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The Journal of Biological Chemistry Sep 2001The Escherichia coli RuvB protein is a motor protein that forms a complex with RuvA and promotes branch migration of Holliday junctions during homologous recombination....
A unique beta-hairpin protruding from AAA+ ATPase domain of RuvB motor protein is involved in the interaction with RuvA DNA recognition protein for branch migration of Holliday junctions.
The Escherichia coli RuvB protein is a motor protein that forms a complex with RuvA and promotes branch migration of Holliday junctions during homologous recombination. This study describes the characteristics of two RuvB mutants, I148T and I150T, that do not promote branch migration in the presence of RuvA. These RuvB mutants hydrolyzed ATP and bound duplex DNA with the same efficiency as wild-type RuvB, but the mutants did not form a complex with RuvA and were defective in loading onto junction DNA in a RuvA-assisted manner. A recent crystallographic study revealed that Ile(148) and Ile(150) are in a unique beta-hairpin that protrudes from the AAA(+) ATPase domain of RuvB. We propose that this beta-hairpin interacts with hydrophobic residues in the mobile third domain of RuvA and that this interaction is vital for the RuvA-assisted loading of RuvB onto Holliday junction DNA.
Topics: Adenosine Triphosphatases; Adenosine Triphosphate; Amino Acid Sequence; Bacterial Proteins; DNA; DNA Helicases; DNA Repair; DNA-Binding Proteins; Escherichia coli Proteins; Molecular Sequence Data
PubMed: 11427534
DOI: 10.1074/jbc.M103611200 -
Journal of Gastrointestinal Surgery :... Nov 2007Mucin-producing tumor in the bile duct is referred to clinically as mucin-producing bile duct tumor (MPBT). Intraductal papillary neoplasm of the biliary tract that...
Mucin-producing tumor in the bile duct is referred to clinically as mucin-producing bile duct tumor (MPBT). Intraductal papillary neoplasm of the biliary tract that resembles an intraductal papillary mucinous neoplasm (IPMN) of the pancreas is a rare category of MPBT and is not well characterized. We, herein, report a case of MPBT of the caudate lobe of the liver that showed papillary growth and communicated with the bile duct of the caudate lobe and protruded into the common hepatic duct. Histologically, MPBT cells showed papillary overgrowth with abundant mucinous secretions, resembling an IPMN of the pancreas. The MPBT cells showed the same immunostaining pattern as that of cells from IPMN of the pancreas.
Topics: Bile Duct Neoplasms; Cholangiopancreatography, Magnetic Resonance; Female; Hepatic Duct, Common; Humans; Immunohistochemistry; Liver Neoplasms; Magnetic Resonance Imaging; Middle Aged; Mucins
PubMed: 17922173
DOI: 10.1007/s11605-007-0133-z -
General Thoracic and Cardiovascular... Mar 2009We report a rare type of aneurysm of the sinus of Valsalva. The orifice of the aneurysm was in the right sinus of Valsalva and protruded superiorly, which is a direction...
We report a rare type of aneurysm of the sinus of Valsalva. The orifice of the aneurysm was in the right sinus of Valsalva and protruded superiorly, which is a direction not typical of right sinus of Valsalva aneurysms. Intraoperatively, it became clear that the aneurysm was located in the right sinus of Valsalva with extracardiac protrusion. Inspection through the aortotomy revealed that the orifice of the aneurysm opened between the orifice of the right coronary artery and the commissure between the right and left coronary cusps. The aneurysm was obliterated with a pledgeted suture from outside the orifice of the aneurysm. Early prophylactic surgical treatment of the aneurysm makes the operation simple and prevents subsequent development of complications, such as compression of the coronary artery, thrombosis, and/or spontaneous rupture.
Topics: Abnormalities, Multiple; Aortic Aneurysm; Aortography; Cardiac Surgical Procedures; Heart Defects, Congenital; Humans; Incidental Findings; Infant; Male; Sinus of Valsalva; Suture Techniques; Tomography, X-Ray Computed; Treatment Outcome; Vascular Surgical Procedures
PubMed: 19280312
DOI: 10.1007/s11748-008-0340-x -
PloS One 2022Colorectal cancer (CRC) can be classified into four consensus molecular subtypes (CMS) according to genomic aberrations and gene expression profiles. CMS is expected to...
BACKGROUND
Colorectal cancer (CRC) can be classified into four consensus molecular subtypes (CMS) according to genomic aberrations and gene expression profiles. CMS is expected to be useful in predicting prognosis and selecting chemotherapy regimens. However, there are still no reports on the relationship between the morphology and CMS.
METHODS
This retrospective study included 55 subjects with T2 CRC undergoing surgical resection, of whom 30 had the depressed type and 25 the protruded type. In the classification of the CMS, we first defined cases with deficient mismatch repair as CMS1. And then, CMS2/3 and CMS4 were classified using an online classifier developed by Trinh et al. The staining intensity of CDX2, HTR2B, FRMD6, ZEB1, and KER and the percentage contents of CDX2, FRMD6, and KER are input into the classifier to obtain automatic output classifying the specimen as CMS2/3 or CMS4.
