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PubMed2001

On-site solid-phase extraction and laboratory analysis of ultra-trace synthetic musks in municipal sewage effluent using gas chromatography-mass spectrometry in the full-scan mode.

Fragrance materials such as synthetic musks in aqueous samples, are normally determined by gas chromatography-mass spectrometry in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of 1-1 samples. Full-scan mass spectra are required to verify that a target analyte has been found by comparison with the mass spectra of fragrance compounds in the National Institute of Standards and Technology (NIST) mass spectral library. A 1-1 sample usually provides insufficient analyte for full scan data acquisition. This paper describes an on-site extraction method developed at the US Environmental Protection Agency (Las Vegas, NV, USA) for synthetic musks from 60 l of wastewater effluent. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for a wide array of synthetic musks. Quantification of these compounds was achieved from the full-scan data directly, without the need to acquire SIM data. The detection limits obtained with this method are an order of magnitude lower than those obtained from liquid-liquid and other solid-phase extraction methods. This method is highly reproducible, and recoveries ranged from 80 to 97% in spiked sewage treatment plant effluent. The high rate of sorbent-sample mass transfer eliminated the need for a methanolic activation step, which reduced extraction time, labor, and solvent use. More samples could be extracted in the field at lower cost. After sample extraction, the light-mass cartridges are easily transported and stored.

Fatty Acids, Monounsaturated↗
PubMed1993

Documenting nursing and health care history in the mid-Atlantic region.

The records of health care institutions can be of great value to library patrons. Yet, librarians rarely provide these unique resources because records must be collected, arranged, and described before they can be useful to patrons. The University of Pennsylvania's Center for the Study of the History of Nursing conducted a survey of health care agencies in the mid-Atlantic region to locate records created by area health care institutions. The goals of this project were to develop a database of primary source materials, to place organizational records with enduring value at suitable repositories, and to assist in the development of in-house archival programs at agencies keeping records. In-house programs provide health care institutions with a systematic way to preserve their records for administrative, legal, fiscal, and research use. Such programs also facilitate access to information, reduce cost through records management, and promote an institution through preservation and use of its historical records. The survey demonstrated that record keeping is not coordinated in most institutions, and that institutional awareness of the organization or content of records is minimal.

Archives↗
PubMed1988

Genomic structure and evolution of the human pepsinogen A multigene family.

A human cosmid library was screened with a pepsinogen A (PGA) cDNA probe, yielding 18 clones with (parts of) one, two or three PGA genes. By aligning these cosmids a restriction map of a PGA gene quadruplet was obtained in which the four genes are arranged in a highly ordered fashion in a head-to-tail orientation. Using the length in kilobases of the large polymorphic EcoRI fragment of the PGA genes, this quadruplet can be described as 15.0-12.0-12.0-16.6. An AvaII polymorphism allowed us to identify the two PGA haplotypes of the individual whose DNA had been cloned in the cosmid library to be a gene triplet and a gene quadruplet. By comparing the restriction maps of the central 12.0 genes in these multiplets to those of the flanking 15.0 and 16.6 genes, we postulate that these central genes arose from unequal but homologous crossing over between two 15.0-16.6 gene pairs. This hypothesis provides for the creation of a variety of haplotypes by additional cross overs and mutations. Southern blots of family and population material supports the existance of at least five common PGA haplotypes, including a single-gene haplotype, giving rise to a large number of different EcoRI patterns. The single PGA gene is probably the reciprocal crossing over product. Comparison between the DNA and protein polymorphisms suggests further micro-heterogeneity in the different PGA haplotypes.

Biological Evolution↗
PubMed2003

Beneficial properties of single-domain antibody fragments for application in immunoaffinity purification and immuno-perfusion chromatography.

