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1.
Nucleic Acids Res ; 51(22): e113, 2023 Dec 11.
Article in English | MEDLINE | ID: mdl-37941133

ABSTRACT

Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (aRMCE), able to provide monoclonality, precise genomic integration and uniform transgene expression. Via optimized nocodazole-mediated mitotic arrest, 20% target gene replacement efficiency was achieved without antibiotic selection, and the improved aRMCE efficiency was applicable to a variety of tested cell clones, transgene targets and transfection methods. As a demonstration of this versatile method, we performed directed evolution of fragment crystallizable (Fc), for which error-prone libraries of over 107 variants were constructed and displayed as IgG on surface of CHO cells. Diversities of constructed libraries were validated by deep sequencing, and panels of novel Fc mutants were identified showing improved binding towards specific Fc gamma receptors and enhanced effector functions. Due to its large cargo capacity and compatibility with different mutagenesis approaches, we expect this mammalian cell platform technology has broad applications for directed evolution, multiplex genetic assays, cell line development and stem cell engineering.


Subject(s)
Recombinases , Cricetinae , Animals , Recombinases/genetics , Cricetulus , CHO Cells , Transfection , Cell Cycle
2.
Neuroradiology ; 66(5): 825-834, 2024 May.
Article in English | MEDLINE | ID: mdl-38438630

ABSTRACT

PURPOSE: The elastase-induced aneurysm (EIA) model in rabbits has been proposed for translational research; however, the adjustment of aneurysm neck size remains challenging. In this study, the technical feasibility and safety of balloon neck-plasty to create a wide-necked aneurysm in rabbit EIA model were investigated. METHODS: Male New Zealand White rabbits (N = 15) were randomly assigned to three groups: group A, EIA creation without neck-plasty; group B, neck-plasty immediately after EIA creation; group C, neck-plasty 4 weeks after EIA creation. The diameter of balloon used for neck-plasty was determined 1 mm larger than origin carotid artery diameter. All rabbits were euthanized 4 weeks after their final surgery. Aneurysm neck, height, dome-to-neck (D/N) ratio, and histologic parameters were compared among the groups. RESULTS: Aneurysm creation was technically successful in 14 out of 15 rabbits (93.3%), with one rabbit experiencing mortality due to an adverse anesthetic event during the surgery. Saccular and wide-necked aneurysms were successfully created in all rabbits. Aneurysm neck was significantly greater in groups B and C compared to group A (all P < .05). D/N ratio was significantly lower in groups B and C compared to group A (all P < .05). Additionally, tunica media thickness, vessel area, and luminal area were significantly greater in groups B and C compared to group A (all P < .05). These variables were found to be significantly greater in group B compared to group C (all P < .05). CONCLUSION: The creation of a wide-necked aneurysm using balloon neck-plasty after elastase induction in rabbits has been determined to be technically feasible and safe.


Subject(s)
Intracranial Aneurysm , Male , Rabbits , Animals , Intracranial Aneurysm/pathology , Pancreatic Elastase/adverse effects , Disease Models, Animal , Carotid Artery, Common
3.
Molecules ; 29(11)2024 May 30.
Article in English | MEDLINE | ID: mdl-38893448

ABSTRACT

Epilepsy is a prevalent neurological disorder characterized by recurrent seizures. Validamycin A (VA) is an antibiotic fungicide that inhibits trehalase activity and is widely used for crop protection in agriculture. In this study, we identified a novel function of VA as a potential anti-seizure medication in a zebrafish epilepsy model. Electroencephalogram (EEG) analysis demonstrated that VA reduced pentylenetetrazol (PTZ)-induced seizures in the brains of larval and adult zebrafish. Moreover, VA reduced PTZ-induced irregular movement in a behavioral assessment of adult zebrafish. The developmental toxicity test showed no observable anatomical alteration when the zebrafish larvae were treated with VA up to 10 µM within the effective range. The median lethal dose of VA in adult zebrafish was > 14,000 mg/kg. These results imply that VA does not demonstrate observable toxicity in zebrafish at concentrations effective for generating anti-seizure activity in the EEG and alleviating abnormal behavior in the PTZ-induced epileptic model. Furthermore, the effectiveness of VA was comparable to that of valproic acid. These results indicate that VA may have a potentially safer anti-seizure profile than valproic acid, thus offering promising prospects for its application in agriculture and medicine.


