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PubMed2026

From Variability to Consensus: Rescoring Harmonizes Peptide Identification across Diverse Search Engines and Data Sets.

Peptide-spectrum match (PSM) rescoring has become standard in proteomics workflows, improving peptide identification accuracy across diverse search engines. Despite the availability of multiple rescoring strategies, systematic comparisons spanning several search engines, data sets, and database configurations remain limited. Here, we benchmarked seven publicly available search engines, evaluating standard target-decoy-based false discovery rate (FDR) estimation alongside Percolator, MS2Rescore, and Oktoberfest across four data sets acquired on different mass spectrometry platforms in data-dependent mode and searched against protein databases of varying size and composition. Rescoring substantially increased identification consensus and reduced variability between search engines, with prediction-based approaches yielding the largest gains. While database size had limited impact for human data sets, it significantly affected identification rates on a metaproteomic data set. Entrapment-based evaluation indicated generally adequate FDR control across methods, although prediction-based rescoring exhibited a higher tendency toward FDR underestimation in specific configurations. Overall, advanced rescoring strategies harmonize peptide identification outcomes across search engines, thereby enhancing robustness and comparability in proteomics analyses. However, careful feature selection and appropriate database choice remain essential to ensure reliable FDR control and optimal performance across diverse experimental settings.

Search Engine↗

PubMed1995

Transmembrane signaling by the aspartate receptor: engineered disulfides reveal static regions of the subunit interface.

Ligand binding to the periplasmic domain of the transmembrane aspartate receptor generates an intramolecular conformational change which spans the bilayer and ultimately signals the cytoplasmic CheA histidine kinase, thereby triggering chemotaxis. The receptor is a homodimer stabilized by the interface between its two identical subunits: the present study investigates the role of the periplasmic and transmembrane regions of this interface in the mechanism of transmembrane signaling. Free cysteines and disulfide bonds are engineered into selected interfacial positions, and the resulting effects on the transmembrane signal are assayed by monitoring in vitro regulation of kinase activity. Three of the 14 engineered cysteine pairs examined, as well as six of the 14 engineered disulfides, cause perturbations of the interface structure which essentially destroy transmembrane regulation of the kinase. The remaining 11 cysteine pairs, and eight engineered disulfides covalently linking the two subunits at locations spanning positions 18-75, are observed to retain significant transmembrane kinase regulation. The eight functional disulfides positively identify adjacent faces of the two N-terminal helices in the native receptor dimer and indicate that large regions of the periplasmic and transmembrane subunit interface remain effectively static during the transmembrane signal. The results are consistent with a model in which the subunit interface plays a structural role, while the second membrane-spanning helix transmits the ligand-induced signal across the bilayer to the kinase binding domain. The effects of engineered cysteines and disulfides on receptor methylation in vitro are also measured, enabling direct comparison of the in vitro methylation and phosphorylation assays.

Cell Membrane↗

PubMed1996

Furilisin: a variant of subtilisin BPN' engineered for cleaving tribasic substrates.

The serine protease, subtilisin BPN', was engineered to cleave proteins after tribasic sequences in a manner that resembles the substrate specificity of furin, one of the mammalian subtilisin homologs that processes prohormones. As a starting point we used a double mutant of subtilisin BPN' (N62D/ G166D) that showed substantial preference for cleaving after sequences having consecutive dibasic residues (namely, at the P1 and P2 substrate positions) [Ballinger et al. (1995) Biochemistry 34, 13312-13319]. Additional specificity for basic residues was engineered at the P4 position by introducing subtilisin-to-furin substitutions at three hydrophobic residues that composed the S4 subsite (Y104, I107, and L126). Initial attempts to incorporate a Y104D or I107E mutation or the Y104D/I107E double mutation into the dibasic specific enzyme failed to generate the processed enzyme. The problem was traced to the inability of the mutant prosubtilisins to process themselves and fold correctly. Replacing the natural processing site sequence (AHAY) with a good furin substrate sequence (RHKR) resulted in expression of the triple subtilisin mutant (N62D/Y104D/G166D) we call "furilisin". Furilisin hydrolyzes synthetic tribasic substrates (succinyl-RAKR-pNA or succinyl-KAKR-pNA) with high catalytic efficiency (kcat/K(m) > 3 x 10(5) M-1 s-1) and discriminates in favor of Arg versus Ala at the P4 position by a factor of 360. The overall specificity change versus the wild-type enzyme was dramatic. For example, succinyl-RAKR-pNA was cleaved approximately 60000 times faster than succinyl-AAPF-pNA, a good substrate for wild-type subtilisin. Similarly, furilisin was inhibited (K1* = 29 nM) by a variant of the turkey ovomucoid third domain inhibitor that contained an engineered furin substrate site (RCKR decreases) [Lu et al. (1993) J. Biol. Chem. 268, 14583-14585] and not by one having a good wild-type subtilisin substrate sequence (ACTL decreases). Interestingly, the extreme changes in substrate specificity resulted from substantial synergy between the engineered subsites. These studies provide a basic example of how to manipulate substrate specificity in a modular fashion, thereby creating an engineered-enzyme that may be useful as a protein processing tool.

