Cloning and deletion mutagenesis using direct protein-protein interaction on an expression vector. Identification of the calmodulin binding domain of alpha-fodrin

We have screened a lambda gt11 library, constructed with mouse macrophage cDNA, in order to isolate clones that code for calmodulin binding proteins. We have developed a new approach for this purpose using radioactive calmodulin (produced by genetic engineering) to detect fusion proteins that interact with this protein with high affinity. A cDNA clone that codes for mouse macrophage fodrin was isolated, sequenced and identified. By deleting part of the sequence the calmodulin binding domain was located on the fodrin sequence. The site is situated on repeat 11 of fodrin and probably on the extra arm of this repeat. The method we developed is widely applicable to site-directed mutagenesis of interacting proteins.     

The structure of the carbohydrate units of the carboxyl-terminal peptide of procollagen as elucidated by 500 MHz 1H-NMR spectroscopy

The oligosaccharides of chick embryo type I procollagen were isolated from the carboxyl-terminal propeptide fragment by exhaustive digestion with papain and pronase, and then purified as a mixture of glycopeptides. The structures of the oligosaccharides were established by high-resolution ¹H-NMR spectroscopy and found to be a mixture with respect to the non-reducing terminal residues as shown below:

The percentages refer to the relative amount of those mannose residues present in the mixture. The data suggest that the oligosaccharides are a microheterogeneous mixture of high-mannose type glycans containing between six and nine mannose residues per carbohydrate unit. Such carbohydrate chains, although not uncommon for glycoproteins, had never been found before for collagen or collagen-related compounds.     

Recent advances in ABE fermentation: hyper-butanol producing Clostridium beijerinckii BA101

This is an overview of the mutant strain Clostridium beijerinckii BA101 which produces solvents (acetone–butanol–ethanol, ABE) at elevated levels. This organism expresses high levels of amylases when grown on starch. C. beijerinckii BA101 hydrolyzes starch effectively and produces solvent in the concentration range of 27–29 g l⁻¹. C. beijerinckii BA101 has been characterized for both substrate and butanol inhibition. Supplementing the fermentation medium (MP2) with sodium acetate enhances solvent production to 33 g l⁻¹. The results of studies utilizing commercial fermentation medium and pilot plant-scale reactors are consistent with the results using small-scale reactors. Pervaporation, a technique to recover solvents, has been applied to fed-batch reactors containing C. beijerinckii BA101, and solvent production as high as 165 g l⁻¹ has been achieved. Immobilization of C. beijerinckii BA101 by adsorption and use in a continuous reactor resulted in reactor productivity of 15.8 g l⁻¹ h⁻¹. Recent economic studies employing C. beijerinckii BA101 suggested that butanol can be produced at US$0.20–0.25 lb⁻¹ by employing batch fermentation and distillative recovery. Application of new technologies such as pervaporation, fed-batch culture, and immobilized cell reactors is expected to further reduce these prices. Journal of Industrial Microbiology & Biotechnology (2001) 27, 287–291. Received 12 September 2000/ Accepted in revised form 27 January 2001     

The effect of diethyl- -fluoroglutarate on phosphates and glutamate in slices of rabbit cerebral cortex

Abstract— The diethyl ester of α-fluoroglutarate (DEFG), an inhibitor of glutamate dehydrogenase, was prepared, and its effect on glutamate and phosphates in slices of rabbit cerebral cortex was examined. The primary effect of the drug on cortical slices incubating in a Krebs-Ringer glucose medium was to decrease the tissue levels of glutamate in association with decreased levels and turnover of high-energy phosphates. Assimilation of exogenous glutamate by the slices was partially blocked in the presence of the drug and severely depressed oxidative phosphorylation resulted when glutamate and DEFG were both present in the incubation mixture. The results suggested a significant relationship between the activity of cerebral glutamate dehydrogenase and oxidative phosphorylation. During incubation in a Krebs-Ringer glucose medium the endogenous pool of free amino acids in the cortical slice partitioned with the medium. Little or no glutamate, aspartate or GABA was present in the medium after incubation, but glycine, alanine, threonine, serine and glutamine did partition to varying degrees, with over one-half of the glutamine present in the incubation medium. With the exception of ‘leakage’ of aspartate, the partitioning patterns were relatively unaffected by the presence of added glutamate or DEFG.     