Subject(s)
Anticonvulsants , Disease Models, Animal , Epilepsy , Pentylenetetrazole , Zebrafish , Animals , Anticonvulsants/pharmacology , Anticonvulsants/therapeutic use , Pentylenetetrazole/adverse effects , Epilepsy/drug therapy , Epilepsy/chemically induced , Seizures/drug therapy , Seizures/chemically induced , Electroencephalography , Valproic Acid/pharmacology , Larva/drug effects , Brain/drug effects , Brain/pathology , Inositol/analogs & derivatives
4.
Exp Dermatol ; 31(5): 743-752, 2022 05.
Article in English | MEDLINE | ID: mdl-34882846

ABSTRACT

Matrix metalloproteinases (MMPs) play a key role in tissue remodelling by cleaving extracellular matrix (ECM) components. In the skin, UV irradiation increases expression of MMPs that causes dysregulation of ECM homeostasis in dermis, leading to acceleration of skin aging. However, the mediator(s) that links UV irradiation to the upregulation of MMPs have not been fully defined. Previously, we showed that UVB irradiation activated transglutaminase 2 (TG2) in keratinocytes, eliciting an inflammatory response by activating NF-κB signalling. In this study, we reported the role of TG2 in mediating the UVB-induced expression of MMP-1. In human dermal fibroblasts, UVB irradiation enhanced the expression and activity of TG2, which in turn promotes the expression of MMP-1. Analyses of MMP-1 promoter showed that activation of the NF-κB signalling pathway, rather than AP-1, was responsible for the TG2-mediated upregulation of MMP-1. Moreover, Western blot analysis revealed that TG2 increased the activity of NF-κB by inhibiting degradation of p65 in the nucleus. Furthermore, ex vivo skin from TG2-knockout mice exhibited significantly reduced levels of MMP-1 compared to that from wild-type mice. These results indicate that TG2 functions as a mediator for the UVB-induced expression of MMP-1 in dermal fibroblasts, providing a new target for preventing skin photodamage.


Subject(s)
Matrix Metalloproteinase 1 , Protein Glutamine gamma Glutamyltransferase 2 , Animals , Fibroblasts/metabolism , Matrix Metalloproteinase 1/genetics , Matrix Metalloproteinase 1/metabolism , Matrix Metalloproteinase 3/metabolism , Matrix Metalloproteinases/metabolism , Mice , NF-kappa B/metabolism , Skin/metabolism , Ultraviolet Rays/adverse effects
5.
Proc Natl Acad Sci U S A ; 116(33): 16314-16319, 2019 08 13.
Article in English | MEDLINE | ID: mdl-31363054

ABSTRACT

Critical for diverse biological processes, proteases represent one of the largest families of pharmaceutical targets. To inhibit pathogenic proteases with desired selectivity, monoclonal antibodies (mAbs) hold great promise as research tools and therapeutic agents. However, identification of mAbs with inhibitory functions is challenging because current antibody discovery methods rely on binding rather than inhibition. This study developed a highly efficient selection method for protease inhibitory mAbs by coexpressing 3 recombinant proteins in the periplasmic space of Escherichia coli-an antibody clone, a protease of interest, and a ß-lactamase modified by insertion of a protease cleavable peptide sequence. During functional selection, inhibitory antibodies prevent the protease from cleaving the modified ß-lactamase, thereby allowing the cell to survive in the presence of ampicillin. Using this method to select from synthetic human antibody libraries, we isolated panels of mAbs inhibiting 5 targets of 4 main protease classes: matrix metalloproteinases (MMP-14, a predominant target in metastasis; MMP-9, in neuropathic pain), ß-secretase 1 (BACE-1, an aspartic protease in Alzheimer's disease), cathepsin B (a cysteine protease in cancer), and Alp2 (a serine protease in aspergillosis). Notably, 37 of 41 identified binders were inhibitory. Isolated mAb inhibitors exhibited nanomolar potency, exclusive selectivity, excellent proteolytic stability, and desired biological functions. Particularly, anti-Alp2 Fab A4A1 had a binding affinity of 11 nM and inhibition potency of 14 nM, anti-BACE1 IgG B2B2 reduced amyloid beta (Aß40) production by 80% in cellular assays, and IgG L13 inhibited MMP-9 but not MMP-2/-12/-14 and significantly relieved neuropathic pain development in mice.


