Cancer cell-secreted proteomes as a basis for searching potential tumor markers: nasopharyngeal carcinoma as a model

Nasopharyngeal carcinoma (NPC) is commonly diagnosed late due to its deep location and vague symptoms. To identify biomarkers for early NPC diagnosis, secreted proteomes of two NPC cell lines were analyzed. Proteins in the NPC cell-line cultured media were systematically identified by SDS-PAGE combined with MALDI-TOF MS. Twenty-three proteins were found in cultured media from both NPC cell lines. Among them, fibronectin, Mac-2 binding protein (Mac-2 BP), and plasminogen activator inhibitor 1 (PAI-1) were further confirmed by Western blot analysis. These three proteins were highly expressed in NPC biopsies, but weakly or not expressed in normal nasopharyngeal tissues. The serum levels of the three proteins were significantly higher in NPC patients (n = 46) than in normal controls (n = 47) (p < 0.01). NPC nude mice model (n = 9) also showed elevated levels of serum Mac-2 BP and PAI-1 compared with tumor-free mice (n = 9) (p < 0.01). Systematic analysis of cancer cell-secreted proteomes combined with animal tumor models can be a feasible, convenient strategy for searching multiple potential tumor markers. Furthermore, our work shows that fibronectin, Mac-2 BP, and PAI-1 may be potential markers for diagnosis of NPC.     

Chitosan bearing pendant cyclodextrin as a carrier for controlled protein release

The objective of this work was to investigate the possibility of chitosan bearing β-cyclodextrin (CDen-g-CS) nanocomplexes for controlled protein release. CDen-g-CS was synthesized by a one-step procedure with N-succinylated chitosan and mono(6-(2-aminoethyl)amino-6-deoxy)-β-cyclodextrin in the presence of the water-soluble carbodiimide. The amount of β-CD grafted was up to 62.1 wt%. In vitro cytotoxicity against NIH 3T3 cells showed that CDen-g-CS was not cytotoxic and no significant difference of cytotoxicity was found between CDen-g-CS groups. Self-assembled nanocomplexes between CDen-g-CS and insulin were in the size range of 190–328 nm, with positive electrical charge (+3.7 to +25.5 mV) and high loading efficiency (37.7%). Insulin release in vitro was affected by the medium pH and the composition of copolymer. These results demonstrated that CDen-g-CS copolymer was a new promising vehicle for controlled protein release.     

Chitosan as a Component of Pea-Fusarium solani Interactions

Chitosan, a polymer of β-1,4-linked glucosamine residues with a strong affinity for DNA, was implicated in the pea pod-Fusarium solani interaction as an elicitor of phytoalexin production, an inhibitor of fungal growth and a chemical which can protect pea tissue from infection by F. solani f. sp. pisi. Purified Fusarium fungal cell walls can elicit phytoalexin production in pea pod tissue. Enzymes from acetone powders of pea tissue release eliciting components from the F. solani f. sp. phaseoli cell walls. Hydrochloric acid-hydrolyzed F. solani cell walls are about 20% glucosamine. The actual chitosan content of F. solani cell walls is about 1%. However, chitosan assays and histochemical observations indicate that chitosan content of F. solani spores and adjacent pea cells increases following inoculation. Dormant F. solani spores also accumulate chitosan. Concentrations of nitrous acid-cleaved chitosan as low as 0.9 microgram per milliliter and 3 micrograms per milliliter elicit phytoalexin induction and inhibit germination of F. solani macroconidia, respectively. When chitosan is applied to pea pod tissue with or prior to F. solani f. sp. pisi, the tissue is protected from infection.     

Functional group and substructure searching as a tool in metabolomics

Background

A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases.

Methodology

We have developed a database named “Biochemical Substructure Search Catalogue” (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest.

Conclusions

This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed.     

Chitosan from Syncephalastrum racemosum used as a film support for lipase immobilization

Chitosan from a native Mucoralean strain, Syncephalastrum racemosum, isolated from herbivorous dung (Northeast-Brazil), was used as a film support for lipase immobilization. S. racemosum showed highest chitosan yield (152 mg g dry mycelia weight(-1); 15.2% of dry mycelia weight) among the nine strains screened, which presented 89% D-glucosamine. A chitosan film was used for lipase (EC 3.1.1.3) immobilization using glutaraldehyde as a bifunctional agent. The immobilized lipase retained 47% (12.6 micromol s(-1) m(-2)) of its initial catalytic activity after four cycles of reaction. This result is comparable (same order of magnitude) to that of the enzyme immobilized on film made from commercially available crustacean chitosan.     

Presynaptic unsilencing: searching for a mechanism

Nascent synaptic networks have a high incidence of silent synapses. In this issue of Neuron, Shen et al. show that a brief burst of action potentials rapidly awaken silent synapses by increasing the availability of synaptic vesicles for fusion through BDNF-triggered presynaptic actin remodeling mediated by the small GTPase Cdc42.     

