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Linear and Nonlinear Optics of Broad-Band Laser Pulses: Diffraction. ACS OMEGA 2024; 9:20648-20657. [PMID: 38764665 PMCID: PMC11097181 DOI: 10.1021/acsomega.4c02996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024]
Abstract
The typical spectrally limited laser pulse in the near-infrared region is narrow-band up to 40-50 fs. Its spectral width Δk is much smaller than the carrying wavenumber k0 (Δk ≪ k0) . For such kinds of pulses, on distances of a few diffraction lengths, the diffraction is of a Fresnel's type and their evolution can be described correctly in the frame of the well-known paraxial evolution equation. The technology established in 1985 of amplification through chirping of laser pulses triggered remarkable progress in laser optics along with the construction of femtosecond (fs) laser facilities producing high intensity fields of the order of 1015-1021 W/cm2. However, the duration of the pulse was quickly shortened from picoseconds down to 5-6 fs, which have a broad-band nature (Δk ∼ k0). The linear and nonlinear propagation dynamics of broad-band pulses is quite different form their narrow-band counterparts. Here, we review the appropriate theoretical approach to study the evolution of the pulse. Moreover, we shed light on the different diffraction regimes inherent to both narrow-band and broad-band laser pulses and compare them to unveil the main differences. Using this very method, in subsequent papers, we will investigate the influence of the dispersion and nonlinearity on the laser pulse propagation in isotropic media.
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Nuclear patterns of phosphatidylinositol 4,5- and 3,4-bisphosphate revealed by super-resolution microscopy differ between the consecutive stages of RNA polymerase II transcription. FEBS J 2024. [PMID: 38734927 DOI: 10.1111/febs.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Phosphatidylinositol phosphates are powerful signaling molecules that orchestrate signaling and direct membrane trafficking in the cytosol. Interestingly, phosphatidylinositol phosphates also localize within the membrane-less compartments of the cell nucleus, where they participate in the regulation of gene expression. Nevertheless, current models of gene expression, which include condensates of proteins and nucleic acids, do not include nuclear phosphatidylinositol phosphates. This gap is partly a result of the missing detailed analysis of the subnuclear distribution of phosphatidylinositol phosphates and their relationships with gene expression. Here, we used quantitative dual-color direct stochastic optical reconstruction microscopy to analyze the nanoscale co-patterning between RNA polymerase II transcription initiation and elongation markers with respect to phosphatidylinositol 4,5- or 3,4-bisphosphate in the nucleoplasm and nuclear speckles and compared it with randomized data and cells with inhibited transcription. We found specific co-patterning of the transcription initiation marker P-S5 with phosphatidylinositol 4,5-bisphosphate in the nucleoplasm and with phosphatidylinositol 3,4-bisphosphate at the periphery of nuclear speckles. We showed the specific accumulation of the transcription elongation marker PS-2 and of nascent RNA in the proximity of phosphatidylinositol 3,4-bisphosphate associated with nuclear speckles. Taken together, this shows that the distinct spatial associations between the consecutive stages of RNA polymerase II transcription and nuclear phosphatidylinositol phosphates exhibit specificity within the gene expression compartments. Thus, in analogy to the cellular membranes, where phospholipid composition orchestrates signaling pathways and directs membrane trafficking, we propose a model in which the phospholipid identity of gene expression compartments orchestrates RNA polymerase II transcription.
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Tetracoordinate Co(II) complexes with semi-coordination as stable single-ion magnets for deposition on graphene. Phys Chem Chem Phys 2023; 25:29516-29530. [PMID: 37901907 PMCID: PMC10631493 DOI: 10.1039/d3cp01426f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023]
Abstract
We present a theoretical and experimental study of two tetracoordinate Co(II)-based complexes with semi-coordination interactions, i.e., non-covalent interactions involving the central atom. We argue that such interactions enhance the thermal and structural stability of the compounds, making them appropriate for deposition on substrates, as demonstrated by their successful deposition on graphene. DC magnetometry and high-frequency electron spin resonance (HF-ESR) experiments revealed an axial magnetic anisotropy and weak intermolecular antiferromagnetic coupling in both compounds, supported by theoretical predictions from complete active space self-consistent field calculations complemented by N-electron valence state second-order perturbation theory (CASSCF-NEVPT2), and broken-symmetry density functional theory (BS-DFT). AC magnetometry demonstrated that the compounds are field-induced single-ion magnets (SIMs) at applied static magnetic fields, with slow relaxation of magnetization governed by a combination of quantum tunneling, Orbach, and direct relaxation mechanisms. The structural stability under ambient conditions and after deposition was confirmed by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Theoretical modeling by DFT of different configurations of these systems on graphene revealed n-type doping of graphene originating from electron transfer from the deposited molecules, confirmed by electrical transport measurements and Raman spectroscopy.
