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PubMed2025

SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.

Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired by a multiplex segmented selected ion monitoring (msSIM) technique, which sequentially applies multiple isolation cycles with the quadrupole using a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching using a well-defined spectral library. We applied the SLB-msSIM method to interrogate cellular heterogeneity in various pancreatic cancer cell lines, revealing common and distinct functional traits among PANC-1, MIA-PaCa2, AsPc-1, HPAF, and normal HPDE cells. Furthermore, for the first time, our novel data revealed the diverse cell trajectories of individual PANC-1 cells during the induction and reversal of epithelial-mesenchymal transition (EMT). Collectively, our results demonstrate that SLB-msSIM is a highly sensitive and robust platform, applicable to a wide range of instruments for single-cell proteomic studies. SUMMARY: We present the SLB-msSIM method, a conceptually unique approach in mass spectrometry-based single-cell proteomics that significantly enhances sensitivity and robustness. This innovative platform enables detailed analysis of the proteome landscape, capturing cellular heterogeneity, trajectories, and phenotypes at a single-cell resolution. Utilizing the SLB-msSIM technique, we identified both common and distinct functional traits among various pancreatic cancer cell lines and normal cells. Moreover, our study unveiled new insights into the diverse cell trajectories of individual cancer cells during the induction and reversal of epithelial-mesenchymal transition (EMT). In summary, the SLB-msSIM method offers a highly sensitive and robust platform for single-cell proteomic studies, with broad applicability across different instruments.

Single-Cell Analysis↗

PubMed2002

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase.

Molecular dynamics trajectories for the bovine mitochondrial F(1)-ATPase are used to demonstrate the motions and interactions that take place during the elementary (120 degrees rotation) step of the gamma subunit. The results show how rotation of the gamma subunit induces the observed structural changes in the catalytic beta subunits. Both steric and electrostatic interactions contribute. An "ionic track" of Arg and Lys residues on the protruding portion of the gamma subunit plays a role in guiding the motions of the beta subunits. Experimental data for mutants of the DELSEED motif and the hinge region are interpreted on the basis of the molecular dynamics results. The trajectory provides a unified dynamic description of the coupled subunit motions involved in the 120 degrees rotation cycles of F(1)-ATPase.

Crystallography, X-Ray↗

PubMed1993

CURVATURE: software for the analysis of curved DNA.

Software is presented to plot the sequence-dependent spatial trajectory of the DNA double helix and/or distribution of curvature along the DNA molecule. The nearest-neighbor wedge model is implemented to calculate overall DNA path using local helix parameters: helix twist angle, wedge (deflection) angle and direction (of deflection) angle. The procedures described proved to be very convenient as tools for investigation of a relationship between overall DNA curvature and its gel electrophoretic mobility. All parameters of the model had been estimated from experimental data. Using these wedge parameters the program takes, as input, any DNA sequence and calculates the likely degree of curvature at each point along the molecule. This information is displayed both graphically and in the form of simplified representations of curved double helices. The Software, CURVATURE, can thus be used to investigate possible roles of curvature in modulation of gene expression and for location of curved portions of DNA, which may play an important role in sequence-specific protein--DNA interactions.

Algorithms↗

PubMed2000

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.

Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. Within the RNase H fold a new family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition to the previously characterized RuvC family. The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and AQUIFEX: Endonuclease VII of phage T4 is shown to serve as a structural template for many nucleases, including MCR:A and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the lambda exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This analysis resulted in the prediction of numerous previously unnoticed nucleases, some of which are likely to be new restriction enzymes.

Amino Acid Sequence↗

PubMed2006

Variable time lag and backward ejection in full-dimensional analysis of strong-field double ionization.

Ensembles of 400,000 two-electron trajectories in three space dimensions are used with Newtonian equations of motion to track atomic double ionization under very strong laser fields. We report a variable time lag between e-e collision and double ionization, and find that the time lag plays a key role in the emergence directions of the electrons. These are precursors to production of electron momentum distributions showing substantial new agreement with experimental data.

Journal Article↗

PubMed1991

Reconstruction of shifting elbow joint compliant characteristics during fast and slow movements.