Amino Acid Sequence↗

PubMedDate not supplied

Change is necessary in a biological engineering curriculum.

Success of a Biological Engineering undergraduate educational program can be measured in a number of ways, but however it is measured, a presently successful program can translate into an unsuccessful program if it cannot adjust to different conditions posed by technical advances, student characteristics, and academic pressures. Described in this paper is a Biological Engineering curriculum that has changed significantly since its transformation from Agricultural Engineering in 1993. As a result, student numbers have continued to climb, specific objectives have emerged, and unique courses have been developed. The Biological Resources Engineering program has evolved into a program that emphasizes breadth, fundamentals, communications skills, diversity, and practical engineering judgment.

Curriculum↗

PubMed2003

Plastics disassembly versus bulk recycling: engineering design for end-of-life electronics resource recovery.

Annual plastic flows through the business and consumer electronics manufacturing supply chain include nearly 3 billion lb of high-value engineering plastics derived from petroleum. The recovery of resource value from this stream presents critical challenges in areas of materials identification and recycling process design that demand new green engineering technologies applied together with life cycle assessment and ecological supply chain analysis to create viable plastics-to-plastics supply cycles. The sustainable recovery of potentially high-value engineering plastics streams requires that recyclers either avoid mixing plastic parts or purify later by separating smaller plastic pieces created in volume reduction (shredding) steps. Identification and separation constitute significant barriers in the plastics-to-plastics recycling value proposition. In the present work, we develop a model that accepts randomly arriving electronic products to study scenarios by which a recycler might identify and separate high-value engineering plastics as well as metals. Using discrete eventsimulation,we compare current mixed plastics recovery with spectrochemical plastic resin identification and subsequent sorting. Our results show that limited disassembly with whole-part identification can produce substantial yields in separated streams of recovered engineering thermoplastics. We find that disassembly with identification does not constitute a bottleneck, but rather, with relatively few workers, can be configured to pull the process and thus decrease maximum staging space requirements.

Conservation of Natural Resources↗

PubMed2006

Improved subtilisin YaB production in Bacillus subtilis using engineered synthetic expression control sequences.

Alkaline elastase YaB, a favorable meat tenderizer, is an extracellular subtilisin-type protease produced by wild strain alkalophilic Bacillus YaB. The gene ale coding for subtilisin YaB with its own expression control sequence has been cloned and expressed in Bacillus subtilis, but at levels much lower than in the parental strain Bacillus YaB. This study investigates the influence of various expression control sequences including expression control sequences of cdd and veg from B. subtilis, a synthetic expression control sequence (SECS), and engineered synthetic expression control sequences (engineered SECSs) on the expression of subtilisin YaB in B. subtilis. The engineered SECSs were generated by using the Polymerase Chain Reaction; their UP element, Shine-Dargarno (SD) sequence, or both were different from those of the native SECS. The expression efficiencies of SECS and engineered SECSs were higher than those of expression control sequences of ale, cdd, and veg. Substitution of the SD sequence of SECS resulted in higher expression of subtilisin YaB than substitution of the UP element, whereas combined substitution of both gave the highest expression. These results demonstrate that engineering of SECSs is an approach for improving subtilisin YaB production in B. subtilis. Moreover, it is suggested that these enginnered SECSs could potentially be used to express homologous and heterologous proteins in B. subtilis at high level.

