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Searching for folded proteins in vitro and in silico.

Understanding the sequence determinants of protein structure, stability and folding is critical for understanding how natural proteins have evolved and how proteins can be engineered to perform novel functions. The complexity of the protein folding problem requires the ability to search large volumes of sequence space for proteins with specific structural or functional characteristics. Here we describe our efforts to identify novel proteins using a phage-display selection strategy from a 'mini-exon' shuffling library generated from the yeast genome and from completely random sequence libraries, and compare the results to recent successes in generating novel proteins using in silico protein design.

Evolution, Molecular↗

Monitoring photodynamic therapy of localized infections by bioluminescence imaging of genetically engineered bacteria.

The increasing occurrence of multi-antibiotic resistant microbes has led to the search for alternative methods of killing pathogens and treating infections. Photodynamic therapy (PDT) uses the combination of non-toxic dyes and harmless visible light to produce reactive oxygen species that can kill mammalian and microbial cells. Although the photodynamic inactivation of bacteria has been known for over a hundred years, its use to treat infections has not been much developed. This may be partly due to the difficulty of monitoring the effectiveness of PDT in animal models of infection. In order to facilitate this monitoring process, we have developed a procedure that uses bioluminescent genetically engineered bacteria and a light sensitive imaging system to allow real-time visualization of infections. When these bacteria are treated with PDT in vitro, the loss of luminescence parallels the loss of colony-forming ability. We have developed several models of infections in wounds and soft-tissue abscesses in mice that can be followed by bioluminescence imaging. The size and intensity of the infection can be sequentially monitored in a non-invasive fashion in individual mice in real-time. When photosensitizers are introduced into the infected tissue followed by illumination with red light, a light-dose dependent loss of luminescence is seen. If the bacterium is invasive, the loss of luminescence correlates with increased survival of the mice, whilst animals in control groups die of sepsis within five days. Healing of the PDT treated wounds is not impaired and may actually be improved. This approach can allow many animal models of localized infections to be accurately monitored for efficacy of treatment by PDT.

Animals↗

Engineering biodiversity with type II polyketide synthase genes.

A very important task in the ongoing search for new clinically useful drugs is the generation of large numbers of structurally diverse compounds. The emerging field of combinatorial biosynthesis, in which nature's chemical capabilities are exploited in a combinatorial 'mix-and-match' fashion, has generated libraries of novel molecules representing great structural diversity which are not available naturally or readily generated through (combinatorial) synthesis. Novel polyketides have been generated by manipulating type II iterative polyketide synthase (PKS) systems that express a variety of combinations of a minimal PKS with ketoreductases, cyclases, and other tailoring enzymes, resulting in a set of design rules to rationally engineer new metabolites. Engineering studies with the Streptomyces coelicolor whiE (spore pigment) and the 'Streptomyces maritimus' enterocin type II PKS provide additional insight on designing diverse assemblies of aromatic, as well as nonaromatic, polyketides.

Anti-Bacterial Agents↗

Structural and human cellular assessment of a novel microsphere-based tissue engineered scaffold for bone repair.

The limitations of current grafting materials have driven the search for synthetic alternatives for the regeneration of trabecular bone. A variety of biodegradable polymer foams composed of 85/15 poly(lactide-co-glycolide) (PLAGA) have been evaluated for such uses. However, structural limitations may restrict the clinical use of these scaffolds. We have developed a novel sintered microsphere scaffold with a biomimetic pore system equivalent to the structure of trabecular bone. By modifying processing parameters, several different sintered microsphere structures were fabricated. Optimization of the structure dealt with modifications to sphere diameter and heating time. Compressive testing illustrated a trend between microsphere diameter and modulus, where increased microsphere diameter resulted in decreased modulus. In addition, evaluation of the pore system showed a positive correlation between sphere diameter and pore diameter. Mercury porosimetry showed increased median pore size with an increased microsphere diameter. Heating time modifications showed that compressive modulus was dependent on the period of heating with longer heating times resulting in higher moduli. It was also shown that heating time did not affect the pore structure. Analysis of the structural data indicated that the microsphere matrix sintered for 4h at a temperature of 160 degrees C with a microsphere diameter of 600-710 microm resulted in an optimal, biomimetic structure with range in pore diameter of 83-300 microm, a median pore size of 210 microm, 35% porosity, and a compressive modulus of 232 MPa. An in vitro evaluation of human osteoblasts seeded onto the sintered matrix indicated that the structure was capable of supporting the attachment and proliferation of cells throughout its pore system. Immunofluorescent staining of actin showed that the cells were proliferating three-dimensionally through the pore system. The stain for osteocalcin was used and showed that cells maintained phenotypic expression for this bone specific protein. Through this work, it was shown that an osteoconductive PLAGA scaffold with a pore system used as a reverse template to the structure of trabecular bone could be fabricated through the sintered microsphere method.