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Ion-Conducting Composites of Polymers and Nematic Liquid Crystals. ACS OMEGA 2023; 8:9684-9701. [PMID: 36969472 PMCID: PMC10034833 DOI: 10.1021/acsomega.2c07816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
In the present mini-review are discussed the findings reported in the last five years on the ion-conducting composites of polymers and molecules of nematic liquid crystals (NLCs), as well as their applications at present and in the future. Nowadays, free-standing and flexible thin films of such organic composite electrolytes synthesized from plastics and nematic soft matter are among the technically important materials and components for use in energy storage and conversion devices and in organic soft electronics, sensorics, and mechatronics. Although the physicochemical mechanisms and effects in the ion-conducting polymer/NLCs composites are well understood, the possibility to find additional ways for improving their electrical conductivity and dielectric and mechanical properties is a challenge. The efforts in this research direction are important for the development of novel ion-conductor materials and further diversification of their applications. This mini-review is focused on the key characteristics of ion-conducting polymer/NLCs composites and the new trends in their fabrication. With relevant examples, the vast research opportunities, some proposed improvements, and the creative ideas associated with these advanced materials and their intelligent use are outlined.
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Recent advances in deciphering oligodendrocyte heterogeneity with single-cell transcriptomics. Front Cell Neurosci 2022; 16:1025012. [PMID: 36313617 PMCID: PMC9606807 DOI: 10.3389/fncel.2022.1025012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Oligodendrocytes (OL) have been for decades considered a passive, homogenous population of cells that provide support to neurons, and show a limited response to pathological stimuli. This view has been dramatically changed by the introduction of powerful transcriptomic methods that have uncovered a broad spectrum of OL populations that co-exist within the healthy central nervous system (CNS) and also across a variety of diseases. Specifically, single-cell and single-nucleus RNA-sequencing (scRNA-seq, snRNA-seq) have been used to reveal OL variations in maturation, myelination and immune status. The newly discovered immunomodulatory role suggests that OL may serve as targets for future therapies. In this review, we summarize the current understanding of OL heterogeneity in mammalian CNS as revealed by scRNA-seq and snRNA-seq. We provide a list of key studies that identify consensus marker genes defining the currently known OL populations. This resource can be used to standardize analysis of OL related datasets and improve their interpretation, ultimately leading to a better understanding of OL functions in health and disease.
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Optimization of China's provincial carbon emission transfer structure under the dual constraints of economic development and emission reduction goals. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:50335-50351. [PMID: 35229264 DOI: 10.1007/s11356-022-19288-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The contradiction between China's economic development and the reduction of carbon emission is increasingly deepening along with the complex carbon emission transfer. Optimizing provincial-level carbon emission transfer in China is important for facilitating economic development and carbon emission reduction. Under these dual constraints, this study uses the slacks-based measure, marginal abatement cost, and geographically and temporally weighted regression models to measure the economic and carbon emission reduction effects and the carbon emission reduction baseline. Then, the optimization strategy and path of provincial carbon emission transfer network structure are proposed to provide policy support for achieving the dual goals of economic development and carbon emission reduction in China. This article draws the following important research conclusions. First, under the three economic development scenarios, provinces in the eastern coastal developed regions are capable of completing the expected carbon emission reduction, whereas the underdeveloped provinces in the central and northern regions are not. Second, from the perspective of the economic effect of carbon emission transfer, carbon emission transfer from most provinces promotes economic development, whereas carbon emission transfer from a few economically underdeveloped provinces hinders economic development. Third, from the perspective of the carbon emission reduction impact of carbon emission transfer, carbon emission transfer in the northeast region has a negative impact on carbon emission reduction, and carbon emission transfer in developed regions also has a negative impact on carbon emission reduction. Fourth, the optimization of the carbon emission transfer can be divided into four categories.
