Zoraptera is one of the smallest and least known insect orders, with only 47 described species, mostly known from tropical regions. Data on their distribution remain largely scattered throughout the extensive and often old and/or not easily accessible literature. Recent changes in the supraspecific classification of the order, combined with recent discoveries of new species and other taxonomic changes, have made the understanding of the distribution of Zoraptera even less clear. To summarize and update the knowledge of the worldwide distribution of Zoraptera, we have compiled a data resource of occurrence records: Zoraptera Occurrence Dataset. The dataset contains up-to-date information on the distribution of all zorapteran species according to the latest classification. The dataset is regularly curated and updated with new records from the literature and revised records from iNaturalist and GBIF.
- MeSH
- hmyz * klasifikace MeSH
- rozšíření zvířat MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- dataset MeSH
The geometry of the terrestrial magnetized environment, or geospace, varies widely in space and time due to the Earth's magnetic field interactions with the interplanetary medium. A spacecraft's location in geospace is only approximately determined by its coordinates since the environment is inhomogeneous, with distinct physical processes occurring in different regions. Knowing the location in the geospace offers a strong support for data analysis. This paper introduces a new dataset, Geospace Region and Magnetospheric Boundary identification (GRMB), which provides labelled positions for each Cluster spacecraft over the whole mission, with respect to the local environment. This continuous labelling is based on manual selection, supported by browsing 44 different Cluster data products. The GRMB dataset includes 15 labels spanning from the plasmasphere to solar wind regions. Its consistency is validated over 7 years against reference lists and by the physical properties of the GRMB regions. Over those years, Cluster spent a similar proportion of the time (≈15%) in the regions labelled lobe, plasmasheet, plasmasheet transition region, magnetosheath and solar wind.
- Publikační typ
- časopisecké články MeSH
A large body of evidence suggests that hypoxia drives aggressive molecular features of malignant cells irrespective of cancer type. Non-Hodgkin lymphomas (NHL) are the most common hematologic malignancies characterized by frequent involvement of diverse hypoxic microenvironments. We studied the impact of long-term deep hypoxia (1% O2) on the biology of lymphoma cells. Only 2 out of 6 tested cell lines (Ramos, and HBL2) survived ≥ 4 weeks under hypoxia. The hypoxia-adapted (HA)b Ramos and HBL2 cells had a decreased proliferation rate accompanied by significant suppression of both oxidative phosphorylation and glycolytic pathways. Transcriptome and proteome analyses revealed marked downregulation of genes and proteins of the mitochondrial respiration complexes I and IV, and mitochondrial ribosomal proteins. Despite the observed suppression of glycolysis, the proteome analysis of both HA cell lines showed upregulation of several proteins involved in the regulation of glucose utilization including the active catalytic component of prolyl-4-hydroxylase P4HA1, an important druggable oncogene. HA cell lines demonstrated increased transcription of key regulators of auto-/mitophagy, e.g., neuritin, BCL2 interacting protein 3 (BNIP3), BNIP3-like protein, and BNIP3 pseudogene. Adaptation to hypoxia was further associated with deregulation of apoptosis, namely upregulation of BCL2L1/BCL-XL, overexpression of BCL2L11/BIM, increased binding of BIM to BCL-XL, and significantly increased sensitivity of both HA cell lines to A1155463, a BCL-XL inhibitor. Finally, in both HA cell lines AKT kinase was hyperphosphorylated and the cells showed increased sensitivity to copanlisib, a pan-PI3K inhibitor. In conclusion, our data report on several shared mechanisms of lymphoma cell adaptation to long-term hypoxia including: 1. Upregulation of proteins responsible for glucose utilization, 2. Degradation of mitochondrial proteins for potential mitochondrial recycling (by mitophagy), and 3. Increased dependence on BCL-XL and PI3K-AKT signaling for survival. In translation, inhibition of glycolysis, BCL-XL, or PI3K-AKT cascade may result in targeted elimination of HA lymphoma cells.
- Publikační typ
- časopisecké články MeSH
Most of our knowledge of protein structure and function originates from experiments performed with purified proteins resuspended in dilute, buffered solutions. However, most proteins function in crowded intracellular environments with complex compositions. Significant efforts have been made to develop tools to study proteins in their native cellular settings. Among these tools, in-cell NMR spectroscopy has been the sole technique for characterizing proteins in the intracellular space of living cells at atomic resolution and physiological temperature. Nevertheless, due to technological constraints, in-cell NMR studies have been limited to asynchronous single-cell suspensions, precluding obtaining information on protein behavior in different cellular states. In this study, we present a methodology that allows for obtaining an atomically resolved NMR readout of protein structure and interactions in living human cells synchronized in specific cell cycle phases and within 3D models of human tissue. The described approach opens avenues for investigating how protein structure or drug recognition responds to cell-cell communication or changes in intracellular space composition during transitions among cell cycle phases.