RESULTS
According to the results yielded by the online classifier, of the 30 depressed-type cases, 15 (50%) were classified as CMS2/3 and 15 (50%) as CMS4. Of the 25 protruded-type cases, 3 (12%) were classified as CMS1 and 22 (88%) as CMS2/3. All of the T2 CRCs classified as CMS4 were depressed CRCs. More malignant pathological findings such as lymphatic invasion were associated with the depressed rather than protruded T2 CRC cases.
CONCLUSIONS
Depressed-type T2 CRC had a significant association with CMS4, showing more malignant pathological findings such as lymphatic invasion than the protruded-type, which could explain the reported association between CMS4 CRC and poor prognosis.
Topics: Humans; Biomarkers, Tumor; Colorectal Neoplasms; Prognosis; Retrospective Studies; Transcriptome
PubMed: 36264865
DOI: 10.1371/journal.pone.0273566 -
Evidence-based Complementary and... 2022Tongue diagnosis is a convenient and noninvasive clinical practice of traditional Chinese medicine (TCM), having existed for thousands of years. Prickle, as an essential...
Tongue diagnosis is a convenient and noninvasive clinical practice of traditional Chinese medicine (TCM), having existed for thousands of years. Prickle, as an essential indicator in TCM, appears as a large number of red thorns protruding from the tongue. The term "prickly tongue" has been used to describe the flow of qi and blood in TCM and assess the conditions of disease as well as the health status of subhealthy people. Different location and density of prickles indicate different symptoms. As proved by modern medical research, the prickles originate in the fungiform papillae, which are enlarged and protrude to form spikes like awn. Prickle recognition, however, is subjective, burdensome, and susceptible to external factors. To solve this issue, an end-to-end prickle detection workflow based on deep learning is proposed. First, raw tongue images are fed into the Swin Transformer to remove interference information. Then, segmented tongues are partitioned into four areas: root, center, tip, and margin. We manually labeled the prickles on 224 tongue images with the assistance of an OpenCV spot detector. After training on the labeled dataset, the super-resolutionfaster-RCNN extracts advanced tongue features and predicts the bounding box of each single prickle. We show the synergy of deep learning and TCM by achieving a 92.42% recall, which is 2.52% higher than the previous work. This work provides a quantitative perspective for symptoms and disease diagnosis according to tongue characteristics. Furthermore, it is convenient to transfer this portable model to detect petechiae or tooth-marks on tongue images.
PubMed: 36185091
DOI: 10.1155/2022/5899975 -
Proceedings of the National Academy of... Jun 2006High-resolution structures of macromolecular complexes offer unparalleled insight into the workings of biological systems and hence the interplay of these systems in...
High-resolution structures of macromolecular complexes offer unparalleled insight into the workings of biological systems and hence the interplay of these systems in health and disease. We have adopted a multifaceted approach to understanding the pathogenically important structure of P-pili, the class I adhesion pili from pyelonephritic Escherichia coli. Our approach combines electron cryomicroscopy, site-directed mutagenesis, homology modeling, and energy calculations, resulting in a high-resolution model of PapA, the major structural element of these pili. Fitting of the modeled PapA subunit into the electron cryomicroscopy data provides a detailed view of these pilins within the supramolecular architecture of the pilus filament. A structural hinge in the N-terminal region of the subunit is located at the site of a newly resolved electron density that protrudes from the P-pilus surface. The structural flexibility provided by this hinge is necessary for assembly of P-pili, illustrating one solution to construction of large macromolecular complexes from small repeating units. These data support our hypothesis that domain-swapped pilin subunits transit the outer cell membrane vertically and rotate about the hinge for final positioning into the pilus filament. Our data confirm and supply a structural basis for much previous genetic, biochemical, and structural data. This model of the P-pilus filament provides an insight into the mechanism of assembly of a macromolecular complex essential for initiation of kidney infection by these bacteria.
Topics: Bacterial Adhesion; Cryoelectron Microscopy; Escherichia coli; Escherichia coli Proteins; Fimbriae Proteins; Fimbriae, Bacterial; Models, Molecular; Mutagenesis, Site-Directed; Protein Conformation
PubMed: 16782819
DOI: 10.1073/pnas.0509620103 -
The Journal of Invasive Cardiology May 2017A 62-year-old man was referred for percutaneous coronary intervention of a severe circumflex lesion. The guidewire became entangled in the previously implanted left...
A 62-year-old man was referred for percutaneous coronary intervention of a severe circumflex lesion. The guidewire became entangled in the previously implanted left anterior descending artery stent. The left main was engaged with a second guide catheter, followed by balloon dilations, various microcatheters, and laser atherectomy. The wire eventually fractured without protruding into the aorta. The circumflex lesion was stented with two stents, followed by left main stenting that covered the fragment. Caution should be used when wiring through stents; wire fracture can be treated with stent implantation, as long as the wire fragment does not protrude into the aorta.