Subject(s)
Antibodies, Monoclonal/immunology , Peptide Hydrolases/genetics , Protease Inhibitors/immunology , Recombinant Proteins/immunology , Alzheimer Disease/immunology , Alzheimer Disease/therapy , Amino Acid Sequence/genetics , Amyloid Precursor Protein Secretases/genetics , Amyloid Precursor Protein Secretases/immunology , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/genetics , Amyloid beta-Peptides/immunology , Animals , Antibodies, Monoclonal/biosynthesis , Antibodies, Monoclonal/pharmacology , Aspartic Acid Endopeptidases/genetics , Aspartic Acid Endopeptidases/immunology , Aspergillosis/immunology , Aspergillosis/therapy , Cathepsin B/genetics , Cathepsin B/immunology , Escherichia coli/genetics , Humans , Matrix Metalloproteinase 14/genetics , Matrix Metalloproteinase 14/immunology , Matrix Metalloproteinase 9/genetics , Matrix Metalloproteinase 9/immunology , Matrix Metalloproteinase Inhibitors/immunology , Matrix Metalloproteinase Inhibitors/metabolism , Mice , Neoplasms/immunology , Neoplasms/therapy , Peptide Hydrolases/chemistry , Peptide Hydrolases/immunology , Periplasm/genetics , Protease Inhibitors/pharmacology , Proteolysis/drug effects , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Recombinant Proteins/pharmacology , Serine Proteases/genetics , Serine Proteases/immunology
6.
Int J Mol Sci ; 23(5)2022 Feb 28.
Article in English | MEDLINE | ID: mdl-35269849

ABSTRACT

UV-irradiation induces the secretion of double-stranded RNA (dsRNA) derived from damaged noncoding RNAs in keratinocytes, which enhance the expression of matrix metalloproteinases (MMP) in non-irradiated dermal fibroblasts, leading to dysregulation of extracellular matrix homeostasis. However, the signaling pathway responsible for dsRNA-induced MMP expression has not been fully understood. Transglutaminase 2 (TG2) is an enzyme that modifies substrate proteins by incorporating polyamine or crosslinking of proteins, thereby regulating their functions. In this study, we showed that TG2 mediates dsRNA-induced MMP-1 expression through NF-κB activation. Treatment of poly(I:C), a synthetic dsRNA analogue binding to toll-like receptor 3 (TLR3), generates ROS, which in turn activates TG2 in dermal fibroblast. Subsequently, TG2 activity enhances translocation of p65 into the nucleus, where it augments transcription of MMP. We confirmed these results by assessing the level of MMP expression in Tlr3-/-, TG2-knockdowned and Tgm2-/- dermal fibroblasts after poly(I:C)-treatment. Moreover, treatment with quercetin showed dose-dependent suppression of poly(I:C)-induced MMP expression. Furthermore, ex vivo cultured skin from Tgm2-/- mice exhibited a significantly reduced level of MMP mRNA compared with those from wild-type mice. Our results indicate that TG2 is a critical regulator in dsRNA-induced MMP expression, providing a new target and molecular basis for antioxidant therapy in preventing collagen degradation.


Subject(s)
Matrix Metalloproteinase 1 , RNA, Double-Stranded , Animals , Cells, Cultured , Fibroblasts/metabolism , Matrix Metalloproteinase 1/genetics , Matrix Metalloproteinase 1/metabolism , Matrix Metalloproteinase 3/genetics , Matrix Metalloproteinase 3/metabolism , Mice , Poly I-C/pharmacology , Protein Glutamine gamma Glutamyltransferase 2 , RNA, Double-Stranded/metabolism , Toll-Like Receptor 3/genetics , Toll-Like Receptor 3/metabolism
7.
J Appl Clin Med Phys ; 22(5): 110-116, 2021 May.
Article in English | MEDLINE | ID: mdl-33934495

ABSTRACT

In this study, we assessed how image quality depends on the angle of tilt of a flex tilt coil supporting device during an MRI examination. All measurements were performed with an American College of Radiology (ACR) MRI phantom using a flex tilt coil supporting device. All images were analyzed using an automatic assessment method following the ACR MRI accreditation guidance. Image quality was compared between acquisitions grouped according to the angle of tilt of the coil supporting device: group A (Flat mode), group B (10˚), and group C (18˚). All measured image qualities were within the ACR recommended criteria, regardless of the angle of tilt of the flex tilt coil supporting device. However, statistically significant differences between the three groups were found for slice thickness, position accuracy, image intensity uniformity, and SNR (P < 0.05, ANOVA). The flex tilt coil supporting device can provide sufficient image quality, passing the criteria of the ACR MRI guideline, despite differences in slice thickness, slice position accuracy, image intensity uniformity, and SNR according to the angle of tilt.


