cap affinity except for the mononucleotide analogs, consistent with the crystallographic observation of the second base stacking on this residue. Our spectroscopic studies showed that contrary to the other known cap-binding proteins, the first two nucleotides of a capped-RNA are indispensable for its specific recognition by CBC. Differences in the cap binding of CBC compared with the eukaryotic translation initiation factor 4E (eIF4E) are analyzed and discussed regarding replacement of CBC by eIF4E.
Activity-dependent polyadenylation in neurons
Authors: DU LING , RICHTER JOEL D.
Published: July 2005

Activity-dependent changes in protein synthesis modify synaptic efficacy. One mechanism that regulates mRNA translation in the synapto-dendritic compartment is cytoplasmic polyadenylation, a process controlled by CPEB, the cytoplasmic polyadenylation element (CPE)-specific RNA binding protein. In neurons, very few mRNAs are known CPEB substrates, and none appear to be responsible for the effects on plasticity that are found in the CPEB knockout mouse. These results suggest that the translation of other mRNAs is regulated by CPEB. To identify them, we have developed a functional assay based on the polyadenylation of brain-derived mRNAs injected into Xenopus oocytes, a surrogate system that carries out this 3′ end processing event in an efficient manner. The polyadenylated RNAs were isolated by binding to and thermal elution from poly(U) agarose and identified by microarray analysis. Selected sequences that were positive for polyadenylation were cloned and retested for polyadenylation by injection into oocytes. These sequences were then examined for activity-dependent polyadenylation in cultured hippocampal neurons. Finally, the levels of two proteins encoded by polyadenylated mRNAs were examined in glutamate-stimulated synaptoneurosomes. These studies show that many mRNAs undergo activity-dependent polyadenylation in neurons and that this process coincides with increased translation in the synapto-dendritic compartment.
Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit
Authors: GU SHAN-QING , JÖCKEL JOHANNES , BEINKER PHILIPP , WARNECKE JENS , SEMENKOV YURI P. , RODNINA MARINA V. , WINTERMEYER WOLFGANG
Published: July 2005

The signal recognition particle (SRP) from Escherichia coli consists of 4.5S RNA and protein Ffh. It is essential for targeting ribosomes that are translating integral membrane proteins to the translocation pore in the plasma membrane. Independently of Ffh, 4.5S RNA also interacts with elongation factor G (EF-G) and the 30S ribosomal subunit. Here we use a cross-linking approach to probe the conformation of 4.5S RNA in SRP and in the complex with the 30S ribosomal subunit and to map the binding site. The UV-activatable cross-linker p-azidophenacyl bromide (AzP) was attached to positions 1, 21, and 54 of wild-type or modified 4.5S RNA. In SRP, cross-links to Ffh were formed from AzP in all three positions in 4.5S RNA, indicating a strongly bent conformation in which the 5′ end (position 1) and the tetraloop region (including position 54) of the molecule are close to one another and to Ffh. In ribosomal complexes of 4.5S RNA, AzP in both positions 1 and 54 formed cross-links to the 30S ribosomal subunit, independently of the presence of Ffh. The major cross-linking target on the ribosome was protein S7; minor cross-links were formed to S2, S18, and S21. There were no cross-links from 4.5S RNA to the 50S subunit, where the primary binding site of SRP is located close to the peptide exit. The functional role of 4.5S RNA binding to the 30S subunit is unclear, as the RNA had no effect on translation or tRNA translocation on the ribosome.
Methodology for Evaluating and Optimizing Infrared Interpretations
Authors: Saperstein David D.
Published: July 2005

With the use of spectral information, a means is reported for evaluating and optimizing infrared (IR) interpretations. A procedure is described for numerically estimating the spectral difference between the interpreted IR spectrum and a synthetic spectrum composed of the characteristic subspectra of the functional groups in the interpretation. The expectation value assigned to each functional group by an interpreter can then be modified to minimize the estimated numerical differences and improve the quality of the interpretation.
Effects of the synthetic estrogen ethinylestradiol on early life stages of mink frogs and green frogs in the wild and in situ
Authors: Park Bradley J. , Kidd Karen
Published: July 2005

