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To increase the coating thickness and service life of the FeNiCrMo coating, a plasma transferred arc (PTA) double-track alloying technique was employed to enhance the surface triboperformance of the ductile iron. Optical microscopy (OM), X-ray diffraction (XRD), electron probe X-ray microanalyzer (EPMA), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Vickers hardness tester, and tribological tester were subsequently used to evaluate the effect of the double alloying treatment tracks on the microstructure and triboperformance of the coating. The results indicate that the content of the cementite in the sample with a double-track treatment increases 3.90 wt.% and the content of the martensite decreases 13.04 wt.% compared with the sample with a single-track treatment, which results in the maximum microhardness of the sample fabricated by double track increasing from 837 ± 10 HV0.2 for the sample fabricated by single track to 871 ± 7 HV0.2. Thus, the wear rate is lower than that of the sample with a single-track treatment. In addition, the distribution of alloying elements is more uniform and coating thickness is higher in the double track than those of the single-track-treated one. Therefore, the double-track PTA alloying treatment is favored for hardfacing ductile iron with a FeNiCrMo alloy coating due to its enhanced triboperformance and longer service life.
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Deoxyribonucleic acid (DNA) is the blueprint of life, and cost-effective methods for its long-term storage could have many potential benefits to society. Here we present the method of in situ cryosilicification of whole blood cells, which allows long-term preservation of DNA. Importantly, our straightforward approach is inexpensive, reliable, and yields cryosilicified samples that fulfill the essential criteria for safe, long-term DNA preservation, namely robustness against external stressors, such as radical oxygen species or ultraviolet radiation, and long-term stability in humid conditions at elevated temperatures. Our approach could enable the room temperature storage of genomic information in book-size format for more than one thousand years (thermally equivalent), costing only 0.5 $/person. Additionally, our demonstration of 3D-printed DNA banking artefacts, could potentially allow 'artificial fossilization'.
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ADN , Rayos Ultravioleta , Humanos , ADN/genética , Conservación de la Sangre/métodos , Preservación Biológica/métodos , OxígenoRESUMEN
DNA damage repair (DDR) is critical in maintaining normal cellular function and genome integrity and is associated with cancer risk, progression, and therapeutic response. However, there is still a lack of a thorough understanding of the effects of DDR genes' expression level in cancer progression and therapeutic resistance. Therefore, we defined a tumor-related DDR score (TR-DDR score), utilizing the expression levels of 20 genes, to quantify the tumor signature of DNA damage repair pathways in tumors and explore the possible function and mechanism for the score among different cancers. The TR-DDR score has remarkably predictive power for tumor tissues. It is a more accurate indicator for the response of chemotherapy or immunotherapy combined with the tumor-infiltrating lymphocyte (TIL) and G2M checkpoint score than the pre-existing predictors (CD8 or PD-L1). This study points out that the TR-DDR score generally has positive correlations with patients of advanced-stage, genome-instability, and cell proliferation signature, while negative correlations with inflammatory response, apoptosis, and p53 pathway signature. In the context of tumor immune response, the TR-DDR score strongly positively correlates with the number of T cells (CD4+ activated memory cells, CD8+ cells, T regs, Tfh) and macrophages M1 polarization. In addition, by difference analysis and correlation analysis, COL2A1, MAGEA4, FCRL4, and ZIC1 are screened out as the potential modulating factors for the TR-DDR score. In summary, we light on a new biomarker for DNA damage repair pathways and explore its possible mechanism to guide therapeutic strategies and drug response prediction.
