bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divergence pattern of animal gene families and relationship with the Cambrian explosion
Authors: Miyata Takashi , Suga Hiroshi 
Published: August 2002

AbstractThere are many gene families that are specific to multicellular animals. These have either diverged from ancestral genes that are shared with fungi and/or plants or evolved from an ancestral gene unique to animals. The evolution of gene families involved in cell–cell communication and developmental control has been studied to establish whether the number of member genes increased dramatically immediately prior to or in concert with the Cambrian explosion. A molecular phylogeny‐based analysis of several animal‐specific gene families has revealed that gene diversification by duplication occurred during two active periods interrupted by a long intervening quiescent period. Intriguingly, the Cambrian explosion is situated in the silent period, indicating that there is no direct link between the first burst of gene diversification and the Cambrian explosion itself. The importance of gene recruitment as a possible molecular mechanism for morphological diversity, and its possible role for the Cambrian explosion, are discussed. BioEssays 23:1018–1027, 2001. © 2001 John Wiley & Sons, Inc.
Genetics of the Drosophila flight muscle myofibril: a window into the biology of complex systems
Authors: Vigoreaux Jim O. 
Published: August 2002

AbstractThis essay reviews the long tradition of experimental genetics of the Drosophila indirect flight muscles (IFM). It discusses how genetics can operate in tandem with multidisciplinary approaches to provide a description, in molecular terms, of the functional properties of the muscle myofibril. In particular, studies at the interface of genetics and proteomics address protein function at the cellular scale and offer an outstanding platform with which to elucidate how the myofibril works. Two generalizations can be enunciated from the studies reviewed. First, the study of mutant IFM proteomes provides insight into how proteins are functionally organized in the myofibril. Second, IFM mutants can give rise to structural and contractile defects that are unrelated, a reflection of the dual function that myofibrillar proteins play as fundamental components of the sarcomeric framework and biochemical “parts” of the contractile “engine”. BioEssays 23:1047–1063, 2001. © 2001 John Wiley & Sons, Inc.
Viability, strength, and fragmentation of Saccharopolyspora erythraea in submerged fermentation
Authors: Stocks S. M. , Thomas C. R. 
Published: August 2002

AbstractTwo fermentations of the commercially impor‐tant erythromycin‐producing filamentous bacterium Saccharopolyspora erythraea were conducted in defined media. One was glucose‐limited and the other nitrate‐limited. The viability of the hyphae was determined using the fluorescent stain BacLightTM (Molecular Probes, Eugene, OR). Also, the force required to strain hyphae to breakage was determined using micromanipulation and a sensitive force transducer. In both fermentations, fragmentation coincided with the appearance of regions in the mycelia with permeabilised membranes (considered nonviable). Under glucose‐limitation, hyphal breaking force rose to 1,050 ± 130 nN at the end of the growth phase and fell to an undetectable value as a result of glucose exhaustion. Under nitrate‐limitation, hyphal breaking force fell from 900 ± 160 nN during the growth phase to 550 ± 40 nN in the stationary phase. In both cases image analysis showed that the dimensions of mycelia were of the same order, suggesting that the major factor influencing fragmentation was the appearance of nonviable regions (assumed to be weak). The location in which nonviable regions first appear within hyphae could not be determined because of their appearance coinciding with fragmentation. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 75: 702–709, 2001.
Expression of functional mammalian P450 2E1 in hairy root cultures
Authors: Banerjee Suchitra , Shang Tanya Q. , Wilson Angela M. , Moore Allison L. , Strand Stuart E. , Gordon Milton P. , Lafferty Doty Sharon 
Published: August 2002

AbstractP450 2E1 is an important mammalian liver enzyme known to metabolize a wide range of compounds including several common environmental pollutants. The medicinal plant,Atropa belladonna, was transformed withAgrobacterium rhizogenescontaining a binary vector with rabbit P450 2E1 in either the sense or antisense orientation. The resulting “hairy roots” were isolated and grown in liquid medium. Production of P450 2E1 protein was verified in the roots containing the 2E1 gene in the sense orientation. Transgenic and control root cultures were dosed with the environmental pollutant, trichloroethylene (TCE), and were analyzed for the TCE metabolites, chloral and trichloroethanol. The root cultures expressing the mammalian P450 2E1 had increased levels of the metabolites compared to the levels in the control roots. This method represents a quick way to screen transformants for expression of foreign genes before regeneration of whole plants, and also as a possible source of foreign protein for purification. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 462–466, 2002; DOI 10.1002/bit.10151
Toluene biofiltration by the fungus Scedosporium apiospermum TB1
Authors: García‐Peña E. I. , Hernández S. , Favela‐Torres E. , Auria R. , Revah S. 
Published: August 2002