Bacillus subtilis↗

PubMed2003

Cancer incidence among marine engineers, a population-based study (Iceland).

OBJECTIVES: Marine engineers are in their occupation exposed to different chemicals, organic solvents, exhaust gases, oils, and petroleum products, and were formerly exposed to asbestos. The aim was to study the cancer pattern, with particular attention to lung and bladder cancer, in an Icelandic cohort of marine engineers, indirectly controlling for their smoking habits. METHODS: A cohort of 6603 male marine engineers was followed up from 1955 to 1998, a total of 167,715 person-years. The cohort was record linked by the engineers' personal identification numbers to population-based registers containing the vital and emigration status and cancer diagnosis. Standardized incidence ratios (SIRs) were calculated for all cancers and different cancer sites in relation to different lag time and year of graduation. Information on smoking habits was obtained by administering a questionnaire to a sample of the cohort (n = 1,501). RESULTS: In the total cohort 810 cancers were observed, whereas 794 were expected (SIR 1.0, 95% CI 1.0-1.1), and significantly increased risk of stomach cancer (SIR 1.3, 95% CI 1.0-1.5) and lung cancer (SIR 1.2, 95% CI 1.0-1.5) was found. Increased risk of all cancers (SIR 1.2, 95% CI 1.1-1.3), stomach cancer (SIR 1.5, 95% CI 1.1-1.9), lung cancer (SIR 1.4, 95% CI 1.2-1.8), pleural mesothelioma (SIR 4.8, 95% CI 1.3-12.3), and urinary bladder cancer (SIR 1.3, 95% CI 1.0-1.8) were observed when a 40-year lag time was applied. The engineers' smoking habits were similar to those in a sample of the general population. The predictive value for lung cancer was 1.03. CONCLUSIONS: The increased risk for mesothelioma is possibly attributable to the previous asbestos exposure. The excess of lung cancer could also be related to asbestos exposure. The high incidence of stomach cancer, lung cancer, and bladder cancer may be related to exposure to chemical risk factors, such as oils and petroleum products, as confounding due to smoking seems to be ruled out. In the light of the limited exposure information in the present study the importance of the different occupational exposures needs to be evaluated in further studies.

Adult↗

PubMed2003

Cardiac tissue engineering, ex-vivo: design principles in biomaterials and bioreactors.

Cardiac tissue engineering has emerged as a promising approach to replace or support an infarcted cardiac tissue and thus may hold a great potential to treat and save the lives of patients with heart diseases. By its broad definition, tissue engineering involves the construction of tissue equivalents from donor cells seeded within 3-D biomaterials, then culturing and implanting the cell-seeded scaffolds to induce and direct the growth of new, healthy tissue. In this review, we present an up-to-date summary of the research in cardiac tissue engineering, with an emphasis on the design principles and selection criteria that have been used in two key technologies employed in tissue engineering, (1) biomaterials technology, for the creation of 3-D porous scaffolds which are used to support and guide the tissue formation from dissociated cells, and (2) bioreactor cultivation of the 3-D cell constructs during ex-vivo tissue engineering, which aims to duplicate the normal stresses and flows experienced by the tissues.

Biocompatible Materials↗

PubMed2004

Polymeric scaffolds for bone tissue engineering.

Bone tissue engineering is a rapidly developing area. Engineering bone typically uses an artificial extracellular matrix (scaffold), osteoblasts or cells that can become osteoblasts, and regulating factors that promote cell attachment, differentiation, and mineralized bone formation. Among them, highly porous scaffolds play a critical role in cell seeding, proliferation, and new 3D-tissue formation. A variety of biodegradable polymer materials and scaffolding fabrication techniques for bone tissue engineering have been investigated over the past decade. This article reviews the polymer materials, scaffold design, and fabrication methods for bone tissue engineering. Advantages and limitations of these materials and methods are analyzed. Various architectural parameters of scaffolds important for bone tissue engineering (e.g. porosity, pore size, interconnectivity, and pore-wall microstructures) are discussed. Surface modification of scaffolds is also discussed based on the significant effect of surface chemistry on cells adhesion and function.

