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PubMed1977

[Reverberation of the hindlimb rudimentation on its innervation in squamate reptiles].

When the dimensional reduction of the hind limb begins, a first caudal displacement of the lombar part of the lombo-sacral plexus - which involves the loss of the first root of the sacral part -- appears with a threshold in the increase in the number of presacral vertebrae. This a first indication of the serpentiform tendancy. Others thresholds can conduct to produce the disappearance of the sacral vertebrae and sacral root. The qualitative reduction only concerns the terminal branches of the plexus and does not seem to be associated with the vertebral elongation. If a caudo-proximal reduction of the brachial plexus occurs early in the lepidosaurian line and exists in all the Squamata, even in the Iguana which have well developed limbs, it is not the same for the reduction of the lombo-sacral plexus which does not appear in these Iguana. At last, if the reduction modalities of the both plexus are often differents, their supposed displacements facilitate the extension of the intermediate vertebral region.

Animals↗

PubMed2026

Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics.

In single-cell experiments spanning diverse conditions, distinguishing variation specific to one condition (e.g., treatment) from shared or background variation (e.g., control) is critical for uncovering treatment-specific molecular responses. However, these studies typically yield ultra-high-dimensional data, necessitating effective dimension reduction for reliable biological interpretation. Contrastive dimension reduction methods address this challenge by identifying low-dimensional features enriched in a target dataset relative to a background dataset that captures shared variation. Despite their growing utility, the success of such methods critically depends on the choice of background, yet no formal criterion exists for evaluating or selecting backgrounds. To address this gap, we introduce BasCoD, a statistical testing framework based on spectral subspace inclusion theory, that enables rigorous evaluation and systematic selection of background datasets. Applying BasCoD across a range of single-cell datasets, we show that it effectively identifies suitable backgrounds, substantially improving the contrast and interpretability of the resulting target representations. We further demonstrate how BasCoD can guide the design of contrastive analyses in large-scale single-cell experiments conducted under heterogeneous conditions and elucidate potential interaction effects in perturbation studies.

Single-Cell Analysis↗

PubMed1979

Quantitative coronary angiography: measurement of the "critical" stenosis in patients with unstable angina and single-vessel disease without collaterals.

Quantitative angiographic assessment of proximal coronary artery stenosis was performed in 15 patients with consecutive presentations in two categories defined by clinical and angiographic criteria. Group 1 consisted of 10 patients who had new onset of refractory rest angina and ischemic ST-T changes, but no infarction, single-vessel coronary disease without collateralization, and normal left ventricular (LV) angiograms. Group 2 consisted of five patients who were similar to patients in group 1, but had subendocardial infarction (SEI). Quantitative coronary arteriography, using paired perpendicular angiographic views and digital computation, yielded statistically different lesion dimensions and hemodynamic predictions for the two groups. Minimum stenosis diameters were 0.88 +/- 0.14 (SD) and 0.64 +/- 0.08 mm, respectively, for groups 1 and 2. This corresponded to 72% and 78% diameter reduction and 92% and 95% cross-sectional area reduction for the two groups. These small dimensional differences among lesions in the two groups resulted in large differences in their hemodynamic impact as predicted from classic fluid mechanics theory. We conclude that there are characteristic lesion dimensions for the isolated "critical" stenosis in these selected patients with rest angina. Further small increases in lesions severity result in SEI. Certain practical applications and limitations of these observations are discussed.

Angina Pectoris↗

PubMed1979

Effect of alkylation on the physical properties of simian virus 40 T-antigen species.

