The Bacterial Proteasome at the Core of Diverse Degradation Pathways

Proteasomal protein degradation exists in mycobacteria and other actinobacteria, and expands their repertoire of compartmentalizing protein degradation pathways beyond the usual bacterial types. A product of horizontal gene transfer, bacterial proteasomes have evolved to support the organism's survival under challenging environmental conditions like nutrient starvation and physical or chemical stresses. Like the eukaryotic 20S proteasome, the bacterial core particle is gated and must associate with a regulator complex to form a fully active protease capable of recruiting and internalizing substrate proteins. By association with diverse regulator complexes that employ different recruitment strategies, the bacterial 20S core particle is able to act in different cellular degradation pathways. In association with the mycobacterial proteasomal ATPase Mpa, the proteasome degrades substrates post-translationally modified with prokaryotic, ubiquitin-like protein Pup in a process called pupylation. Upon interaction with the ATP-independent bacterial proteasome activator Bpa, poorly structured substrates are recruited for proteasomal degradation. A potential third degradation route might employ a Cdc48-like protein of actinobacteria (Cpa), for which interaction with the 20S core was recently demonstrated but no degradation substrates have been identified yet. The alternative interaction partners and wide range of substrate proteins suggest that the bacterial proteasome is a modular, functionally flexible and conditionally regulated degradation machine in bacteria that encounter rapidly changing and challenging conditions

Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Troetschel, C., Hamzeh, H., Alvarez, L., Pascal, R., Lavryk, F., Boenigk, W., Koerschen, H. G., Mueller, A., Poetsch, A., Rennhack, A., Gui, L., Nicastro, D., Struenker, T., Seifert, R., & Kaupp, U. B. Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation. Embo Journal, 39(4), (2020): e102723, doi:10.15252/embj.2019102723.Cilia serve as cellular antennae that translate sensory information into physiological responses. In the sperm flagellum, a single chemoattractant molecule can trigger a Ca2+ rise that controls motility. The mechanisms underlying such ultra‐sensitivity are ill‐defined. Here, we determine by mass spectrometry the copy number of nineteen chemosensory signaling proteins in sperm flagella from the sea urchin Arbacia punctulata. Proteins are up to 1,000‐fold more abundant than the free cellular messengers cAMP, cGMP, H+, and Ca2+. Opto‐chemical techniques show that high protein concentrations kinetically compartmentalize the flagellum: Within milliseconds, cGMP is relayed from the receptor guanylate cyclase to a cGMP‐gated channel that serves as a perfect chemo‐electrical transducer. cGMP is rapidly hydrolyzed, possibly via “substrate channeling” from the channel to the phosphodiesterase PDE5. The channel/PDE5 tandem encodes cGMP turnover rates rather than concentrations. The rate‐detection mechanism allows continuous stimulus sampling over a wide dynamic range. The textbook notion of signal amplification—few enzyme molecules process many messenger molecules—does not hold for sperm flagella. Instead, high protein concentrations ascertain messenger detection. Similar mechanisms may occur in other small compartments like primary cilia or dendritic spines.We thank Heike Krause for preparing the manuscript. Financial support by the Deutsche Forschungsgemeinschaft (DFG) via the priority program SPP 1726 “Microswimmers” and the Cluster of Excellence 1023 “ImmunoSensation” is gratefully acknowledged. We thank D. Stoddard for management of the UTSW cryo‐electron microscope facility, which is funded in part by a Cancer Prevention and Research Institute of Texas (CPRIT) Core Facility Award (RP170644). This study was supported by HHS|National Institutes of Health (NIH) grant R01 GM083122 and by CPRIT grant RR140082 to D. Nicastro

Induction of Bim and Bid gene expression during accelerated apoptosis in severe sepsis