We explored the possibility to apply single-domain antibodies from Camelidae for immunoaffinity purification of the ice structuring protein (ISP) from Lolium perenne, which modifies ice crystal growth and therefore has potential application in medicine, biotechnology, agriculture and (frozen) foods. Using phage display together with an appropriate selection method, a group of candidate fragments was isolated from a llama-derived immune library. Affinity chromatography using a purposely selected antibody coupled to a matrix yielded a completely pure and functional ISP. Due to the extreme refolding capabilities and physical stability of single-domain antibodies, the affinity matrix could be regenerated more than 2000 times without loss of capacity, while the fragment's monomeric nature permitted an efficient elution of antigen. The results of this study show that highly pure proteins can be recovered from biological material in a single-step process.

Amino Acid Sequence↗
PubMed2001

HPLC and GC-MS screening of Chinese proprietary medicine for undeclared therapeutic substances.

Traditional Chinese medicine includes raw medicinal materials and Chinese proprietary medicine (CPM). Despite being of natural origin, toxic effects, adulteration with synthetic therapeutic substances and even deaths had been associated with CPM. There is thus a need to develop analytical technique to rapidly screen for undeclared toxic and therapeutic substances in CPM. In this study, a high performance liquid chromatography-diode-array detection method was developed and used to screen for undeclared therapeutic substances in CPM. An ultraviolet (UV) library of 266 drugs had been compiled. Solute identification was performed by comparing the analytical data (UV spectra, retention time and relative retention time) with those of the 266 standards. Gas chromatography-mass spectrometry was used as a confirmation method. These chromatographic methods had been shown to be selective and reproducible in screening for undeclared drugs in CPM. Using the method developed, 41 CPM samples in seven categories were screened for undeclared therapeutic substances. One anti-asthmatic CPM was found to contain codeine.

Chromatography, High Pressure Liquid↗
PubMed2002

The N-myc and c-myc downstream pathways include the chromosome 17q genes nm23-H1 and nm23-H2.

Gain of chromosome 17q material is the most frequent genetic abnormality in neuroblastomas. The common region of gain is at least 375 cR large, which has precluded the identification of genes with a role in neuroblastoma pathogenesis. Neuroblastoma also frequently show amplification of the N-myc oncogene, which correlates closely with 17q gain. Both events are strong predictors of unfavorable prognosis. To identify genes that are part of the N-myc downstream pathway, we constructed SAGE libraries of an N-myc transfected and a control cell line. This identified the chromosome 17q genes nm23-H1 and nm23-H2 as being 6-10 times induced in the N-myc expressing cells. Northern and Western blot analysis confirmed this up-regulation. Time-course experiment shows that both genes are induced within 4 h after N-myc is switched on. Furthermore, we demonstrate also that c-myc can up-regulate nm23-H1 and nm23-H2 expression. Neuroblastoma tumor and cell line panels reveal a striking correlation between N-myc amplification and mRNA and protein expression of both nm23 genes. We show that the nm23 genes are located at the edge of the common region of chromosome 17q gain previously described in neuroblastoma cell lines. Our findings suggest that nm23-H1 and nm23-H2 expression is increased by 17q gain in neuroblastoma and can be further up-regulated by myc overexpression. These observations suggest a major role for nm23-H1 and nm23-H2 in tumorigenesis of unfavorable neuroblastomas.

Chromosomes, Human, Pair 17↗
PubMed1991

A Mr 46,000 human milk fat globule protein that is highly expressed in human breast tumors contains factor VIII-like domains.

The human milk fat globule has proved to be a good source of antigenic material for production of antibodies against surface components of breast epithelial cells. Monoclonal antibodies against one of the major components of the human milk fat globule, which identify a glycoprotein with an apparent molecular weight of 46,000, have been found to be useful for both breast cancer diagnosis and therapy. In order to characterize this Mr 46,000 glycoprotein, specific monoclonal antibodies were used to select complementary DNAs from a lambda gt11 expression library from lactating breast. The largest complementary DNA insert (BA46-1) was 1270 base pairs and encoded 217 amino acids. A single 2.2-kilobase RNA was specifically detected in a variety of carcinoma cell lines, using this complementary DNA probe, and it was overexpressed in some carcinoma lines. The mRNA levels correlated with the level of expression of the antigen in these cell lines as detected by Western blot analysis. Sequence analysis revealed strong homology of the Mr 46,000 glycoprotein with serum factors VIII and V, in the region implicated in phospholipid binding.