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Linking perceived ethical leadership to workplace cheating behavior: A moderated mediation model of moral identity and leader-follower value congruence. CURRENT PSYCHOLOGY 2022; 42:1-13. [PMID: 35729899 PMCID: PMC9204074 DOI: 10.1007/s12144-022-03279-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/05/2022]
Abstract
According to social learning theory, we examine the effect of ethical leadership by investigating how moral identity resulting from ethical leadership influences employees' workplace cheating behaviors. Adopting a moderated mediation framework, this study suggests that leader-follower value congruence moderates the positive relationship between ethical leadership and employees' moral identity and mitigates the indirect effect of ethical leadership on employees' workplace cheating behaviors. The results of this study, drawn from a sample of 243 full-time employees and their direct supervisors, support these hypotheses. As such, this study provides novel theoretical and empirical insights into ethical leadership and workplace cheating behavior.
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Molecular Mechanism of the Anti-Inflammatory Action of Heparin. Int J Mol Sci 2021; 22:10730. [PMID: 34639073 PMCID: PMC8509397 DOI: 10.3390/ijms221910730] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022] Open
Abstract
Our objective is to reveal the molecular mechanism of the anti-inflammatory action of low-molecular-weight heparin (LMWH) based on its influence on the activity of two key cytokines, IFNγ and IL-6. The mechanism of heparin binding to IFNγ and IL-6 and the resulting inhibition of their activity were studied by means of extensive molecular-dynamics simulations. The effect of LMWH on IFNγ signalling inside stimulated WISH cells was investigated by measuring its antiproliferative activity and the translocation of phosphorylated STAT1 in the nucleus. We found that LMWH binds with high affinity to IFNγ and is able to fully inhibit the interaction with its cellular receptor. It also influences the biological activity of IL-6 by binding to either IL-6 or IL-6/IL-6Rα, thus preventing the formation of the IL-6/IL-6Rα/gp130 signalling complex. These findings shed light on the molecular mechanism of the anti-inflammatory action of LMWH and underpin its ability to influence favourably conditions characterised by overexpression of these two cytokines. Such conditions are not only associated with autoimmune diseases, but also with inflammatory processes, in particular with COVID-19. Our results put forward heparin as a promising means for the prevention and suppression of severe CRS and encourage further investigations on its applicability as an anti-inflammatory agent.
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Lipid Polymorphism of the Subchloroplast-Granum and Stroma Thylakoid Membrane-Particles. II. Structure and Functions. Cells 2021; 10:2363. [PMID: 34572012 PMCID: PMC8472583 DOI: 10.3390/cells10092363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/29/2021] [Accepted: 09/04/2021] [Indexed: 12/22/2022] Open
Abstract
In Part I, by using 31P-NMR spectroscopy, we have shown that isolated granum and stroma thylakoid membranes (TMs), in addition to the bilayer, display two isotropic phases and an inverted hexagonal (HII) phase; saturation transfer experiments and selective effects of lipase and thermal treatments have shown that these phases arise from distinct, yet interconnectable structural entities. To obtain information on the functional roles and origin of the different lipid phases, here we performed spectroscopic measurements and inspected the ultrastructure of these TM fragments. Circular dichroism, 77 K fluorescence emission spectroscopy, and variable chlorophyll-a fluorescence measurements revealed only minor lipase- or thermally induced changes in the photosynthetic machinery. Electrochromic absorbance transients showed that the TM fragments were re-sealed, and the vesicles largely retained their impermeabilities after lipase treatments-in line with the low susceptibility of the bilayer against the same treatment, as reflected by our 31P-NMR spectroscopy. Signatures of HII-phase could not be discerned with small-angle X-ray scattering-but traces of HII structures, without long-range order, were found by freeze-fracture electron microscopy (FF-EM) and cryo-electron tomography (CET). EM and CET images also revealed the presence of small vesicles and fusion of membrane particles, which might account for one of the isotropic phases. Interaction of VDE (violaxanthin de-epoxidase, detected by Western blot technique in both membrane fragments) with TM lipids might account for the other isotropic phase. In general, non-bilayer lipids are proposed to play role in the self-assembly of the highly organized yet dynamic TM network in chloroplasts.
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How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription. Int J Mol Sci 2021; 22:6694. [PMID: 34206594 PMCID: PMC8269275 DOI: 10.3390/ijms22136694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.
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A hub-and-spoke nuclear lamina architecture in trypanosomes. J Cell Sci 2021; 134:jcs251264. [PMID: 34151975 PMCID: PMC8255026 DOI: 10.1242/jcs.251264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 05/10/2021] [Indexed: 01/11/2023] Open
Abstract
The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration.
