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At least 19 recordsLinked to original sources
PubMed1991

High resolution biological scanning electron microscopy: a comparative study of low temperature metal coating techniques.

Structural information on the surface of biological specimens can be resolved within molecular dimensions by "in-lens" field emission scanning electron microscopes when cryo-methods are used to adequately preserve the native state of the specimen. The visual definition of molecular surface structures depends largely on the metal coating. The thickness of the coating, as well as the temperature at which it is deposited, are among the most important parameters affecting visual definition. These were evaluated on T4 polyheads and T4D phages using chromium double-axis rotary shadowing (DARS). Micrographs of optimally DARS coated T4 polyheads and T4D phages were compared with chromium planar-magnetron sputtering (PMS) and unidirectional shadowing with platinum/carbon. Metal deposition was carried out at low temperatures during all three procedures. Optimal visual definition of structural details on the surface of DARS coated T4 polyheads and T4D phages (capsomeres of T4 polyheads and their subunits with diameters of 8 and 3 nm; T4D phage tail fibres with a thickness of 3 nm) is achieved at a thickness of the chromium film greater than the minimum required for metal film coalescence. Chromium DARS coating at room temperature resulted in poor structural definition, whereas DARS at specimen temperatures of -85 degrees C and -150 degrees C, with the chromium thickness optimized for each temperature, yielded good visual detail of polyhead substructures. The visual definition was slightly reduced when DARS coating was carried out at a specimen temperature of -250 degrees C. Adequate structural visibility of T4D phage and T4 polyhead surface structures was achieved with the three coating techniques tested.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbon↗
PubMed1986

Beam induced mass loss in high resolution biological microanalysis.

Electron beam induced loss of mass from the organic matrix and from higher Z constituents of biological samples was measured by monitoring bremsstrahlung and peak changes in EDS spectra. When any effects of contamination, extraneous X-rays, beam current drift, specimen drift, and specimen shrinkage were monitored and corrected for, the three types of samples gave consistent and similar results at 296 K. Bremsstrahlung losses averaged 45%, 46% and 50% respectively for muscle homogenate, salivary gland sections and albumin. Sulphur losses average 74%, 72% and 86% for the same three sample types. No other elements suffered significant losses. D1/e for bremsstrahlung averaged 0.14 C/cm2. Bremsstrahlung loss at 93 K began approximately one order of magnitude higher in dose, and the extent of loss varied. Sulphur losses, however, were greatly reduced at low temperatures.

Animals↗
PubMed1981

15N- and 2H-substituted maleimide spin labels: improved sensitivity and resolution for biological EPR studies.

The resolution and sensitivity of electron paramagnetic resonance (EPR) and saturation transfer EPR (ST-EPR) for biological applications are greatly improved by deuteration and substitution of (15)N for (14)N in the spin-labeled probe N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)maleimide (MSL). The EPR and ST-EPR spectra of the deuterated analogue [(2)H]MSL and the (15)N-substituted and deuterated derivative [(15)N, (2)H]MSL were compared with those of the parent MSL. The [(15)N, (2)H]MSL showed the greatest gain in sensitivity and the most marked sharpening of spectral features. These improvements were due to (i) a reduction in the spectral linewidths resulting from the relatively weak hyperfine interactions of the unpaired electron with deuterium and (ii) spectral simplification due to a reduction in the number of nuclear manifolds from three to two in replacing (14)N with (15)N. In the freely tumbling state, the spectra of [(15)N, (2)H]MSL and [(2)H]MSL showed 10-fold and 5-fold increases, respectively, in signal heights compared to MSL. To study the slow tumbling frequencies characteristic of biological molecules, the MSL and its derivatives were covalently bound to the enzyme glyceraldehyde-3-phosphate dehydrogenase [GAPDHaase; D-glyceraldehyde-3-phosphate:NAD(+) oxidoreductase (phosphorylating), EC 1.2.1.12] on cysteine-149 of the catalytic site. The EPR and ST-EPR spectra of [(15)N, (2)H]MSL and [(2)H]MSL adducts showed 3- and 1.5-fold gains in sensitivity, respectively. More important, there were striking increases in resolution, particularly for [(15)N, (2)H]MSL over MSL. These improvements were observed throughout the correlation time range from 0.1 musec to 1 msec. The EPR spectrum of [(15)N, (2)H]MSL-GAPDHase at X-band showed no overlap of the two nuclear manifolds; therefore, all the elements of the A and g tensors could be measured directly from the spectrum. The increase in sensitivity and resolution of the (15)N- and deuterium-substituted spin labels permitted quantitative simulation of the EPR and ST-EPR spectra of a labeled protein. Computation time was reduced 90% by (15)N substitution. Use of (15)N-substituted and deuterated spin probes substantially improved characterization of the motional properties of a protein.

Computers↗
PubMed1992

Assessment of resolution in biological electron crystallography.