Actins↗

A 3D structure database of components from Chinese traditional medicinal herbs.

This article described a 3D structure database of components extracted from Chinese Traditional Medicinal (CTM) herbs. It offers not only basic molecular properties and optimized 3D structure of the compounds but also detailed information on their herbal origin, including basic herbal category (e.g. English name, Latin name, and family), effective parts, and clinical effects. An easy to use, interactive GUI browser allows users to perform various searches via complex logical query builder. Combined with the latest network database engine (MySQL), it can achieve excellent performance under both a local network and an Internet environment. We have tested it on the design of inhibitors of NS3-NS4A protease. Results show that the structure database of components extracted from Chinese medicinal herbs can be a rich source in searching the lead compound.

Databases, Factual↗

A genetic screen to identify sequences that mediate protein oligomerization in Escherichia coli.

Many proteins assemble as oligomeric complexes and in several cases a distinct domain mediates the interaction between the subunits. The identification of new oligomerization modules is relevant to comprehend both the architecture and the evolution of protein sequences and also for protein engineering applications. Using the bacteriophage lambda repressor dimerization assay, we searched Escherichia coli genomic libraries for sequences able to mediate protein oligomerization in vivo. We identified short peptides that can substitute very effectively the dimerizing domain of the repressor. Most of these peptides belong to open reading frames that are normally not expressed in the bacterial cell.

Amino Acid Sequence↗

Wound healing in cell studies and animal model experiments by Low Level Laser Therapy; were clinical studies justified? a systematic review.

Based on results of cell studies and animal experiments, clinical trials with Low Level Laser Therapy (LLLT) were performed, which finally did not demonstrate a beneficial effect on outcome of wound healing. The aim of this study was to investigate whether the evidence from cell studies and animal experiments with respect to wound healing was unequivocally in favour of LLLT, which would imply that these models might be adequate to predict treatment response in patients, or that the data of cell studies and animal experiments were inconclusive, which would mean that the clinical trials were based on insufficient evidence. We performed a systematic review of cell studies and animal experiment with LLLT on wound healing. Manuscripts were identified by searching Medline, Embase, and SPIE (the International Society for Optical Engineering). We assessed whether studies showed a beneficial effect of active treatment or not. The effect size was expressed in standardised mean difference [(SMD) the mean outcome measure of the treatment group minus the mean outcome measure of the control group, divided by the pooled standard deviation of these measurements]. In-depth analyses were performed on (1) studies in which inflicted wounds on animals were irradiated and evaluated; (2) studies with primary outcome measures on dimensions with direct reference to wound healing (ranging from acceleration of wound closure to epithelialisation, but excluding surrogate dimensions with regard to wound healing; in this case: tensile strength); (3) animal studies with 'true controls'; (4) studies in which animals functioned as their 'own controls' and (5) studies with the highest methodological quality score. The 36 included studies contained 49 outcome parameters of which 30 reported a positive effect of laser irradiation and 19 did not. Eleven studies presented exact data about the effect of active treatment and controls. The pooled effect size (SMD) over 22 outcome measures of these studies was - 1.05 (95% Cl: - 1.67 to - 0.43) in favour of LLLT. Methodological quality of the studies was poor. In-depth analysis of studies showed no significant pooled effect size in studies with highest methodological quality scores [0.06 (95% CI:- 0.42 to 0.53)]. Summarising the data of cell studies and animal experiments, reviewed in this manuscript, these studies failed to show unequivocal evidence to substantiate the decision for trials with LLLT in a large number of patients. In fact, there were no differences between the results of these experiments and clinical studies. Remarkably, we found that (almost from the introduction on) animal experiments and clinical studies that address the biological effects of LLLT on wound healing, ran simultaneously, rather than in sequence. We conclude that this type of phototherapy should not be considered a valuable (adjuvant) treatment for this selected, generally therapy-refractory condition in humans.