The purpose of this study was to experimentally investigate the applicability of the equilibrium-point hypothesis to the dynamics of single-joint movements. Subjects were trained to perform relatively slow (movement time 600-1000 ms) or fast (movement time 200-300 ms) single-joint elbow flexion movements against a constant extending torque bias. They were instructed to reproduce the same time pattern of central motor command for a series of movements when the external torque could slowly and unpredictably increase, decrease, or remain constant. For fast movements, the total muscle torque was calculated as a sum of external and inertial components. Analysis of the data allowed reconstruction of the elbow joint compliant characteristics at different times during execution of the learned motor command. "Virtual" trajectories of the movements, representing time-varying changes in a central control parameter, were reconstructed and compared with the "actual" trajectories. For slow movements, the actual trajectories lagged behind the virtual ones. There were no consistent changes in the joint stiffness during slow movements. Similar analysis of experiments without voluntary movements demonstrated a lack of changes in the central parameters, supporting the assumption that the subjects were able to keep the same central motor command in spite of externally imposed unexpected torque perturbations. For the fast movements, the virtual trajectories were N-shaped, and the joint stiffness demonstrated a considerable increase near the middle of the movement. These findings contradict an hypothesis of monotonic joint compliant characteristic translation at a nearly constant rate during such movements.

Adult↗

PubMedDate not supplied

[Evaluation of the fate of young patients treated in therapeutic communities].

This study was attempted to analyse the trajectories of patients who have left a therapeutic community centre since two and a half years. The statistical analysis has permitted us to show that a series of variables concerning personal, family or medical history have a repercussion on these trajectories. The study shows that patients who have become less dependent on assisting psychiatric networks are better integrated in the relational and social networks.

Adult↗

PubMed2006

Classification of patterns of delirium severity scores over time in an elderly population.

OBJECTIVES: To describe and classify individual trajectories of 15-day changes in delirium severity. METHODS: A longitudinal hospital-based study was carried out with 230 medical inpatients aged 65 and over admitted to St Mary's Hospital in Montreal, Canada, between 1996 and 1999, diagnosed with delirium at enrollment, and who had at least four measurements of delirium severity during the next 15 days. Delirium severity was assessed using the Delirium Index (DI). To classify patients' individual trajectories, we applied a new method that relies on principal factor analysis and cluster analysis. We used multiple linear regression to investigate if clusters were associated with DI scores measured at an 8-week follow-up. Multivariable Cox's proportional hazards regression was used to assess whether the clusters were associated with survival over the next 12 months. RESULTS: Individual patterns were classified into five clusters: Steady (n = 89, 38.9%), Fluctuating (n = 36, 15.7%), Worsening (n = 15, 6.6%), Fast Improve-ment (n = 26, 11.3%), and Slow Improvement (n = 63, 27.5%). The Fast Improvement cluster had much lower prevalence of dementia (38.5% vs. 55.6% to 77.8% in other clusters, p = 0.003). Subjects whose 2-week patterns were classified as Fast or Slow Improvement had a significantly lower DI at 8 weeks than those in the Steady or Fluctuating clusters. The Worsening cluster had the largest percentage of deaths. The Fast Improvement and Worsening clusters initially had a high risk of death in the first 2 weeks (adjusted relative risks of approximately 3 and 6, respectively) but that risk decreased rapidly thereafter. CONCLUSION: Two-week trajectories of delirium severity were associated with short-term mortality and delirium severity at 8-week follow-up.

Aged↗

PubMed1987

Analysis of the flagellar bending waves of ejaculated ram sperm.

The variability of flagellar movement, illustrated by the highly heterogeneous nature of the ejaculated sperm population of the ram, was analyzed by the use of a stroboscopic technique and an adapted microphotographic 24 X 36 camera system. The multiple-moving-exposures (MME) records give very distinct successive sequences of the flagellar beats and are particularly suitable for the analysis of bend development and propagation along the tail. With this technique, the parameters of the flagellar bending waves of ejaculated ram sperm have been determined. Most of the sperm have planar flagellar beatings; few are rolling under the conditions of observation. The trajectories of the gametes are mostly linear; nevertheless, some have circular paths. The analysis of bending has been focused on two examples for which the difference in the progressiveness ratio was maximum. The circular pathways for ram spermatozoa are linked to an asymmetry between principal and reverse bend probably induced by differences in wave propagation evidenced along the flagellum. A typical sperm flagellar movement may be related either to the conditions of the observations or to some differences in the maturation process of the sperm.

Animals↗

PubMed2005

Compatibility of postural behavior induced by two aspects of visual feedback: time delay and scale display.