AbstractThe performance of biofilters inoculated with the fungus Scedosporium apiospermum was evaluated. This fungus was isolated from a biofilter which operated with toluene for more than 6 months. The experiments were performed in a 2.9 L reactor packed with vermiculite or with vermiculite‐granular activated carbon as packing material. The initial moisture content of the support and the inlet concentration of toluene were 70% and 6 g/m3, respectively. As the pressure drop increased from 5–40 mm H2O a strong initial growth was observed. Stable operation was maintained for 20 days with a moisture content of 55% and a biomass of 33 mg biomass/g dry support. These conditions were achieved with intermittent addition of culture medium, which permitted a stable elimination capacity (EC) of 100 g/m3reactorh without clogging. Pressure drop across the bed and CO2 production were related to toluene elimination. Measurement of toluene, at different levels of the biofilter, showed that the system attained higher local EC (200 g/m3rh) at the reactor outlet. These conditions were related to local humidity conditions. When the mineral medium was added periodically before the EC decreases, EC of approximately 258 g/m3rh were maintained with removal efficiencies of 98%. Under these conditions the average moisture content was 60% and 41 mg biomass/g dry support was produced. No sporulation was observed. Evaluation of bacterial content and activities showed that the toluene elimination was only due to S. apiospermum catabolism. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 76: 61–69, 2001.
Process for degradation of nitrobenzene: Combining electron beam irradiation with biotransformation
Authors: Zhao Jian‐Shen , Ward Owen P. , Lubicki Piotr , Cross James D. , Huck Peter 
Published: August 2002

AbstractElectron beam irradiations of aqueous solutions containing 15–30 mg/L of nitrobenzene at 60 kGy dose removed 78% of the contaminant. Three mononitrophenols were detected as by‐products of electron beam treatment of nitrobenzene. A mixed culture enriched on a mixture of 2‐, 3‐, and 4‐nitrophenol degraded both the residual nitrobenzene and the nitrophenol products. Percentage removal of nitrobenzene increased with increasing electron beam dose. This observation led to the conceptual design of a two‐stage electron beam microbial process for degradation of nitrobenzene. Three groups of pure isolates were characterized from the mixed culture based on their abilities to grow on cor‐ responding nitrophenol substrates: Group A, 2NP−3NP−4NP+; Group B, 2NP+3NP+4NP−; and Group C, 2NP−3NP+4NP−. Bacteria that grew on 3‐NP transformed nitrobenzene into ammonia in the electron beam‐treated nitrobenzene samples. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 73: 306–312, 2001.
Fluorescent detection of cyanobacterial DNA using bacterial magnetic particles on a MAG‐microarray
Authors: Matsunaga Tadashi , Nakayama Hideki , Okochi Mina , Takeyama Haruko 
Published: August 2002

AbstractBacterial magnetic particles (BMPs) were used for the identification of cyanobacterial DNA. Genus‐specific oligonucleotide probes for the detection of Anabaena spp., Microcystis spp., Nostoc spp., Oscillatoria spp., and Synechococcus spp. were designed from the variable region of the cyanobacterial 16S rDNA of 148 strains. These oligonucleotide probes were immobilized on BMPs via streptavidin‐biotin conjugation and employed for magnetic‐capture hybridization against digoxigenin‐labeled cyanobacterial 16S rDNA. Bacterial magnetic particles were magnetically concentrated, spotted in 100‐μm‐size microwell on MAG‐microarray, and the fluorescent detection was performed. This work details the development of an automated technique for the magnetic isolation, the concentration of hybridized DNA, and the detection of specific target DNA on MAG‐microarray. The entire process of hybridization and detection was automatically performed using a magnetic‐separation robot and all five cyanobacterial genera were successfully discriminated. © 2001 John Wiley & Sons, Inc., Biotechnol Bioeng 73: 400–405, 2001.
Effects of charged water‐soluble polymers on the stability and activity of yeast alcohol dehydrogenase and subtilisin Carlsberg
Authors: Foreman Trudi M. , Khalil Mona , Meier Paul , Brainard James R. , Vanderberg Laura A. , Sauer Nancy N. 
Published: August 2002