Animals↗

Software for computational peptide identification from MS-MS data.

Protein identification in biological samples is an important task in drug discovery research. Protein identification is nowadays regularly performed by tandem mass spectrometry (MS-MS). Because of the difficulty of measuring intact proteins using MS-MS, typically a protein is enzymically digested into peptides and the MS-MS spectrum of each peptide is measured. Computational methods are then invoked to identify the peptides, which are later combined together to identify the protein. The most recognized peptide identification software packages can be classified into four categories: database searching, de novo sequencing, sequence tagging and consensus of multiple engines.

Databases, Protein↗

Psychometric properties of measurement tools for quantifying knee joint position and movement: a systematic review.

This systematic review critically evaluates literature on the reliability and validity of measurement tools for quantifying knee joint angles and knee movement. A search was conducted of seven medical databases and one biomedical engineering database, yielding 43 articles that reported reliability or validity. Tools for quantifying knee joint angles included standard handheld goniometers, fluid-based goniometers, gravity-based goniometers, photographs and two dimensional (2-D) motion analysis. Knee movement was measured with electrogoniometers, 2-D and three dimensional (3-D) motion analysis. Intraclass correlation coefficients for testing knee angles ranged from 0.51-1.00 for intratester reliability and 0.43-0.99 for intertester reliability. For quantifying knee position, sequential MRI and 2-D had the least error of measurement, followed by hand held goniometers and photographs. For dynamic measurements, electrogoniometers and 3-D motion analysis were most reliable and had low error of measurement. Strong concurrent validity was found between hand held goniometers and radiographs, as well as between hand held goniometers and 3-D motion analysis.

Arthrometry, Articular↗

Semi-automatic construction of the Chinese-English MeSH using Web-based term translation method.

Due to language barrier, non-English users are unable to retrieve the most updated medical information from the U.S. authoritative medical websites, such as PubMed and MedlinePlus. A few cross-language medical information retrieval (CLMIR) systems have been utilizing MeSH (Medical Subject Heading) with multilingual thesaurus to bridge the gap. Unfortunately, MeSH has yet not been translated into traditional Chinese currently. We proposed a semi-automatic approach to constructing Chinese-English MeSH based on Web-based term translation. The system provides knowledge engineers with candidate terms mining from anchor texts and search-result pages. The result is encouraging. Currently, more than 19,000 Chinese-English MeSH entries have been complied. This thesaurus will be used in Chinese-English CLMIR in the future.

Chi-Square Distribution↗

Eukaryotic coupled translation of tandem cistrons: identification of the influenza B virus BM2 polypeptide.

Previous nucleotide sequence analysis of RNA segment 7 of influenza B virus indicated that, in addition to the reading frame encoding the 248 amino acid M1 protein, there is a second overlapping reading frame (BM2ORF) of 585 nucleotides that has the coding capacity for 195 amino acids. To search for a polypeptide product derived from BM2ORF, a genetically engineered beta-galactosidase-BM2ORF fusion protein was expressed in Escherichia coli and a polyclonal rabbit antiserum was raised to the purified fusion protein. This antiserum was used to identify a polypeptide, designated BM2 protein (Mr approximately equal to 12,000), that is synthesized in influenza B virus-infected cells. To understand the mechanism by which the BM2 protein is generated from influenza B virus RNA segment 7, a mutational analysis of the cloned DNA was performed and the altered DNAs were expressed in eukaryotic cells. The expression patterns of the M1 and BM2 proteins from the altered DNAs indicate that the BM2 protein initiation codon overlaps with the termination codon of the M1 protein in an overlapping translational stop-start pentanucleotide, TAATG, and that the expression of the BM2 protein requires 5'-adjacent termination of M1 synthesis. Our data suggest that a termination-reinitiation scheme is used in translation of a bicistronic mRNA derived from influenza B virus RNA segment 7, and this strategy has some analogy to prokaryotic coupled stop-start translation of tandem cistrons.

Animals↗

Using views for retrieving data from extremely heterogeneous databanks.

