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PubMed2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.

MOTIVATION: Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. RESULTS: We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. AVAILABILITY AND IMPLEMENTATION: It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Quantitative Trait Loci↗
PubMed1995

Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry.

A new method for automatically assigning proton-proton NOESY spectra is described and demonstrated for simulated and experimental spectra of the proteins dendrotoxin K, alpha-amylase inhibitor tendamistat and the DNA-binding domain of the 434 repressor protein. The method assigns the NOESY spectrum and calculates three-dimensional protein structures simultaneously, using a list of proton chemical shifts and 3JNH alpha coupling constants. An ensemble of structures is iteratively calculated by self-correcting distance geometry from unambiguous and selected ambiguous NOESY cross peaks. New structure based filters recognize the correct constraints from the ambiguous cross peak list. For the first round of assignment neither a preliminary initial structure nor a sufficient set of unambiguous NOESY cross peaks is needed. The method can also be applied to cross peak lists containing hundreds of noise peaks. For an assumed tolerance of +/- 0.01 ppm in the chemical shifts of the peak positions, only about 10% of the NOESY cross peaks can be unambiguously assigned based on their chemical shifts alone. Our automated method assigned about 80% of all cross peaks with this chemical shift tolerance, and 95 to 99% of the assignments were correct. The average pairwise RMSD for the backbone atoms of the ten best final structures is about 1.5 A in all three proteins and the previously determined NMR solution structures are always embedded in this structure bundle. We regard our method as a highly practical tool for automatic calculation of three-dimensional protein structures from NMR spectra with minimal human interference.

Computer Simulation↗
PubMed2000

Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias.

The cortex of the brain is organized into clear horizontal layers, laminae, which subserve much of the connectional anatomy of the brain. We hypothesize that there is also a vertical anatomical organization that might subserve local interactions of neuronal functional units, in accord with longstanding electrophysiological observations. We develop and apply a general quantitative method, inspired by analogous methods in condensed matter physics, to examine the anatomical organization of the cortex in human brain. We find, in addition to obvious laminae, anatomical evidence for tightly packed microcolumnar ensembles containing approximately 11 neurons, with a periodicity of about 80 microm. We examine the structural integrity of this new architectural feature in two common dementing illnesses, Alzheimer disease and dementia with Lewy bodies. In Alzheimer disease, there is a dramatic, nearly complete loss of microcolumnar ensemble organization. The relative degree of loss of microcolumnar ensembles is directly proportional to the number of neurofibrillary tangles, but not related to the amount of amyloid-beta deposition. In dementia with Lewy bodies, a similar disruption of microcolumnar ensemble architecture occurs despite minimal neuronal loss. These observations show that quantitative analysis of complex cortical architecture can be applied to analyze the anatomical basis of brain disorders.

Alzheimer Disease↗
PubMed2006

Allostatic load is associated with symptoms in chronic fatigue syndrome patients.

OBJECTIVES: To further explore the relationship between chronic fatigue syndrome (CFS) and allostatic load (AL), we conducted a computational analysis involving 43 patients with CFS and 60 nonfatigued, healthy controls (NF) enrolled in a population-based case-control study in Wichita (KS, USA). We used traditional biostatistical methods to measure the association of high AL to standardized measures of physical and mental functioning, disability, fatigue and general symptom severity. We also used nonlinear regression technology embedded in machine learning algorithms to learn equations predicting various CFS symptoms based on the individual components of the allostatic load index (ALI). METHODS: An ALI was computed for all study participants using available laboratory and clinical data on metabolic, cardiovascular and hypothalamic-pituitary-adrenal (HPA) axis factors. Physical and mental functioning/impairment was measured using the Medical Outcomes Study 36-item Short Form Health Survey (SF-36); current fatigue was measured using the 20-item multidimensional fatigue inventory (MFI); frequency and intensity of symptoms was measured using the 19-item symptom inventory (SI). Genetic programming, a nonlinear regression technique, was used to learn an ensemble of different predictive equations rather just than a single one. Statistical analysis was based on the calculation of the percentage of equations in the ensemble that utilized each input variable, producing a measure of the 'utility' of the variable for the predictive problem at hand. Traditional biostatistics methods include the median and Wilcoxon tests for comparing the median levels of subscale scores obtained on the SF-36, the MFI and the SI summary score. RESULTS: Among CFS patients, but not controls, a high level of AL was significantly associated with lower median values (indicating worse health) of bodily pain, physical functioning and general symptom frequency/intensity. Using genetic programming, the ALI was determined to be a better predictor of these three health measures than any subcombination of ALI components among cases, but not controls.

Adult↗
PubMed1986

RNA secondary structure formation during transcription.