Fourteen healthy adults were tested to assess the potential influence on stance maintenance of two parts of the visual feedback technique (display scale and time delay). The task consisted in their keeping a spot on the screen representing their center of pressure, CoP (i.e. successive points of application of the ground reaction forces detected by the force platform on which they were standing) to a minimum size. The analysis focused on elementary motions computed from the complex CoP trajectories, that is the horizontal motion of the center of gravity (CoG(h)) and the difference between the CoP and the vertical projection of the center of gravity (CoP-CoG(v)). The former is recognized as the main variable in postural control, and several interesting features can be extracted from the latter. The results indicate that setting a delay and increasing the display scale induce substantial reductions in CoP-CoG(v) and CoG(h) displacements, respectively. Interestingly, when the two effects are combined, these single effects cohabit quite happily. Fractional Brownian motion modeling of these trajectories revealed clearly that, in each case, these effects originate principally from poor or improved control, respectively. This feature confirms that these elementary motions are involved differently in the postural system and that study of the complex CoP might not be of great interest. By generating opposing but complementary trends, the visual feedback technique should thus be perceived as a promising tool for inducing particular postural behavior in healthy and disabled individuals.

Adult↗

PubMed1993

Evaluating the special role of time in the control of handwriting.

Claims that time has a special role in the control of writing and the specific claim that writing time is absolutely invariant across changes in writing size are evaluated in two experiments. The first examined writing time for 24 undergraduate subjects who produced the string eyleyl with the dominant hand or arm in blocked repetitions having different vertical size targets. These variations produced small but systematic changes in writing time. The second experiment explored whether the small range of writing-time variation observed in experiment 1 was due to structural or strategic limitations. This experiment showed, for four undergraduate subjects, that writing time can be varied precisely across a wide range (0.6 to 1.66 of 'normal') while maintaining shape and vertical size constant. Taken together, these experiments suggest that, although relative stroke timing is approximately maintained, absolute timing is not critical to writing. The limited range of writing times typically observed should, rather, be ascribed to a strategic gradient that, along with other influences, broadly defines preferred writing times. This paper also describes a new application of Generalized Procrustes Analysis of shape, and this procedure is applied to the trajectories generated in both experiments. Although several small failures are noted, these analyses generally confirmed previous claims that shape is invariant across changes in writing time, size, and writing with the hand versus the arm. This result is a necessary buttress to the conclusions just described. Shape variability was also assessed in these analyses. This variability soared as writing time was reduced from normal, but showed only a small, insignificant increase as writing time was increased from normal. There were also small, predictable changes in spatial variability across changes in size and effector.

Adult↗

PubMed1996

Molecular dynamics of amphotericin B. II. Dimer in water.

Molecular dynamics simulations were performed for a dimer of the antifungal antibiotic, amphotericin B, in water. In the first step of the work three appropriately selected versions of the dimer structure were taken into consideration. In each version antibiotic molecules were placed antiparallel with polar and ionizable groups outside the hydrophobic core formed by polyene chromophores. During short dynamic simulations versions of the dimer structure were compared in respect of the energy of dimerization. The highest energy was observed for the structure in which polyene chromophores superimposed each other as much as possible and this version was subjected to the main simulation. The analysis of 66 snapshot geometries stored during 33 ps dynamic trajectory allowed us to draw three main conclusions: (i) the relative orientation of the amino-sugar moiety and chromophore as well as conformation of the antibiotic macrolide ring were different in both molecules and could exhibit dynamic changes, (ii) the dimer structure exhibited intrinsic asymmetry which could be responsible for characteristic circular dichroism spectra of the aggregated form of the antibiotic, (iii) relatively high stability of the dimer structure resulted not only from hydrophobic interactions between chromophores but also from hydrogen bonds networks that were observed around polar terminals of antibiotic molecules. Implications of these features of the dimer structure for its susceptibility on the ionic state of carboxyl and/or amino groups are also discussed.

Amphotericin B↗

PubMed2006

Rapid determination of complex mixtures by dual-column gas chromatography with a novel stationary phase combination and spectrometric detection.

