bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate
Authors: Nadaf Javad , Gilbert Hélène , Pitel Frédérique , Berri Cécile M , Feve Katia , Beaumont Catherine , Duclos Michel J , Vignal Alain , Porter Tom E , Simon Jean , Aggrey Samuel E , Cogburn Larry A , Le Bihan-Duval Elisabeth
Published: June 2007

Background

Meat technological traits (i.e. meat pH, water retention and color) are important considerations for improving further processing of chicken meat. These quality traits were originally characterized in experimental lines selected for high (HG) and low (LG) growth. Presently, quantitative trait loci (QTL) for these traits were analyzed in an F2 population issued from the HG × LG cross. A total of 698 animals in 50 full-sib families were genotyped for 108 microsatellite markers covering 21 linkage groups.

Results

The HG and LG birds exhibit large differences in body weight and abdominal fat content. Several meat quality traits [pH at 15 min post-slaughter (pH15) and ultimate pH (pHu), breast color-redness (BCo-R) and breast color-yellowness (BCo-Y)] were lower in HG chickens. In contrast, meat color-lightness (BCo-L) was higher in HG chickens, whereas meat drip loss (DL) was similar in both lines. HG birds were more active on the shackle line. Association analyses were performed using maximum-likelihood interval mapping in QTLMAP. Five genome-wide significant QTLs were revealed: two for pH15 on GGA1 and GGA2, one for DL on GGA1, one for BCo-R and one for BCo-Y both on GGA11. In addition, four suggestive QTLs were identified by QTLMAP for BCo-Y, pHu, pH15 and DL on GGA1, GGA4, GGA12 and GGA14, respectively. The QTL effects, averaged on heterozygous families, ranged from 12 to 31% of the phenotypic variance. Further analyses with QTLExpress confirmed the two genome-wide QTLs for meat color on GGA11, failed to identify the genome-wide QTL for pH15 on GGA2, and revealed only suggestive QTLs for pH15 and DL on GGA1. However, QTLExpress qualified the QTL for pHu on GGA4 as genome-wide.

Conclusion

The present study identified genome-wide significant QTLs for all meat technological traits presently assessed in these chickens, except for meat lightness. This study highlights the effects of divergent selection for growth rate on some behavioral traits, muscle biochemistry and ultimately meat quality traits. Several QTL regions were identified that are worthy of further characterization. Some QTLs may in fact co-localize, suggesting pleiotropic effects for some chromosomal regions.
Computational prediction of Pho regulons in cyanobacteria
Authors: Su Zhengchang , Olman Victor , Xu Ying
Published: June 2007

Background

Phosphorus is an essential element for all life forms. However, it is limiting in most ecological environments where cyanobacteria inhabit. Elucidation of the phosphorus assimilation pathways in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. However, a systematic study of the Pho regulon, the core of the phosphorus assimilation pathway in a cyanobacterium, is hitherto lacking.

Results

We have predicted and analyzed the Pho regulons in 19 sequenced cyanobacterial genomes using a highly effective scanning algorithm that we have previously developed. Our results show that different cyanobacterial species/ecotypes may encode diverse sets of genes responsible for the utilization of various sources of phosphorus, ranging from inorganic phosphate, phosphodiester, to phosphonates. Unlike in E. coli, some cyanobacterial genes that are directly involved in phosphorus assimilation seem to not be under the regulation of the regulator SphR (orthologue of PhoB in E coli.) in some species/ecotypes. On the other hand, SphR binding sites are found for genes known to play important roles in other biological processes. These genes might serve as bridging points to coordinate the phosphorus assimilation and other biological processes. More interestingly, in three cyanobacterial genomes where no sphR gene is encoded, our results show that there is virtually no functional SphR binding site, suggesting that transcription regulators probably play an important role in retaining their binding sites.

Conclusion

The Pho regulons in cyanobacteria are highly diversified to accommodate to their respective living environments. The phosphorus assimilation pathways in cyanobacteria are probably tightly coupled to a number of other important biological processes. The loss of a regulator may lead to the rapid loss of its binding sites in a genome.
Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli
Authors: Gutierrez-Ríos Rosa María , Freyre-Gonzalez Julio A , Resendis Osbaldo , Collado-Vides Julio , Saier Milton , Gosset Guillermo
Published: June 2007

Background

Glucose is the preferred carbon and energy source for Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzyme activities in response to the presence of this sugar. To determine the extent of the cellular response to glucose, we applied an approach combining global transcriptome and regulatory network analyses.

Results

Transcriptome data from isogenic wild type and crp
- strains grown in Luria-Bertani medium (LB) or LB + 4 g/L glucose (LB+G) were analyzed to identify differentially transcribed genes. We detected 180 and 200 genes displaying increased and reduced relative transcript levels in the presence of glucose, respectively. The observed expression pattern in LB was consistent with a gluconeogenic metabolic state including active transport and interconversion of small molecules and macromolecules, induction of protease-encoding genes and a partial heat shock response. In LB+G, catabolic repression was detected for transport and metabolic interconversion activities. We also detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. Cluster analysis of a subset of genes revealed that CRP mediates catabolite repression for most of the genes displaying reduced transcript levels in LB+G, whereas Fis participates in the upregulation of genes under this condition. An analysis of the regulatory network, in terms of topological functional units, revealed 8 interconnected modules which again exposed the importance of Fis and CRP as directly responsible for the coordinated response of the cell. This effect was also seen with other not extensively connected transcription factors such as FruR and PdhR, which showed a consistent response considering media composition.