AbstractRemarkable increases in enzyme catalytic stability resulting from addition of charged water‐soluble polymers have recently been reported, suggesting that use of these polymers may be an attractive general strategy for enzyme stabilization. To test the proposed hypothesis that coulombic forces between water‐soluble polymers and enzymes are primarily responsible for enzyme stabilization, we examined the catalytic stability and activity of two enzymes in the presence of polymers differing in net charge. All polymers tested increased enzyme lifetimes, regardless of their net charge, suggesting that stabilization of these enzymes by water‐soluble polymers is not solely dependent on simple electrostatic interactions between the polymers and enzymes. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 76: 241–246, 2001.
High‐performance liquid chromatographic profiling of fluorescent labelled N‐glycans on glycoproteins
Authors: Yuen C.‐T. , Gee C. K. , Jones C. 
Published: August 2002

AbstractMonitoring protein glycosylation is becoming increasingly important as novel recombinant glycoprotein therapeutics, such as glycoprotein hormones, cytokines and clotting factors, are introduced into clinical use. In this report, we describe an HPLC strategy and an improved and simplified pre‐column derivatization procedure to profile N‐linked glycans obtained from a variety of commercially available glycoproteins as examples. N‐Glycans were first released by peptide:N‐glycosidase F and labelled with the fluorescent label, 4‐aminobenzoic acid by reductive amination. The labelled N‐Glycans were then resolved by normal‐phase HPLC and the N‐glycan profile could be further improved by separating the N‐glycans first according to charge by anion‐exchange HPLC prior to the normal‐phase HPLC. If required, identification of the fractionated derivatized oligosaccharides can be determined by mass spectrometry. The whole profiling process is simple and can be implemented in most laboratories. Because of the high sensitivity, batch glycan‐analysis of low‐yield recombinant glycoproteins such as samples in ampoules or obtained in the early stage of production development is possible. Copyright © 2002 John Wiley & Sons, Ltd.
Determination of 24,25‐dihydroxyvitamin D3 in human plasma using liquid chromatography‐mass spectrometry after derivatization with a Cookson‐type reagent
Authors: Higashi Tatsuya , Awada Dalsuke , Shimada Kazutake 
Published: August 2002

AbstractA practical LC‐MS method for determination of (24R)‐24,25‐dihydroxyvitamin D3 [24,25(OH)2D3] in human plasma has been developed using derivatization with a Cookson‐type reagent, 4‐[4‐(6‐methoxy‐2‐benzoxazolyl)phenyl]‐1,2,4‐triazoline‐3,5‐dione (MBOTAD). The derivatization with MBOTAD significantly improved the ionization efficiency of the analyte with a detection limit of 18 fmol [equivalent to 7.5 pg of 24,25(OH)2D3] per injection. The method employed protein precipitation with acetonitrile, purification with OASIS HLB cartridge and silica gel column, derivatization with MBOTAD and atmospheric pressure chemical ionization MS detection. The mass spectrometer was operated in the positive‐ion mode of mass chromatography and [26,26,26,27,27,27‐2H6]‐24,25(OH)2D3 was used as an internal standard. The intra‐ and inter‐assay coefficients of variation were below 3.4 and 2.5%, respectively, and the analytical recovery of 24,25(OH)2D3 was quantitative. Assay linearity was obtained in the range of 0.05–1.2 ng per tube and the limit of quantitation was 0.23 ng/mL for a 0.3 mL plasma aliquot. The developed method was applied to plasma samples obtained from volunteers and gave satisfactory results. Copyright © 2001 John Wiley & Sons, Ltd.
Abbreviations used:

CPBA

Competitive protein binding assay

DBP

vitamin D binding protein

DMEQ7AD

4‐[2‐(6,7‐dimethoxy‐4‐methyl‐3‐oxo‐3,4‐dihydroxyvitaminyl)ethyl]‐1,2,4‐triazoline‐3,5‐dione

MBOTAD

4‐[4‐(6‐methoxy‐2‐benzoxazolyl)phenyl]‐1,2,4‐triazoline‐3,5‐dione

1,25(OH)2D3

1α,25‐dihydroxyvitamin D3

24,25(OH)2D3

(24R)‐24,25‐dihydroxyvitamin D3

25,26(OH)2D3

25,26‐dihydroxyvitamin D3

PTAD

4‐phenyl‐1,2,4‐triazoline‐3,5‐dione
Use of fluorescently labelled deoxyribonuclease I to spatially measure G‐actin levels in migrating and non‐migrating cells
Authors: Cramer L. P. , Briggs L. J. , Dawe H. R. 
Published: August 2002