Animals↗

PubMed2006

Technology Insight: adult stem cells in cartilage regeneration and tissue engineering.

Articular cartilage, the load-bearing tissue of the joint, has limited repair and regeneration potential. The scarcity of treatment modalities for large chondral defects has motivated attempts to engineer cartilage tissue constructs that can meet the functional demands of this tissue in vivo. Cartilage tissue engineering requires three components: cells, scaffold, and environment. Adult stem cells, specifically multipotent mesenchymal stem cells, are considered the cell type of choice for tissue engineering, because of the ease with which they can be isolated and expanded and their multilineage differentiation capabilities. Successful outcome of cell-based cartilage tissue engineering ultimately depends on the proper differentiation of stem cells into chondrocytes and the assembly of the appropriate cartilaginous matrix to achieve the load-bearing capabilities of the natural articular cartilage. Multiple requirements, including growth factors, signaling molecules, and physical influences, need to be met. Adult mesenchymal stem-cell-based tissue engineering is a promising technology for the development of a transplantable cartilage replacement to improve joint function.

Cartilage, Articular↗

PubMed2006

Engineered heart tissue grafts improve systolic and diastolic function in infarcted rat hearts.

The concept of regenerating diseased myocardium by implantation of tissue-engineered heart muscle is intriguing, but convincing evidence is lacking that heart tissues can be generated at a size and with contractile properties that would lend considerable support to failing hearts. Here we created large (thickness/diameter, 1-4 mm/15 mm), force-generating engineered heart tissue from neonatal rat heart cells. Engineered heart tissue formed thick cardiac muscle layers when implanted on myocardial infarcts in immune-suppressed rats. When evaluated 28 d later, engineered heart tissue showed undelayed electrical coupling to the native myocardium without evidence of arrhythmia induction. Moreover, engineered heart tissue prevented further dilation, induced systolic wall thickening of infarcted myocardial segments and improved fractional area shortening of infarcted hearts compared to controls (sham operation and noncontractile constructs). Thus, our study provides evidence that large contractile cardiac tissue grafts can be constructed in vitro, can survive after implantation and can support contractile function of infarcted hearts.

Animals↗

PubMed2002

Functional analysis of the tissue-engineered stomach wall.

We have established a method for in situ tissue engineering of the stomach in a canine model using an acellular collagen scaffold graft. The current study was conducted to evaluate the functional aspects of the tissue-engineered stomach wall. The anterior wall of the stomach in beagle dogs was replaced with a collagen sponge scaffold measuring 4 x 4 cm. At 16 weeks after implantation, the animals were sacrificed and the stomach specimens were evaluated immunohistochemically and physiologically. Regeneration of the proton pump and thin muscle layer, which are essential for mechanical and chemical digestion by the stomach, was observed in the tissue-engineered gastric tissue. However, acetylcholine-induced contraction was not observed in the tissue-engineered stomach wall. Although there is still room for improvement, the tissue-engineered stomach wall had a highly organized structure, and it is anticipated that this approach could eventually become an alternative for stomach reconstruction after gastrectomy.

Animals↗

PubMed2003

Structure and function of the temporomandibular joint disc: implications for tissue engineering.

