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Journal of Molecular Biology Feb 2024The width of the periplasmic space of Gram-negative bacteria is only about 25-30 nm along the long axis of the cell, which affects free diffusion of (macro)molecules....
The width of the periplasmic space of Gram-negative bacteria is only about 25-30 nm along the long axis of the cell, which affects free diffusion of (macro)molecules. We have performed single-particle displacement measurements and diffusion simulation studies to determine the impact of confinement on the apparent mobility of proteins in the periplasm of Escherichia coli. The diffusion of a reporter protein and of OsmY, an osmotically regulated periplasmic protein, is characterized by a fast and slow component regardless of the osmotic conditions. The diffusion coefficient of the fast fraction increases upon osmotic upshift, in agreement with a decrease in macromolecular crowding of the periplasm, but the mobility of the slow (immobile) fraction is not affected by the osmotic stress. We observe that the confinement created by the inner and outer membranes results in a lower apparent diffusion coefficient, but this can only partially explain the slow component of diffusion in the particle displacement measurements, suggesting that a fraction of the proteins is hindered in its mobility by large periplasmic structures. Using particle-based simulations, we have determined the confinement effect on the apparent diffusion coefficient of the particles for geometries akin the periplasmic space of Gram-negative bacteria.
Topics: Diffusion; Escherichia coli; Escherichia coli Proteins; Osmotic Pressure; Periplasm; Single Molecule Imaging
PubMed: 38143021
DOI: 10.1016/j.jmb.2023.168420 -
Science Advances Apr 2024Phase modulation has scarcely been mentioned in diffusive physical systems because the diffusion process does not carry the momentum like waves. Recently, non-Hermitian...
Phase modulation has scarcely been mentioned in diffusive physical systems because the diffusion process does not carry the momentum like waves. Recently, non-Hermitian physics provides a unique perspective for understanding diffusion and shows prospects in thermal phase regulation, exemplified by the discovery of anti-parity-time (APT) symmetry in diffusive systems. However, precise control of thermal phase remains elusive hitherto and can hardly be realized, due to the phase oscillations. Here we construct the PT-symmetric diffusive systems to achieve the complete suppression of thermal phase oscillation. The real coupling of diffusive fields is readily established through a strong convective background, and the decay-rate detuning is enabled by thermal metamaterial design. We observe the phase transition of PT symmetry breaking with the symmetry-determined amplitude and phase regulation of coupled temperature fields. Our work shows the existence of PT symmetry in dissipative energy exchanges and provides unique approaches for harnessing the mass transfer of particles, wave dynamics in strongly scattering systems, and thermal conduction.
PubMed: 38640240
DOI: 10.1126/sciadv.adn1746 -
Human Brain Mapping Jul 2023This study investigated associations between psychological resilience and characteristics of white matter microstructure in pediatric concussion. This is a case control... (Randomized Controlled Trial)
Randomized Controlled Trial
This study investigated associations between psychological resilience and characteristics of white matter microstructure in pediatric concussion. This is a case control study and a planned substudy of a larger randomized controlled trial. Children with an acute concussion or orthopedic injury were recruited from the emergency department. Participants completed both the Connor-Davidson Resilience Scale 10 and an MRI at 72 h and 4-weeks post-injury. The association between resiliency and fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) at both timepoints were examined. We examined whether these associations were moderated by group. The association between resiliency captured at 72 h and diffusion tensor imaging metrics at 4 weeks was also investigated. Clusters were extracted using a significance threshold of threshold-free cluster enhancement corrected p < .05. A total of 66 children with concussion (median (IQR) age = 12.88 (IQR: 11.80-14.36); 47% female) and 29 children with orthopedic-injury (median (IQR) age = 12.49 (IQR: 11.18-14.01); 41% female) were included. A negative correlation was identified in the concussion group between 72 h resilience and 72 h FA. Meanwhile, positive correlations were identified in the concussion group with concussion between 72 h resilience and both 72 h MD and 72 h RD. These findings suggest that 72 h resilience is associated with white matter microstructure of the forceps minor, superior longitudinal fasciculus, and anterior thalamic radiation at 72 h post-concussion. Resilience seems to be associated with neural integrity only in the acute phase of concussion and thus may be considered when researching concussion recovery.
Topics: Humans; Child; Female; Male; White Matter; Diffusion Tensor Imaging; Brain; Resilience, Psychological; Benchmarking; Case-Control Studies; Brain Concussion; Anisotropy
PubMed: 37126608
DOI: 10.1002/hbm.26321 -
Bioinformatics (Oxford, England) Sep 2023As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest...
MOTIVATION
As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios.
RESULTS
To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA-miRNA network.
AVAILABILITY AND IMPLEMENTATION
The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php.
Topics: Humans; Diffusion; Glioma; MicroRNAs; Mutation; RNA, Messenger
PubMed: 37624931
DOI: 10.1093/bioinformatics/btad520 -
Quantitative Imaging in Medicine and... Jan 2024Diffusion tensor imaging (DTI) has been implemented in a breadth of scientific investigations of optic neuropathies, though it has yet to be fully adopted for diagnosis... (Review)
Review
BACKGROUND AND OBJECTIVE
Diffusion tensor imaging (DTI) has been implemented in a breadth of scientific investigations of optic neuropathies, though it has yet to be fully adopted for diagnosis or prognosis. This is potentially due to a lack of standardization and weak replication of results. The aim of this investigation was to review DTI results from studies specific to three distinct optic neuropathies in order to probe its current clinical utility.