We analyzed large and small species of T-antigen by immunoprecipitation and two-dimensional gel electrophoresis. The T-antigen species were subjected to electrophoresis either directly or after reduction and alkylation with N-ethylmaleimide. Treatment with N-ethylmaleimide improved the resolution of large-T by two-dimensional gel electrophoresis and was a requirement for the resolution of small-t antigen on two dimensional gels. Large-T did not form a discrete protein spot, but rather formed a streak from approximately pH 6.5 to 6.9 on isoelectric focusing gels. Small-t formed a sharp protein spot at approximately pH 7.2 when subjected to electrophoresis under non-equilibrium conditions which extended the pH gradient to include proteins with basic isoelectric points. Treatment with N-ethylmaleimide decreased the mobility of the T-antigen species during sodium dodecyl sulfate gel electrophoresis. We suggest that the apparent increase in molecular weight was due to the association of N-ethylmaleimide with cysteine-rich regions of these proteins. Viable deletion mutants of simian virus 40 which do not induce the synthesis of small-t but product small-t-related polypeptides were used to localize the cysteine-rich region of small-t to between 0.54 and 0.59 on the genetic map of simian virus 40.

Alkylation↗

PubMed1977

A two-dimensional thin layer chromatographic procedure for the sequential analysis of oligonucleotides employing tritium post-labeling.

Two dimensional PEI-cellulose thin layer chromatography can resolve sequentially degraded oligonucleotide fragments of tRNA. This technique entails the sequential degradation of the oligonucleotide with snake venom phosphodiesterase in the presence of bacterial alkaline phosphatase, and periodate oxidation followed by tritiated sodium borohydride reduction of the 3' terminal nucleoside. Subsequently the tritiated oligonucleotide fragments were resolved by two dimensional PEI-cellulose TLC. The results of these experiments indicate that, in some cases, the complete nucleotide sequence of a large oligonucleotide fragment may be determined by interpretation of the observed mobility shifts, thereby eliminiating the need for additional analysis of the oligonucleotide. In addition, the use of two-dimensional rather than one-dimensional resolution of the tritium labeled fragments allows for a complete separation of any interfering background spots from the sequentially degraded oligonucleotides. This procedure was applied to the complete nucleotide sequence analysis of several ribonuclease T1Val and ribonuclease A digestion products from human placenta tRNA.

Base Sequence↗

PubMed1977

Platelet membrane defects in Glanzmann's thrombasthenia. Evidence for decreased amounts of two major glycoproteins.

Platelets from patients with Glanzmann's thrombasthenia have a distinct molecular alteration of the plasma membrane surface, namely decreased amounts of a major glycoprotein designated as IIb (apparent mol wt 142,000). To identify other possible surface defects of thrombasthenic platelets, we labeled the membrane polypeptides of normal and thrombasthenic platelets by two different techniques: lactoperoxidase-catalyzed iodination and galactose oxidase oxidation, followed by reduction with tritiated sodium borohydride. Labeling patterns were determined after the polypeptides were separated by two-dimensional polyacrylamide gel electrophoresis. Before the second dimension was run, platelet samples were incubated with a reducing agent, beta-mercapto-ethanol, to cleave the disulfide bonds of certain glycoproteins; the resulting changes in electrophoretic mobility permitted better resolution of individual molecules. Comparison of the labeled polypeptides of normal and thrombasthenic samples after reduction indicated decreased labeling of two major glycoproteins in thrombasthenic platelets: IIb and III (apparent mol wt 114,000). The relative proportions of radioactivity incorporated by these polypeptides were about 60 and 80% less than control values, respectively. With either Coomassie Blue or periodic acid-Schiff's reagent, glycoprotein III stained much less intensely in thrombasthenic compared to normal samples, indicating that the observed labeling deficit was caused by a decreased concentration of the molecule rather than steric inaccessibility on the membrane surface. Analysis of normal plasma membranes by affinity chromatography showed that glycoprotein IIb has receptors for lectin from Lens culinaris, the common lentil, whereas III does not. We conclude that a characteristic feature of Glanzmann's thrombasthenia is a decreased concentration of two discrete glycoproteins in the platelet plasma membrane.

Blood Platelet Disorders↗

PubMed1977

Heterogeneity of the cold-insoluble globulin of human plasma (CIg), a circulating cell surface protein.