A new approach has been proposed for predicting the kinetic ensemble of the RNA secondary structures during chain growth. It is based on an analysis of time intervals in structural reconstruction. The Markov chain employed for describing structural reconstruction was modelled on the Monte Carlo method. A calculation was made of possible secondary structures formed during transcription. An algorithm has also been suggested for the search of a helix with a bulge type defect in which a cooperative effect is retained. Kinetic ensembles of the SD-sites and initiation regions of the polycistronic mRNA transcribed from ATP operon E. coli were calculated. A correlation between the secondary structures of these mRNA regions and the relative cistronic expression was established.

Base Sequence↗
PubMed2025

Granular Hydrogels as Brittle Yield Stress Fluids.

While granular hydrogels are increasingly used in biomedical applications, methods to capture their rheological behavior generally consider shear-thinning and self-healing properties or produce ensemble metrics (e.g., dynamic moduli) while neglecting transient yielding and unyielding processes. Combining oscillatory shear testing with Brittility (Bt) via the Kamani-Donley-Rogers (KDR) model, this work shows that granular hydrogels behave as brittle yield stress fluids. This work quantifies steady and transient rheology as a function of microgel properties and granular composition for polyethylene glycol and gelatin microgels. The KDR model with Bt captures granular hydrogel behavior for a wide range of design parameters, reducing the complex rheology to a determination of model parameters. In granular mixtures, this work observes monotonic dependencies of the elastic modulus, structural viscosity, and brittility upon granular composition, while the yield stress is lower for mixtures. Microgel size distribution and polymer fraction are the most influential parameters in monolithic granular hydrogels, while microgel size and packing density are less impactful. The model robustly captures self-healing behavior and reveals that granular hydrogel relaxation accelerates with an increased small-amplitude strain rate. This quantitative framework is an important step toward rational design of granular hydrogels for applications ranging from injection and in situ stabilization to 3D bioprinting.

brittility↗
PubMed2000

Ion-beam thinning. An atomistic view by molecular dynamics simulations

The purpose of this study is to offer a view of ion beam thinning at atomistic level. Therefore, a computer simulation of the type molecular dynamics is used to study the evolution of a stepped silicon surface undergoing ion bombardment. According to the methods used in radiation damage studies, the effect of the impinging beam is described by constructing a large ensemble of trajectories of displaced silicon atoms. The effects of the beam parameters, such as energy and angle, as well as the ones arising from the surface topography, are obtained from the properties of this ensemble. The results of the simulations are discussed in the light of the mesoscopic models of surface evolution.

Journal Article↗
PubMed1994

Modeling compact denatured states of proteins.

We propose a model for the conformations of compact denatured states of globular proteins: that they are broad ensembles of chain backbone conformations that involve common localized hydrophobic clustering and helical contacts, depending on the amino acid sequence. We construct representative ensembles for chain lengths up to 136 monomers on three-dimensional cubic lattices using the "hydrophobic zippers" method (Fiebig & Dill, 1993). We find that model conformations with radii of gyration about 20% larger than native conformations commonly have bimodal distributions of P(r), of the pairwise interatomic distances, r, and Kratky plots in agreement with recent small-angle X-ray scattering (Sosnick & Trewhella, 1992; Flanagan et al., 1992; Kataoka et al., 1993; Flanagan et al., 1993) experiments on three different proteins. We also find that the lattice model of the Shortle 1-136 fragment of staphylococcal nuclease does not appear capable of forming a single hydrophobic core by hydrophobic zippering, consistent with experiments.

Amino Acid Sequence↗
PubMed2005

A simple method to predict protein flexibility using secondary chemical shifts.

Protein motions play a critical role in many biological processes, such as enzyme catalysis, allosteric regulation, antigen-antibody interactions, and protein-DNA binding. NMR spectroscopy occupies a unique place among methods for investigating protein dynamics due to its ability to provide site-specific information about protein motions over a large range of time scales. However, most NMR methods require a detailed knowledge of the 3D structure and/or the collection of additional experimental data (NOEs, T1, T2, etc.) to accurately measure protein dynamics. Here we present a simple method based on chemical shift data that allows accurate, quantitative, site-specific mapping of protein backbone mobility without the need of a three-dimensional structure or the collection and analysis of NMR relaxation data. Further, we show that this chemical shift method is able to quantitatively predict per-residue RMSD values (from both MD simulations and NMR structural ensembles) as well as model-free backbone order parameters.

Carbon Isotopes↗
PubMed2002

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy.