Estrogenic contaminants are known to disrupt growth and development in amphibians. Field-based research is needed to elucidate their potential impacts on wild populations. Hatch success, larval growth and development rates, and gonad development were examined in native amphibians exposed to low ng/L concentrations of 17α-efhinylestradiol (EE2) in a whole-lake addition experiment at the Experimental Lakes Area, northwestern Ontario, Canada. Egg masses were reared in situ in the EE2-amended lake and in two reference lakes in 2001 and 2002. Hatching success was reduced significantly in green frogs (Rana clamitans) but not in mink frogs (Rana septentrionalis) exposed to EE2. Ethinylestradiol had no consistent effect on mass or development stage of hatchlings in the early larval stages of the caging study. Ethinylestradiol had no effect on sex ratios of either species in situ, and no intersex gonads were observed in exposed or reference green frog tadpoles or in reference mink frog tadpoles. However, 5.6% (total n = 18) and 12.5% (total n = 56) of EE2-exposed mink frog tadpoles were intersex in the 2001 and 2002 caging studies, respectively. Wild mink frog tadpoles also were examined, and EE2 had no effect on sex ratios. No intersex gonads were observed in reference lake tadpoles or in tadpoles from the experimental lake prior to EE2 additions; however, 2.4, 0, and 28.6% of wild EE2-exposed first-year tadpoles had intersex gonads (2001, 2002, and 2003, respectively). These results indicate that exposure to EE2 in the wild and in situ at concentrations comparable to those detected in effluents and, occasionally, in surface waters can impact gonad development and hatch success in native amphibians.
Reproductive, physiological, and biochemical responses in juvenile female rainbow trout (oncorhynchus mykiss) exposed to sediment from pulp and paper mill industrial discharge areas
Authors: Orrego Rodrigo , Moraga-Cid Gustavo , González Margarita , Barra Ricardo , Valenzuela Ariel , Burgos Abed , Gavilán Juan F.
Published: July 2005

Four pulp and paper mills discharge their effluents in the same section of the Biobio River in central southern Chile. Pulp mill effluents are a very complex mixture with characteristics that depend on the type of raw material, the process technology, and the effluent treatment. To investigate the effect of pulp mill effluent discharges, immature Oncorhynchus mykiss were exposed to river sediments in the laboratory for 29 d. Three sampling areas were defined in a spatial gradient in the river: Preimpact, impact, and postimpact zones relative to the pulp and paper mill discharge areas. Ethoxyresorufin-O-deethylase activities were significantly higher in fish exposed to impact and postimpact sediments when compared to those exposed to preimpact sediments, and higher levels of vitellogenin were observed in the plasma of female fish exposed to impact and postimpact sediments. Histological analysis of the gonadal tissue showed an induction of gonadal maturation in fish exposed to sediment coming from the impact and postimpact zones (oocytes in a vitellogenic state). No site differences were observed in erythrocytes, although differences were noted in the leukocytes in the exposure areas. Finally, the biomarker approach showed evidence that the sediment associated with pulp mill effluent discharges produces some effects in fish under laboratory conditions.
Presence and estrogenicity of anthracene derivatives in coastal japanese waters
Authors: Kurihara Ryo , Shiraishi Fujio , Tanaka Noriho , Hashimoto Shinya
Published: July 2005

An analytical method was developed to measure levels of anthracene (ANT) and its derivative compounds 9,10-anthraquinone (ATQ) and eight hydroxy-anthraquinones (hATQs) in seawater from Tokyo Bay and Suruga Bay, Japan. The hATQs produced through photochemical reaction of ANT are known to be toxic. Seawater samples contained ANT at levels ranging from <0.2 to 4.7 ng/L, ATQ from 3.9 to 200 ng/L, 1-hydroxyanthraquinone (1-hATQ) from <0.9 to 5.3 ng/L, and 2-hATQ from 1.6 to 5.5 ng/L. The yeast two-hybrid system was also used to evaluate the estrogenic activity of these compounds. Estrogen agonist and antagonist tests with or without rat liver S9 were carried out. Some compounds showed estrogenic activity: The strongest (2-hydroxyanthraquinone) was of similar potency to p-nonylphenol. Concentrations of some estrogenic derivatives in the samples were higher than those of the parent ANT. Polycyclic aromatic hydrocarbons (PAHs) such as ANT appear able to be transformed into toxic compounds in the environment when they are irradiated by sunlight, so it is important to monitor not only PAHs but also hydroxyl-PAH-quinones in the environment.
Laboratory culture and life-cycle experiments with the benthic amphipod melita plumulosa (zeidler)
Authors: Hyne Ross V. , Gale Sharyn A. , King Catherine K.
Published: July 2005