The cold-insoluble globulin of human plasma (CIg), a circulating cell surface protein, exists in multiple molecular forms. Most molecules are found as two chain (MR approximately 220 000 per chain) disulfide-bridged dimeric units but several minor components of smaller size have also been identified; based upon their migration rates in dodecyl sulfate gel electrophoretic experiments, the smaller molecules characterized in this study range in molecular size from 235 000 to 146 000. The component of molecular weight 235 000 apparently represents a two chain disulfide-bridged derivative of larger parent molecules (one chain of 220 000 plus a smaller remnant), whereas smaller CIg components appear to be single chain proteins. These observations plus electrophoretic analyses of samples of plasmic digests of CIg indicate that the interchain disulfide bridging in the two chain molecule is located in a segment within approx. 175 residues of the NH2- or COOH-terminus.

Dithiothreitol↗

PubMed1979

Flow cytometry as a new method for the measurement of electrophoretic mobility of erythrocytes using membrane charge staining by fluoresceinated polycations.

The binding of FITC-labeled poly-L-ornithine and poly-L-lysine to fresh or neuraminidase treated human, rat or rabbit erythrocytes was investigated by simultaneous cell volume and cell membrane fluorescence measurements in a flow cytometer. The cell volume was converted into cell surface and the distribution curve of the fluorescence/micrometer2 cell surface was calculated from all histogram classes by a computer program. The mean fluorescence/micrometer2 cell surface as a measure of the density of the negative charges on the cell surface was directly proportional to the elctrophoretic mobility of the erythrocytes, showing that polycation binding can effectively be used for the measurement of the electrophoretic mobility of erythrocytes. The computer fitting of the experimental two parameter histograms by two dimensional Gaussian normal distributions was found to be a very efficient way of data reduction, and a good separation of overlapping cell clusters was possible even in the case of low total numbers of cells in the histogram.

Animals↗

PubMed1979

Myocardial ischemia. Relationship between local flow, function and ST-segment elevation.

The significance of reductions in local myocardial flow on mechanical function and intramural electrocardiograms (ECG) was studied in anesthetized open-chest dogs. Local dimensional changes in the anterior wall of the left ventricle were recorded by ultrasonic technique. By platinum electrodes in the same region, both intramural ECG and hydrogen tension were recorded. Local flow was calculated from hydrogen desaturation curves. At approx. 25% flow reduction (constriction of the left anterior descending coronary artery (LAD)) local enddiastolic dilation and reduced systolic shortening appeared. Significant ST-segment elevation first appeared with flow reduction of 50%. After complete LAD-occlusions, enddiastolic dilation appeared within 20 sec, ST-segment elevation 40 sec later. It is concluded that mechanical and electrical events can be dissociated during acute myocardial ischemia: enddiastolic dilation and reduced systolic shortening are more sensitive indicators of moderate reductions in myocardial tissue flow than ST-segment elevation.

Animals↗

PubMed1979

Visualization of multidimensional spectra in flow cytometry.

Flow data from a cell sorter have been processed by hardwired circuits which include amplification, discrimination, coincidence requirements, peak sensing and holding, A-D conversion, and a computerized pulse height analysis with storage of the spectra obtained. Two dimensional spectra can be stored directly in memory, on tape and disk. Three and four parametric cellular events can be recorded on line during the flow measurement in a sequential mode on tape for subsequent recall. Simple processing of these data can be performed for displaying of two dimensional projections from these multidimensional spaces based on threshold conditions for the remaining parameters. Interfaced transmission of the stored data to a large scale computer enables more sophisticated data analysis. Data reduction by means of a multidimensional probability analysis has been carried out in order to transfer the spectra to a computerized picture system for display. This system creates perspective two-dimensional images from a three-dimensional data space. Frequency can be converted into grey levels. Hard copy in color (color as the third dimension and color intensity as frequency) simplifies the visualization of multiparametric flow data sets.

Animals↗

PubMed1978

Regulation and characterization of protein products coded by the nif (nitrogen fixation) genes of Klebsiella pneumoniae.