Topics: Angioplasty, Balloon, Coronary; Atherectomy; Cardiac Catheters; Coronary Angiography; Coronary Artery Disease; Device Removal; Equipment Failure; Follow-Up Studies; Humans; Laser Therapy; Male; Middle Aged; Risk Assessment; Stents; Treatment Outcome
PubMed: 28441644
DOI: No ID Found -
Cell Sep 2000TFIIH is a multiprotein complex required for both transcription and DNA repair. Single particles of human TFIIH were revealed by electron microscopy and image processing...
TFIIH is a multiprotein complex required for both transcription and DNA repair. Single particles of human TFIIH were revealed by electron microscopy and image processing at a resolution of 3.8 nm. TFIIH is 16 x 12.5 x 7.5 nm in size and is organized into a ring-like structure from which a large protein domain protrudes out. A subcomplex assembled from five recombinant core subunits also forms a circular architecture that can be superimposed on the ring found in human TFIIH. Immunolabeling experiments localize several subunits: p44, within the ring structure, forms the base of the protruding protein density which includes the cdk7 kinase, cyclin H, and MAT1. Within the ring structure, p44 was flanked on either side by the XPB and XPD helicases. These observations provide us with a quartenary organizational model of TFIIH.
Topics: Antibodies, Monoclonal; Cyclin H; Cyclin-Dependent Kinases; Cyclins; DNA Helicases; DNA-Binding Proteins; HeLa Cells; Humans; Image Processing, Computer-Assisted; Macromolecular Substances; Microscopy, Immunoelectron; Models, Molecular; Multiprotein Complexes; Protein Serine-Threonine Kinases; Protein Structure, Quaternary; Proteins; RNA, Messenger; Recombinant Proteins; Transcription Factor TFIIH; Transcription Factors; Transcription Factors, TFII; Transcription, Genetic; Xeroderma Pigmentosum Group D Protein; Cyclin-Dependent Kinase-Activating Kinase
PubMed: 11007478
DOI: 10.1016/s0092-8674(00)00082-9 -
Surgery Today Aug 2011We describe how we performed retroperitoneoscopic surgery for a 15.5-cm fibroepithelial polyp, which originated in the lowest portion of the right upper ureter,...
We describe how we performed retroperitoneoscopic surgery for a 15.5-cm fibroepithelial polyp, which originated in the lowest portion of the right upper ureter, protruded intermittently into the bladder, and caused ureteral invagination. To our knowledge, this is the first report of the retroperitoneoscopic management of ureteral invagination caused by a long fibroepithelial polyp.
Topics: Adult; Endoscopy; Female; Humans; Neoplasms, Fibroepithelial; Pelvic Organ Prolapse; Polyps; Retroperitoneal Space; Ureteral Neoplasms
PubMed: 21773903
DOI: 10.1007/s00595-010-4422-x -
Molecular Immunology Apr 2000The crystal structure of the Fv molecule from a human monoclonal IgM cryoglobulin (Mez) was determined at 2.6 A resolution. Amino acid sequences of framework regions...
The crystal structure of the Fv molecule from a human monoclonal IgM cryoglobulin (Mez) was determined at 2.6 A resolution. Amino acid sequences of framework regions (FR) of the Mez light (L) and heavy (H) chain variable domains (VL and VH) are highly similar to their counterparts in another human Fv (Pot) previously subjected to X-ray analysis in our laboratory. As expected, the three-dimensional (3-D) structures of FR are quite similar in the two proteins, as are four of the six complementarity-determining regions (CDRs): CDRs 1 and 2 for both L and H chains. Absence of Pro 95L from the LCDR3 loop in Mez VL (relative to Pot LCDR3) results in compression of this loop and creates more space in the VL-VH interface. In the two IgMs, HCDR3 conformations differ significantly from all previously defined conformations for these loops. Pot has a 12-residue HCDR3 that collapses to fill all available space in the VL-VH domain interface, resulting in the formation of a relatively flat platform for antigen binding. In Mez, the HCDR3 is two residues longer and is comprehensively different. A semi-rigid ascending segment dominated by a Pro-Pro-Tyr sequence protrudes out into solvent. The descending portion has the sequence Gly-Trp-Gly-Gly-Gly, which promotes high local flexibility. This segment folds across the VL-VH domain interface to interact with residues in LCDR3. These features partition the Mez active site into two compartments, a large cavity between VL and VH and a smaller cavity lined entirely by constituents of the three heavy chain CDRs. Such an unusual topographical feature indicates why the Mez IgM does not bind to the Fc portion of intact human IgG antibodies in immunoassays yet interacts with high avidity with many Fc-derived octapeptides. The cavities are expected to be the repositories for the Fc-derived peptides, while the semi-rigid protrusion of the Mez HCDR3 prevents the close approach of another macromolecule (e.g. intact IgG) to the active site.
Topics: Amino Acid Sequence; Antibody Affinity; Complementarity Determining Regions; Crystallography, X-Ray; Humans; Immunoglobulin M; Ligands; Models, Molecular; Molecular Sequence Data; Peptides; Protein Conformation; Sequence Deletion; Sequence Homology, Amino Acid; Static Electricity; Water
PubMed: 11000403
DOI: 10.1016/s0161-5890(00)00049-3