AbstractLamellipodium protrusion is linked to actin filament disassembly in migrating fibroblasts [Cramer, 1999: Curr. Biol. 9:1095–1105]. To further study this relationship, we have identified a method to specifically and sensitively detect G‐actin in distinct spatial locations in motile cells using deoxyribonuclease I (DNase I). Although DNase I can bind both G‐ and F‐actin in vitro [Mannherz et al., 1980: Eur. J. Biochem. 95:377–385], when cells were fixed in formaldehyde and permeabilized in detergent, fluorescently‐labelled DNase I specifically stained G‐actin and not F‐actin. 92–98% of actin molecules were stably retained in cells during fixation and permeabilization. Further, increasing or decreasing cellular G‐actin concentration by treating live cells with latrunculin‐A or jasplakinolide, respectively, caused a respective increase and decrease in DNase I cell‐staining intensity as expected. These changes in DNase I fluorescence intensity accurately reflected increases and decreases in cellular G‐actin concentration independently measured in lysates prepared from drug‐treated live cells (regression coefficient = 0.98). This shows that DNase I cell‐staining is very sensitive using this method. Applying this method, we found that the ratio of G‐/F‐actin is lower in both the lamellipodium and in a broad band immediately behind the lamellipodium in migrating compared to non‐migrating fibroblasts. Thus, we predict that protrusion of the lamellipodium in migrating fibroblasts requires tight coupling to filament disassembly at least in part because G‐actin is relatively limited within and behind the lamellipodium. This is the first report to directly demonstrate high sensitivity of cell‐staining for any G‐actin probe and this, together with the ready commercial accessibility of fluorescently‐labelled DNase I, make it a simple, convenient, and sensitive tool for cell‐staining of G‐actin. Cell Motil. Cytoskeleton 51:27–38, 2002. © 2002 Wiley‐Liss, Inc.
Multiple antibodies to titin immunoreact with AHNAK and localize to the mitotic spindle machinery
Authors: Wernyj Roman P. , Ewing Charles M. , Isaacs William B. 
Published: August 2002

AbstractRecently, the large filamentous striated‐muscle protein titin has been observed in non‐muscle cells, and, in one instance, has been proposed to have a nuclear function as a chromosomal component contributing to structure and elasticity. In this study, we sought to further characterize the presumptive nuclear isoform of titin. Immunofluorescence microscopy with multiple titin‐specific monoclonal antibodies shows localization to the nucleus in interphase cells and to the spindle machinery in mitotic cells in all cell types examined; localization to condensed chromosomes is not observed. An abundant 700‐kDa phosphoprotein is the predominant species immunoprecipitated with these antibodies. Sequencing of peptide fragments of the immunopurified protein reveals identity to AHNAK, a nuclear phosphoprotein, an identification that was confirmed by Western blot analysis with antibodies to AHNAK and peptide fragmentation patterns. Sequence comparison suggests similarities between the repetitive heptad ϕ±ϕP±ϕ± motif in AHNAK and the PEVK region of titin, potentially explaining the cross‐reactivity observed between AHNAK antibodies and titin antibodies. Interestingly, although some AHNAK antibodies stain interphase nuclei, no evidence of mitotic spindle localization is seen, suggesting that the identity of the protein at the latter location is more closely related to titin than AHNAK. This concept is further supported by observations that cell lines not expressing AHNAK have similar antititin antibody localization to the mitotic spindle. We conclude that (1) multiple titin antibodies, particularly those recognizing the PEVK region, cross‐react with AHNAK, and (2) the mitotic spindle staining observed with antititin antibodies is most likely due to the association of titin or a titin‐like molecule with this structure. Cell Motil. Cytoskeleton 50:101–113, 2001. © 2001 Wiley‐Liss, Inc.
Precise microdissection of human bladder carcinomas reveals divergent tumor subclones in the same tumor
Authors: Cheng Liang , Gu Jian , Ulbright Thomas M. , MacLennan Gregory T. , Sweeney Christopher J. , Zhang Shaobo , Sanchez Katya , Koch Michael O. , Eble John N. 
Published: August 2002