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Daño del ADN , Neoplasias , Reparación del ADN , Humanos , Factores Inmunológicos/uso terapéutico , Inmunoterapia , Neoplasias/tratamiento farmacológico , Neoplasias/terapia , Transducción de SeñalRESUMEN
Pseudomonas is a large and diverse genus within the Gammaproteobacteria known for its important ecological role in the environment. These bacteria exhibit versatile features of which the ability of heterotrophic nitrification and aerobic denitrification can be applied for nitrogen removal from the wastewater. A novel denitrifying bacterium, designated JM10B5aT, was isolated from the pond water for juvenile Litopenaeus vannamei. The phylogenetic, genomic, physiological, and biochemical analyses illustrated that strain JM10B5aT represented a novel species of the genus Pseudomonas, for which the name Pseudomonas oligotrophica sp. nov. was proposed. The effects of carbon sources and C/N ratios on denitrification performance of strain JM10B5aT were investigated. In addition, the results revealed that sodium acetate was selected as the optimum carbon source for denitrification of this strain. Besides, strain JM10B5aT could exhibit complete nitrate removal at the low C/N ratio of 3. Genomic analyses revealed that JM10B5aT possessed the functional genes including napA, narG, nirS, norB, and nosZ, which might participate in the complete denitrification process. Comparative genomic analyses indicated that many genes related to aggregation, utilization of alkylphosphonate and tricarballylate, biosynthesis of cofactors, and vitamins were contained in the genome of strain JM10B5aT. These genomic features were indicative of its adaption to various niches. Moreover, strain JM10B5aT harbored the complete operons required for the biosynthesis of vibrioferrin, a siderophore, which might be conducive to the high denitrification efficiency of denitrifying bacterium at low C/N ratio. Our findings demonstrated that the strain JM10B5aT could be a promising candidate for treating wastewater with a low C/N ratio.
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Coronary artery disease (CAD) is considered one of the leading causes of death worldwide. Although dysregulation of long non-coding RNAs (lncRNAs) has been reported to be associated with the initiation and progression of CAD, the knowledge regarding their specific functions as well their physiological/pathological significance in CAD is very limited. In this study, we aimed to systematically analyze immune-related lncRNAs in CAD and explore the relationship between key immune-related lncRNAs and the immune cell infiltration process. Based on differential expression analysis of mRNAs and lncRNAs, an immune-related lncRNA-mRNA weighted gene co-expression network containing 377 lncRNAs and 119 mRNAs was constructed. LINC01480 and AL359237.1 were identified as the hub immune-related lncRNAs in CAD using the random forest-recursive feature elimination and least absolute shrinkage and selection operator logistic regression. Furthermore, 93 CAD samples were divided into two subgroups according to the expression values of LINC01480 and AL359237.1 by consensus clustering analysis. By performing gene set enrichment analysis, we found that cluster 2 enriched more cardiovascular risk pathways than cluster 1. The immune cell infiltration analysis of ischemic cardiomyopathy (ICM; an advanced stage of CAD) samples revealed that the proportion of macrophage M2 was upregulated in the LINC01480 highly expressed samples, thus suggesting that LINC01480 plays a protective role in the progression of ICM. Based on the findings of this study, lncRNA LINC01480 may be used as a novel biomarker and therapeutic target for CAD.
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Two novel bacterial strains, designated as DN00404T and DN04309T, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404T and DN04309T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404T were short rod-shaped and those of DN04309T were long rod-shaped. Strain DN00404T was found to grow at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.5) and in 0-2.0â% (w/v) NaCl (optimum, 1.0â%). Strain DN04309T was found to grow at 15-45 °C (optimum, 20-37 °C), at pH 5.5-11.0 (optimum, 7.5) and in 0-4.0â% (w/v) NaCl (optimum, 0.5â%). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus Sphingobacterium and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0-96.0â% ANI and 70.0â% dDDH for species delineation. The genomic DNA G+C contents of strains DN00404T and DN04309T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C15â:â0 and summed feature 3 (C16â:â1 ω6c and/or C16â:â1 ω7c), which were similar to those of other species of this genus. The two major fatty acids C16â:â0 and iso-C17â:â0 3-OH were also found in strain DN00404T. Based on genotypic and phenotypic characteristics, two novel species of the genus Sphingobacterium are proposed: Sphingobacterium micropteri sp. nov. with DN00404T (=GDMCC 1.1865T=KACC 21924T) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309T (=GDMCC 1.1984T=KCTC 82348T) as the type strain.