Information in molecular biology or biology in general is contained in a multitude of different databanks each specializing in a certain area. This specialization is useful since it improves the maintainability of the data and the flexibility of the overall structure which until now manages to exist without almost any standards. However, information gathering from these extremely heterogeneous sources is difficult since the desired data may be scattered over many databanks. This paper presents the concept of views implemented in the retrieval system SRS that uses links between databanks and a sophisticated parsing engine for information extraction to provide a flexible way of searching and obtaining data across databank boundaries. The implementation provides homogeneous access to all databanks using two types of views: the list-view which displays selected data-fields in their original format and the table-view available for HTML and plain ASCII text which tries to represent the data in a format independent from that of the source databank.

Amino Acid Sequence↗

Hepatic tissue engineering for adjunct and temporary liver support: critical technologies.

The severe donor liver shortage, high cost, and complexity of orthotopic liver transplantation have prompted the search for alternative treatment strategies for end-stage liver disease, which would require less donor material, be cheaper, and less invasive. Hepatic tissue engineering encompasses several approaches to develop adjunct internal liver support methods, such as hepatocyte transplantation and implantable hepatocyte-based devices, as well as temporary extracorporeal liver support techniques, such as bioartificial liver assist devices. Many tissue engineered liver support systems have passed the "proof of principle" test in preclinical and clinical studies; however, they have not yet been found sufficiently reliably effective for routine clinical use. In this review we describe, from an engineering perspective, the progress and remaining challenges that must be resolved in order to develop the next generation of implantable and extracorporeal devices for adjunct or temporary liver assist.

Biomedical Technology↗

Characteristics of Israeli women studying nursing compared to women studying education and engineering.

This study examined the demographic characteristics, vocational personality, and sex-role orientation of Israeli women studying nursing compared to women studying education and engineering. The convenience sample was 176 university students. The instrument included a demographic inventory, Holland's Self-Directed Search (SDS) questionnaire, and the Sex-Role Orientation Attitude questionnaire. Nursing and education students had Holland's "social" personality types and engineering students were more "realistic" or "investigative". Nursing and engineering students were significantly more feminist in their orientation than education majors. Nursing students were nontraditional women who had traditional family backgrounds, yet were nontraditional in their feminist orientation. With nursing's move into colleges and universities, the need for academically qualified applicants has intensified. Developing a better understanding of the unique nature of nursing and nursing students is a challenge.

Adult↗

Tissue engineering meniscus: cells and matrix.

Tissue engineering, a relatively new field of research, was born as a result of a search for solutions to the limited alternatives currently used to replace structure and function lost because of failure or loss of tissues throughout the body. The field merges advances in cell biology, growth factor therapy, and material design. It encourages creation of tissue-engineered menisci for repair and replacement therapy and offers a means for developing a better understanding of meniscal cell and matrix biology.

Animals↗

Design and development of a search interface for an information gathering tool.

In order to design effective and usable search interfaces it is essential to fully understand the characteristics of the users and the tasks they perform. In this paper we describe how to use human-centered approach to design a usable search interface. We first conducted user and task analyses of the application domain--Biomedical Engineers' log notes at NASA Johnson Space Center. From these analyses we identified what functions the users want, the tasks they perform, and a coding system for the vocabulary used by the users to log entries in the log notes. We then implemented a prototype of human-centered search interface by using the results of the user and task analyses and by applying other human-centered principles. Finally we discussed the implications of human-centered design for general health information systems.

Information Storage and Retrieval↗

Probing metabolic pathways with isotopic tracers: insights from mammalian metabolic physiology.

Metabolic Engineering offers an opportunity to forge a link between metabolic physiologists, working with mammalian systems and metabolic engineers. Many parallels may be drawn between the specific modification of metabolic networks to improve cellular properties and the analysis of metabolic networks in search of causes of disease. At the core of both fields is the measurement of fluxes. This issue of Metabolic Engineering highlights important topics: mammalian metabolic physiology where estimating fluxes is challenging. The challenges come from compartmentation of metabolites, from dilution of tracer by endogenous pools, and from the difficulty of sampling relevant pools. The common theme across these investigations is the use of isotopic tracers. The wide variety of tracers and tracer analysis techniques in use in mammalian metabolic physiology reflects the complexity of the systems under study. In presenting these examples from the field of mammalian metabolic physiology, our goal is to strengthen the linkages between physiologists and engineers as we develop our knowledge and appreciation of the complexity of metabolic networks.

Animals↗