Two hundred and thirty-five Nif- strains of Klebsiella pneumoniae were characterized by two-dimensional polyacrylamide gel electrophoresis. Forty-two of these strains were tested further by in vitro acetylene reduction assays. By these techniques, nine nif-coded polypeptides were identified, and eight of these were assigned to specific nif genes. Nitrogenase component I required nifK and nifD, which coded for the beta and alpha subunits, and nifB, -E, and -N were required for the iron-molybdenum cofactor, which is a part of the active site of nitrogenase. nifH coded for the structural protein of component II, and nifM and nifS products seemed to be necessary for the synthesis of an active component II. There were two genes, nifF and nifJ, that were required for N2 fixation in vivo but not for N2 fixation in vitro. There were at least two cases (nifE and nifN, nifK and nifD) of two proteins that seemed to require each other for stability in vivo. Regulation of N2 fixation is apparently complex, and this is reflected by the assignment of regulatory functions to the gene products of nifA, nifL, nifK, nifD, nifH, and NIFJ.

Bacterial Proteins↗

PubMed1979

Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis.

When double helical DNA is exposed to conditions favoring partial melting in polyacrylamide gels, its electrophoretic mobility undergoes a sharp cooperative transition, resulting in a large reduction in mobility. In the present experiments, where the transition is effected at a uniform temperature of 60 degrees C in a concentration gradient of a urea-formamide mixture, each Eco RI fragment of lambda or E. coli DNA exhibits the mobility transition at a characteristic concentration of the denaturant. The sudden retardation of fragments moving toward higher denaturant concentration in the gradient results in a pattern of sharpened zones in order depending upon nucleotide sequence, rather than size, and only very slightly dependent upon the time after the last fragment has been retarded. When combined with length-dependent electrophoresis in agarose in the perpendicular direction, this system provides a two-dimensional separation of fragments. The resolving power of the system is demonstrated by the clear resolution of over 250 fragments of the Eco RI digest of E. coli DNA. Corresponding fragments from an isogenic lambda lysogen of E. coli are found in the same positions, and additional fragments unique to the lysogen are evident.

Coliphages↗

PubMed1979

Sulphydryl oxidase: oxidation of sulphydryl groups and the formation of three-dimensional structure in proteins.

Sulphydryl oxidase, an enzyme isolated from milk, catalyses the de novo synthesis of disulphide bonds. Thiol groups in amino acids or their derivatives, peptides, and proteins are oxidized; molecular oxygen serves as the electron acceptor and undergoes a two-electron reduction to hydrogen peroxide. Michaelis constants vary considerably amongst various substrates; glutathione is a particularly good substrate. Inhibition studies and oxidation of 1,3-diphenylisobenzofuran suggest a mechanism involving an electron transfer to singlet O2 forming an enzyme-bound hydroperoxy group. Evidence for a direct interaction of the enzyme with horseradish peroxidase was also obtained. Although protein-folding appears to be thermodynamically favoured, rates of spontaneous acquisition of functional three-dimensional structures in disulphide-containing proteins have appeared disturbingly slow. In the presence of sulphydryl oxidase, functional structure is rapidly acquired by both reductively unfolded ribonuclease A and reductively denatured immobilized chymotrypsinogen A as judged by restoration of native fluorescence characteristics and biological activity. Preliminary data suggest that unlike thiol:protein-disulphide oxidoreductase, protein-disulphide isomerase, or GSSG/GSH redox systems, sulphydryl oxidase does not permit a 'reshuffling' of disulphide bonds.

Animals↗

PubMed1977

The sialoglycoprotein subunits of human placental brush border membranes characterized by two-two-dimensional electrophoresis.

A brush border membrane enriched fraction was isolated from human full-term placenta. This membrane fraction exhibited large membrane fragments with microvilli projecting from the basal membrane in electron micrographs and was enriched tenfold in alkaline phosphatase, a brush border enzyme marker. The sialoglycoproteins associated with this membrane fraction were tritiated by mild periodate oxidation of sialic acid and reduction with tritiated NaBH4. The membranes were solubilized in 8 M urea, 2 percent Triton X-100, and the tritiated glycoprotein subunits were reduced with beta-mercaptoethanol and characterized by 2-dimensional poly-acrylamide gel electrophoresis using a method similar to that described by O'Farrell and Bhakdi, Knüferman, and Wallach. The tritiated subunits were detected in the gels by autofluorography. The 2-dimensional subunit "maps" resolved at least 17 major sialoglycoprotein subunits whereas only 10 major periodate-Schiff reagent staining components were resolved by 1-dimensional SDS polyacrylamide gel electrophoresis. Placental alkaline phosphatase (PAP) was identified on the subunit maps by inclusion of 32P-labeled PAP in the tritiated membrane sample. The 32P-labeled PAP corresponded to a major tritiated sialoglycoprotein subunit, which was heterogeneous with respect to charge as demonstrated by 3 closely running spots of the same molecular weight.