ABSTRACT: INTRODUCTION: In transgenic animal models of sepsis, members of the Bcl-2-family of proteins regulate lymphocyte apoptosis and survival of sepsis. This study investigates the gene regulation of pro- and anti-apoptotic members of the Bcl-2-family of proteins in patients with early stage severe sepsis. METHODS: In this prospective case-control study patients were recruited from three intensive care units in a university hospital. Sixteen patients were enrolled as soon as they fulfilled the criteria of severe sepsis. Ten critically ill but non-septic patients and eleven healthy volunteers served as controls. Blood samples were immediately obtained at inclusion. To confirm the presence of accelerated apoptosis in the patient groups, caspase-3 activation and phosphatidylserine (PS) externalization in CD4+, CD8+ and CD19+ lymphocyte subsets were assessed by flow cytometry. Specific mRNA's of Bcl-2 family members were quantified from whole blood by real-time polymerase chain reaction. To test for statistical significance, Kruskal-Wallis testing with Dunn's multiple comparison test for post hoc testing was performed. RESULTS: In all lymphocyte populations caspase-3 (p<0.05) was activated, which was reflected in an increased PS externalization (p<0.05). Accordingly, lymphocyte counts were decreased in early severe sepsis. In CD4+ T-cells (p<005) and in B-cells (p<0.001) the Bcl-2 protein was decreased in severe sepsis. Gene expression of the BH3-only Bim was massively upregulated as compared to critically ill patients (p<0.001) and 51.6 fold as compared to healthy controls (p<0.05). Bid was increased 12.9 fold compared to critically ill (p<0.001). In the group of the mitochondrial apoptosis-inducers, Bak was upregulated 5.6 fold, while the expression of Bax showed no significant variations. By contrast, the pro-survival members Bcl-2 and Bcl-xl were both downregulated in severe sepsis (p<0.001, p<0.05). CONCLUSIONS: In early severe sepsis a gene expression pattern with induction of the pro-apoptotic Bcl-2 family members Bim, Bid and Bak and a downregulation of the anti-apoptotic Bcl-2 and Bcl-xl was observed in peripheral blood. This constellation may affect cellular susceptibility to apoptosis and complex immune dysfunction in sepsis

BASEWECS - Influence of the Baltic Sea and its annual ice coverage on the water and energy budget of the Baltic Sea

BASEWECS is a contribution to the German Climate Research Program DEKLIM. The project started in May 2001 and lasted until December 2004. BASEWECS aimed at the investigation of the influence of the Baltic Sea and its annual ice coverage on the water and energy budget of the BALTEX are

Kinetics of maternal immunity against rabies in fox cubs (Vulpes vulpes)

BACKGROUND: In previous experiments, it was demonstrated that maternal antibodies (maAb) against rabies in foxes (Vulpes vulpes) were transferred from the vixen to her offspring. However, data was lacking from cubs during the first three weeks post partum. Therefore, this complementary study was initiated. METHODS: Blood samples (n = 281) were collected from 64 cubs (3 to 43 days old) whelped by 19 rabies-immune captive-bred vixens. Sera was collected up to six times from each cub. The samples were analysed by a fluorescence focus inhibition technique (RFFIT), and antibody titres (nAb) were expressed in IU/ml. The obtained data was pooled with previous data sets. Subsequently, a total of 499 serum samples from 249 cubs whelped by 54 rabies-immune vixens were fitted to a non-linear regression model. RESULTS: The disappearance rate of maAb was independent of the vixens' nAb-titre. The maAb-titre of the cubs decreased exponentially with age and the half-life of the maAb was estimated to be 9.34 days. However, maAb of offspring whelped by vixens with high nAb-titres can be detected for longer by RFFIT than that of offspring whelped by vixens with relatively low nAb-titres. At a mean critical age of about 23 days post partum, maAb could no longer be distinguished from unspecific reactions in RFFIT depending on the amount of maAb transferred by the mother. CONCLUSIONS: The amount of maAb cubs receive is directly proportional to the titre of the vixen and decreases exponentially with age below detectable levels in seroneutralisation tests at a relatively early age

Interference effects in the photorecombination of argonlike Sc3+ ions: Storage-ring experiment and theory