Fast GC separations of a broad range of analytes are demonstrated using a capillary column coated with a novel immobilized ionic liquid (IIL) stationary phase. Both completely cross-linked and partially cross-linked columns were evaluated, yielding approximately 1600 and approximately 2000 theoretical plates per meter, respectively. Enhanced separation is demonstrated using a dual-column ensemble comprised of an IIL column, a commercially coated Rtx-1 column, and a pneumatic valve connecting the inlet to the junction point between the two columns. Enhanced separation of 20 components, with two sets of co-eluting peaks is shown in approximately 150 s, while sacrificing only a length of time equivalent to the sum of the stop flow pulses, or about 15.5 s. A novel application of a band trajectory model that shows band position as a function of analysis time as analytes move through the column ensemble is employed to determine pulse application times. The model predicts component retention times within a few seconds. Another method of selectivity enhancement of the IIL stationary phase-coated columns is demonstrated using a differential mobility spectrometer (DMS) that provides a second dimension separation based on ion mobility in a high-frequency electrical field. The DMS is able to separate all but one set of co-eluting components from the IIL column. The separation of 13 components found in the headspace above U.S. currency is demonstrated using the IIL column in a dual-column ensemble as well as with the DMS.

Chromatography, Gas↗

PubMed2025

Identification of marginal zone B cells in head and neck cancer with immunomodulatory characteristics.

INTRODUCTION: Recently we observed high numbers of marginal zone B cells (MZBs) within murine head and neck squamous cell carcinoma (HNSCC) with immunosuppressive potential. To date, MZBs have not been linked to tumor development or tumor prevention. OBJECTIVES: Based on our previous findings the present study aimed to validate the presence of MZB in HNSCC and to investigate their possible implications in tumorigenesis and prognosis. METHODS: Flow cytometry was used to uncover MZB within tumors and blood of HNSCC patients. A single-cell RNA sequencing cohort of 118 HNSCC patients across different disease stages and 6 healthy donors (HDs) was compiled. Comparative transcriptomic profiling of B lymphocytes between HNSCC and HDs were performed. Downstream analysis, such as pathway enrichment, cell-cell communication, pseudotime trajectory inference, survival correlation, and spatial transcriptomics were applied. RESULTS: Two MZB subsets were revealed in tissues and blood of HNSCC patients and HDs. The tumor-associated MZBs were featured with hypoxia stress and viral-related hallmark genes. MZB-2, characterized by elevated expression of activation markers and immune-regulatory genes, displayed strong interactions with CD4+ T cells and antigen-presenting cells. These interactions were supported by costimulatory signals in HDs but were absent in HNSCC patients. Co-localization of MZB-2, germinal center B cell (GCB), and CD4+ follicular helper T cell (Tfh) was detected in HNSCC, suggesting the presence of an intratumoral MZB-Tfh-GCB axis. Clinically, MZB-2 abundance was associated with favorable prognosis in early-stage HNSCC, but not in advanced disease. Immunosuppressive gene signatures were not exclusive to MZBs, indicating that they do not represent a purely regulatory B cell phenotype. CONCLUSION: Our findings demonstrate an immunomodulatory role of MZBs in tumor immunity, balancing antigen presentation, cytokine signaling, and immune suppression. The association of MZB-2 with improved prognosis in early-stage HNSCC highlights its potential as a beneficial regulator of antitumor immunity during early tumor progression.

Humans↗

PubMed2006

A method to synchronise video cameras using the audio band.

This paper proposes and evaluates a novel method for synchronisation of video cameras using the audio band. The method consists in generating and transmitting an audio signal through radio frequency for receivers connected to the microphone input of the cameras and inserting the signal in the audio band. In a software environment, the phase differences among the video signals are calculated and used to interpolate the synchronous 2D projections of the trajectories. The validation of the method was based on: (1) Analysis of the phase difference changes as a function of time of two video signals. (2) Comparison between the values measured with an oscilloscope and by the proposed method. (3) Estimation of the improvement in the accuracy in the measurements of the distance between two markers mounted on a rigid body during movement applying the method. The results showed that the phase difference changes in time slowly (0.150 ms/min) and linearly, even when the same model of cameras are used. The values measured by the proposed method and by oscilloscope showed equivalence (R2=0.998), the root mean square of the difference between the measurements was 0.10 ms and the maximum difference found was 0.31 ms. Applying the new method, the accuracy of the 3D reconstruction had a statistically significant improvement. The accuracy, simplicity and wide applicability of the proposed method constitute the main contributions of this work.

Biomechanical Phenomena↗

PubMed2006

Spatial and kinematic features of apraxic movement depend on the mode of execution.