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Mineral Carbonation of Biomass Ashes in Relation to Their CO 2 Capture and Storage Potential. ACS OMEGA 2021; 6:14598-14611. [PMID: 34124483 PMCID: PMC8190880 DOI: 10.1021/acsomega.1c01730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/11/2021] [Indexed: 05/27/2023]
Abstract
Short-term stored, long-term stored, and weathered biomass ashes (BAs) produced from eight biomass varieties were studied to define their composition, mineral carbonation, and CO2 capture and storage (CCS) potential by a combination of methods. Most of these BAs are highly enriched in alkaline-earth and alkaline oxides, and the minerals responsible for CCS in them include carbonates such as calcite, kalicinite, and fairchildite, and to a lesser extent, butschliite and baylissite. These minerals are a result of reactions between alkaline-earth and alkaline oxyhydroxides in BA and flue CO2 gas during biomass combustion and atmospheric CO2 during BA storage and weathering. The mineral composition of the short-term stored, long-term stored, and weathered BAs is similar; however, there are increased proportions of carbonates and especially bicarbonates in the long-term stored BAs and particularly weathered BAs. The carbonation of BAs based on the measurement of CO2 volatilization determined in fixed temperature ranges is approximately 1-27% (mean 11%) for short-term stored BAs, 2-33% (mean 18%) for long-term stored BAs, and 2-34% (mean 22%) for weathered BAs. Hence, biomass has some extra CCS potential because of sequestration of atmospheric CO2 in BA, and the forthcoming industrial bioenergy production in a sustainable way can contribute for decreasing CO2 emissions and can reduce the use of costly CCS technologies.
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CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation. Int J Mol Sci 2021; 22:5394. [PMID: 34065512 PMCID: PMC8161014 DOI: 10.3390/ijms22105394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multisubunit cullin-RING ubiquitin ligase 4 (CRL4)-DCAF12 recognizes the C-terminal degron containing acidic amino acid residues. However, its physiological roles and substrates are largely unknown. Purification of CRL4-DCAF12 complexes revealed a wide range of potential substrates, including MOV10, an "ancient" RNA-induced silencing complex (RISC) complex RNA helicase. We show that DCAF12 controls the MOV10 protein level via its C-terminal motif in a proteasome- and CRL-dependent manner. Next, we generated Dcaf12 knockout mice and demonstrated that the DCAF12-mediated degradation of MOV10 is conserved in mice and humans. Detailed analysis of Dcaf12-deficient mice revealed that their testes produce fewer mature sperms, phenotype accompanied by elevated MOV10 and imbalance in meiotic markers SCP3 and γ-H2AX. Additionally, the percentages of splenic CD4+ T and natural killer T (NKT) cell populations were significantly altered. In vitro, activated Dcaf12-deficient T cells displayed inappropriately stabilized MOV10 and increased levels of activated caspases. In summary, we identified MOV10 as a novel substrate of CRL4-DCAF12 and demonstrated the biological relevance of the DCAF12-MOV10 pathway in spermatogenesis and T cell activation.
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The food web in a subterranean ecosystem is driven by intraguild predation. Sci Rep 2021; 11:4994. [PMID: 33654189 PMCID: PMC7925651 DOI: 10.1038/s41598-021-84521-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
Trophic interactions of cave arthropods have been understudied. We used molecular methods (NGS) to decipher the food web in the subterranean ecosystem of the Ardovská Cave (Western Carpathians, Slovakia). We collected five arthropod predators of the species Parasitus loricatus (gamasid mites), Eukoenenia spelaea (palpigrades), Quedius mesomelinus (beetles), and Porrhomma profundum and Centromerus cavernarum (both spiders) and prey belonging to several orders. Various arthropod orders were exploited as prey, and trophic interactions differed among the predators. Linear models were used to compare absolute and relative prey body sizes among the predators. Quedius exploited relatively small prey, while Eukoenenia and Parasitus fed on relatively large prey. Exploitation of eggs or cadavers is discussed. In contrast to previous studies, Eukoenenia was found to be carnivorous. A high proportion of intraguild predation was found in all predators. Intraspecific consumption (most likely cannibalism) was detected only in mites and beetles. Using Pianka's index, the highest trophic niche overlaps were found between Porrhomma and Parasitus and between Centromerus and Eukoenenia, while the lowest niche overlap was found between Parasitus and Quedius. Contrary to what we expected, the high availability of Diptera and Isopoda as a potential prey in the studied system was not corroborated. Our work demonstrates that intraguild diet plays an important role in predators occupying subterranean ecosystems.