Conclusion

This work allowed the identification of eight interconnected regulatory network modules that includes CRP, Fis and other transcriptional factors that respond directly or indirectly to the presence of glucose. In most cases, each of these modules includes genes encoding physiologically related functions, thus indicating a connection between regulatory network topology and related cellular functions involved in nutrient sensing and metabolism.
Porto-systemic shunt using adrenal vein as a conduit; an alternative procedure for spleno – renal shunt
Authors: Aydin Unal , Yazici Pinar , Kilic Murat
Published: June 2007

Background

Currently, portal hypertension is still big problem for the patients with serious liver diseases. Variceal bleeding is one of the most important complications of portal hypertension. In case of failure of endoscopic and combined medical treatments, surgical decompressive shunts are required. We emphasized an alternative splenorenal shunt procedure using adrenal vein as a conduit.

Case presentation

A 26-year-old male suffered from recurrent variceal bleeding was considered for surgical therapy. Although we planned to perform a distal splenorenal shunt procedure, it was observed to be difficult. Therefore left adrenal vein was used as a conduit between left renal vein and splenic vein after splenic artery was ligated. He did well and was discharged from the hospital on the postoperative day 6. In the follow up period for nine months, endoscopic and ultrasonographic examinations were normal.

Conclusion

We concluded that, in case of failure to perform distal splenorenal shunt due to technical problems, alternative porto-systemic shunt procedure using the adrenal vein as a vascular conduit can be safely employed.
In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach
Authors: Dell'Orco Daniele , De Benedetti Pier Giuseppe , Fanelli Francesca
Published: June 2007

Background

Molecular recognition between enzymes and proteic inhibitors is crucial for normal functioning of many biological pathways. Mutations in either the enzyme or the inhibitor protein often lead to a modulation of the binding affinity with no major alterations in the 3D structure of the complex.

Results

In this study, a rigid body docking-based approach has been successfully probed in its ability to predict the effects of single and multiple point mutations on the binding energetics in three enzyme-proteic inhibitor systems. The only requirement of the approach is an accurate structural model of the complex between the wild type forms of the interacting proteins, with the assumption that the architecture of the mutated complexes is almost the same as that of the wild type and no major conformational changes occur upon binding. The method was applied to 23 variants of the ribonuclease inhibitor-angiogenin complex, to 15 variants of the barnase-barstar complex, and to 8 variants of the bovine pancreatic trypsin inhibitor-β Trypsin system, leading to thermodynamic and kinetic estimates consistent with in vitro data. Furthermore, simulations with and without explicit water molecules at the protein-protein interface suggested that they should be included in the simulations only when their positions are well defined both in the wild type and in the mutants and they result to be relevant for the modulation of mutational effects on the association process.

Conclusion

The correlative models built in this study allow for predictions of mutational effects on the thermodynamics and kinetics of association of three substantially different systems, and represent important extensions of our computational approach to cases in which it is not possible to estimate the absolute free energies. Moreover, this study is the first example in the literature of an extensive evaluation of the correlative weights of the single components of the ZDOCK score on the thermodynamics and kinetics of binding of protein mutants compared to the native state.

Finally, the results of this study corroborate and extend a previously developed quantitative model for in silico predictions of absolute protein-protein binding affinities spanning a wide range of values, i.e. from -10 up to -21 kcal/mol.

The computational approach is simple and fast and can be used for structure-based design of protein-protein complexes and for in silico screening of mutational effects on protein-protein recognition.
BK virus associated meningoencephalitis in an AIDS patient treated with HAART
Authors: Vidal José E , Fink Maria C , Cedeno-Laurent Filiberto , Delbue Serena , Ferrante Pasquale , Dauar Rafi F , Filho Francisco Bonasser , Nogueira Roberta Schiavon , Calore Eduardo E , Pannuti Claudio S , Roberto Trujillo J , Penalva de Oliveira Augusto C
Published: June 2007

A severely immune-suppressed AIDS patient was suspected of suffering from BK virus (BKV) meningoencephalitis, after being studied for common causes of neurological complications of co-infectious origin. Polymerase chain reaction (PCR) and sequence analysis of cerebrospinal fluid and brain samples, confirmed the presence of BKV. His clinical condition improved along with the regression of brain lesions, after modifications on his antiretroviral regime. Five months after discharge, the patient was readmitted because of frequent headaches, and a marked inflammatory reaction was evidenced by a new magnetic resonance imaging (MRI). The symptoms paralleled a rising CD4+ lymphocyte count, and immune reconstitution syndrome was suspected. This is the first non-postmortem report of BKV meningoencephalitis in an AIDS patient, showing clinical and radiographic improvement solely under HAART.
Repressor element-1 silencing transcription factor/neuronal restrictive silencer factor (REST/NRSF) can regulate HSV-1 immediate-early transcription via histone modification
Authors: Pinnoji Rajeswara C , Bedadala Gautam R , George Beena , Holland Thomas C , Hill James M , Hsia Shao-chung V
Published: June 2007

Background

During primary infection of its human host, Herpes Simplex Virus Type-1 (HSV-1) establishes latency in neurons where the viral genome is maintained in a circular form associated with nucleosomes in a chromatin configration. During latency, most viral genes are silenced, although the molecular mechanisms responsible for this are unclear. We hypothesized that neuronal factors repress HSV-1 gene expression during latency. A search of the HSV-1 DNA sequence for potential regulatory elements identified a Repressor Element-1/Neuronal Restrictive Silencer Element (RE-1/NRSE) located between HSV-1 genes ICP22 and ICP4. We predicted that the Repressor Element Silencing Transcription Factor/Neuronal Restrictive Silencer Factor (REST/NRSF) regulates expression of ICP22 and ICP4.