Cell Fractionation↗

PubMed2026

Toxicoproteomic analysis reveals arsenic-induced alterations in eye lens proteins of Labeo rohita.

Arsenic occurs extensively in the environment and is classified as a potent carcinogenic substance in humans. Prolonged intake of water contaminated with arsenic results in the development of arsenicosis. In the present study, a toxicoproteomic approach was employed to elucidate arsenic-induced alterations in lens proteins using a fish model. Juveniles of Labeo rohita were exposed to sodium meta-arsenite (NaAsO2) at concentrations of 5, 10, 15, and 20 ppm for a period of 10 days in triplicate experimental groups. Soluble lens proteins were analyzed using one- and two-dimensional gel electrophoresis, immunoblotting of αA-crystallin and MALDI-TOF mass spectrometry. Cataract development was observed at arsenic concentrations ≥ 15 ppm. Proteomic analyses revealed concentration-dependent alterations in lens protein abundance, including significant reductions in βB1, βB2, and βA2b-crystallin, small heat shock protein and skeletal α-actin (p < 0.05). In addition, αA, βA2, and βA2a-crystallin exhibited reduced abundance trends, although these changes were not statistically significant. Two-dimensional immunoblotting revealed 15 distinct αA-crystallin isoforms in control lenses, several of which showed a progressive decrease with increasing arsenic exposure, culminating in complete degradation at 20 ppm. These findings demonstrate that arsenic exposure is associated with substantial alterations in lens crystallins and other proteins involved in structural organization and protein homeostasis, coinciding with cataract development at higher exposure concentrations. The identified proteins may serve as potential toxicoproteomic biomarkers of lens damage in aquatic organisms and provide a foundation for future studies investigating the molecular mechanisms of arsenic-induced lens toxicity.

Animals↗

PubMed1976

[Ultrasound examination in obstructive biliary disease (author's transl)].

Ultrasound examination with a two-dimensional recording technique has proved increasingly useful in obstructive biliary disease and in abnormalities of the liver parenchyma causing a reduction in biliary contrast excretion. In particular, hydrops of the gall bladder, cholelithiasis and choledocholithiasis and choledocholithiasis can be demonstrated where there is biliary obstruction. Analysis of various planes of section is particularly useful in showing obstruction due to the head of the pancreas. The introduction of grey scale techniques and focussed transducers of various frequencies and sizes, suggests that there will be further improvements in the sonographic diagnosis of the hilum of the liver and of the intrahepatic biliary passages.

Adult↗

PubMed2026

Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.

This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.

Soil Microbiology↗

PubMed1979

Analyses of oligosaccharides by tagging the reducing end with a fluorescent compound. I. Application to glycoproteins.

The reducing end sugar of an oligosaccharide and 2-aminopyridine were linked by means of reductive amination with sodium cyanoborohydride. The fluorescent derivative of the oligosaccharide thus obtained, which had a positive charge, was subjected to two-dimensional paper electrophoresis. In the first direction, the sugar derivative moved according to its degree of polymerization, and in the second direction, it moved according to the structure of the borate complex. In this way fluorescent derivatives of saccharides were mapped on a sheet of paper. The method was applied to some known mono- and oligosaccharides and to the saccharides obtained by nitrous deamination of the oligosaccharide portions of glycoproteins (fetuin, Take-amylase A, and ovalbumin). The fingerprints thus obtained were characteristic of the chemical structures of the original oligosaccharides.

Aminopyridines↗