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Acuicultura , Filogenia , Sphingobacterium , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Sphingobacterium/clasificación , Sphingobacterium/aislamiento & purificación , AguaRESUMEN
Based on a fluorescence "on-off-on" strategy, we fabricated a simple and highly sensitive DNA-based fluorescence biosensor for the detection of micro (mi)RNA from carbon dots (CDs) and graphene oxide (GO) without complicated and time-consuming operations. CDs were successfully synthesized and conjugated to the end of a single-stranded fuel DNA that was adsorbed onto the surface of GO through π-π stacking, resulting in fluorescence quenching. In the presence of the target miRNA let-7a, the fuel DNA was desorbed from the GO surface, and fluorescence was restored through two successive toehold-mediated strand displacement reactions on double-stranded DNA-modified gold nanoparticles. The target miRNA let-7a was recycled, leading to signal amplification. The concentration of let-7a was proportional to the degree of fluorescence recovery. Under optimal conditions, there was a good linear relationship between the relative fluorescence intensity and let-7a concentration in the range of 0.01-1 nM, with a detection limit of 7.8 pM. With its advantages of signal amplification and high biocompatibility, this fluorescence sensing strategy can be applied to the detection of a variety of target miRNAs and can guide the design of novel biosensors with improved properties.
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BACKGROUND: Lung cancer screening using low-dose computed tomography (LDCT) often leads to unnecessary biopsy because of the low specificity among patients with pulmonary nodules ≤10 mm. Circulating genetically abnormal cells (CACs) can be used to discriminate lung cancer from benign lung disease. To examine the diagnostic value of CACs in detecting lung cancer for patients with malignant pulmonary nodules ≤10 mm. METHODS: In this prospective study, patients with pulmonary nodules ≤10 mm who were detected at four hospitals in China from January 2019 to January 2020 were included. CACs were detected using fluorescence in-situ hybridization. All patients were confirmed as lung cancer or benign disease by further histopathological examination. Multivariable logistic regression models were established to detect the presence of lung cancer using CACs and other associated characteristics. Receiver operating characteristic analysis was used to evaluate the performance of CACs for lung cancer diagnosis. RESULTS: Overall, 125 patients were included and analyzed. When the cutoff value of CACs was >2, the sensitivity and specificity for lung cancer were 70.5 and 86.4%. Male (OR = 0.330, P = 0.005), maximum solid nodule (OR = 2.362, P = 0.089), maximum nodule located in upper lobe (OR = 3.867, P = 0.001), and CACs >2 (OR = 18.525, P < 0.001) met the P < 0.10 criterion for inclusion in the multivariable models. The multivariable logistic regression model that included the dichotomized CACs (>2 vs. ≤2) and other clinical factors (AUC = 0.907, 95% CI = 0.842-0.951) was superior to the models that only considered dichotomized CACs or other clinical factors and similar to the model with numerical CACs and other clinical factors (AUC = 0.913, 95% CI = 0.850-0.956). CONCLUSION: CACs presented a significant diagnostic value in detecting lung cancer for patients with pulmonary nodules ≤10 mm.
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PURPOSE: Available biomarkers lack sensitivity for an early lung cancer. Circulating genetically abnormal cells (CACs) occur early in tumorigenesis. To determine the diagnostic value of CACs in blood detected by 4-color fluorescence in situ hybridization (FISH) for lung cancer. METHODS: This was a prospective study of patients with pulmonary nodules ≤ 30 mm detected between 10/2019 and 01/2020 at four tertiary hospitals in China. All patients underwent a pathological examination of lung nodules found by imaging and were grouped as malignant and benign. CACs were detected by 4-color FISH. Patients were divided into the training and validation cohorts. Receiver operating characteristics analysis was used to analyze the diagnosis value of CACs. RESULTS: A total of 205 participants were enrolled. Using a cut-off value of ≥ 3, blood CACs achieved areas under the curve (AUCs) of 0.887, 0.823, and 0.823 for lung cancer in the training and validation cohorts, and all patients, respectively. CACs had high diagnostic values across all tumor sizes and imaging lesion types. CACs were decreased after surgery (median, 4 vs. 1, P < 0.001) in the validation set. The CAC status between blood and tissues was highly consistent (kappa = 0.909, P < 0.001). The AUC of CAC (0.823) was higher than that of CEA (0.478), SCC (0.516), NSE (0.506), ProGRP (0.519), and CYFRA21-1 (0.535) (all P < 0.001). CONCLUSION: CACs might have a high value for the early diagnosis of lung cancer. These findings might need to be validated in future studies. Evidence suggested homology in genetic aberrations between the CACs and the tumor cells.