Knowledge about the dependency of apraxic movements on the mode of execution may enhance the understanding of apraxia and of the cerebral representation of actions. We examined a common tool-use action in nine patients with left hemisphere damage and apraxia. Arm movements during the use of a handsaw were measured and tested in three different modes of execution: pantomime, pantomime with a bar shaped like the handle of the saw, and actual sawing. Analysis concentrated on spatial and kinematic features of the wrist trajectories during these repetitive movements. In healthy control subjects, both pantomime conditions differed from actual use mainly by larger amplitudes during miming. Apraxic patients executed large proportions of their pantomiming movements in an incorrect direction away from the appropriate anteroposterior direction, while other movement features were normal. The availability of the handle-like bar did not improve performance. During actual use, movement direction was constraint by mechanical demands. In this condition patients moved with moderately decreased velocity. However, this deficit was not related to the errors in movement direction characteristic of pantomiming. These data suggest that pantomiming and actual execution of an action are dictated by different external requirements and constraints, pantomiming serves to convey information, while actual use has to obey the mechanical demands of the task. Due to these differences, spatial and kinematic movement features in healthy subjects vary between the modes of execution, movements are differently vulnerable to apraxia, and deficits in patients may dissociate.

Adult↗

PubMed2001

Atmospheric aerosol over Vermont: chemical composition and sources.

Aerosol chemical composition data for PM2.5 samples collected during the period from 1988 to 1995 at Underhill, VT, were analyzed. Sulfur and black carbon mass concentrations ranged from 0.01 to 6.5 microg m(-3) and from 0.05 to 2.2 microg m(-3), respectively, while the total fine aerosol mass concentration ranged from 0.2 to 51.1 microg m(-3). Seasonal variations with maxima during the summer and minima in winter/spring were observed for sulfur and the fine mass concentrations. No annual pattern was observed for black carbon. Seasonal variations for most of the other anthropogenic species had maxima in winter and spring and minima in the summer. A factor analysis method, positive matrix factorization (PMF), utilizing error estimates of the data to provide optimum data point scaling was used to obtain information about possible sources of the aerosol. An 11-factor solution was obtained. The six sources representing wood burning, coal and oil combustion, coal combustion emissions plus photochemical sulfate production, metal production plus municipal waste incineration, and emissions from motor vehicles were identified. Emissions from smelting of nonferrous metal ores, arsenic smelting, and soil particles and particles with high concentrations of Na were also identified by PMF. Potential source contribution function (PSCF) analysis combines the aerosol data with the air parcel backward trajectories. PSCF was applied to identify possible source areas and pathways that give rise to the observed high particulate mass concentrations from these 11 sources. The CAPITA Monte Carlo trajectory model was used to obtain 10 sets of 5-day air parcel back trajectories arriving every 2 h for the 7-yr period from 1988 to 1995. The PSCF plot for the black carbon factor shows high probabilities in the area surrounding the sampling site, indicating a strong local influence from residential wood combustion in northern New England and southwestern Quebec. Similar large potential source areas in the midwestern United States were identified for the two coal combustion factors. The midwestern United States was also identified as the source region for the Zn-Pb factor. The oil combustion factor was associated with the east coast of the United States. The results for the Pb-Mn factor suggests high probability over the nearby Montreal urban area and the areas in the midwestern United States. The windblown dust emissions from the areas to the north are significant contributors for the soil factor. Canadian Ni smelters are the main sources for the As factor, although there is some contribution from coal-fired power plants to the south and west of Underhill, VT. It is concluded that the combination of the two receptor modeling methods, PMF and PSCF, provides an effective way in identifying atmospheric aerosol sources and their likely locations. Emissions from different anthropogenic activities as well as secondary aerosol production are the main sources of aerosol measured in Vermont. Fuel combustion, local wood smoke, municipal waste incineration, and the secondary sulfate production collectively accounted for about 87% of the fine mass concentrations measured in Vermont.

Aerosols↗

PubMed2005

Narrative development in bilingual kindergarteners: can Arthur help?

This study examined the effects of the children's TV program Arthur on the development of narrative skills over an academic year for Spanish-speaking English-language learners. In October, February, and June of their kindergarten year, children were asked to tell a story, in English, prompted by 3 pictures. Before the 2nd and 3rd assessments, half of the 108 children were randomly assigned to view Arthur 3 times a week during school hours, and the other half, which formed the control group, viewed the children's program Between the Lions on the same schedule. Individual growth modeling analysis showed that children who viewed Arthur had steeper growth trajectories than those who viewed Between the Lions. Boys displayed better English narrative skills than girls but no difference in narrative growth rate. The results suggest that certain educational TV programs can assist in some aspects of the language development of bilingual children.

Child, Preschool↗