Results

Transient cotransfection indicated that REST/NRSF inhibited the activity of both promoters. In contrast, cotransfection of a mutant form of REST/NRSF encoding only the DNA-binding domain of the protein resulted in less inhibition. Stably transformed cell lines containing episomal reporter plasmids with a chromatin structure showed that REST/NRSF specifically inhibited the ICP4 promoter, but not the ICP22 promoter. REST/NRSF inhibition of the ICP4 promoter was reversed by histone deacetylase (HDAC) inhibitor Trichostatin A (TSA). Additionally, chromatin immuno-precipitation (ChIP) assays indicated that the corepressor CoREST was recruited to the proximity of ICP4 promoter and that acetylation of histone H4 was reduced in the presence of REST/NRSF.

Conclusion

Since the ICP4 protein is a key transactivator of HSV-1 lytic cycle genes, these results suggest that REST/NRSF may have an important role in the establishment and/or maintenance of HSV-1 gene silencing during latency by targeting ICP4 expression.
Downregulation of Selective microRNAs in Trigeminal Ganglion Neurons Following Inflammatory Muscle Pain
Authors: Bai Guang , Ambalavanar Rajini , Wei Dong , Dessem Dean
Published: June 2007

Active regulation of gene expression in the nervous system plays an important role in the development and/or maintenance of inflammatory pain. MicroRNA (miRNA) negatively regulates gene expression via posttranscriptional or transcriptional inhibition of specific genes. To explore the possible involvement of miRNA in gene regulation during inflammatory pain, we injected complete Freund's adjuvant (CFA) unilaterally into the rat masseter muscle and quantified changes in neuron-specific mature miRNAs in the trigeminal ganglion (TG). Real-time reverse-transcription polymerase chain reaction revealed significant, but differential, downregulation of mature miR-10a, −29a, −98, −99a, −124a, −134, and −183 in the ipsilateral mandibular division (V3) of the TG within 4 hr after CFA. In contrast, levels of tested miRNAs did not change significantly in the contralateral V3 or the ipsilateral ophthalmic and maxillary divisions of the TG from inflamed rats, nor in the ipsilateral V3 of saline-injected animals. The downregulated miRNAs recovered differentially to a level equal to or higher than that in naive animals. Full recovery time varied with miRNA species but was at least 4 days. Expression and downregulation of some miRNAs were further confirmed by in situ hybridization of TG neurons that innervate the inflamed muscle. Although neurons of all sizes expressed these miRNAs, their signals varied between neurons. Our results indicate that miRNA species specific to neurons are quickly regulated following inflammatory muscle pain.
Zac1 functions through TGFβIIto negatively regulate cell number in the developing retina
Authors: Ma Lin , Cantrup Robert , Varrault Annie , Colak Dilek , Klenin Natalia , Götz Magdalena , McFarlane Sarah , Journot Laurent , Schuurmans Carol
Published: June 2007

Background

Organs are programmed to acquire a particular size during development, but the regulatory mechanisms that dictate when dividing progenitor cells should permanently exit the cell cycle and stop producing additional daughter cells are poorly understood. In differentiated tissues, tumor suppressor genes maintain a constant cell number and intact tissue architecture by controlling proliferation, apoptosis and cell dispersal. Here we report a similar role for two tumor suppressor genes, the Zac1 zinc finger transcription factor and that encoding the cytokine TGFβII, in the developing retina.

Results

Using loss and gain-of-function approaches, we show that Zac1 is an essential negative regulator of retinal size. Zac1 mutants develop hypercellular retinae due to increased progenitor cell proliferation and reduced apoptosis at late developmental stages. Consequently, supernumerary rod photoreceptors and amacrine cells are generated, the latter of which form an ectopic cellular layer, while other retinal cells are present in their normal number and location. Strikingly, Zac1 functions as a direct negative regulator of a rod fate, while acting cell non-autonomously to modulate amacrine cell number. We implicate TGFβII, another tumor suppressor and cytokine, as a Zac1-dependent amacrine cell negative feedback signal. TGFβII and phospho-Smad2/3, its downstream effector, are expressed at reduced levels in Zac1 mutant retinae, and exogenous TGFβII relieves the mutant amacrine cell phenotype. Moreover, treatment of wild-type retinae with a soluble TGFβ inhibitor and TGFβ receptor II (TGFβRII) conditional mutants generate excess amacrine cells, phenocopying the Zac1 mutant phenotype.