- MeSH
- buněčný cyklus * MeSH
- konformace proteinů MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie metody MeSH
- nukleární magnetická rezonance biomolekulární metody MeSH
- proteiny chemie metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- proteiny MeSH
Replication stress, particularly in hard-to-replicate regions such as telomeres and centromeres, leads to the accumulation of replication intermediates that must be processed to ensure proper chromosome segregation. In this study, we identify a critical role for the interaction between RECQ4 and MUS81 in managing such stress. We show that RECQ4 physically interacts with MUS81, targeting it to specific DNA substrates and enhancing its endonuclease activity. Loss of this interaction, results in significant chromosomal segregation defects, including the accumulation of micronuclei, anaphase bridges, and ultrafine bridges (UFBs). Our data further demonstrate that the RECQ4-MUS81 interaction plays an important role in ALT-positive cells, where MUS81 foci primarily colocalise with telomeres, highlighting its role in telomere maintenance. We also observe that a mutation associated with Rothmund-Thomson syndrome, which produces a truncated RECQ4 unable to interact with MUS81, recapitulates these chromosome instability phenotypes. This underscores the importance of RECQ4-MUS81 in safeguarding genome integrity and suggests potential implications for human disease. Our findings demonstrate the RECQ4-MUS81 interaction as a key mechanism in alleviating replication stress at hard-to-replicate regions and highlight its relevance in pathological conditions such as RTS.
- MeSH
- chromozomální nestabilita MeSH
- DNA vazebné proteiny * metabolismus genetika MeSH
- endonukleasy * metabolismus genetika MeSH
- helikasy RecQ * metabolismus genetika MeSH
- homeostáza telomer MeSH
- lidé MeSH
- mutace MeSH
- replikace DNA * MeSH
- Rothmundův-Thomsonův syndrom * genetika metabolismus MeSH
- segregace chromozomů MeSH
- telomery * metabolismus genetika MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA vazebné proteiny * MeSH
- endonukleasy * MeSH
- helikasy RecQ * MeSH
- MUS81 protein, human MeSH Prohlížeč
- RECQL4 protein, human MeSH Prohlížeč
Single-molecule localization microscopy (SMLM) allows imaging beyond the diffraction limit. Detection of molecules is a crucial initial step in SMLM. False positive detections, which are not quantitatively controlled in current methods, are a source of artifacts that affect the entire SMLM analysis pipeline. Furthermore, current methods lack standardization, which hinders reproducibility. Here, we present an optimized molecule detection method which combines probabilistic thresholding with theoretically optimal filtering. The probabilistic thresholding enables control over false positive detections while optimal filtering minimizes false negatives. A theoretically optimal Poisson matched filter is used as a performance benchmark to evaluate existing filtering methods. Overall, our approach allows the detection of molecules in a robust, single-parameter and user-unbiased manner. This will minimize artifacts and enable data reproducibility in SMLM.
- Publikační typ
- časopisecké články MeSH
Studying the self-assembly of chiral molecules in two dimensions offers insights into the fundamentals of crystallization. Using scanning tunneling microscopy, we examine an uncommon aggregation of polyaromatic chiral molecules on a silver surface. Dense packing is achieved through a chiral triangular tiling of triads, with N and N ± 1 molecules at the edges. The triangles feature a random distribution of mirror-isomers, with a significant excess of one isomer. Chirality at the domain boundaries causes a lateral shift, producing three distinct topological defects where six triangles converge. These defects partially contribute to the formation of supramolecular spirals. The observation of different equal-density arrangements suggests that entropy maximization must play a crucial role. Despite the potential for regular patterns, all observed tiling is aperiodic. Differences from previously reported aperiodic molecular assemblies, such as Penrose tiling, are discussed. Our findings demonstrate that two-dimensional molecular self-assembly can be governed by topological constraints, leading to aperiodic tiling induced by intermolecular forces.
- Publikační typ
- časopisecké články MeSH
Data compression algorithms tend to reduce information entropy, which is crucial, especially in the case of images, as they are data intensive. In this regard, lossless image data compression is especially challenging. Many popular lossless compression methods incorporate predictions and various types of pixel transformations, in order to reduce the information entropy of an image. In this paper, a block optimisation programming framework Φ is introduced to support various experiments on raster images, divided into blocks of pixels. Eleven methods were implemented within Φ , including prediction methods, string transformation methods, and inverse distance weighting, as a representative of interpolation methods. Thirty-two different greyscale raster images with varying resolutions and contents were used in the experiments. It was shown that Φ reduces information entropy better than the popular JPEG LS and CALIC predictors. The additional information associated with each block in Φ is then evaluated. It was confirmed that, despite this additional cost, the estimated size in bytes is smaller in comparison to the sizes achieved by the JPEG LS and CALIC predictors.