Subject(s)
Accreditation , Magnetic Resonance Imaging , Humans , Phantoms, Imaging
8.
Biochemistry ; 59(40): 3802-3812, 2020 10 13.
Article in English | MEDLINE | ID: mdl-32997500

ABSTRACT

Macromolecular protease inhibitors and camelid single-domain antibodies achieve their enzymic inhibition functions often through protruded structures that directly interact with catalytic centers of targeted proteases. Inspired by this phenomenon, we constructed synthetic human antibody libraries encoding long CDR-H3s, from which highly selective monoclonal antibodies (mAbs) that inhibit multiple proteases were discovered. To elucidate their molecular mechanisms, we performed in-depth biochemical characterizations on a panel of matrix metalloproteinase (MMP)-14 inhibitory mAbs. Assays included affinity and potency measurements, enzymatic kinetics, a competitive enzyme-linked immunosorbent assay, proteolytic stability, and epitope mapping followed by quantitative analysis of binding energy changes. The results collectively indicated that these mAbs of convex paratopes were competitive inhibitors recognizing the vicinity of the active cleft, with their significant epitopes scattered across the north and south rims of the cleft. Remarkably, identified epitopes were the surface loops that were highly diverse among MMPs and predominately located at the prime side of the proteolytic site, shedding light on the mechanisms of target selectivity and proteolytic resistance. Substrate sequence profiling and paratope mutagenesis further suggested that mAb 3A2 bound to the active-site cleft in a canonical (substrate-like) manner, by direct interactions between 100hNLVATP100m of its CDR-H3 and subsites S1-S5' of MMP-14. Overall, synthetic mAbs carrying convex paratopes can achieve efficient inhibition and thus hold great therapeutic promise for effectively and safely targeting biomedically important proteases.


Subject(s)
Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/pharmacology , Matrix Metalloproteinase 14/metabolism , Matrix Metalloproteinase Inhibitors/chemistry , Matrix Metalloproteinase Inhibitors/pharmacology , Animals , Camelids, New World , Catalytic Domain/drug effects , Humans , Immunoglobulin Fab Fragments/chemistry , Immunoglobulin Fab Fragments/pharmacology , Models, Molecular , Proteolysis/drug effects
9.
Biotechnol Bioeng ; 117(12): 3664-3676, 2020 12.
Article in English | MEDLINE | ID: mdl-32716053

ABSTRACT

Matrix metalloproteinase-12 (MMP-12), also known as macrophage elastase, is a potent inflammatory mediator and therefore an important pharmacological target. Clinical trial failures of broad-spectrum compound MMP inhibitors suggested that specificity is the key for a successful therapy. To provide the required selectivity, monoclonal antibody (mAb)-based inhibitors are on the rise. However, poor production of active recombinant human MMP-12 catalytic domain (cdMMP-12) presented a technical hurdle for its inhibitory mAb development. We hypothesized that this problem could be solved by designing an expression-optimized cdMMP-12 mutant without structural disruptions at its reaction cleft and surrounding area, and thus isolated active-site inhibitory mAbs could maintain their binding and inhibition functions toward wild-type MMP-12. We combined three advances in the field-PROSS algorithm for cdMMP-12 mutant design, convex paratope antibody library construction, and functional selection for inhibitory mAbs. As a result, isolated Fab inhibitors showed nanomolar affinity and potency toward cdMMP-12 with high selectivity and high proteolytic stability. Particularly, Fab LH11 targeted the reaction cleft of wild-type cdMMP-12 with 75 nM binding KD and 23 nM inhibition IC50 . We expect that our methods can promote the development of mAbs inhibiting important proteases, many of which are recalcitrant to functional production.


Subject(s)
Antibodies, Monoclonal/chemistry , Matrix Metalloproteinase 12/chemistry , Matrix Metalloproteinase Inhibitors/chemistry , Antibodies, Monoclonal/genetics , Humans , Matrix Metalloproteinase 12/genetics , Protein Domains
10.
Pediatr Radiol ; 50(11): 1570-1578, 2020 10.
Article in English | MEDLINE | ID: mdl-32591981