Conclusion

We show here that Zac1 has an essential role in cell number control during retinal development, akin to its role in tumor surveillance in mature tissues. Furthermore, we demonstrate that Zac1 employs a novel cell non-autonomous strategy to regulate amacrine cell number, acting in cooperation with a second tumor suppressor gene, TGFβII, through a negative feedback pathway. This raises the intriguing possibility that tumorigenicity may also be associated with the loss of feedback inhibition in mature tissues.
The p160 Steroid Receptor Coactivator 2, SRC-2, Regulates Murine Endometrial Function and Regulates Progesterone-Independent and -Dependent Gene Expression
Authors: Jeong Jae-Wook , Lee Kevin Y. , Han Sang Jun , Aronow Bruce J. , Lydon John P. , O’Malley Bert W. , DeMayo Francesco J.
Published: June 2007

The role of the p160 steroid receptor coactivator 2 (SRC-2) in the regulation of uterine function and progesterone (P4) signaling was investigated by determining the expression pattern of SRC-2 in the murine uterus during pregnancy and the impact of SRC-2 ablation on uterine function and global uterine gene expression in response to progesterone. SRC-2 is expressed in the endometrial luminal and glandular epithelium from pregnancy d 0.5. SRC-2 is then expressed in the endometrial stroma on pregnancy d 2.5–3.5. Once the embryo is implanted, SRC-2 is expressed in the endometrial stromal cells in the secondary decidual zone. This compartmental expression of SRC-2 can be mimicked by treatment of ovariectomized mice with estrogen and P4. Ablation of SRC-2 in the uterus resulted in a significant reduction in the ability of the uterus to undergo a hormonally induced decidual reaction. Microarray analysis of RNA from uteri of wild-type and SRC-2−/− mice treated with vehicle or P4 showed that SRC-2 was involved in the ability of progesterone to repress specific genes. This microarray analysis also revealed that the uteri of SRC-2−/− mice showed alterations in genes involved in estrogen receptor, Wnt, and bone morphogenetic protein signaling. This analysis indicates that SRC-2 regulates uterine function by modulating the regulation of developmentally important signaling molecules and the ability of P4 to repress specific genes.
Efficiency of a self-aminoacylating ribozyme: Effect of the length and base-composition of its 3′ extension
Authors: Lehmann Jean , Reichel Amy , Buguin Axel , Libchaber Albert
Published: June 2007

Variants of a previously described small self-aminoacylating ribozyme are tested in order to uncover the potentialities of a 3′ extension responsible for the esterification. The base-composition and the length of this specific part of the ribozyme are investigated. Very short extensions can still reach the active site, reflecting the small persistence length of RNA. The yield of aminoacylation is particularly high for ribozymes with extensions made up of a poly-U, for which a maximum of efficiency is observed for a total length of about 10 nucleotides. A simple model describing the behavior of this region of the ribozyme can account for the data.
Stability of Complexes of Alkali Metal Cations with Tetraethyl p-tert-Butylcalix[4]arene Tetraacetate in the Water–Nitrobenzene Extraction System
Authors: Makrlík E. , Vaňura P.
Published: June 2007

From extraction experiments and γ-activity measurements, the exchange extraction constants corresponding to the general equilibrium M+(aq) + NaL+(nb) ⇔ ML+(nb) + Na+(aq) taking place in the two-phase water–nitrobenzene system (L = tetraethyl p-tert-butylcalix[4]arene tetraacetate; aq = aqueous phase, nb = nitrobenzene phase) were evaluated. Further, the stability constants of the ML+ complexes in water saturated nitrobenzene were calculated; they were found to increase in the cation order Cs+ < Rb+ < K+ < Li+ < Na+.
Fluorescence Quenching of Xanthene Dyes by TiO2
Authors: Kathiravan A. , Anbazhagan V. , Jhonsi M. Asha , Renganathan R.
Published: June 2007

The fluorescence quenching of xanthene dyes by TiO2 has been investigated using steady state technique. The dyes used are eosin, rhodamine B, rhodamine 6G. The quenching was found to obey Stern-Volmer equation and the corresponding Stern-Volmer plots were linear in the range of quencher concentration used [0–5 × 10--5] M. The quenching rate constant (k
q) is in the range of 0.77–8.30 × 1012 M-1 s-1. This study reveals effective quenching of xanthene dyes with TiO2. The quenching of xanthene dyes followed electron transfer mechanism.
Oxygen Tension Regulates Survival and Fate of Mouse Central Nervous System Precursors at Multiple Levels
Authors: Chen Hui-Ling , Pistollato Francesca , Hoeppner Daniel J. , Ni Hsiao-Tzu , McKay Ronald D.G. , Panchision David M.
Published: June 2007

Despite evidence that oxygen regulates neural precursor fate, the effects of changing oxygen tensions on distinct stages in precursor differentiation are poorly understood. We found that 5% oxygen permitted clonal and long-term expansion of mouse fetal cortical precursors. In contrast, 20% oxygen caused a rapid decrease in hypoxia-inducible factor 1α and nucleophosmin, followed by the induction of p53 and apoptosis of cells. This led to a decrease in overall cell number and particularly a loss of astrocytes and oligodendrocytes. Clonal analysis revealed that apoptosis in 20% oxygen was due to a complete loss of CD133loCD24lo multipotent precursors, a substantial loss of CD133hiCD24lo multipotent precursors, and a failure of remaining CD133hiCD24lo cells to generate glia. In contrast, committed neuronal progenitors were not significantly affected. Switching clones from 5% to 20% oxygen only after mitogen withdrawal led to a decrease in total clone numbers but an even greater decrease in oligodendrocyte-containing clones. During this late exposure to 20% oxygen, bipotent glial (A2B5+) and early (platelet-derived growth factor receptor α) oligodendrocyte progenitors appeared and disappeared more quickly, relative to 5% oxygen, and late stage O4+ oligodendrocyte progenitors never appeared. These results indicate that multipotent cells and oligodendrocyte progenitors are more susceptible to apoptosis at 20% oxygen than committed neuronal progenitors. This has important implications for optimizing ex vivo production methods for cell replacement therapies.