Protein folding is inherently a heterogeneous process because of the very large number of microscopic pathways that connect the myriad unfolded conformations to the unique conformation of the native structure. In a first step towards the long-range goal of describing the distribution of pathways experimentally, Förster resonance energy transfer (FRET) has been measured on single, freely diffusing molecules. Here we use this method to determine properties of the free-energy surface for folding that have not been obtained from ensemble experiments. We show that single-molecule FRET measurements of a small cold-shock protein expose equilibrium collapse of the unfolded polypeptide and allow us to calculate limits on the polypeptide reconfiguration time. From these results, limits on the height of the free-energy barrier to folding are obtained that are consistent with a simple statistical mechanical model, but not with the barriers derived from simulations using molecular dynamics. Unlike the activation energy, the free-energy barrier includes the activation entropy and thus has been elusive to experimental determination for any kinetic process in solution.

Bacterial Proteins↗
PubMed2006

Stereographic projection path-integral simulations of (HF)n clusters.

We perform several quantum canonical ensemble simulations of (HF)(n) clusters. The HF stretches are rigid, and the stereographic projection path-integral method is employed for the simulation in the resulting curved configuration space. We make use of the reweighted random series techniques to accelerate the convergence of the path-integral simulation with respect to the number of path coefficients. We develop and test estimators for the total energy and heat capacity based on a finite difference approach for non-Euclidean spaces. The quantum effects at temperatures below 400 K are substantial for all sizes. We observe interesting thermodynamic behaviors in the quantum simulations of the octamer and the heptamer.

Journal Article↗
PubMed2004

The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques.

We use single-molecule force spectroscopy to study the kinetics of unfolding of the small protein ubiquitin. Upon a step increase in the stretching force, a ubiquitin polyprotein extends in discrete steps of 20.3 +/- 0.9 nm marking each unfolding event. An average of the time course of these unfolding events was well described by a single exponential, which is a necessary condition for a memoryless Markovian process. Similar ensemble averages done at different forces showed that the unfolding rate was exponentially dependent on the stretching force. Stretching a ubiquitin polyprotein with a force that increased at a constant rate (force-ramp) directly measured the distribution of unfolding forces. This distribution was accurately reproduced by the simple kinetics of an all-or-none unfolding process. Our force-clamp experiments directly demonstrate that an ensemble average of ubiquitin unfolding events is well described by a two-state Markovian process that obeys the Arrhenius equation. However, at the single-molecule level, deviant behavior that is not well represented in the ensemble average is readily observed. Our experiments make an important addition to protein spectroscopy by demonstrating an unambiguous method of analysis of the kinetics of protein unfolding by a stretching force.

Kinetics↗
PubMed2005

Discrete layers of interacting growing protein seeds: convective and morphological stages of evolution.

The growth of several macromolecular seeds uniformly distributed on the bottom of a protein reactor (i.e., a discrete layer of N crystals embedded within a horizontal layer of liquid with no-slip boundaries) under microgravity conditions is investigated for different values of N and for two values of the geometrical aspect ratio of the container. The fluid dynamics of the growth reactor and the morphological (shape-change) evolution of the crystals are analyzed by means of a recently developed moving boundary method based on differential equations coming from the protein "surface incorporation kinetics." The face growth rates are found to depend on the complex multicellular structure of the convective field and on associated "pluming phenomena." This correspondence is indirect evidence of the fact that mass transport in the bulk and surface attachment kinetics are competitive as rate-limiting steps for growth. Significant adjustments in the roll pattern take place as time passes. The convective field undergoes an interesting sequence of transitions to different values of the mode and to different numbers of rising solutal jets. The structure of the velocity field and the solutal effects, in turn, exhibit sensitivity to the number of interacting crystals if this number is small. In the opposite case, a certain degree of periodicity can be highlighted for a core zone not affected by edge effects. The results with no-slip lateral walls are compared with those for periodic boundary conditions to assess the role played by geometrical constraints in determining edge effects and the wavelength selection process. The numerical method provides "microscopic" and "morphological" details as well as general rules and trends about the macroscopic evolution (i.e., "ensemble behaviors") of the system.

Binding Sites↗
PubMed2006

Thermostat with a local heat-bath coupling for exact energy conservation in dissipative particle dynamics.

We present a Markov process which models particle hydrodynamics with conservation of the first three momenta. This is achieved by extending the [Peters, Europhys. Lett. 66, 311 (2004)] and [Lowe, Europhys. Lett. 47, 145 (1999)] method to incorporate energy conservation. The equivalence of the energy conserving Peters method and dissipative particle dynamics with energy conservation (DPDE) in the limit of a vanishing time step is shown. Simple numerical experiments clearly demonstrate the applicability of the methods. This overcomes current limitations of DPDE in the study of complex fluids in the (N,V,E) ensemble.

Journal Article↗
PubMedDate not supplied

Signal and noise in modulation transfer function determinations using the slit, wire, and edge techniques.