ABSTRACT

BACKGROUND: Image sharpness is commonly degraded on cardiac CT images reconstructed using iterative reconstruction algorithms. OBJECTIVE: To compare the image quality of cardiac CT between raw-data-based and model-based iterative reconstruction algorithms developed by the same CT vendor in children and young adults with congenital heart disease. MATERIALS AND METHODS: In 29 patients with congenital heart disease, we reconstructed 39 cardiac CT datasets using raw-data-based and model-based iterative reconstruction algorithms. We performed quantitative analysis of image sharpness using distance25-75% and angle25-75% on a line density profile across an edge of the descending thoracic aorta in addition to CT attenuation, image noise, signal-to-noise ratio and contrast-to-noise ratio. We compared these quantitative image-quality measures between the two algorithms. RESULTS: CT attenuation did not show significant differences between the algorithms (P>0.05) except in the aorta. Image noise was small but significantly higher in the model-based algorithm than in the raw-data-based algorithm (4.8±2.3 Hounsfield units [HU] vs. 4.7±2.1 HU, P<0.014). Signal-to-noise ratio (110.2±50.9 vs. 108.4±50.4, P=0.050) and contrast-to-noise ratio (91.0±45.7 vs. 89.6±45.1, P=0.063) showed marginal significance between the two algorithms. The model-based algorithm showed a significantly smaller distance25-75% (1.4±0.4 mm vs. 1.6±0.3 mm, P<0.001) and a significantly higher angle25-75% (77.0±4.3° vs. 74.1±5.7°, P<0.001) than the raw-data-based algorithm. CONCLUSION: Compared with the raw-data-based algorithm, the model-based iterative reconstruction algorithm demonstrated better image sharpness and higher image noise on cardiac CT in patients with congenital heart disease.


Subject(s)
Algorithms , Heart Defects, Congenital/diagnostic imaging , Multidetector Computed Tomography , Radiographic Image Interpretation, Computer-Assisted/methods , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Retrospective Studies , Signal-To-Noise Ratio
11.
Sensors (Basel) ; 20(16)2020 Aug 09.
Article in English | MEDLINE | ID: mdl-32784913

ABSTRACT

This paper proposes a novel online object-packing system which can measure the dimensions of every incoming object and calculate its desired position in a given container. Existing object-packing systems have the limitations of requiring the exact information of objects in advance or assuming them as boxes. Thus, this paper is mainly focused on the following two points: (1) Real-time calculation of the dimensions and orientation of an object; (2) Online optimization of the object's position in a container. The dimensions and orientation of the object are obtained using an RGB-D sensor when the object is picked by a manipulator and moved over a certain position. The optimal position of the object is calculated by recognizing the container's available space using another RGB-D sensor and minimizing the cost function that is formulated by the available space information and the optimization criteria inspired by the way people place things. The experimental results show that the proposed system successfully places the incoming various shaped objects in their proper positions.

12.
Int J Mol Sci ; 21(3)2020 Jan 25.
Article in English | MEDLINE | ID: mdl-31991788

ABSTRACT

Transglutaminase 2 (TG2) is a Ca2+-dependent enzyme, which regulates various cellular processes by catalyzing protein crosslinking or polyamination. Intracellular TG2 is activated and inhibited by Ca2+ and GTP binding, respectively. Although aberrant TG2 activation has been implicated in the pathogenesis of diverse diseases, including cancer and degenerative and fibrotic diseases, the structural basis for the regulation of TG2 by Ca2+ and GTP binding is not fully understood. Here, we produced and analyzed a Ca2+-containing TG2 crystal, and identified two glutamate residues, E437 and E539, as Ca2+-binding sites. The enzymatic analysis of the mutants revealed that Ca2+ binding to these sites is required for the transamidase activity of TG2. Interestingly, we found that magnesium (Mg2+) competitively binds to the E437 and E539 residues. The Mg2+ binding to these allosteric sites enhances the GTP binding/hydrolysis activity but inhibits transamidase activity. Furthermore, HEK293 cells transfected with mutant TG2 exhibited higher transamidase activity than cells with wild-type TG2. Cells with wild-type TG2 showed an increase in transamidase activity under Mg2+-depleted conditions, whereas cells with mutant TG2 were unaffected. These results indicate that E437 and E539 are Ca2+-binding sites contributing to the reciprocal regulation of transamidase and GTP binding/hydrolysis activities of TG2 through competitive Mg2+ binding.