Disclosure of potential conflicts of interest is found at the end of this article.
A Novel, Immortal, and Multipotent Human Neural Stem Cell Line Generating Functional Neurons and Oligodendrocytes
Authors: De Filippis Lidia , Lamorte Giuseppe , Snyder Evan Y. , Malgaroli Antonio , Vescovi Angelo L.
Published: June 2007

The discovery and study of neural stem cells have revolutionized our understanding of the neurogenetic process, and their inherent ability to adopt expansive growth behavior in vitro is of paramount importance for the development of novel therapeutics based on neural cell replacement. Recent advances in high-throughput assays for drug development and gene discovery dictate the need for rapid, reproducible, long-term expansion of human neural stem cells (hNSCs). In this view, the complement of wild-type cell lines currently available is insufficient. Here we report the establishment of a stable human neural stem cell line (immortalized human NSCs [IhNSCs]) by v-myc-mediated immortalization of previously derived wild-type hNSCs. These cells demonstrate three- to fourfold faster proliferation than wild-type cells in response to growth factors but retain rather similar properties, including multipotentiality. By molecular biology, biochemistry, immunocytochemistry, fluorescence microscopy, and electrophysiology, we show that upon growth factor removal, IhNSCs completely downregulate v-myc expression, cease proliferation, and differentiate terminally into three major neural lineages: astrocytes, oligodendrocytes, and neurons. The latter are functional, mature cells displaying clear-cut morphological and physiological features of terminally differentiated neurons, encompassing mostly the GABAergic, glutamatergic, and cholinergic phenotypes. Finally, IhNSCs produce bona fide oligodendrocytes in fractions up to 20% of total cell number. This is in contrast to the negligible propensity of hNSCs to generate oligodendroglia reported so far. Thus, we describe an immortalized hNSC line endowed with the properties of normal hNSCs and suitable for developing the novel, reliable assays and reproducible high-throughput gene and drug screening that are essential in both diagnostics and cell therapy studies.

Disclosure of potential conflicts of interest is found at the end of this article.
Manipulating Nitrogen Release from Nitrogen‐Rich Crop Residues using Organic Wastes under Field Conditions
Authors: Chaves Barbara , De Neve Stefaan , Boeckx Pascal , Van Cleemput Oswald , Hofman Georges
Published: June 2007

Following mineralization of N‐rich crop residues, large amounts of mineral N can be released into the soil. Manipulating N mineralization of crop residues may be an option to reduce NO3− in soil. The potential to manipulate the N release from vegetable crop residues by using organic wastes was tested under field conditions. At the start of the experiment, cauliflower (Brassica oleracea L. var. botrytis L.) residues (∼73 Mg fresh matter ha−1) together with an immobilizer waste (∼5 Mg C ha−1 of straw, green waste compost, sawdust, or paper sludge) were incorporated into a silt loam soil. After 154 d, a remineralizing waste (∼1 Mg C ha−1 of vinasse or dairy sludge) was incorporated. During the field experiment, the mineral N content in the soil was measured at regular time intervals, and net N release, NO3− leaching, and denitrification were simulated using a N mineralization–immobilization model coupled to a NO3− leaching model. Straw, green waste compost, and sawdust were able to immobilize between 54 and 68% of the N released by the cauliflower residues and reduced NO3− leaching by 56 to 68%. Paper sludge released an extra amount of N due to its low C/N ratio. No consistent remineralization of N could be found in any of the treatments, probably due to an unsuitable composition of the remineralizer wastes. Manipulating N release of N‐rich crop residues by using organic wastes may be a suitable method to reduce NO3− leaching; however, stimulating remineralization of immobilized N by the start of the following spring may not be easy to achieve.
Edaphic Controls on Soil Organic Carbon Retention in the Brazilian Cerrado: Texture and Mineralogy
Authors: Zinn Yuri L. , Lal Rattan , Bigham Jerry M. , Resck Dimas V. S.
Published: June 2007