The resolution of images or density maps produced by electron microscopy and electron crystallography can be objectively defined in terms of the spatial frequency of the highest resolution diffraction spot, or Fourier coefficient, included in the data processing. In practice, this objective definition of resolution is expected to be too optimistic if the amplitudes of the highest resolution structure factors are too weak, if the population of high resolution reflections is too sparse, or if the signal-to-noise ratio of the high resolution data is too low. Calculated examples are presented here which illustrate how the apparent resolution in images of a membrane protein, bacteriorhodopsin, can be reduced from a nominal value of 3.5 A by weak amplitudes, sparse data or high noise levels. These calculations provide concrete examples which can serve as a guide when estimating whether the objective definition of image resolution is likely to correspond to a practical, structurally useful estimate of image resolution.

Bacteriorhodopsins↗
PubMed1992

Towards high resolution SEM of biological objects.

The major task of biological high resolution SEM and TEM is to provide structural information for correlating structure and function. It is the only methodology with the inherent power needed to observe structures down to molecular dimensions within the context of complex biological systems. Specimen preparation and imaging techniques should therefore be directed towards the preservation and imaging of the smallest significant details in order to fully exploit this unique, integrating feature of biological electron microscopy, complementing the progress of the techniques used in cell biology, biochemistry, and molecular biology.

Animals↗
PubMed1988

Resolution and biological properties of three N-terminal analogues of recombinant human interleukin-1 beta.

Recombinant human interleukin-1 beta (rhuIL-1 beta) was purified to apparent homogeneity using standard procedures. The protein was characterized by N-terminal sequence analysis and found to consist of three forms: Met (20%), Ala (75%), and des-Ala (5%). Utilizing TSK SP 5PW HPLC, each form was resolved and analyzed by 2-D acrylamide gel electrophoresis. The analogues were identical in molecular mass (17,500 d) but differed in pI (Met, pI = 6.7; Ala, pI = 6.8; des-Ala, pI = 6.8). Bioactivity measurements, using the C3H/HeJ thymocyte proliferation assay, showed that native Ala rhuIL-1 beta was 300-400% more active than des-Ala rhuIL-1 beta, and was 400-600% more active than Met rhuIL-1 beta protein.

Animals↗
PubMed1979

T7-induced DNA polymerase. Characterization of associated exonuclease activities and resolution into biologically active subunits.

Bacteriophage T7-induced DNA polymerase has been isolated by a procedure suitable for large scale use and which yields near homogeneous enzyme. In addition to previously described DNA polymerase activity and 3' to 5' exonucleolytic activity on single stranded DNA (Grippo, P., and Richardson, C. C. (1971) J. Biol. Chem. 246, 6867-6873), the enzyme also possesses a highly active exonuclease which hydrolyzes duplex substrates with 3' to 5' directionality. The native polymerase has been dissociated using 6 M guanidine HCl and resolved into biologically active subunits: T7 gene 5 protein and Escherichia coli thioredoxin. The phage-specified subunit obtained by this procedure is deficient in DNA polymerase and double strand exonuclease activities, with deficiencies in these activities being apparent at the level of a single turnover. However, it possesses near normal levels of a single strand hydrolytic activity which is identical to that associated with the native polymerase with respect to substrate specificity and suppression of hydrolysis by low levels of deoxyribonucleoside 5'-triphosphates. Thioredoxin forms a molecular complex with the T7 gene 5 protein, and addition of the host protein restores restores DNA polymerase and double strand exonuclease activities to near normal levels.

DNA-Directed DNA Polymerase↗
PubMed2026

Coagulation activation is associated with genomic-instability-related features in TP53-mutated AML and MDS: routine laboratory patterns beyond classical disseminated intravascular coagulation.