The temporomandibular joint (TMJ) disc is a little understood structure that, unfortunately, exhibits a plethora of pathologic disorders. Tissue engineering approaches may be warranted to address TMJ disc pathophysiology, but first a clear understanding of structure-function relationships needs to be developed, especially as they relate to the regenerative potential of the tissue. In this review, we correlate the biochemical content of the TMJ disc to its mechanical behavior and discuss what this correlation infers for tissue engineering studies of the TMJ disc. The disc of the TMJ exhibits a somewhat biconcave shape, being thicker in the anterior and posterior bands and thinner in the intermediate zone. The disc, which is certainly an anisotropic and nonhomogeneous tissue, consists almost entirely of type I collagen with trace amounts of type II and other types. In general, collagen fibers in the intermediate zone appear to run primarily in an anteroposterior direction and in a ringlike fashion around the periphery. Collagen orientation is reflected in higher tensile stiffness and strength in the center anteroposteriorly than mediolaterally and in the anterior and posterior bands than the intermediate zone mediolaterally. Tensile tests have shown the disc is stiffer and stronger in the direction of the collagen fibers. Elastin fibers in general appear along the collagen fibers and most likely function in restoring and retaining disc form after loading. The 2 primary glycosaminoglycans of the disc by far are chondroitin sulfate and dermatan sulfate, although their distribution is not clear. Compression studies are conflicting, but evidence suggests the disc is compressively stiffest in the center. Only a few tissue engineering studies of the TMJ disc have been performed to date. Tissue engineering studies must take advantage of existing information for experimental design and construct validation, and more research is necessary to characterize the disc to create a clearer picture of our goals in tissue engineering the TMJ disc.

Compressive Strength↗

PubMed2002

Fetal tissue engineering: in utero tracheal augmentation in an ovine model.

BACKGROUND/PURPOSE: This study was aimed at comparing fetal tissue engineering with autologous free grafting in an ovine model of in utero tracheal repair. METHODS: Chondrocytes were isolated from both elastic and hyaline cartilage specimens harvested from fetal lambs and expanded in vitro. Cells were seeded dynamically onto biodegradable scaffolds, which then were maintained in a rotating bioreactor for 6 to 8 weeks. Constructs subsequently were implanted into fetal tracheas (n = 15), in a heterologous fashion (group I). In group II, fetuses (n = 5) received autologous free grafts of elastic cartilage harvested from the ear as tracheal implants. In vivo specimens were harvested for histologic analysis at different time-points postimplantation. RESULTS: In the 12 of 15 surviving fetuses of group I, all constructs were found to resemble normal hyaline cartilage, engraft well despite their heterologous origin, and display time-dependent epithelialization derived from the native trachea. All autologous free grafts were engrafted and epithelialized at birth, retaining histologic characteristics of elastic cartilage, but were more deformed than engineered constructs. Of the lambs allowed to reach term, 5 of 5 in the engineered group and 4 of 5 in the free graft group could breathe spontaneously. CONCLUSIONS: (1) Tissue-engineered cartilage, as well as autologous free grafts, can be implanted successfully into the fetal trachea, resulting in engraftment and function. (2) Engineered cartilage provides enhanced structural support after implantation into the fetal trachea when compared with free grafts. Prenatal tracheoplasty may prove useful for the treatment of severe congenital tracheal malformations.

Animals↗

PubMed2004

Flap prefabrication and prelamination with tissue-engineered cartilage.

In reconstructive surgery, the integration of tissue-engineered cartilage in a prefabricated free flap may make it possible to generate flaps combining a variety of tissue components, to meet the special requirements of particular defects. One aim of the present study was to investigate prefabrication of a microvascular free flap by implanting a vessel loop under a skin flap in a rabbit model. A second aim was to report on the authors' preliminary experiences in prelaminating prefabricated flaps with autologous tissue-engineered cartilage, in terms of matrix development, inflammatory reaction, and host-tissue interaction. The flap was prefabricated by implanting a vessel loop under a random-pattern abdominal skin flap. The tissue-engineered cartilage constructs were made by isolating chondrocytes from auricular biopsies. Following a period of amplification, the cells were seeded onto a non-woven scaffold made of a hyaluronic-acid derivative and cultivated for 2 weeks. One cell-biomaterial construct was placed beneath the prefabicated flap, and two additional constructs were placed subcutaneously and intramuscularly. In addition, a biomaterial sample without cells was placed subcutaneously to provide a control. All implanted specimens were left in position for 6 or 12 weeks. Neovascularization in the prefabricated flap and biomaterial construct was analyzed by angiography. After explantation, the specimens were examined by histologic and immunohistochemical methods. The prefabricated flaps showed a well-developed network of blood vessels between the implanted vessel loop and the original random-pattern blood supply. The tissue-engineered constructs remained stable in size and showed signs of tissue similar to hyaline cartilage, as evidenced by the expression of cartilage-specific collagen type II and proteoglycans. No inflammatory reactions were observed. The physiologic environment of the autologous rabbit model provided favorable conditions for matrix deposition and maturation of the cell-biomaterial constructs. These initial results demonstrated the potential of prefabricating an axial perfused flap, combined with tissue-engineered cartilage, thus creating functionally competent tissue components for reconstructive surgery with minimal donor-site morbidity.