Subject(s)
Aminoacyltransferases/metabolism , Binding Sites , Calcium/metabolism , GTP-Binding Proteins/metabolism , Guanosine Triphosphate/metabolism , Magnesium/metabolism , Transglutaminases/metabolism , Amino Acid Sequence , Aminoacyltransferases/chemistry , Binding, Competitive , Calcium/chemistry , Enzyme Activation , GTP-Binding Proteins/chemistry , Guanosine Triphosphate/chemistry , Humans , Hydrolysis , Magnesium/chemistry , Models, Biological , Molecular Conformation , Protein Binding , Protein Glutamine gamma Glutamyltransferase 2 , Structure-Activity Relationship , Transglutaminases/chemistry
13.
Microb Cell Fact ; 16(1): 73, 2017 Apr 28.
Article in English | MEDLINE | ID: mdl-28454584

ABSTRACT

BACKGROUND: As regulators of multifunctional metalloproteinases including MMP, ADAM and ADAMTS families, tissue inhibitors of metalloproteinases (TIMPs) play a pivotal role in extracellular matrix remodeling, which is involved in a wide variety of physiological processes. Since abnormal metalloproteinase activities are related to numerous diseases such as arthritis, cancer, atherosclerosis, and neurological disorders, TIMPs and their engineered mutants hold therapeutic potential and thus have been extensively studied. Traditional productions of functional TIMPs and their N-terminal inhibitory domains (N-TIMPs) rely on costly and time-consuming insect and mammalian cell systems, or tedious and inefficient refolding from denatured inclusion bodies. The later process is also associated with heterogeneous products and batch-to-batch variation. RESULTS: In this study, we developed a simple approach to directly produce high yields of active TIMPs in the periplasmic space of Escherichia coli without refolding. Facilitated by disulfide isomerase (DsbC) co-expression in protease-deficient strain BL21 (DE3), N-TIMP-1/-2 and TIMP-2 which contain multiple disulfide bonds were produced without unwanted truncations. 0.2-1.4 mg purified monomeric TIMPs were typically yielded per liter of culture media. Periplasmically produced TIMPs exhibited expected inhibition potencies towards MMP-1/2/7/14, and were functional in competitive ELISA to elucidate the binding epitopes of MMP specific antibodies. In addition, prepared N-TIMPs were fully active in a cellular context, i.e. regulating cancer cell morphology and migration in 2D and 3D bioassays. CONCLUSION: Periplasmic expression in E. coli is an excellent strategy to recombinantly produce active TIMPs and N-TIMPs.


Subject(s)
Escherichia coli/metabolism , Periplasm/enzymology , Tissue Inhibitor of Metalloproteinase-1/genetics , Tissue Inhibitor of Metalloproteinase-1/metabolism , Tissue Inhibitor of Metalloproteinase-2/genetics , Tissue Inhibitor of Metalloproteinase-2/metabolism , Cloning, Molecular , Epitopes/immunology , Humans , Metalloproteases/antagonists & inhibitors , Periplasm/metabolism , Protein Disulfide-Isomerases/genetics , Protein Disulfide-Isomerases/metabolism , Protein Folding , Recombinant Proteins/metabolism , Solubility , Tissue Inhibitor of Metalloproteinase-1/chemistry , Tissue Inhibitor of Metalloproteinase-1/pharmacology , Tissue Inhibitor of Metalloproteinase-2/chemistry , Tissue Inhibitor of Metalloproteinase-2/pharmacology
14.
Chembiochem ; 17(13): 1198-201, 2016 07 01.
Article in English | MEDLINE | ID: mdl-27151886

ABSTRACT

The genetic code in most organisms codes for 20 proteinogenic amino acids or translation stop. In order to encode more than 20 amino acids in the coding system, one of stop codons is usually reprogrammed to encode a non-proteinogenic amino acid. Although this approach works, usually only one amino acid is added to the amino acid repertoire. In this study, we incorporated non-proteinogenic amino acids into a protein by using a sense codon. As all the codons are allocated in the universal genetic code, we destroyed all the tRNA(Arg) in a cell-free protein synthesis system by using a tRNA(Arg) -specific tRNase, colicin D. Then by supplementing the system with tRNACCU , the translation system was partially restored. Through this creative destruction, reprogrammable codons were successfully created in the system to encode modified lysines along with the 20 proteinogenic amino acids.


Subject(s)
Arginine/genetics , Directed Molecular Evolution , Genetic Code , Codon , Colicins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Green Fluorescent Proteins/biosynthesis , Green Fluorescent Proteins/genetics , Protein Biosynthesis/genetics , RNA, Transfer, Arg/genetics , RNA, Transfer, Arg/metabolism
15.
Methods Mol Biol ; 2747: 243-256, 2024.
Article in English | MEDLINE | ID: mdl-38038945

ABSTRACT

Targeting dysregulated protease expression and/or abnormal substrate proteolysis, highly selective inhibition of pathogenic proteases by monoclonal antibodies (mAbs) presents an attractive therapeutic approach for the treatment of diseases including cancer. Herein, we report a functional selection method for protease inhibitory mAbs by periplasmic co-expression of three recombinant proteins-a protease of interest, an antibody Fab library, and a modified ß-lactamase TEM-1. We validate this approach by isolation of highly selective and potent mAbs inhibiting human matrix metalloproteinase 9 (MMP9).