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Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Detección Precoz del Cáncer/métodos , Hibridación Fluorescente in Situ/métodos , Neoplasias Pulmonares/diagnóstico , Células Neoplásicas Circulantes/patología , Anciano , Biomarcadores de Tumor/análisis , Biomarcadores de Tumor/sangre , Carcinoma de Pulmón de Células no Pequeñas/sangre , Carcinoma de Pulmón de Células no Pequeñas/cirugía , Femenino , Colorantes Fluorescentes/análisis , Humanos , Neoplasias Pulmonares/sangre , Neoplasias Pulmonares/cirugía , Masculino , Persona de Mediana Edad , Valor Predictivo de las Pruebas , Estudios Prospectivos , Sensibilidad y EspecificidadRESUMEN
Biomolecules and organelles usually undergo changes to their structure or form as a result of mechanical stretching or stimulation. It is critical to be able to observe these changes and responses, which trigger mechano-chemical coupling or signal transduction. Advanced techniques have been developed to observe structure and form during manipulation; however, these require sophisticated methods. We have developed a simple approach to observe fine structure after stretching without fluorophore labeling. DNAs or molecules on the cell surface were bound to magnetic microbeads, followed by stretching with a magnetic field. After fixing, staining, and drying, the samples were examined by scanning electron microscopy with no need to build a functional surface with complex processes. Straight DNAs were observed rather than random-walk-like loose polymers. In our cellular experiment, the magnetic beads were bound to a Jurkat cell and formed a rosette which was later stuck to the substrate. A 41.3 µm filament on the base of a filopodium was pulled out via integrin from a cell. Therefore, our method can reveal long structures up to hundreds of micrometers at nanometer resolution after stretching or twisting. Our approach could have wide applications in structure-function studies of biomolecules, and in mechanobiology and cell biology when diffraction cannot used.
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CsgA is a major protein subunit of Escherichia coli biofilms and plays key roles in bacterial adhesion and invasion. CsgA proteins can self-assemble into amyloid nanofibers, characterized by their hierarchical structures across multiple length scales, outstanding strength and their structural robustness under harsh environments. Here, magnetic tweezers were used to study the force spectra of CsgA protein at fibril levels. The two ends of a single nanofiber were directly connected between a magnetic bead and a glass slide using a previously reported tag-free method. We showed that a wormlike chain model could be applied to fit the typical force-extension curves of CsgA nanofibers and to estimate accordingly the mechanical properties. The bending stiffness of nanofibers increased with increasing diameters. The changes in extension of single CsgA fibers were found to be up to 17 fold that of the original length, indicating exceptional tensile properties. Our results provide new insights into the tensile properties of bacterial amyloid nanofibers and highlight the ultrahigh structural stability of the Escherichia coli biofilms.
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DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA "braiding" experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements.
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Proteínas Bacterianas/metabolismo , ADN Nucleotidiltransferasas/metabolismo , ADN Superhelicoidal/metabolismo , Recombinación Genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , ADN Nucleotidiltransferasas/química , ADN Nucleotidiltransferasas/genética , ADN Superhelicoidal/química , Proteínas de Unión al ADN/metabolismo , Factor Proteico para Inverción de Estimulación/metabolismo , Modelos Químicos , Modelos Genéticos , Modelos Moleculares , Conformación de Ácido Nucleico , Plásmidos/genética , Mutación Puntual , Conformación Proteica , Subunidades de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Rotación , Salmonella/enzimologíaRESUMEN
Histone H1 binds to linker DNA between nucleosomes, but the dynamics and biological ramifications of this interaction remain poorly understood. We performed single-molecule experiments using magnetic tweezers to determine the effects of H1 on naked DNA in buffer or during chromatin assembly in Xenopus egg extracts. In buffer, nanomolar concentrations of H1 induce bending and looping of naked DNA at stretching forces below 0.6 pN, effects that can be reversed with 2.7-pN force or in 200 mM monovalent salt concentrations. Consecutive tens-of-nanometer bending events suggest that H1 binds to naked DNA in buffer at high stoichiometries. In egg extracts, single DNA molecules assemble into nucleosomes and undergo rapid compaction. Histone H1 at endogenous physiological concentrations increases the DNA compaction rate during chromatin assembly under 2-pN force and decreases it during disassembly under 5-pN force. In egg cytoplasm, histone H1 protects sperm nuclei undergoing genome-wide decondensation and chromatin assembly from becoming abnormally stretched or fragmented due to astral microtubule pulling forces. These results reveal functional ramifications of H1 binding to DNA at the single-molecule level and suggest an important physiological role for H1 in compacting DNA under force and during chromatin assembly.