Soil organic carbon (SOC) retention is a function of climate, vegetation, drainage, and management interactions, but also of intrinsic soil properties such as texture, mineralogy, and structure. To assess these edaphic controls, three soils of the Brazilian savanna (Cerrado) under similar climate, vegetation, and slope but of contrasting texture were sampled to 1‐m depth and characterized for textural, chemical, and mineralogical properties, and SOC concentration (in bulk samples and clay, silt, and sand fractions). The basic assumption was that SOC particle size determines its retention mechanism: colloidal forms are retained by sorption, while particulate organic matter (>20 μm) can occur outside or inside aggregates. It was hypothesized that SOC retention is controlled simultaneously by soil texture, mineralogy, and depth. The three soils are clayey, loamy, and sandy Haplustox, all kaolinitic with minor contents of Fe and Al oxides, vermiculite, and illite. The SOC concentrations in particle size fractions were inversely related to the content of the respective fraction in soil (SOC dilution effect), thus SOC partition is better assessed by determination of SOC pools in each particle size on a total soil mass basis rather than on a size‐fraction concentration basis. The positive linear relations between SOC and clay + silt concentrations in bulk soil were explained mostly by greater clay‐sized SOC pools, which could be modeled as a function of clay content (related to specific surface area) and depth. Quantitative clay mineralogy showed that bulk SOC and clay‐sized SOC pools were well correlated with Fe oxides in topsoil and amorphous Al oxides in subsoil, but this mineralogical control is secondary to the textural control, since it depends on clay content.
Edaphic Controls on Soil Organic Carbon Retention in the Brazilian Cerrado: Soil Structure
Authors: Zinn Yuri L. , Lal Rattan , Bigham Jerry M. , Resck Dimas V. S.
Published: June 2007

Soil structure can be an important factor affecting soil organic carbon (SOC), but it is also a dynamic property affected by texture, mineralogy, land use, soil fauna, and also SOC. Assuming that structure affects SOC mostly by occlusion of particulate organic matter (POM) within aggregates, it was hypothesized that structure exerts a major control on SOC retention in soils of the Brazilian Cerrado region. Water‐stable aggregates (WSA) were obtained from the 1‐m depth of three different‐textured, uncultivated soils. The mean weight diameter (MWD) of WSA was used as a structural indicator, and SOC concentrations were determined in intact WSA and their respective sand fractions (estimating occluded POM). Clay + silt content in bulk soils was correlated with MWD in all depths but more strongly in the top 10 cm. Although equally correlated with clay + silt contents, SOC concentrations were well correlated with MWD only in the 0‐ to 5‐cm layer. Sand‐free SOC concentrations in WSA fractions were proportional to sand content, indicating that the SOC dilution effect reported in particle size fractionations occurs naturally in the soil fabric. Occlusion of POM within aggregates was proportional to clay + silt contents, but this did not result in larger total POM pools, and the weak correlations obtained did not warrant predictive models. Aggregates produced by macrofauna comprised a minor but significant part of the soil and were mostly SOC enriched. We concluded that the structural control on SOC retention is less significant than the textural and mineralogical controls, since aggregation depends on those properties and is not as strongly correlated with SOC concentration and POM occlusion.
Pore Shrinkage Dependency of Inorganic and Organic Soils on Wetting and Drying Cycles
Authors: Peng X. , Horn R. , Smucker A.
Published: June 2007

Cycles of wetting and drying (WD) occur naturally in soils and affect the pore structure through altered hydraulic stresses. Two organic‐rich soils, a Eutric Histosol and a Histic Gleysol, and two inorganic soils, a Calcic Gleysol and a Dystric Gleysol, ranging in texture and microstructure, were investigated. Undisturbed soil samples were predried to either −100 kPa water potential by using a ceramic plate or to 30°C by using an oven and then resaturated for one or three WD cycles. In addition, different combinations defined by the intensity, frequency, and sequence of WD cycles were analyzed. Soil structure was altered significantly if the intensity of drying was severe at 30°C, while drying to −100 kPa had only a small effect. The frequency and sequence of WD cycles did not alter the structure and shrinkage behavior significantly. Compared with the initial pore volume, intense WD cycles decreased it by 23.6 to 60.1% in the two organic‐rich soils, whereas it increased by 1.5 to 4.8% in the silty Calcic Gleysol and by 3.6 to 15.1% in the clayey Dystric Gleysol. Both organic‐rich soils showed more shrinkage but less swelling than did the two inorganic soils. Intense WD cycles altered the water potential vs. void ratio curves of the two organic‐rich soils more gradually, while steeper patterns were observed for the two inorganic soils. This study shows that the changes in soil structure and pore shrinkage depend mostly on the maximum intensity of previous WD cycles.
Overestimation of Phosphorus Adsorption Capacity in Reduced Soils: An Artifact of Typical Batch Adsorption Experiments
Authors: Brand-Klibanski S. , Litaor M. I. , Shenker M.
Published: June 2007

Although soil reduction often results in P release to soil solutions, many researchers have observed an increased maximum P adsorption (Smax) following soil reduction. We hypothesized that this result is an experimental artifact caused by exposure of the reduced soils to aerobic conditions and by the use of high P additions, which may result in precipitation. Four semiarid altered wetland soils were incubated under reduced conditions, followed by reoxidation, and their P‐adsorption characteristics were measured under atmospheric and N2–atmosphere conditions. During the reductive incubation, soluble P and Fe concentrations increased. In one of the soils, P and Fe were monitored after reoxidation and both were found to decrease. The reduction–reoxidation cycle has led to increased Smax values. Under an N2 atmosphere, the equilibrium P concentrations at zero adsorption (EPC0) of all soils were higher than those determined under atmospheric conditions, whereas no significant changes were observed in Smax values. Oversaturation of the equilibrating solutions with respect to P minerals suggested P precipitation and overestimation of Smax at high added P concentrations under both aerobic and N2–atmosphere conditions. We conclude that aerobic batch experiments of reduced soils are affected by P adsorption to newly in‐tube‐formed ferric oxides. In accordance, we stress the importance of the EPC0 rather than the Smax as an informative measure of P adsorption, and the need for using low‐P experiments and maintaining anaerobic conditions in evaluating P adsorption of reduced soils.
Relationships between Soybean Yield, Soil pH, and Soil Carbonate Concentration
Authors: Rogovska Natalia P. , Blackmer Alfred M. , Mallarino Antonio P.
Published: June 2007