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X-ray microtomography-based atlas of mouse cranial development. Gigascience 2021; 10:giab012. [PMID: 33677535 PMCID: PMC7936920 DOI: 10.1093/gigascience/giab012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/21/2020] [Accepted: 02/02/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND X-ray microtomography (μCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological information about the structures prominent in the development of future face, brain, and sensory organs. The development of facial skeleton tracked in these μCT data provides a valuable background for further studies of congenital craniofacial diseases and normal development. FINDINGS In this work, reusable tomographic data from 7 full 3D scans of mouse embryo heads are presented and made publicly available. The ages of these embryos range from E12.5 to E18.5. The samples were stained by phosphotungstic acid prior to scanning, which greatly enhanced the contrast of various tissues in the reconstructed images and enabled precise segmentation. The images were obtained on a laboratory-based μCT system. Furthermore, we provide manually segmented masks of mesenchymal condensations (for E12.5 and E13.5) and cartilage present in the nasal capsule of the scanned embryos. CONCLUSION We present a comprehensive dataset of X-ray 3D computed tomography images of the developing mouse head with high-quality manual segmentation masks of cartilaginous nasal capsules. The provided μCT images can be used for studying any other major structure within the developing mouse heads. The high quality of the manually segmented models of nasal capsules may be instrumental to understanding the complex process of the development of the face in a mouse model.
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Characterization of ALBA Family Expression and Localization in Arabidopsis thaliana Generative Organs. Int J Mol Sci 2021; 22:1652. [PMID: 33562109 PMCID: PMC7914821 DOI: 10.3390/ijms22041652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ALBA DNA/RNA-binding proteins form an ancient family, which in eukaryotes diversified into two Rpp25-like and Rpp20-like subfamilies. In most studied model organisms, their function remains unclear, but they are usually associated with RNA metabolism, mRNA translatability and stress response. In plants, the enriched number of ALBA family members remains poorly understood. Here, we studied ALBA dynamics during reproductive development in Arabidopsis at the levels of gene expression and protein localization, both under standard conditions and following heat stress. In generative tissues, ALBA proteins showed the strongest signal in mature pollen where they localized predominantly in cytoplasmic foci, particularly in regions surrounding the vegetative nucleus and sperm cells. Finally, we demonstrated the involvement of two Rpp25-like subfamily members ALBA4 and ALBA6 in RNA metabolism in mature pollen supported by their co-localization with poly(A)-binding protein 3 (PABP3). Collectively, we demonstrated the engagement of ALBA proteins in male reproductive development and the heat stress response, highlighting the involvement of ALBA4 and ALBA6 in RNA metabolism, storage and/or translational control in pollen upon heat stress. Such dynamic re-localization of ALBA proteins in a controlled, developmentally and environmentally regulated manner, likely reflects not only their redundancy but also their possible functional diversification in plants.
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Abstract
Geomagnetic fields interfere with the accumulation of iron in the human brain. Magnetic sensing of the human brain provides compelling evidence of new electric mechanisms in human brains and may interfere with the evolution of neurodegenerative diseases. We revealed that the human brain may have a unique susceptibility to conduct electric currents as feedback of magnetic dipole fluctuation in superparamagnetic grains. These grains accumulate and grow with brain aging. The electric feedback creates an electronic noise background that depends on geomagnetic field intensity and may compromise functional stability of the human brain, while induced currents are spontaneously generated near superparamagnetic grains. Grain growth due to an increase of iron mobility resulted in magnetic remanence enhancement during the final years of the studied brains.
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Influence of fluorophore and linker length on the localization and trafficking of fluorescent sterol probes. Sci Rep 2020; 10:22053. [PMID: 33328481 PMCID: PMC7745015 DOI: 10.1038/s41598-020-78085-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
Fluorescent sterol probes, comprising a fluorophore connected to a sterol backbone by means of a linker, are promising tools for enabling high-resolution imaging of intracellular cholesterol. In this study, we evaluated how the size of the linker, site of its attachment and nature of the fluorophore, affect the localization and trafficking properties of fluorescent sterol probes. Varying lengths of linker using the same fluorophore affected cell penetration and retention in specific cell compartments. A C-4 linker was confirmed as optimal. Derivatives of heterocyclic sterol precursors attached with identical C-4 linker to different fluorophores at diverse positions also showed significant differences in their binding properties to various intracellular compartments and kinetics of trafficking. Two novel red-emitting probes with good cell permeability, fast intracellular labelling and slightly different distribution displayed very promising characteristics for sterol probes. These probes also strongly labelled endo/lysosomal compartment in cells with pharmacologically disrupted cholesterol transport, or with a genetic mutation of cholesterol transporting protein NPC1, that overlapped with filipin staining of cholesterol. Overall, the present study demonstrates that the physicochemical properties of the fluorophore/linker pairing determine the kinetics of uptake and distribution and subsequently influence the applicability of final probes.