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Ensamble y Desensamble de Cromatina , ADN/metabolismo , Histonas/metabolismo , Proteínas de Xenopus/metabolismo , Animales , Extractos Celulares , Núcleo Celular/efectos de los fármacos , Núcleo Celular/metabolismo , ADN/química , ADN/genética , Femenino , Histonas/química , Histonas/genética , Cinética , Masculino , Nocodazol/farmacología , Conformación de Ácido Nucleico/efectos de los fármacos , Nucleosomas/metabolismo , Óvulo/metabolismo , Cloruro de Potasio/química , Cloruro de Potasio/farmacología , Unión Proteica/efectos de los fármacos , Espermatozoides/metabolismo , Moduladores de Tubulina/farmacología , Proteínas de Xenopus/química , Proteínas de Xenopus/genética , Xenopus laevisRESUMEN
Binding of selectins to P-selectin glycoprotein ligand-1 (PSGL-1) mediates tethering and rolling of leukocytes on the endothelium during inflammation. Previous measurements obtained with a flow-chamber assay have shown that mutations of three tyrosines at the PSGL-1 N-terminus (Y46, Y48, and Y51) increase the reverse rates and their sensitivity to the force of bonds with P- and L-selectin. However, the effects of these mutations on the binding affinities and forward rates have not been studied. We quantified these effects by using an adhesion frequency assay to measure two-dimensional affinity and kinetic rates at zero force. Wild-type PSGL-1 has 2.2- to 8.5-fold higher binding affinities for P- and L-selectin than PSGL-1 mutants with two of three tyrosines substituted by phenylalanines, and 9.6- to 49-fold higher affinities than the PSGL-1 mutant with all three tyrosines replaced. In descending order, the affinity decreased from wild-type to Y48/51F, Y46/51F, Y46/48F, and Y46/48/51F. The affinity differences were attributed to major changes in the forward rate and minor changes in the reverse rate, suggesting that these tyrosines regulate the accessibility of PSGL-1 to P- and L-selectin via electrostatic interactions, which is supported by molecular-dynamics simulations. Our results provide insights into the structure-function relationship of receptor-ligand binding at a single-residue level.
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Sustitución de Aminoácidos , Membrana Celular/metabolismo , Selectina L/metabolismo , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Selectina-P/metabolismo , Tirosina , Animales , Células CHO , Cricetinae , Cricetulus , Humanos , Cinética , Glicoproteínas de Membrana/genética , Simulación de Dinámica Molecular , Unión Proteica , Estructura Terciaria de Proteína , Electricidad EstáticaRESUMEN
Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the force-extension measurements were in thermodynamic equilibrium. We, therefore, could use a thermodynamic Maxwell relation to deduce the change of protein number on a single DNA due to varied force. For the binding of both HU and Fis under conditions studied, numbers of bound proteins decreased as force was increased. Our experiments showed that most of the bound HU proteins were driven off the DNA at 6.3 pN for HU concentrations lower than 150 nM; our HU data were fit well by a statistical-mechanical model of protein-induced bending of DNA. In contrast, a significant amount of Fis proteins could not be forced off the DNA at forces up to 12 pN and Fis concentrations up to 20 nM. This thermodynamic approach may be applied to measure changes in numbers of a wide variety of molecules bound to DNA or other polymers. Force-dependent DNA binding by proteins suggests mechano-chemical mechanisms for gene regulation.