BACKGROUND: Disseminated intravascular coagulation (DIC) is a serious complication of acute myeloid leukemia (AML) associated with poor prognosis. In TP53-mutated AML and myelodysplastic syndrome (MDS), however, the classical ISTH criteria rarely identify overt DIC, although bleeding and thrombotic complications are well documented in acute leukaemia. We hypothesized that these patients exhibit a lower-grade, subclinical coagulation activation that is associated with the underlying genomic-instability-related features of TP53-mutant disease. METHODS: We retrospectively analyzed 107 consecutive patients with TP53-mutated AML (n = 52) or high-risk MDS (MDS, n = 55), median age 65 years, diagnosed and initially evaluated at our centre between 2018 and 2025. Seven routine coagulation markers and 46 co-mutated genes were evaluated for associations with overall survival (OS) using univariate and multivariable Cox regression, continuous dose-response modeling, and unsupervised k-means clustering. Internal validity was assessed by 1000 bootstrap resamples. RESULTS: Overt DIC according to ISTH criteria was rare (15%). Subclinical activation was common: 50% of patients had a D-dimer &#x2265;1&#xa0;&#x3bc;g/mL, 41% a fibrinogen &#x2265;4&#xa0;g/L, and 29% an INR &#x2265;1.2. In univariate analysis, D-dimer, fibrinogen, INR, prothrombin time, and activated partial thromboplastin time were each associated with OS (HR 1.33-1.38 per SD; all p < 0.05). Complex karyotype correlated with higher D-dimer (median 1.39 vs. 0.60&#xa0;&#x3bc;g/mL, p = 0.022) and fibrinogen (3.91 vs. 2.53&#xa0;g/L, p = 0.007), while TP53 variant allele frequency (VAF) showed modest positive correlations with D-dimer (&#x3c1; = 0.21), INR (&#x3c1; = 0.27), and PT (&#x3c1; = 0.27; all p < 0.05). Clustering identified three coagulation phenotypes: Silent (51%), Thrombo-inflammatory (31%), and Consumption-like (18%), showing a graded but statistically non-significant gradient in molecular features and a stepwise decline in median OS (14, 10 and 8 months; log-rank p = 0.041). After adjustment for complex karyotype, TP53 VAF, and favorable co-mutation count, the Consumption-like phenotype was associated with a non-significant increased risk (HR 1.83, 95% CI 0.92-3.65, p = 0.084), whereas favorable co-mutation pathways remained independently protective (HR 0.56, 95% CI 0.35-0.90, p = 0.016). CONCLUSION: In TP53-mutated AML/MDS, coagulation activation intensity is associated with the degree of genomic instability. The three phenotypes may add biological resolution beyond classical DIC and cytogenetic risk groups, but represent laboratory patterns rather than validated bleeding or thrombosis prediction tools. However, after accounting for genomic features, phenotypes were not independent predictors of outcome, with complex karyotype, TP53 VAF, and favorable co-mutation count driving prognosis. Because treatment intensity and other clinical confounders were not available, these survival associations are hypothesis-generating. Coagulation profiling remains inexpensive, widely accessible, and offers a practical window into disease biology that warrants prospective validation.

TP53↗
PubMed1987

Visibility and stability of a 12-tungsten atom complex in the scanning transmission electron microscope.

A complex consisting of 12 tungsten atoms has been studied in terms of signal-to-noise (S/N) and dose response in the scanning transmission electron microscope (STEM), to evaluate its suitability for use as a approximately 1 nm resolution biological label. Molecular weight of the complex was measured as a function of radius of integration, and results were in agreement with the calculated formula weight. S/N was highest at the lowest radius of integration (0.25 nm), and decreased monotonically with increasing radius. The complex was clearly visible at a dose of 4 X 10(3) e/nm2, and exhibited negligible mass loss (approximately 8%) after an accumulated dose of 1.28 X 10(5) e/nm2. Beam-induced motion was small, 0.46 nm rms after 4 X 10(4) e/nm2. Some intensity fluctuations were observed between successive scans of the same clusters, for which a diffraction-based explanation is advanced. Upon suitable functionalization, the tungsten complex is expected to complement the undecagold cluster already in use for site-specific labeling.

Chemical Phenomena↗
PubMed2026

Hierarchical modeling of tumor subtypes in cell lines using large-scale genomic datasets.

Cancer cell lines (CLs) are widely used to study tumor biology and drug response, yet their translational relevance is often limited by inaccurate subtype annotations. Existing CL-tumor matching approaches are frequently constrained by flat classification schemes, weak subtype definitions, and the exclusion of normal tissue references, leading to potential confounding of tumor-specific and tissue-of-origin signals. To address these limitations, a hierarchical classification (HC) framework is presented in which CLs are aligned with patient tumors across biological resolutions, from organ to molecular subtype. Gene expression profiles from 802 CLs, 5,612 tumors from The Cancer Genome Atlas (TCGA) , and 8,939 non-cancerous tissues were integrated to separate oncogenic signals from tissue-specific signals. Node-specific features were selected using maximum relevance minimum redundancy, and balanced accuracies of 89% in cross-validation and 75%, and 80% on external datasets were achieved. Through the framework, 43 CLs were reassigned, and clinically relevant underrepresented subtypes were identified.

cancer cell lines↗
PubMed1990

Enantiomers of 8-(3-tert-butylamino-2-hydroxypropoxy)-3,4-dihydro-3-oxo-2H- (1,4)benzothiazine: racemic resolution, chiral synthesis and biological activity.

We report the resolution of racemic (+/-)-1 with (R)-(+)-methylbenzyl isocianate and the synthesis of (R)-1 and (S)-1 via Sharpless chiral epoxidation. The enantio- and tissue-selectivity of such enantiomers, as beta- and alpha-adrenoceptor antagonists, were studied. Compound 1, while confirming the potent beta-blocking activity, displayed a modest enantio-selectivity towards beta 1- and beta 2-adrenoceptors. All the compounds displayed no activity as alpha-adrenoceptor blockers.

Adrenergic alpha-Antagonists↗