In Australia, the collection of estuarine invertebrates from the field for whole-sediment toxicity tests is hindered because of temporal variability in their population densities and distributions. The present study aimed to develop culturing procedures for Melita plumulosa (Zeidler), an epibenthic and intertidal, deposit-feeding amphipod that is native to the southeastern coast of Australia. During a 28-d chronic exposure, the species was tested under a range of salinities (5–35‰), temperatures (14–25°C), and sediment particle sizes (sand to silt). Optimal culture conditions with respect to salinity, temperature, sediment particle size, feeding, and light regimes were determined. Compared to survival, amphipod growth and fertility were better predictors of optimal culture conditions. A life-history experiment was undertaken at the initial culture conditions of 22°C and 35‰ salinity to establish the age at maturity, length of reproductive cycle, and life span for each sex. Under these test conditions, posthatch female M. plumulosa released their first offspring at seven weeks, after which each female produced an average of nine juveniles every 16 d. Male M. plumulosa had an average life span of eight months, whereas females had an average life span of 11 months. Optimal culturing conditions established in the present study have been incorporated into toxicity test procedures with this species and are being used to maximize reproductive output of this species in laboratory cultures to provide a supply of juveniles for routine use in whole-sediment toxicity tests.
A short-term sublethal in situ toxicity assay with hediste diversicolor (polychaeta) for estuarine sediments based on postexposure feeding
Authors: Moreira Susana Maria , Moreira-Santos Matilde , Guilhermino Lúcia , Ribeiro Rui
Published: July 2005

This study evaluated a short-term sublethal endpoint for in situ toxicity assays for estuarine sediments, based on postexposure feeding of the polychaete Hediste (Nereis) diversicolor Müller. A method for precisely quantifying postexposure feeding rates of H. diversicolor was established under laboratory conditions using Artemia franciscana Kellog nauplii. The sensitivity of the postexposure feeding response to copper was investigated by comparing postexposure feeding rates to growth and lethality. The 48-h and 96-h median lethal concentration (LC50) of copper were 241 and 125 μg/L, respectively, whereas the 48-h median inhibitory concentration (IC50) for postexposure feeding and the 20-d IC50 for growth were 52 and 25 μg/L of copper, respectively. The influence of different exposure conditions (substrate, temperature, salinity, food availability, and light) on H. diversicolor postexposure feeding was assessed; temperature and salinity were found to influence significantly postexposure feeding. The effectiveness of the proposed in situ assay was investigated by deploying it at two reference and six contaminated Portuguese estuaries. A 48-h exposure period was followed by a 1-h postexposure feeding period. High organism recoveries (89–100%) were obtained. Postexposure feeding was depressed significantly (17–90%) at all contaminated sites relatively to reference sites. The proposed in situ assay with H. diversicolor was shown to be a potential useful tool for estuarine sediment toxicity testing.
Influence of water temperature on acetylcholinesterase activity in the pacific tree frog (hyla regilla)
Authors: Johnson Catherine S. , Schwarzbach Steven E. , Henderson John D. , Wilson Barry W. , Tjeerdema Ronald S.
Published: July 2005

This investigation evaluated whether acetylcholinesterase (AChE) in Pacific tree frogs (Hyla regilla) from different geographical locations was influenced by different temperatures during early aquatic life stages, independent of pesticide exposure. Tadpoles were collected from both a California coastal pond and a Sierra Nevada mountain range pond, USA. Groups of frogs from each location were raised in temperatures representative of either the Sierra Nevada (8°C) or the coastal (19°C) location. Metamorphs from both locations raised as tadpoles at 19°C had AChE activities of 42.3 and 38.7 nm/min/mg protein, while those raised as tadpoles at 8°C had activities of 26.9 and 28.2 nm/min/mg protein. A two-way analysis of variance revealed temperature to be the significant factor in determining AChE activity (F = 22.3, p < 0.001), although origin was not important (F = 0.09, p = 0.75). Interpretations regarding the influence of pesticides upon AChE activity in Pacific tree frogs must consider the influence of environmental temperature to enable cross-population comparisons.
Reduction in acute toxicity of soils to terrestrial oligochaetes following the removal of bioavailable polycyclic aromatic hydrocarbons with mild supercritical carbon dioxide extraction
Authors: Hawthorne Steven B. , Lanno Roman , Kreitinger Joseph P.
Published: July 2005