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Active surveillance for antibodies confirms circulation of lyssaviruses in Palearctic bats. BMC Vet Res 2020; 16:482. [PMID: 33302915 PMCID: PMC7731468 DOI: 10.1186/s12917-020-02702-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Palearctic bats host a diversity of lyssaviruses, though not the classical rabies virus (RABV). As surveillance for bat rabies over the Palearctic area covering Central and Eastern Europe and Siberian regions of Russia has been irregular, we lack data on geographic and seasonal patterns of the infection. RESULTS To address this, we undertook serological testing, using non-lethally sampled blood, on 1027 bats of 25 species in Bulgaria, the Czech Republic, Poland, Russia and Slovenia between 2014 and 2018. The indirect enzyme-linked immunosorbent assay (ELISA) detected rabies virus anti-glycoprotein antibodies in 33 bats, giving an overall seroprevalence of 3.2%. Bat species exceeding the seroconversion threshold included Myotis blythii, Myotis gracilis, Myotis petax, Myotis myotis, Murina hilgendorfi, Rhinolophus ferrumequinum and Vespertilio murinus. While Myotis species (84.8%) and adult females (48.5%) dominated in seropositive bats, juveniles of both sexes showed no difference in seroprevalence. Higher numbers tested positive when sampled during the active season (10.5%), as compared with the hibernation period (0.9%). Bat rabies seroprevalence was significantly higher in natural habitats (4.0%) compared with synanthropic roosts (1.2%). Importantly, in 2018, we recorded 73.1% seroprevalence in a cave containing a M. blythii maternity colony in the Altai Krai of Russia. CONCLUSIONS Identification of such "hotspots" of non-RABV lyssavirus circulation not only provides important information for public health protection, it can also guide research activities aimed at more in-depth bat rabies studies.
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In vivo Reporters for Visualizing Alternative Splicing of Hormonal Genes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E868. [PMID: 32650629 PMCID: PMC7412054 DOI: 10.3390/plants9070868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
Rapid progress in plant molecular biology in recent years has uncovered the main players in hormonal pathways and characterized transcriptomic networks associated with hormonal response. However, the role of RNA processing, in particular alternative splicing (AS), remains largely unexplored. Here, using example genes involved in cytokinin signaling, brassinosteroid synthesis and auxin transport, we present a set of reporters devised to visualize their AS events in vivo. These reporters show a differential tissue-specific expression of certain transcripts and reveal that expression of some of the them can be changed by the application of the exogenous hormone. Finally, based on the characterized AS event of the PIN7 auxin efflux carrier, we designed a system that allows a rapid genetic screening for the factors upstream of this AS event. Our innovative toolset can be therefore highly useful for exploring novel regulatory nodes of hormonal pathways and potentially helpful for plant researchers focusing on developmental aspects of AS.
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Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis. Biomolecules 2020; 10:E242. [PMID: 32033404 PMCID: PMC7072406 DOI: 10.3390/biom10020242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are industrially important oxidoreductases employed in lignocellulose saccharification. Using advanced time-resolved mass spectrometric techniques, we elucidated the structural determinants for substrate-mediated stabilization of the fungal LPMO9C from Neurosporacrassa during catalysis. LPMOs require a reduction in the active-site copper for catalytic activity. We show that copper reduction in NcLPMO9C leads to structural rearrangements and compaction around the active site. However, longer exposure to the reducing agent ascorbic acid also initiated an uncoupling reaction of the bound oxygen species, leading to oxidative damage, partial unfolding, and even fragmentation of NcLPMO9C. Interestingly, no changes in the hydrogen/deuterium exchange rate were detected upon incubation of oxidized or reduced LPMO with crystalline cellulose, indicating that the LPMO-substrate interactions are mainly side-chain mediated and neither affect intraprotein hydrogen bonding nor induce significant shielding of the protein surface. On the other hand, we observed a protective effect of the substrate, which slowed down the autooxidative damage induced by the uncoupling reaction. These observations further complement the picture of structural changes during LPMO catalysis.
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