Amino Acid Sequence↗
PubMed2001

Prognostic factor studies in oncology: osteosarcoma as a clinical example.

OBJECTIVE: Prognostic factor studies are abundant in oncology. Nevertheless, most of them have very limited impact on clinical practice, in part because many of them have a low statistical power. The importance of statistical power is illustrated using bootstrap resampling of data from a series of osteosarcoma patients. METHODS AND MATERIALS: Osteosarcoma is a rare disease, the incidence being just a few cases per million person-years in the Western World. Very few Phase III studies have been conducted in the disease, and much knowledge on therapeutic progress has come from Phase II studies. This has caused controversy concerning the validity of historical controls, which again has stimulated interest in the identification of prognostic factors in this disease. A literature search in the National Library of Medicine MEDLINE database was performed to identify prognostic factor studies in osteosarcoma published between 1975 and 1998. Monte Carlo methods, so-called bootstrap resampling, are used to investigate the importance of sample size based on survival data for a previously published series of 158 osteosarcomas treated with surgery alone. RESULTS: Most published studies are too small to provide useful information on prognostic factors in osteosarcoma. Three-quarters of the papers reviewed included less than 100 patients with osteosarcoma. More than 20 different potential prognostic factors were included in these papers. Inherent differences between studies and poor reporting hamper a synthesis of information from various studies. The results from the bootstrap resampling illustrate how the majority of published studies would miss even quite significant prognostic factors. CONCLUSIONS: An effort is needed to improve the design, conduct, and reporting of prognostic studies in oncology.

Bone Neoplasms↗
PubMed1986

Isolation of biologically active RNA from human autopsy for the study of cystic fibrosis.

Biologically active RNA has been isolated from several tissues implicated in the pathogenesis of the genetic disease cystic fibrosis. To ensure that mRNA from stomach and pancreas has not been degraded, it must be isolated within 2 h postmortem, while intact RNA can be isolated from lung material up to 20 h postmortem. It is imperative that tissue removed during autopsy be dispersed in a strong denaturant buffer (guanidine isothiocyanate) to inactivate nucleases. While stomach and pancreas yields of RNA are low, relative to the amount of gland material, yields of RNA from lung samples are sufficient for the further isolation of mRNA by oligo(dT)-cellulose chromatography. The biological integrity of subsequently isolated mRNA has been assessed by AMV-reverse transcriptase cDNA synthesis as well as by in vitro translation. Protein products generated in this manner show distinct differences from mRNA translation patterns of age- and sex-matched controls when compared with mRNA from CF samples. R0t analysis of cDNA libraries thus generated indicates that the complexity of such libraries is representative of the starting RNA species.

Autopsy↗
PubMed1993

Molecular cloning and characterization of ficolin, a multimeric protein with fibrinogen- and collagen-like domains.