Three soil samples contaminated with polycyclic aromatic hydrocarbons (PAHs) that caused 100% mortality to terrestrial oligochaetes were extracted with supercritical carbon dioxide to remove the bioavailable fraction of PAHs. Although the remaining PAH concentrations were high after supercritical fluid extraction (SFE), 650 to 8,000 mg/kg, acute toxicity to Eisenia fetida and Enchytraeus albidus essentially was eliminated. These results demonstrate that mild SFE with pure carbon dioxide preferentially extracts PAH molecules that are bioavailable toxicologically to the oligochaetes, although biologically unavailable PAHs are not extracted, suggesting that SFE could be used for the removal of toxicity due to hydrophobic organic chemicals in soils during toxicity identification evaluations.
Aqueous photolysis of 8:2 fluorotelomer alcohol
Authors: Gauthier Suzanne A. , Mabury Scott A.
Published: July 2005

The 8:2 fluorotelomer alcohol (8:2 FTOH) was photodegraded in aqueous hydrogen peroxide solutions, synthetic field water (SFW) systems, and Lake Ontario (Canada) water samples. It was found to undergo indirect photolysis, with the data suggesting that the hydroxyl radical was the main degradation agent and that nitrate promoted photolysis whereas dissolved organic carbon inhibited it. The half-lives of 8:2 FTOH were 0.83 ± 0.20 h (10 mM H2O2), 38.0 ± 6.0 h (100 μM H2O2), 30.5 ± 8.0 to 163.1 ± 3.0 h (SFW systems), and 93.2 ± 10.0 h (Lake Ontario). No significant loss of the parent compound by direct photolysis could be observed. The major monitored products were the 8:2 fluorotelomer aldehyde, the 8:2 fluorotelomer acid (8:2 FTCA), and perfluorooctanoate (PFOA); the minor monitored products were the 8:2 fluorotelomer unsaturated acid (8:2 FTUCA) and perfluorononanoate (PFNA). The intermediates, 8:2 FTCA and 8:2 FTUCA, were photodegraded to verify the degradation pathway, and a mechanism for the photolysis was proposed whereby the end products of the photolysis pathway were PFOA (major) and PFNA (minor).
Trophic level and macronutrient shift effects associated with the weaning process in the postclassic Maya
Authors: Williams Jocelyn S. , White Christine D. , Longstaffe Fred J.
Published: July 2005

The weaning process was investigated at two Maya sites dominated by Postclassic remains: Marco Gonzalez (100 BC–AD 1350) and San Pedro (1400–AD 1650), Belize. Bone collagen and bioapatite were analyzed from 67 individuals (n ≤ 6 years = 15, n > 6 years = 52). Five isotopic measures were used to reconstruct diet and weaning: stable nitrogen‐ and carbon‐isotope ratios in collagen, stable carbon‐ and oxygen‐isotope ratios in bioapatite, and the difference in stable carbon‐isotope values of coexisting collagen and bioapatite. Nitrogen‐isotope ratios in infant collagen from both sites are distinct from adult females, indicating a trophic level effect. Collagen‐to‐bioapatite differences in infant bone from both sites are distinct from adult females, indicating a shift in macronutrients. Oxygen‐isotope ratios in infant bioapatite from both sites are also distinct from adult females, indicating the consumption of breast milk. Among infants, carbon‐ and nitrogen‐isotope ratios vary, indicating death during different stages in the weaning process. The ethnohistoric and paleopathological literature on the Maya indicate cessation of breast‐feeding between ages 3–4 years. Isotopic data from Marco Gonzalez and San Pedro also indicate an average weaning age of 3–4 years. Based on various isotopic indicators, weaning likely began around age 12 months. This data set is not only important for understanding the weaning process during the Postclassic, but also demonstrates the use of collagen‐to‐bioapatite spacing as an indicator of macronutrient shifts associated with weaning. Am J Phys Anthropol 127:, 2005. © 2005 Wiley‐Liss, Inc.