NH2-terminal sequence of calf fetuin

Calf fetuin, one of the 3 major known fetal proteins has been isolated by a two-step purification procedure and characterized by aminoacid composition. The purified glycoprotein, which consisted of a single chain, was submitted to 47 steps of automatic aminoacid sequencing, allowing to determine 44 positions. This section of the molecule was devoid of carbohydrates. Comparison of this sequence with a variety of detectable potentially related protein did not allow to point to any detectable homology.     

Occurrence of Strongyloides stercoralis in Yunnan Province, China, and comparison of diagnostic methods

Background

Strongyloides stercoralis is a neglected soil-transmitted helminth species, and there is a lack of parasitologic and epidemiologic data pertaining to this parasite in China and elsewhere. We studied the local occurrence of S. stercoralis in a village in Yunnan province, China, and comparatively assessed the performance of different diagnostic methods.

Methodology/Principal Findings

Multiple stool samples from a random population sample were subjected to the Kato-Katz method, an ether-concentration technique, the Koga agar plate method, and the Baermann technique. Among 180 participants who submitted at least 2 stool samples, we found a S. stercoralis prevalence of 11.7%. Males had a significantly higher prevalence than females (18.3% versus 6.1%, p = 0.011), and infections were absent in individuals <15 years of age. Infections were only detected by the Baermann (highest sensitivity) and the Koga agar plate method, but neither with the Kato-Katz nor an ether-concentration technique. The examination of 3 stool samples rather than a single one resulted in the detection of 62% and 100% more infections when employing the Koga agar plate and the Baermann technique, respectively. The use of a mathematical model revealed a ‘true’ S. stercoralis prevalence in the current setting of up to 16.3%.

Conclusions/Significance

We conclude that S. stercoralis is endemic in the southern part of Yunnan province and that differential diagnosis and integrated control of intestinal helminth infections needs more pointed emphasis in rural China.     

Identification of staphylococcal enterotoxin B domains involved in binding to cultured human kidney proximal tubular cells: imparting proliferation and death

Studies suggest that staphylococcal enterotoxin B (SEB) is initially harbored in the kidney by binding to digalactosylceramide molecules in the proximal tubular cells. However, little is known in regard to the peptide motif within SEB that binds to these cells and imparts toxic effects. Herein, using human kidney proximal tubular cells (PTs) we have performed a systematic study on the binding of various peptides and peptide analogs of SEB and demonstrate a structure-functional relationship. Using [(125)I]labeled SEB peptides, we show a high affinity and displaceable binding of SEB 191-220 to human PT cells. Binding was mitigated by the use of antibody against SEB, by digalactosylceramide (the putative receptor), and by the use of endoglycoceramidase, which selectively removes the oligosaccharide backbones from glycosphingolipids. Our structure/ functional studies revealed that peptide 130-160 induces a concentration-dependent increase in programmed cell death/ apoptosis in human proximal tubular cells. Mechanistic studies further suggest that SEB/SEB peptide (130-160) impart apoptosis via the activation of neutral sphingomyelinase, which hydrolizes sphingomyelin to ceramide and phosphocholine. SEB 130-160 mediated apoptosis was mitigated by preincubation of cells with antibody against SEB and an SEB 130-160 antibody.     

GeneCite: a stand-alone open source tool for high-throughput literature and pathway mining

Systematic extraction of relevant biological facts from available massive scientific knowledge source is emerging as a significant task for the science community. Its success depends on several key factors, including the precision of a given search, the time of its accomplishment, and the communicative prowess of the mined information to the users. GeneCite - a stand-alone Java-based high-throughput data mining tool - is designed to carry out these tasks for several important knowledge sources simultaneously, allowing the users to integrate the results and interpret biological significance in a time-efficient manner. GeneCite provides an integrated high-throughput search platform serving as an information retrieval (IR) tool for probing online literature database (PubMed) and the sequence-tagged sites' database (UniSTS), respectively. It also operates as a data retrieval (DR) tool to mine an archive of biological pathways integrated into the software itself. Furthermore, GeneCite supports a retrieved data management system (DMS) showcasing the final output in a spread-sheet format. Each cell of the output file holds a real-time connection (hyperlink) to the given online archive reachable at the users' convenience. The software is free and currently available online www.bioinformatics.org; www.wrair.army.mil/Resources.     

Common molecular pathways involved in human CD133+/CD34+ progenitor cell expansion and cancer

Background  

Uncovering the molecular mechanism underlying expansion of hematopoietic stem and progenitor cells is critical to extend current therapeutic applications and to understand how its deregulation relates to leukemia. The characterization of genes commonly relevant to stem/progenitor cell expansion and tumor development should facilitate the identification of novel therapeutic targets in cancer.