bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract

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.
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

Abstract
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.
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

Abstract
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

Abstract
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.
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 propertiesCelecoxib 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 tabletsBuccoadhesive 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 evaluationValdecoxib, 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.
Use of ceric ammonium sulphate and two dyes, methyl orange and indigo carmine, in the determination of lansoprazole in pharmaceuticals
Authors: Basavaiah Kanakapura , Ramakrishna Veeraiah , Kumar Urdigere 
Published: June 2007

Use of ceric ammonium sulphate and two dyes, methyl orange and indigo carmine, in the determination of lansoprazole in pharmaceuticalsTwo spectrophotometric methods are proposed for the assay of lansoprazole (LPZ) in bulk drug and in dosage forms using ceric ammonium sulphate (CAS) and two dyes, methyl orange and indigo carmine, as reagents. The methods involve addition of a known excess of CAS to LPZ in acid medium, followed by determination of residual CAS by reacting with a fixed amount of either methyl orange, measuring the absorbance at 520 nm (method A), or indigo carmine, measuring the absorbance at 610 nm (method B). In both methods, the amount of CAS reacted corresponds to the amount of LPZ and the measured absorbance was found to increase linearly with the concentration of LPZ, which is corroborated by the correlation coefficients of 0.9979 and 0.9954 for methods A and B, respectively. The systems obey Beer's law for 0.5-7.0 μg mL-1and 0.25-3.0 μg mL-1for methods A and B, respectively. The apparent molar absorptivities were calculated to be 3.0 x 104and 4.4 x 104L mol-1cm-1for methods A and B, respectively. The limits of detection (LOD) and quantification (LOQ) were calculated to be 0.08 and 0.25 μg mL-1for method A, and 0.09 and 0.27 μg mLs-1for method B, respectively. The intra-day and inter-day precision and accuracy of the methods were evaluated according to the current ICH guidelines. Both methods were of comparable accuracy (er≤ 2 %). Also, both methods are equally precise as shown by the relative standard deviation values < 1.5%. No interference was observed from common pharmaceutical adjuvants. The accuracy of the methods was further ascertained by performing recovery studies using the standard addition method. The methods were successfully applied to the assay of LPZ in capsule preparations and the results were statistically compared with those of the literature UV-spectrophotometric method by applying Student'st-test andF-test.