Subject(s)
Matrix Metalloproteinase Inhibitors , Peptide Hydrolases , Humans , Peptide Hydrolases/metabolism , Matrix Metalloproteinase Inhibitors/pharmacology , Antibodies, Monoclonal , Endopeptidases/metabolism , Proteolysis
16.
Nat Commun ; 15(1): 1695, 2024 Feb 24.
Article in English | MEDLINE | ID: mdl-38402240

ABSTRACT

Prominent techniques such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and rapid kits are currently being explored to both enhance sensitivity and reduce assay time for diagnostic tests. Existing commercial molecular methods typically take several hours, while immunoassays can range from several hours to tens of minutes. Rapid diagnostics are crucial in Point-of-Care Testing (POCT). We propose an approach that integrates a time-series deep learning architecture and AI-based verification, for the enhanced result analysis of lateral flow assays. This approach is applicable to both infectious diseases and non-infectious biomarkers. In blind tests using clinical samples, our method achieved diagnostic times as short as 2 minutes, exceeding the accuracy of human analysis at 15 minutes. Furthermore, our technique significantly reduces assay time to just 1-2 minutes in the POCT setting. This advancement has the potential to greatly enhance POCT diagnostics, enabling both healthcare professionals and non-experts to make rapid, accurate decisions.


Subject(s)
Communicable Diseases , Deep Learning , Humans , Rapid Diagnostic Tests , Point-of-Care Testing , Enzyme-Linked Immunosorbent Assay , Sensitivity and Specificity , Point-of-Care Systems
17.
Appl Microbiol Biotechnol ; 97(10): 4665-75, 2013 May.
Article in English | MEDLINE | ID: mdl-22846900

ABSTRACT

Quorum sensing gives rise to biofilm formation on the membrane surface, which in turn causes a loss of water permeability in membrane bioreactors (MBRs) for wastewater treatment. Enzymatic quorum quenching was reported to successfully inhibit the formation of biofilm in MBRs through the decomposition of signal molecules, N-acyl homoserine lactones (AHLs). The aim of this study was to elucidate the mechanisms of quorum quenching in more detail in terms of microbial population dynamics and proteomics. Microbial communities in MBRs with and without a quorum quenching enzyme (acylase) were analyzed using pyrosequencing and compared with each other. In the quorum quenching MBR, the rate of transmembrane pressure (TMP) rise-up was delayed substantially, and the proportion of quorum sensing bacteria with AHL-like autoinducers (such as Enterobacter, Pseudomonas, and Acinetobacter) also decreased in the entire microbial community of mature biofilm in comparison to that in the control MBR. These factors were attributed to the lower production of extracellular polymeric substances (EPS), which are known to play a key role in the formation of biofilm. Proteomic analysis using the Enterobacter cancerogenus strain ATCC 35316 demonstrates the possible depression of protein expression related to microbial attachments to solid surfaces (outer membrane protein, flagellin) and the agglomeration of microorganisms (ATP synthase beta subunit) with the enzymatic quorum quenching. It has been argued that changes in the microbial population, EPS and proteins via enzymatic quorum quenching could inhibit the formation of biofilm, resulting in less biofouling in the quorum quenching MBR.


Subject(s)
Bioreactors , Enzymes/metabolism , Proteomics , Quorum Sensing
18.
PLoS One ; 18(1): e0280395, 2023.
Article in English | MEDLINE | ID: mdl-36649351

ABSTRACT

Some cerebral arterial silicone phantoms have been used in preclinical evaluations. However, typical silicone-based phantoms are limited in their capacity to reproduce real contrast filling dynamics of the human cerebral artery. This study aimed to develop a cerebral arterial silicone phantom to analyze the feasibility of real contrast filling dynamics. The fluid circulation phantom system consisted of a cerebral arterial silicone phantom without or with additional devices, a pump, an injection system, a pressure-monitoring system, a constant-temperature bath, and a venous drainage container. Vascular resistance was reproduced with a plastic cistern only or a plastic cistern filled with a sponge pad. Three phantom groups were constructed as follows: a) the cerebral arterial silicone phantom used as the control group (type A), b) phantom with the incorporated plastic cistern (type B), and c) phantom with the incorporated plastic cistern filled with a sponge pad (type C). The contrast concentration-time curve patterns of the three groups obtained from digital subtraction angiography (DSA) were compared. Consequently, the DSA pattern of the type C phantom was the most similar to that obtained from the control group as the reference data, which showed the broadest full-width-at-half-maximum and the area under the curve values and the highest maximum contrast concentration. In conclusion, we could emulate the arterial contrast filling dynamics of clinical cerebral angiography by applying a small cistern filled with a sponge pad at the drainage side of the phantom.