We have previously identified and purified transforming growth factor-beta 1 (TGF-beta 1)-binding proteins from porcine uterus membranes (Ichijo, H., Rönnstrand, L., Miyagawa, K., Ohashi, H., Heldin, C.-H., and Miyazono, K. (1991) J. Biol. Chem. 266, 22459-22464). One of these TGF-beta 1-binding proteins, with a molecular weight of 40,000, was purified to homogeneity and subjected to amino acid sequence analysis. The amino acid sequences obtained were used to isolate two closely related cDNA clones from a porcine uterus cDNA library. The deduced amino acid sequences revealed that both cDNAs encoded proteins that were mainly composed of fibrinogen-like and collagen-like domains. Therefore, they were denoted ficolin-alpha and ficolin-beta. Expression of ficolin-alpha and -beta cDNA in mammalian cells revealed that ficolin forms dimers, trimers, and several higher order of oligomers, whose molecular weights fit well with those of the purified TGF-beta 1-binding proteins from porcine uterus. Moreover, immunoblotting analysis using a peptide anti-serum against ficolin indicated that the TGF-beta 1-binding proteins identified in porcine uterus are ficolin-alpha, -beta, and their oligomers or closely related molecules. However, recombinant ficolin-alpha and -beta did not bind TGF-beta 1, despite the similarities in molecular weights and immunoreactivity with the material from the natural source. It is possible that a specific posttranslational modification of ficolin or interaction with another component is needed for TGF-beta 1 binding. Analysis by Northern blotting revealed that the expression of ficolin-alpha mRNA is relatively restricted and most abundant in placenta and lung. On the other hand, ficolin-beta was mainly expressed in skeletal muscle. The in vivo functions of ficolin will be discussed.

Amino Acid Sequence↗
PubMed2006

Conformational selectivity of peptides for single-walled carbon nanotubes.

Carbon nanotubes show promising prospects for applications ranging from molecular electronics to ultrasensitive biosensors. An important aspect to understanding carbon nanotube properties is their interactions with biomolecules such as peptides and proteins, as these interactions are important in our understanding of nanotube interactions with the environment, their use in cellular systems, as well as their interface with biological materials for medical and diagnostic applications. Here we report the sequence and conformational requirements of peptides for high-affinity binding to single-walled carbon nanotubes (SWNTs). A new motif, X(1)THX(2)X(3)PWTX(4), where X(1) is G or H, X(2) is H or D or null, X(3) is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. The high affinity binding of the motif to SWNTs required constrained conformations which were achieved through either the extension of the amino acid sequence (e.g., LLADTTHHRPWT) or the addition of a constrained disulfide bond (e.g., CGHPWTKC). This motif shows specific high-affinity to the currently studied SWNTs, compared to previously reported peptides. The conformations of the identified peptides in complex with SWNTs were also characterized with a variety of biophysical methodologies including CD, fluorescence, NMR spectroscopy, and molecular modeling.

Amino Acid Sequence↗
PubMed1998

Kinetic analysis of the mechanism and specificity of protein-disulfide isomerase using fluorescence-quenched peptides.

Protein-disulfide isomerase (PDI) is an abundant folding catalyst in the endoplasmic reticulum of eukaryotic cells. PDI introduces disulfide bonds into newly synthesized proteins and catalyzes disulfide bond isomerizations. We have synthesized a library of disulfide-linked fluorescence-quenched peptides, individually linked to resin beads, for two purposes: 1) to probe PDI specificity, and 2) to identify simple, sensitive peptide substrates of PDI. Using this library, beads that became rapidly fluorescent by reduction by human PDI were selected. Amino acid sequencing of the bead-linked peptides revealed substantial similarities. Several of the peptides were synthesized in solution, and a quantitative characterization of pre-steady state kinetics was carried out. Interestingly, a greater than 10-fold difference in affinity toward PDI was seen for various substrates of identical length. As opposed to conventional PDI assays involving larger polypeptides, the starting material for this assay is homogenous. It is furthermore simple and highly sensitive (requires less than 0.5 microgram of PDI/assay) and thus opens the possibility for quantitative determination of PDI activity and specificity.

Amino Acid Sequence↗
PubMed2005

Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1.

Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes nano-sized magnetites, referred to as magnetosomes, aligned intracellularly in a chain. The potential of this nano-sized material is growing and will be applicable to broad research areas. It has been expected that genome analysis would elucidate the mechanism of magnetosome formation by magnetic bacteria. Here we describe the genome of Magnetospirillum sp. AMB-1 wild type, which consists of a single circular chromosome of 4967148 bp. For identification of genes required for magnetosome formation, transposon mutagenesis and determination of magnetosome membrane proteins were performed. Analysis of a non-magnetic transposon mutant library focused on three unknown genes from 2752 unknown genes and three genes from 205 signal transduction genes. Partial proteome analysis of the magnetosome membrane revealed that the membrane contains numerous oxidation/reduction proteins and a signal response regulator that may function in magnetotaxis. Thus, oxidation/reduction proteins and elaborate multidomain signaling proteins were analyzed. This comprehensive genome analysis will enable resolution of the mechanisms of magnetosome formation and provide a template to determine how magnetic bacteria maintain a species-specific, nano-sized, magnetic single domain and paramagnetic morphology.

Bacterial Proteins↗
PubMed2006

Improving the quality of randomized controlled trials in Chinese herbal medicine, part III: quality control of Chinese herbal medicine used in randomized controlled trials.

OBJECTIVE: To discuss quality control of Chinese herbal medicine (CHM) in randomized controlled trials (RCTs), and to provide suggestions for improving this aspect in future clinical study in this therapeutic area. METHODS: A search of the Cochrane Library was conducted to identify RCTs of CHM. Quality control information reported in those RCTs was then assessed independently. RESULTS: The search yielded a total of 167 RCTs of CHM for a variety of conditions. A total of 11 CHM preparations were used in those RCTs. Only one trial discussed quality control of the CHM interventions used. Issues affecting the safety and efficacy of CHM products used in RCTs were discussed including standardization of raw herbal materials, processing methods, screening for product contamination, and effects of combination products. CONCLUSION: The overall quality of reporting of RCTs of CHM was poor, reflecting the need for improvements in reporting future clinical trials in this area. RECOMMENDATIONS: To improve quality control of CHM used in RCTs in future, we recommend developing and implementing guidelines such as Good Agricultural Practice (GAP) for Chinese crude drugs, and current Good Manufacturing Practice (GMP) specific to CHM products. Chemical analyses of individual herbs of CHM and combination products are also recommended to provide reference standards for quality control.

Drugs, Chinese Herbal↗
PubMed1989

Isolation and partial sequencing of the human prothymosin alpha gene family. Evidence against export of the gene products.

Prothymosin alpha and thymosin alpha 1 are believed to be thymus-derived, hormone-like materials with immunomodulatory functions performed outside the cell. These functions are inconsistent with the existence of a full length cDNA clone that does not encode an amino-terminal signal peptide or several consecutive hydrophobic residues. A study of the prothymosin alpha mRNAs and genes was undertaken in search of evidence for secreted forms of the protein. Prothymosin alpha mRNA was localized exclusively on free, rather than membrane-bound, polysomes. Upon screening cosmid and plasmid libraries totaling 2 X 10(6) clones, a gene family consisting of six members was identified. Sequence information from the 5'-ends of all the genes indicated that none encodes an amino-terminal signal peptide. One of the genes, apparently by means of alternate splicing, gives rise to two prothymosin alpha mRNAs, one of which has an additional internal glutamic acid codon with respect to the other. Comparison of the translated nucleic acid sequences of the five remaining genes with those encoded in the mRNAs revealed 30-98% homology in the first 50 amino acids. These five genes appear to be processed genes and/or pseudogenes. The localization of prothymosin alpha mRNAs on free polysomes, together with the partial nucleotide sequences of the genes, strongly suggest an intracellular function for prothymosin alpha. Therefore, the possibility must be raised that prothymosin alpha and its peptide derivatives act as xenobiotics when introduced into assays of immune function.

Amino Acid Sequence↗
PubMed2004

Region-specific expression and secretion of the fibrinogen-related protein, fgl2, by epithelial cells of the hamster epididymis and its role in disposal of defective spermatozoa.