Angiography↗

PubMed2006

Relevance and safety of telomerase for human tissue engineering.

Tissue engineering holds the promise of replacing damaged or diseased tissues and organs. The use of autologous donor cells is often not feasible because of the limited replicative lifespan of cells, particularly those derived from elderly patients. Proliferative arrest can be overcome by the ectopic expression of telomerase via human telomerase reverse transcriptase (hTERT) gene transfection. To study the efficacy and safety of this potentially valuable technology, we used differentiated vascular smooth muscle cells (SMC) and vascular tissue engineering as a model system. Although we previously demonstrated that vessels engineered with telomerase-expressing SMC had improved mechanics over those grown with control cells, it is critical to assess the phenotypic impact of telomerase expression in donor cells, because telomerase up-regulation is observed in >95% of human malignancies. To study the impact of telomerase in tissue engineering, expression of hTERT was retrovirally induced in SMC from eight elderly patients and one young donor. In hTERT SMC, significant lifespan extension beyond that of control was achieved without population doubling time acceleration. Karyotype changes were seen in both control and hTERT SMC but were not clonal nor representative of cancerous change. hTERT cells also failed to show evidence of neoplastic transformation in functional assays of tumorigenicity. In addition, the impact of donor age on cellular behavior, particularly the synthetic capability of SMC, was not affected by hTERT expression. Hence, this tissue engineering model system highlights the impact of donor age on cellular synthetic function that appears to be independent of lifespan extension by hTERT.

Blood Vessels↗

PubMed1997

Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates.

Protein phosphorylation plays a central role in controlling many diverse signal transduction pathways in all cells. Novel protein kinases are identified at a rapid rate using homology cloning methods and genetic screens or selections; however identification of the direct substrates of kinases has proven elusive to genetic methods because of the tremendous redundancy and overlapping of substrate specificities among protein kinases. We describe the development of a protein engineering-based method to identify the direct substrates of the prototypical protein tyrosine kinase v-Src, which controls fibroblast transformation by the Rous sarcoma virus. To differentiate the substrates of v-Src from all other kinase substrates, we mutated the ATP binding site of v-Src such that the engineered v-Src uniquely accepted an ATP analog. We show that the engineered v-Src kinase displayed catalytic efficiency with the ATP analog, N(6)-(cyclopentyl) ATP, which is similar to the wild-type kinase catalytic efficiency with ATP itself. However, the N(6)-(cyclopentyl) ATP analog was not accepted by the wild-type kinase. Furthermore, the engineered v-Src exhibited the same protein target specificity as wild-type v-Src despite the proximity of the reengineered nucleotide binding site to the phosphoacceptor binding site. The successful engineering of v-Src's active site to accept a unique nucleotide analog provides a unique handle by which the direct substrates of one kinase (v-Src) can be traced in the presence of any number of cellular kinases.

Amino Acid Sequence↗

PubMed2003

Tissue engineering of the gastrointestinal tract for surgical replacement: a nutrition tool of the future?

Optimal nutrition depends on the multiple complex functions performed by the gastrointestinal tract, which range from basic functions such as storage, conduit and mechanical processing to more finely regulated capabilities such as vectorial transport, immune defence and cell signalling. Surgical strategies to supply lacking gastrointestinal tract tissues have relied on either replacement by proxy (surgical substitution) or the introduction of prostheses. Tissue engineering seeks to replace missing tissues with engineered tissues that more accurately reproduce the native physiological and anatomical milieu. It is now possible to engineer several areas of the gastrointestinal tract with high fidelity, and to employ tissue-engineered bowel in replacement in animal models. These replacement models have reflected excellent anatomical and physiological recapitulation of native bowel by the tissue-engineered constructs in vivo.

Animals↗