The modulation transfer function (MTF) of an idealized imaging system can be determined from the Fourier transform of the system's line-spread function (LSF). Three techniques of experimentally determining the LSF require imaging either a slit, wire, or edge. In this paper, these three techniques are modeled theoretically to determine the noise in the calculated MTFs as a function of spatial frequency resulting from both quantum fluctuations and stochastic detector noise. The techniques are compared using the signal-to-noise ratio (SNR) in the MTF, defined as the ratio of the MTF value to the standard deviation in an ensemble of MTF determinations from independent measurements. It is shown that for a specified photon fluence, the edge method MTF has the highest SNR at low spatial frequencies, while that of the slit method is superior at high frequencies. The wire method SNR is always inferior to that of the slit technique. This suggests that the edge method is preferable for measuring parameters such as the low-frequency drop, and the slit method is preferable for determining high-frequency response. The cross-over frequency at which the slit and edge methods are equal (f(e)) for quantum-noise limited systems is a function of the slit width and the length over which the LSF is measured. For detector-noise limited systems, f(e) is dependent on the slit width only. The SNR in all but the quantum-noise limited slit method can therefore be increased by decreasing the length over which the LSF is measured, smoothing the tails of the LSF, or by fitting the tails to an analytic expression.

Fourier Analysis↗
PubMed2026

Physiological sub-typing of cold and freezing injury in Triticum turgidum subspecies with bioinformatic and expression characterization of glutathione reductase.

BACKGROUND: This study examined how different subspecies of Triticum turgidum (T. durum, T. polonicum, T. turanicum) respond to cold and freezing, assessing their water status, stress responses, and antioxidant system, with particular focus on the structure and function of glutathione reductase (TtGR). METHODS: TtGR genes were first identified from the T. turgidum genome using publicly available genomic resources such as Ensembl Plants. Promoter regions (~2 kb upstream) were analyzed to identify cis-regulatory elements using PlantCARE. Gene classification was performed based on predicted subcellular localization and conserved domain features. Plants were subjected to cold acclimation and freezing treatments, and physiological, biochemical, and enzymatic parameters were measured. RESULTS: Bioinformatics analyses identified four TtGR genes in the T. turgidum genome. The genes in two groups: cytosolic (Class I) and chloroplastic (Class II). Gene structure analysis showed a conserved exon-intron organization, while motif analysis confirmed the presence of Nicotinamide Adenine Dinucleotide Phosphate (NADPH)-binding and redox-active domains across all TtGR proteins. Several regulatory sequences in the promoters are involved in cold (DRE), abscisic acid (ABRE), and stress (STRE) responses, indicating that TtGR genes are dynamically regulated in response to environmental changes. Physiological analyses showed that freezing treatment reduces leaf water content in all genotypes, leading to turgor loss, hydrogen peroxide (H2O2) accumulation, and increased malondealdehyte (MDA) levels. However, tolerance mechanisms addressing water stress and membrane damage differ among genotypes. At the biochemical level, activation of the antioxidant defense system occurs in all genotypes. T. turanicum displays strong defense by significantly increasing enzyme activities, ensuring that the ascorbate-glutathione cycle continues under stress. By contrast, T. polonicum, although showing increased overall enzyme activities, experiences a dramatic drop in glutathione reductase (GR) activity at freezing temperatures, which restricts reduced glutathione (GSH) regeneration and creates a functional bottleneck in the antioxidant cycle. T. durum fails to sustain enzyme activities over the stress period, leading to an intermediate-sensitive response. Thus, whereas T. turanicum effectively maintains antioxidant function during freezing, T. polonicum and T. durum exhibit less efficient stress responses, either through enzymatic bottlenecks or a lack of sustained defense. CONCLUSIONS: One of the most striking findings of this study is the observed dissociation between TtGR gene expression levels and enzyme activities. Low temperature limits the link between transcription and enzyme function. The primary determinant of low-temperature tolerance in T. turgidum subspecies is the sustainability of GR enzyme activity and GSH regeneration under freezing conditions.

Triticum↗
PubMed2004

Magnetic moment of the fragmentation-aligned 61Fe (9/2(+)) isomer.

We report on the g factor measurement of an isomer in the neutron-rich (61)(26)Fe (E(*)=861 keV and T(1/2)=239(5) ns). The isomer was produced and spin aligned via a projectile-fragmentation reaction at intermediate energy, the time dependent perturbed angular distribution method being used for the measurement of the g factor. For the first time, due to significant improvements of the experimental technique, an appreciable residual alignment of the nuclear spin ensemble has been observed, allowing a precise determination of its g factor, including the sign: g=-0.229(2). In this way we open the possibility to study moments of very neutron-rich short-lived isomers, not accessible via other production and spin-orientation methods.

Journal Article↗