Soybean [Glycine max (L.) Merrill] often shows symptoms of iron deficiency chlorosis (IDC) on high pH, calcareous soils of the U.S. Midwest. The objective of this study was to assess the variation in soybean yield that could be explained by soil pH and carbonate concentration in Iowa fields. Color aerial images of soybean canopy taken from 2000 to 2002 from 12 fields having acid to calcareous soils were used to select 10 to 28 sampling areas 10 to 25 m2 in size to encompass significant variability in early soybean growth and IDC symptoms in each field. Representative areas 0.93 m2 in size were identified through field observations to collect soil samples and measure grain yield. Soil pH measured to a 15‐cm depth across fields ranged from 5.6 to 8.2 and calcium carbonate equivalent (CCE) ranged from 0 to 30%. Soil CCE varied from 2.5 to 30% as pH ranged from 7.7 to 8.2. Grain yield decreased with increasing pH and CCE in 9 and 11 fields, respectively. Soil pH and CCE explained 30 and 41% of the variability in relative yield across sites, respectively. An alkalinity stress index (ASI) that combined both measurements (pH + 0.14CCE) was developed based on the relative effects of each measurement on yield and explained 45% of the yield variability across sites. The index developed was a better predictor of soybean yield in fields with high‐pH soils than each measurement alone.
Organic Matter in Volcanic Ash Soils under Forest and Páramo along an Ecuadorian Altitudinal Transect
Authors: Nierop Klaas G. J. , Tonneijck Femke H. , Jansen Boris , Verstraten Jacobus M.
Published: June 2007

The volcanic ash soils along an altitudinal transect in Guandera Biological Station in northern Ecuador have been developed under varying vegetation around the upper forest line. Generally, the soils currently covered by forest are composed of Fulvic Andosols (melanic index >1.7) while those under páramo (tropical alpine grasslands) have developed into Melanic Andosols. This vegetation effect on soil formation is believed to be associated with differences in organic matter composition. In this study, we examined whether Fulvic Andosols differed from Melanic Andosols in organic matter composition. Using analytical pyrolysis techniques, we found hardly any differences in the organic matter characteristics related to vegetation cover, not even between soils that supposedly have been covered by forest and páramo for millennia. Small differences were found within the lipid compounds, while the polysaccharides and lignin were virtually absent from the (deeper) mineral soil horizons. The low abundance of polysaccharides in soils that have undergone severe organic matter decomposition is not unusual for most soils, but is uncommon in other Andosols studied with the same pyrolysis techniques.
Soil Aggregate‐ and Particle‐Associated Organic Carbon under Different Land Uses in Nepal
Authors: Shrestha B. M. , Singh B. R. , Sitaula B. K. , Lal R. , Bajracharya R. M.
Published: June 2007

Soil aggregation is an important process of C sequestration and hence a useful strategy to mitigate the increase in concentration of atmospheric CO2We studied water stability of soil aggregates (WSA) and soil organic carbon (SOC) associated with aggregates and primary particles in surface (0–10 cm) and subsurface (10–20 cm) layers of cultivated (khet, irrigated lowland, andbari, rainfed upland) and forest lands (denseShoreaforest, degraded forest and shrub land, pine–Shoreaforest,Shorea–pine–Schimaforest, andSchima–Castanopsisforest) in a mountain watershed of Nepal. Macroaggregates (>2 mm) were abundant in forest soils (41–70%) while microaggregates (<0.5 mm) were abundant (56–63%) in cultivated lands. Pine mixed forest contained more macroaggregates in both layers. Mean WSA in the surface soil was highest inShorea–pine–Schimaforest (96%) and lowest inkhet(74%). Macroaggregates in the surface layers contained 14.9 to 24.8 and 5.5 to 20.7 g kg−1SOC in cultivated and forest soils, respectively, while microaggregates contained 12.5 to 30.8 and 11.9 to 25.4 g kg−1SOC, respectively. The forest soils contained more sand (639–834 g kg−1) and fewer clay particles (49–95 g kg−1) than the cultivated soils. Soils under natural forest, however, were characterized by higher SOC associated with all primary particles. Cultivated soils contained higher amounts of clay but less clay‐associated SOC than forest soils. The relation between clay content and clay‐associated SOC was explained by a quadratic function (R2= 0.45,P= 0.002).
Deterministic and probabilistic approaches to the development of pH total maximum daily loads: a comparative analysis
Authors: Elshorbagy A. , Parasuraman K. , Putz G. , Ormsbee L.
Published: June 2007