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Proteínas de Unión al ADN/química , ADN/química , Proteínas de Escherichia coli/química , Factor Proteico para Inverción de Estimulación/química , Termodinámica , ADN/metabolismo , Proteínas de Unión al ADN/metabolismo , Proteínas de Escherichia coli/metabolismo , Factor Proteico para Inverción de Estimulación/metabolismo , Modelos Estadísticos , Unión ProteicaRESUMEN
HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression.
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Proteínas Bacterianas/metabolismo , Proteínas de Unión al ADN/metabolismo , ADN/química , Tampones (Química) , ADN/metabolismo , Glutamatos/química , Cinética , Unión Proteica , Cloruro de Sodio/químicaRESUMEN
Barrier-to-autointegration factor (BAF) is a protein that has been proposed to compact retroviral DNA, making it inaccessible as a target for self-destructive integration into itself (autointegration). BAF also plays an important role in nuclear organization. We studied the mechanism of DNA condensation by BAF using total internal reflection fluorescence microscopy. We found that BAF compacts DNA by a looping mechanism. Dissociation of BAF from DNA occurs with multiphasic kinetics; an initial fast phase is followed by a much slower dissociation phase. The mechanistic basis of the broad timescale of dissociation is discussed. This behavior mimics the dissociation of BAF from retroviral DNA within preintegration complexes as monitored by functional assays. Thus the DNA binding properties of BAF may alone be sufficient to account for its association with the preintegration complex.
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Proteínas de Unión al ADN/química , ADN/química , Sitios de Unión , Proteínas Portadoras , Cristalografía por Rayos X , ADN/metabolismo , Proteínas de Unión al ADN/metabolismo , Dimerización , Humanos , Microscopía Fluorescente , Conformación Proteica , Pliegue de ProteínaRESUMEN
Mechanics and surface microtopology of the molecular carrier influence cell adhesion, but the mechanisms underlying these effects are not well understood. We used a micropipette adhesion frequency assay to quantify how the carrier stiffness and microtopology affected two-dimensional kinetics of interacting adhesion molecules on two apposing surfaces. Interactions of P-selectin with P-selectin glycoprotein ligand-1 (PSGL-1) were used to demonstrate such effects by presenting the molecules on three carrier systems: human red blood cells (RBCs), human promyelocytic leukemia HL-60 cells, and polystyrene beads. Stiffening the carrier alone or in cooperation with roughing the surface lowered the two-dimensional affinity of interacting molecules by reducing the forward rate but not the reverse rate, whereas softening the carrier and roughing the surface had opposing effects in affecting two-dimensional kinetics. In contrast, the soluble antibody bound with similar three-dimensional affinity to surface-anchored P-selectin or PSGL-1 constructs regardless of carrier stiffness and microtopology. These results demonstrate that the carrier stiffness and microtopology of a receptor influences its rate of encountering and binding a surface ligand but does not subsequently affect the stability of binding. This provides new insights into understanding the rolling and tethering mechanism of leukocytes onto endothelium in both physiological and pathological processes.
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Glicoproteínas de Membrana/metabolismo , Selectina-P/metabolismo , Mapeo de Interacción de Proteínas , Adhesión Celular/fisiología , Células Cultivadas , Células HL-60 , Humanos , Cinética , Glicoproteínas de Membrana/química , Selectina-P/química , Unión Proteica/fisiología , Transporte de Proteínas/fisiologíaRESUMEN
We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening-closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy difference between core histone octamers on and off DNA. Addition of ATP led to highly dynamic behavior with time courses exhibiting processive runs of assembly and disassembly not observed in the ATP-depleted case. With ATP present, application of forces of 2 pN led to nearly complete fiber disassembly. Our study suggests that ATP hydrolysis plays a major role in nucleosome rearrangement and removal and that chromatin in vivo may be subject to highly dynamic assembly and disassembly processes that are modulated by DNA tension.