The cauda epididymidis functions in the storage and protection of mature, fertile spermatozoa. We previously identified a region-specific secretory glycoprotein (termed HEP64) of the hamster proximal cauda epididymidis that specifically bound and coated the nonviable, but not the viable, spermatozoa within the epididymal lumen. In this study we employed expression screening of a hamster epididymal cDNA library to obtain the full-length sequence of HEP64 and to identify it as the fibrinogen-like protein fgl2. Northern blot analysis demonstrated that fgl2 mRNA is highly expressed by the proximal cauda epididymidis in comparison to other hamster tissues examined, and, in situ hybridization analysis of the epididymis revealed that fgl2 mRNA exhibited a region- and principal cell-specific expression pattern. Immunohistochemistry confirmed the association of fgl2 with abnormal spermatozoa in the cauda epididymidis and revealed smaller fgl2-containing particles. Immunoelectron microscopy revealed that fgl2 was distributed throughout an amorphous, "death cocoon," complex assembled onto abnormal spermatozoa and that the smaller fgl2 aggregates consisted of the amorphous material with embedded sperm fragments, organelles, and membrane vesicles. A protocol was developed to isolate an enriched death cocoon fraction. SDS-PAGE and microsequence analyses revealed that the Mr 64,000 fgl2 monomer was assembled into two disulfide-linked oligomers of Mr 260,000 and 280,000. These data demonstrate that the epididymis possesses a specific mechanism to identify and envelop defective spermatozoa with a protein complex containing the fibrinogen-like protein fgl2. We propose that this represents an important protective mechanism not only to shield the viable sperm population from potentially deleterious enzymes released by dying spermatozoa but also to prevent the release of sperm proteins that could initiate an immune response if they escaped the epididymal environment.

Amino Acid Sequence↗
PubMed2003

Anaerobic digestion of manure and mixture of manure with lipids: biogas reactor performance and microbial community analysis.

Anaerobic digestion of cattle manure and a mixture of cattle manure with glycerol trioleate (GTO) was studied in lab-scale, continuously stirred tank reactors (CSTR) operated at 37 degrees C. The reactor codigesting manure and lipids exhibited a significantly higher specific methane yield and a higher removal of VS than the reactor treating manure. Microbial population analysis done by cultivation--most probable number (MPN) test and specific methanogenic activity (SMA) measurement, revealed higher MPN and increased SMA of methanogenic populations of biomass from the reactor codigesting manure and lipids. Spatial microbial distribution and activity was studied in digested materials fractionated into size of particles > 200 microm, 50-200 microm and 0.45-50 microm. With manure, the main pool of methanogenic activity from propionate, butyrate and hydrogen was associated with the particles > 200 microm, while the activity of acetotrophic methanogens was uniformly distributed in all fractions. When digesting manure and lipids, an enhanced methanogenesis was detected both for particles > 200 microm and the 50-200 microm fraction. The molecular methods--temperature gradient gel electrophoresis (TGGE), cloning library and sequencing of 16S rDNA--showed presence of a restricted number of archaeal species in both reactors. The vast majority of clones was phylogenetically most closely related to Methanosarcina siciliae.

Agriculture↗
PubMed1987

Isolation of human Y chromosomal major repetitive sequences from a flow-sorted Y chromosomal library.

The human Y chromosome is highly heterochromatic and consists mainly of repetitive sequences, of which 3.4 kb HaeIII or EcoR1 fragments represent the most abundant species. From a flow-sorted human Y chromosomal library, we isolated 15 clones containing sequences highly homologous to this major repetitive sequence. Although the size of inserts varied from 0.7 to 3.8 kb, their hybridization patterns to human genomic DNA were indistinguishable from each other. These repetitive sequences unambiguously detected the presence of the Y chromosome in a male-female DNA mixture of which 5% was derived from male cells. Thus, these clones would be useful molecular tools to detect contaminating male cells in clinical materials.

Cell Line↗