- Klíčová slova
- Computer science, Information entropy, Inverse distance transform, Prediction, String transformations,
- Publikační typ
- časopisecké články MeSH
Homeostasis of cellular membranes is maintained by fine-tuning their lipid composition. Yeast lipid transporter Osh6, belonging to the oxysterol-binding protein-related proteins family, was found to participate in the transport of phosphatidylserine (PS). PS synthesized in the endoplasmic reticulum is delivered to the plasma membrane, where it is exchanged for phosphatidylinositol 4-phosphate (PI4P). PI4P provides the driving force for the directed PS transport against its concentration gradient. In this study, we employed an in vitro approach to reconstitute the transport process into the minimalistic system of large unilamellar vesicles to reveal its fundamental biophysical determinants. Our study draws a comprehensive portrait of the interplay between the structure and dynamics of Osh6, the carried cargo lipid, and the physical properties of the involved membranes, with particular attention to the presence of charged lipids and to membrane fluidity. Specifically, we address the role of the cargo lipid, which, by occupying the transporter, imposes changes in its dynamics and, consequently, predisposes the cargo to disembark in the correct target membrane.
- MeSH
- biologický transport MeSH
- buněčná membrána * metabolismus MeSH
- fluidita membrány MeSH
- fosfatidylinositolfosfáty metabolismus MeSH
- fosfatidylseriny metabolismus MeSH
- Saccharomyces cerevisiae - proteiny * metabolismus genetika MeSH
- Saccharomyces cerevisiae metabolismus MeSH
- steroidní receptory metabolismus MeSH
- unilamelární lipozómy metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- fosfatidylinositolfosfáty MeSH
- fosfatidylseriny MeSH
- Oxysterol Binding Proteins MeSH
- phosphatidylinositol 4-phosphate MeSH Prohlížeč
- Saccharomyces cerevisiae - proteiny * MeSH
- steroidní receptory MeSH
- unilamelární lipozómy MeSH
The cytokine TNF can trigger highly proinflammatory RIPK1-dependent cell death. Here, we show that the two adapter proteins, TANK and AZI2, suppress TNF-induced cell death by regulating the activation of TBK1 kinase. Mice lacking either TANK or AZI2 do not show an overt phenotype. Conversely, animals deficient in both adapters are born in a sub-Mendelian ratio and suffer from severe multi-organ inflammation, excessive antibody production, male sterility, and early mortality, which can be rescued by TNFR1 deficiency and significantly improved by expressing a kinase-dead form of RIPK1. Mechanistically, TANK and AZI2 both recruit TBK1 to the TNF receptor signaling complex, but with distinct kinetics due to interaction with different complex components. While TANK binds directly to the adapter NEMO, AZI2 is recruited later via deubiquitinase A20. In summary, our data show that TANK and AZI2 cooperatively sustain TBK1 activity during different stages of TNF receptor assembly to protect against autoinflammation.
- MeSH
- adaptorové proteiny signální transdukční * metabolismus genetika MeSH
- buněčná smrt MeSH
- endopeptidasy MeSH
- intracelulární signální peptidy a proteiny metabolismus genetika MeSH
- lidé MeSH
- myši inbrední C57BL MeSH
- myši knockoutované * MeSH
- myši MeSH
- protein-serin-threoninkinasy interagující s receptory * metabolismus genetika MeSH
- protein-serin-threoninkinasy * metabolismus genetika MeSH
- receptory TNF - typ I * metabolismus genetika MeSH
- signální transdukce MeSH
- TNF-alfa * metabolismus MeSH
- TNFAIP3 metabolismus genetika MeSH
- zánět metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- adaptorové proteiny signální transdukční * MeSH
- endopeptidasy MeSH
- gumby protein, mouse MeSH Prohlížeč
- intracelulární signální peptidy a proteiny MeSH
- NEMO protein, mouse MeSH Prohlížeč
- protein-serin-threoninkinasy interagující s receptory * MeSH
- protein-serin-threoninkinasy * MeSH
- receptory TNF - typ I * MeSH
- Ripk1 protein, mouse MeSH Prohlížeč
- Tbk1 protein, mouse MeSH Prohlížeč
- TNF-alfa * MeSH
- Tnfaip3 protein, mouse MeSH Prohlížeč
- TNFAIP3 MeSH
- Tnfrsf1a protein, mouse MeSH Prohlížeč
- Tnip2 protein, mouse MeSH Prohlížeč