The most commonly used deterministic approach to the development of total maximum daily loads (TMDLs) fails to explicitly address issues related to a margin of safety and inherent variability of streamflows in the process of TMDL development. In this paper, the deterministic approach to pH TMDL development for Beech Creek watershed, Muhlenberg County, Kentucky, proposed by Ormsbee, Elshorbagy and Zechman is discussed. The shortcomings and the limitations of the assumptions associated with the deterministic approach are highlighted. An alternative probabilistic approach, to cope with the percentile-based water quality standards based on Monte Carlo simulation, is presented and compared to the deterministic approach. The proposed probabilistic approach provides a deeper insight into the issue of uncertainty and emphasizes the importance of handling the water quality standards and TMDLs in terms of magnitude and frequency rather than a single-valued approach. Expected exceedances and the confidence of compliance with percentile-based standards are estimated. Accordingly, an objective method of estimating the margin of safety for pH TMDLs is proposed.
Spherical crystals of celecoxib to improve solubility, dissolution rate and micromeritic properties
Authors: Gupta Venkadari , Mutalik Srinivas , Patel Madhobhai , Jani Girish
Published: June 2007

Spherical crystals of celecoxib to improve solubility, dissolution rate and micromeritic properties

Celecoxib spherical agglomerates were prepared with polyvinylpyrrolidone (PVP) using acetone, water and chloroform as solvent, non-solvent and bridging liquid, respectively. The agglomerates were characterized by differential scanning calorimetry (DSC), X-ray diffraction (XRD), IR spectroscopic studies and scanning electron microscopy (SEM). The IR spectroscopy and DSC results indicated the absence of any interactions between drug and additives. XRD studies showed a decrease in crystallinity in agglomerates. The crystals exhibited significantly improved micromeritic properties compared to pure drug. The loading efficiency (% or mg drug per 100 mg crystals) was in the range of 93.9 ± 2.3 and 97.3 ± 1.3% (n = 3) with all formulations. The aqueous solubility and dissolution rate of the drug from crystals was significantly (p < 0.05) increased (nearly two times). The solubility andin vitrodrug release rates increased with an increase in PVP concentration (from 2.5 to 10%). The SEM studies showed that the crystal posseses a good spherical shape with smooth and regular surface.
Development and in vitro evaluation of buccoadhesive carvedilol tablets
Authors: Yamsani Vamshi , Gannu Ramesh , Kolli Chandrasekhar , Rao M. , Yamsani Madhusudan
Published: June 2007

Development andin vitroevaluation of buccoadhesive carvedilol tablets

Buccoadhesive tablets of carvedilol were prepared using HPMC K4M, HPMC K15M and Carbopol 934 as mucoadhesive polymers. Fifteen formulations were developed with varying concentrations of polymers. Formulations of the BC or BD series were composed of HPMC K4M or HPMC K15M in ratios of 1:1 to 1:5 whereas in the BE series Carbopol 934 was used (1:0.25 to 1:1.50). The formulations were tested forin vitrodrug release,in vitrobioadhesion, moisture absorption andin vitrodrug permeation through porcine buccal mucosa. Formulation BC3 showed maximum release of the drug (88.7 ± 0.4%) with the Higuchi model release profile and permeated 21.5 ± 2.9% of the drug (flux 8.35 ± 0.291 μg h-1cm-2) permeation coefficient 1.34 ± 0.05 cm h-1) through porcine buccal membrane. BC3 formulation showed 1.62 ± 0.15 N of peak detachment force and 0.24 ± 0.11 mJ of work of adhesion. FTIR results showed no evidence of interaction between the drug and polymers. XRD study revealed that the drug is in crystalline form in the polymer matrix. The results indicate that suitable bioadhesive buccal tablets with desired permeability could be prepared.
Topical dosage form of valdecoxib: Preparation and pharmacological evaluation
Authors: Kesavanarayanan K. , Nappinnai Mohanavelu , Ilavarasan Raju
Published: June 2007

Topical dosage form of valdecoxib: Preparation and pharmacological evaluation

Valdecoxib, a selective COX-2 inhibitor, produces serious side effects when given orally. This has led to its withdrawal. Topical application of valdecoxib was formulated and evaluated for its efficacy and safety. Standard procedures were followed and male Wistar albino rats were used to test the anti-inflammatory effect and effect in hyperalgesic conditions. Ointments, creams, and gels containing valdecoxib 1% (m/m) were prepared. These were tested for physical appearance, pH, spreadability, drug content uniformity,in vitrodiffusion. Gel prepared using Carbopol 940 (F-X) was selected after the analysis of the results. Formulation F-X was evaluated for acute skin irritancy, anti-inflammatory effect, optimum effective concentration of valdecoxib, effect on hyperalgesia, inhibition of the granulation tissue formation and anti-arthritic effect. Determination of valdecoxib in test animals plasma and determining the blood clotting time and bleeding time were conducted to study the safety of topical valdecoxib. Valdecoxib gel containing 1% (m/m) of the drug was significantly (p< 0.05) more effective in inhibiting hyperalgesia associated with inflammation, compared to placebo gel, but exhibited significantly (p< 0.05) lower suppression of inflammation than commercial rofecoxib gel. Concentration of valdecoxib used in the preparation minimizes the risk of systemic effects, as shown by the analysis of rat plasma for the presence of valdecoxib; hence, this may be the alternative to oral preparations. The bleeding and clotting time showed no significant difference before and after application of F-X.