Subject(s)
Silicones , Humans , Cerebral Angiography , Pilot Projects , Feasibility Studies , Angiography, Digital Subtraction
19.
Interv Neuroradiol ; 29(5): 548-554, 2023 Oct.
Article in English | MEDLINE | ID: mdl-35733403

ABSTRACT

BACKGROUND: The purpose of our study was to investigate the safety and effectiveness of a modified technique using a short guiding catheter for instillation of elastase in comparison with the previously described method of creating elastase-induced aneurysm in rabbits. METHODS: Following right common carotid artery (RCCA) access using an arterial sheath and inflating the Fogarty balloon in the subclavian artery, a short guiding catheter was used for the instillation of the elastase in the experimental group (n = 5) while it was performed with a microcatheter in the control group (n = 5). The procedure duration was recorded from the RCCA puncture to the sheath removal. The histological changes were characterized using H&E and Masson's trichrome (MT) staining. RESULTS: The procedure time was 23 ± 2 min in the experimental group and 29 ± 2 min in the control group. All the rabbits (100%) in the experimental group survived without neurologic deficits, but two rabbits (40%) survived in the control group. All aneurysms were created in the saccular shape (100%) with a neck size of 2.3 ± 0.29 mm, a width of 2.75 ± 0.36 mm, and height of 6.37 ± 0.46 mm, and a dome to neck ratio of 1.21 ± 0.23. The aneurysm walls were partly thickened due to the degradation of the media tunica and adventitia proliferation with loss of the internal elastic lamina. CONCLUSION: By using a short guiding catheter, we could instill the elastase in a more effective and safe manner in the creation of the elastase-induced aneurysm model in rabbits.


Subject(s)
Intracranial Aneurysm , Pancreatic Elastase , Animals , Rabbits , Pancreatic Elastase/adverse effects , Disease Models, Animal , Intracranial Aneurysm/diagnostic imaging , Intracranial Aneurysm/therapy , Carotid Artery, Common/surgery , Subclavian Artery
20.
Clin Neuroradiol ; 33(1): 227-235, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36036257

ABSTRACT

PURPOSE: Woven EndoBridge (WEB) was introduced for the endovascular therapy of wide-neck intracranial aneurysms. The safety and efficacy have been evaluated through several meta-analyses. However, these reviews did not cover the expanding indications in detail. Therefore, we aimed to show the changing trends for intracranial aneurysm treatment using the WEB device. METHODS: A systematic review and meta-analysis was conducted with PubMed, Embase, and Cochrane databases. We searched for studies that reported baseline characteristics of aneurysms and the WEB devices, which had treated more than 20 aneurysms consecutively. The pooled proportions of aneurysm indications and used WEB device types were obtained. To evaluate the changing indications for the treated aneurysm size, including the neck diameter, a trend line and linear regression model was measured. RESULTS: A total of 27 cohorts were included encompassing 1831 aneurysms treated with the WEB. A total of 86% were used in the four major locations as on-label indications (middle cerebral artery bifurcation; 34%, anterior communicating artery; 26%, basilar tip; 18%, internal carotid artery terminus; 7%). Among off-label indications, the most common location was the posterior communicating artery (8%), followed by the anterior cerebral artery including the pericallosal artery (6%). The median aneurysm size and neck diameter was 7 mm and 4.6 mm, respectively. The WEB device has been used for the treatment of smaller aneurysms than the initial indication. Also, the proportion for ruptured aneurysm treatment was increased up to 15%. CONCLUSION: The mechanical and technical development of the WEB resulted in expanding the indications for the treatment of intracranial aneurysms. The off-label indications accounted for 14% in total and an increasing number of small aneurysms are treated with WEB devices. Moreover, the proportion for ruptured aneurysm treatment was currently increased up to 14% more than in the beginning.


Subject(s)
Aneurysm, Ruptured , Embolization, Therapeutic , Endovascular Procedures , Intracranial Aneurysm , Humans , Intracranial Aneurysm/diagnostic imaging , Intracranial Aneurysm/therapy , Treatment Outcome , Embolization, Therapeutic/methods , Endovascular Procedures/methods , Retrospective Studies , Aneurysm, Ruptured/therapy
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