AbstractBACKGROUNDHuman bladder carcinoma is thought to arise from a field change that affects the entire urothelium. Whether independently transformed urothelial cell populations exist in the same patient is uncertain.METHODSWe studied the clonality of urinary bladder carcinoma in 18 female patients who underwent cystectomy for urothelial carcinoma. None had multiple tumors. Tumor samples were obtained from different areas of the same tumor. Sixty‐seven tumor samples were analyzed. Tumor genomic DNA was microdissected and extracted from formalin‐fixed, paraffin‐embedded slides. The clonality of urothelial tumors was evaluated on the basis of a polymorphism of the X chromosome‐linked human androgen receptor gene (HUMARA) locus. The technique is dependent on digestion of DNA with the methylation‐sensitive restriction enzyme HhaI, polymerase chain reaction (PCR) amplification of HUMARA locus, and detection of methylation of this locus. With this method, only the methylated HUMARA allele is selectively amplified by PCR.RESULTSEleven of 18 patients were informative. Nonrandom inactivation of the X chromosome was found in 9 of the 11 informative patients (82%). Seven patients showed different patterns of nonrandom X chromosome inactivation for tumor samples obtained from different regions of the same tumor. Two patients showed the same pattern of nonrandom X chromosome inactivation in all samples.CONCLUSIONSSome muscle‐invasive urothelial carcinomas may arise from independently transformed progenitor urothelial cells, supporting the “field effect” theory for bladder carcinogenesis. Cancer 2002;94:104–10. © 2002 American Cancer Society.
Pathologic features of superficial esophageal squamous cell carcinoma with lymph node and distal metastasis
Authors: Araki Koshi , Ohno Shinji , Egashira Akinori , Saeki Hiroshi , Kawaguchi Hidetoshi , Sugimachi Keizo 
Published: August 2002

AbstractBACKGROUNDEndoscopic mucosal resection (EMR) is a less invasive localized treatment for patients with esophageal carcinoma. However, indications for EMR use in cases of superficial esophageal carcinoma are controversial. The authors evaluated histopathologic risk factors for lymph node metastasis and recurrence.METHODSIn the specimens resected, the authors examined depth, the superficial area and the area attached to or infiltrating the lamina muscularis mucosa.RESULTSThe authors found that the superficial area and the attached or infiltrated area reflected the depth of the tumor. However, there was a recurrence of esophageal carcinoma even in m3 cases attached only to the lamina muscularis mucosa.CONCLUSIONSThe authors concluded that m1 and m2 esophageal carcinoma had almost no risk of lymph node metastasis and recurrence no matter how extensive the superficial area. In addition, sm2 and sm3 carcinoma have a high frequency of lymph node metastasis and recurrence. M3 and sm1 carcinoma run the risk of lymph node metastasis and recurrence however small the superficial area and the area attached to or infiltrating the lamina muscularis mucosa. Treatment strategies for patients with superficial esophageal carcinoma, including EMR, should take the above findings into account. Cancer 2002;94:570–5. © 2002 American Cancer Society.
Undifferentiated sarcoma of the liver in childhood
Authors: Bisogno Gianni , Pilz Thorsten , Perilongo Giorgio , Ferrari Andrea , Harms Dieter , Ninfo Vito , Treuner Jorn , Carli Modesto 
Published: August 2002

AbstractBACKGROUNDUndifferentiated (embryonal) sarcoma of the liver (UESL) is a rare childhood hepatic tumor, and it is generally considered an aggressive neoplasm with an unfavorable prognosis.METHODSThe Soft Tissue Sarcoma Italian and German Cooperative Groups enrolled 17 children with UESL in studies conducted between 1979 and 1995. They were treated using the same multimodal approach as for patients with sarcomas including conservative surgery at diagnosis, multiagent chemotherapy, and second‐look operation in cases of residual disease. Radiotherapy was occasionally used (2 of 17 patients).RESULTSTwelve patients are alive with follow‐up ranging from 2.4 to 20 years. Eight underwent complete tumor resection either at diagnosis or after preoperative chemotherapy, and all are currently alive. After initial chemotherapy tumor reduction was evident in six of nine evaluable cases. Overall three patients died of disease and one of a surgical complication. One child died in second complete remission for a non‐disease‐related cause.CONCLUSIONSThe current prognosis of UESL no longer should be regarded as poor. Modern multimodal treatment and supportive therapy have improved survival. Cancer 2002;94:252–7. © 2002 American Cancer Society.