METHODS
We reviewed the DTI literature specific to primary open-angle glaucoma (POAG), optic neuritis (ON), and traumatic optic neuropathy (TON) by systematically searching the PubMed database on March 1, 2023. Four distinct DTI metrics are considered: fractional anisotropy (FA), along with mean diffusivity (MD, axial diffusivity (AD), and radial diffusivity (RD). Results from within-group, between-group, and correlational studies were thoroughly assessed.
KEY CONTENT AND FINDINGS
POAG studies most consistently report a decrease in FA, especially in the optic radiations, followed in prevalence by an increase in RD and then MD, whilst AD yields conflicting results between studies. It is notable that there is not an equal distribution of investigated DTI metrics, with FA utilized the most, followed by MD, RD, and AD. Studies of ON are similar in that the most consistent findings are specific to FA, RD, and MD. These results are specific to the optic nerve and radiation since only one study measured the intermediary regions. More studies are needed to assess the effect that ON has on the tracts of the visual system. Finally, only three studies assessing DTI of TON have been performed to date, displaying low to moderate replicability of results. To improve the level of agreement between studies assessing each optic neuropathy, an increased level of standardization is recommended.
CONCLUSIONS
Both POAG and ON studies have yielded some prevalent DTI findings, both for contrast and correlation-based assessments. Although the clinical need is high for TON, considering the limitations of the current diagnostic tools, too few studies exist to make confident conclusions. Future use of standardized and longitudinal DTI, along with the foreseen methodological and technical improvements, is warranted to effectively study optic neuropathies.
PubMed: 38223128
DOI: 10.21037/qims-23-779 -
Toxins Sep 2023Blue-green algae, or cyanobacteria, may be prevalent in our rivers and tap water. These minuscule bacteria can grow swiftly and form blooms in warm, nutrient-rich water.... (Review)
Review
Blue-green algae, or cyanobacteria, may be prevalent in our rivers and tap water. These minuscule bacteria can grow swiftly and form blooms in warm, nutrient-rich water. Toxins produced by cyanobacteria can pollute rivers and streams and harm the liver and nervous system in humans. This review highlights the properties of 25 toxin types produced by 12 different cyanobacteria genera. The review also covered strategies for reducing and controlling cyanobacteria issues. These include using physical or chemical treatments, cutting back on fertilizer input, algal lawn scrubbers, and antagonistic microorganisms for biocontrol. Micro-, nano- and ultrafiltration techniques could be used for the removal of internal and extracellular cyanotoxins, in addition to powdered or granular activated carbon, ozonation, sedimentation, ultraviolet radiation, potassium permanganate, free chlorine, and pre-treatment oxidation techniques. The efficiency of treatment techniques for removing intracellular and extracellular cyanotoxins is also demonstrated. These approaches aim to lessen the risks of cyanobacterial blooms and associated toxins. Effective management of cyanobacteria in water systems depends on early detection and quick action. Cyanobacteria cells and their toxins can be detected using microscopy, molecular methods, chromatography, and spectroscopy. Understanding the causes of blooms and the many ways for their detection and elimination will help the management of this crucial environmental issue.
Topics: Humans; Drinking Water; Lakes; Ultraviolet Rays; Diffusion; Cyanobacteria Toxins
PubMed: 37756009
DOI: 10.3390/toxins15090582 -
Northern Clinics of Istanbul 2023This article aimed to study two different parameters of basal cell carcinoma (BCC): First, to analyze the expression of antihuman epithelial antigen (Ber-EP4) on the...
OBJECTIVE
This article aimed to study two different parameters of basal cell carcinoma (BCC): First, to analyze the expression of antihuman epithelial antigen (Ber-EP4) on the primary and recurrent BCCs on the head, neck, and other body parts and second, to find Ber-EP4's staining pattern and staining intensities correlation between histological type, demographic data, tumor, and its prognostic parameters.
METHODS
We evaluated the Ber-EP4 staining patterns of 201 patients diagnosed with BCC. We analyzed the possible correlation between the tumor's prognostic parameters and the Ber-EP4 staining intensity and its pattern (peripheral, superficial, or diffused).
RESULTS
In 199 out of the 201 cases, staining was observed. Two cases were unstained. In 25.6% (n=51) of the cases with staining, the staining was weak, on the 25.6% (n=51), it was moderate, and on the 48.8% (n=97), it was severe. The staining pattern was 31.2% (n=62) peripheral, 4.0% (n=8) superficial, 54.7% (n=109) diffuse, and 10.1% (n=20) peripheral and superficial.