Chitosan as a growth stimulator in orchid tissue culture

The effect of shrimp and fungal chitosan on the growth and development of orchid plant meristemic tissue in culture was investigated in liquid and on solid medium. The growth of meristem explants into protocorm-like bodies in liquid medium was accelerated up to 15 times in the presence of chitosan oligomer, the optimal concentration being 15 ppm. The 1 kDa shrimp oligomer was slightly more effective compared to 10 kDa shrimp chitosan and four times more active compared to high molecular weight 100 kDa shrimp chitosan. The 10 kDa fungal chitosan was more effective compared with 1 kDa oligomer. The development of orchid protocorm into differentiated orchid tissue with primary shoots and roots was studied on solid agar medium. The optimal effect, the generation of 5–7 plantlets in 12 weeks was observed in the presence of 20 ppm using either 10 kDa fungal or 1 kDa oligomer shrimp chitosan. The data are consistent with preliminary results from field experiments and confirm unequivocally that a minor amount of chitosan has a profound effect on the growth and development of orchid plant tissue.     

Chitosan sponges as tissue engineering scaffolds for bone formation

Rat calvarial osteoblasts were grown in porous chitosan sponges fabricated by freeze drying. The prepared chitosan sponges had a porous structure with a 100-200 microm pore diameter, which allowed cell proliferation. Cell density, alkaline phosphatase activity and calcium deposition were monitored for up to 56 d culture. Cell numbers were 4 x 10(6) (day 1), 11 x 10(6) (day 28) and 12 x 10(6) (day 56) per g sponge. Calcium depositions were 9 (day 1), 40 (day 28) and 48 (day 56) microg per sponge. Histological results corroborated that bone formation within the sponges had occurred. These results show that chitosan sponges can be used as effective scaffolding materials for tissue engineered bone formation in vitro.     

几丁聚糖在硅橡胶表面作涂层的实验研究

几丁聚糖具有良好的生物相容性和抗菌性,作为生物涂层已经引起了广泛的注意。研究了基体的不同表面处理方法、浸涂次数和几丁聚糖溶液浓度对涂层的表面形貌、结合强度等性能的影响,结果显示,几丁聚糖溶液浓度和硅橡胶表面粗糙度都存在一个最佳取值范围;增加浸涂次数可以改善涂层光洁度,但是对涂层附着力贡献不大;硅橡胶经紫外照射后可以改善几丁聚糖在其上的成膜性能。     

Maternal-fetal attachment: searching for a new definition

Maternal-fetal attachment is the purest source of the powerful attachment relationship, the gradual internalisation of the life within unspoilt by the realities and complexities of early parenting. This qualitative study searches for a definition of attachment utilising a phenomenological framework. An opportunity sample of 10 women in the final trimester of pregnancy was interviewed. Interviews were transcribed and analysed using Glaser & Strauss's (1967) constant comparative methodology. Thirteen key themes were identified, of these 4 were specific to parenting experience. A novel finding contrary to earlier studies was that women reported their overwhelming emotion was not love but an innate desire to protect. Protection, the developmental nature of attachment and importance of the emotional and physical support of a partner or parent form the kernel of an evolving paradigm.     

MPSQ: a web tool for protein-state searching

MPSQ (multi-protein-states query) is a web-based tool for the discovery of protein states (e.g. biological interactions, covalent modifications, cellular localizations). In particular, large sets of genes can be used to search for enriched state transition network maps (NMs) and features facilitating the interpretation of genomic-scale experiments such as microarrays. One NM collects all the catalogued states of a protein as well as the mutual transitions between the states. For the returned NM, graph visualization is provided for easy understanding and to guide further analysis.     

The global trace graph, a novel paradigm for searching protein sequence databases

MOTIVATION: Propagating functional annotations to sequence-similar, presumably homologous proteins lies at the heart of the bioinformatics industry. Correct propagation is crucially dependent on the accurate identification of subtle sequence motifs that are conserved in evolution. The evolutionary signal can be difficult to detect because functional sites may consist of non-contiguous residues while segments in-between may be mutated without affecting fold or function. RESULTS: Here, we report a novel graph clustering algorithm in which all known protein sequences simultaneously self-organize into hypothetical multiple sequence alignments. This eliminates noise so that non-contiguous sequence motifs can be tracked down between extremely distant homologues. The novel data structure enables fast sequence database searching methods which are superior to profile-profile comparison at recognizing distant homologues. This study will boost the leverage of structural and functional genomics and opens up new avenues for data mining a complete set of functional signature motifs. AVAILABILITY: http://www.bioinfo.biocenter.helsinki.fi/gtg. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

ANDY: a general, fault-tolerant tool for database searching on computer clusters

SUMMARY: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used distributed resource management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms. Availability: ANDY is freely available and can be obtained from http://compbio.berkeley.edu/proj/andy. SUPPLEMENTARY INFORMATION: Supplemental data, figures, and a more detailed overview of the software are found at http://compbio.berkeley.edu/proj/andy.