CONCLUSION
Ber-EP4 is the only antibody commonly used for BCC diagnosis; the existence of different staining intensities and patterns in BCC tumor cells in routine dermatopathology practice limit the pathologists. The studies investigating Ber-EP4 staining in BCCs were conducted with very small numbers of cases. In these studies, even the presence of staining in the focal area was considered to be a positive acceptance criterion; the staining intensity and pattern were not evaluated. Therefore, our study is the first study with a high number of cases and the first to include an evaluation of Ber-EP4 staining's intensity and localization.
PubMed: 37829747
DOI: 10.14744/nci.2022.25675 -
Cephalalgia : An International Journal... Dec 2023Diffusion-tensor imaging can be applied to describe the microstructural integrity of the whole brain. As findings about microstructural alterations in migraine are...
BACKGROUND
Diffusion-tensor imaging can be applied to describe the microstructural integrity of the whole brain. As findings about microstructural alterations in migraine are inconsistent, we aimed to replicate the most frequent results and assess a relationship between migraine parameters and changes in microstructure.
METHODS
Diffusion-weighted MRI data of 37 migraine patients and 40 controls were collected. Two indices of diffusion of water molecules, fractional anisotropy and mean diffusivity were used in a voxel-wise analysis. Group comparisons were carried out in SPM12 using age and sex as covariates. Statistically significant results survived family-wise error correction (p < 0.05). Migraine intensity, frequency, and duration were self-reported and correlated with mean fractional anisotropy and mean diffusivity values across clusters.
RESULTS
Migraine patients showed significantly lower fractional anisotropy in occipital regions, and significantly higher fractional anisotropy in thirteen clusters across the brain. Mean diffusivity of migraine patients was significantly decreased in the cerebellum and pons, but it was not increased in any area. Correlation between migraine duration and fractional anisotropy was significantly positive in the frontal cortex and significantly negative in the superior parietal lobule.
CONCLUSION
We suggest that microstructural integrity of the migraine brain is impaired in visual areas and shows duration-related alterations in regions of the default mode network.
Topics: Humans; Diffusion Tensor Imaging; Brain; Migraine Disorders; Diffusion Magnetic Resonance Imaging; Cerebellum
PubMed: 38111172
DOI: 10.1177/03331024231216456 -
Pain Reports Jun 2024Patients with chronic pain frequently report cognitive symptoms that affect memory and attention, which are functions attributed to the hippocampus. Trigeminal neuralgia...
INTRODUCTION
Patients with chronic pain frequently report cognitive symptoms that affect memory and attention, which are functions attributed to the hippocampus. Trigeminal neuralgia (TN) is a chronic neuropathic pain disorder characterized by paroxysmal attacks of unilateral orofacial pain. Given the stereotypical nature of TN pain and lack of negative symptoms including sensory loss, TN provides a unique model to investigate the hippocampal implications of chronic pain. Recent evidence demonstrated that TN is associated with macrostructural hippocampal abnormalities indicated by reduced subfield volumes; however, there is a paucity in our understanding of hippocampal microstructural abnormalities associated with TN.
OBJECTIVES
To explore diffusivity metrics within the hippocampus, along with its functional and structural subfields, in patients with TN.
METHODS
To examine hippocampal microstructure, we utilized diffusion tensor imaging in 31 patients with TN and 21 controls. T1-weighted magnetic resonance images were segmented into hippocampal subfields and registered into diffusion-weighted imaging space. Fractional anisotropy (FA) and mean diffusivity were extracted for hippocampal subfields and longitudinal axis segmentations.
RESULTS
Patients with TN demonstrated reduced FA in bilateral whole hippocampi and hippocampal body and contralateral subregions CA2/3 and CA4, indicating microstructural hippocampal abnormalities. Notably, patients with TN showed significant correlation between age and hippocampal FA, while controls did not exhibit this correlation. These effects were driven chiefly by female patients with TN.
CONCLUSION
This study demonstrates that TN is associated with microstructural hippocampal abnormalities, which may precede and potentially be temporally linked to volumetric hippocampal alterations demonstrated previously. These findings provide further evidence for the role of the hippocampus in chronic pain and suggest the potential for targeted interventions to mitigate cognitive symptoms in patients with chronic pain.
PubMed: 38655236
DOI: 10.1097/PR9.0000000000001159 -
Scientific Reports Sep 2023Due to the unrestricted movement of humans over a wide area, it is important to understand how individuals move between non-adjacent locations in space. In this...
Due to the unrestricted movement of humans over a wide area, it is important to understand how individuals move between non-adjacent locations in space. In this research, we introduce a nonlocal diffusion introduce for dengue, which is driven by integral operators. First, we use the semigroup theory and continuously Fréchet differentiable to demonstrate the existence, uniqueness, positivity and boundedness of the solution. Next, the global stability and uniform persistence of the system are proved by analyzing the eigenvalue problem of the nonlocal diffusion term. To achieve this, the Lyapunov function is derived and the comparison principle is applied. Finally, numerical simulations are carried out to validate the results of the theorem, and it is revealed that controlling the disease's spread can be achieved by implementing measures to reduce the transmission of the virus through infected humans and mosquitoes.
Topics: Animals; Humans; Culicidae; Diffusion; Movement; Dengue
PubMed: 37709860
DOI: 10.1038/s41598-023-42440-3