Absolute total electron-ion recombination rate coefficients of argonlike Sc3+(3s2 3p6) ions have been measured for relative energies between electrons and ions ranging from 0 to 45 eV. This energy range comprises all dielectronic recombination resonances attached to 3p -> 3d and 3p -> 4s excitations. A broad resonance with an experimental width of 0.89 +- 0.07 eV due to the 3p5 3d2 2F intermediate state is found at 12.31 +- 0.03 eV with a small experimental evidence for an asymmetric line shape. From R-Matrix and perturbative calculations we infer that the asymmetric line shape may not only be due to quantum mechanical interference between direct and resonant recombination channels as predicted by Gorczyca et al. [Phys. Rev. A 56, 4742 (1997)], but may partly also be due to the interaction with an adjacent overlapping DR resonance of the same symmetry. The overall agreement between theory and experiment is poor. Differences between our experimental and our theoretical resonance positions are as large as 1.4 eV. This illustrates the difficulty to accurately describe the structure of an atomic system with an open 3d-shell with state-of-the-art theoretical methods. Furthermore, we find that a relativistic theoretical treatment of the system under study is mandatory since the existence of experimentally observed strong 3p5 3d2 2D and 3p5 3d 4s 2D resonances can only be explained when calculations beyond LS-coupling are carried out.Comment: 11 pages, 7 figures, 3 tables, Phys. Rev. A (in print), see also: http://www.strz.uni-giessen.de/~k

The Power Laws of Violence against Women: Rescaling Research and Policies

BACKGROUND: Violence against Women -despite its perpetuation over centuries and its omnipresence at all social levels- entered into social consciousness and the general agenda of Social Sciences only recently, mainly thanks to feminist research, campaigns, and general social awareness. The present article analyzes in a secondary analysis of German prevalence data on Violence against Women, whether the frequency and severity of Violence against Women can be described with power laws. PRINCIPAL FINDINGS: Although the investigated distributions all resemble power-law distributions, a rigorous statistical analysis accepts this hypothesis at a significance level of 0.1 only for 1 of 5 cases of the tested frequency distributions and with some restrictions for the severity of physical violence. Lowering the significance level to 0.01 leads to the acceptance of the power-law hypothesis in 2 of the 5 tested frequency distributions and as well for the severity of domestic violence. The rejections might be mainly due to the noise in the data, with biases caused by self-reporting, errors through rounding, desirability response bias, and selection bias. CONCLUSION: Future victimological surveys should be designed explicitly to avoid these deficiencies in the data to be able to clearly answer the question whether Violence against Women follows a power-law pattern. This finding would not only have statistical implications for the processing and presentation of the data, but also groundbreaking consequences on the general understanding of Violence against Women and policy modeling, as the skewed nature of the underlying distributions makes evident that Violence against Women is a highly disparate and unequal social problem. This opens new questions for interdisciplinary research, regarding the interplay between environmental, experimental, and social factors on victimization

Tightness of slip-linked polymer chains

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops which can exchange length between each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip-links it incorporates and its competition with other segments. When self-avoiding interactions are included, scaling arguments can be used to predict the statistics of segment sizes for certain paraknot configurations.Comment: 10 pages, 6 figures, REVTeX

Robust automated detection of microstructural white matter degeneration in Alzheimer’s disease using machine learning classification of multicenter DTI data

Diffusion tensor imaging (DTI) based assessment of white matter fiber tract integrity can support the diagnosis of Alzheimer’s disease (AD). The use of DTI as a biomarker, however, depends on its applicability in a multicenter setting accounting for effects of different MRI scanners. We applied multivariate machine learning (ML) to a large multicenter sample from the recently created framework of the European DTI study on Dementia (EDSD). We hypothesized that ML approaches may amend effects of multicenter acquisition. We included a sample of 137 patients with clinically probable AD (MMSE 20.6±5.3) and 143 healthy elderly controls, scanned in nine different scanners. For diagnostic classification we used the DTI indices fractional anisotropy (FA) and mean diffusivity (MD) and, for comparison, gray matter and white matter density maps from anatomical MRI. Data were classified using a Support Vector Machine (SVM) and a Naïve Bayes (NB) classifier. We used two cross-validation approaches, (i) test and training samples randomly drawn from the entire data set (pooled cross-validation) and (ii) data from each scanner as test set, and the data from the remaining scanners as training set (scanner-specific cross-validation). In the pooled cross-validation, SVM achieved an accuracy of 80% for FA and 83% for MD. Accuracies for NB were significantly lower, ranging between 68% and 75%. Removing variance components arising from scanners using principal component analysis did not significantly change the classification results for both classifiers. For the scanner-specific cross-validation, the classification accuracy was reduced for both SVM and NB. After mean correction, classification accuracy reached a level comparable to the results obtained from the pooled cross-validation. Our findings support the notion that machine learning classification allows robust classification of DTI data sets arising from multiple scanners, even if a new data set comes from a scanner that was not part of the training sample

Gravitational clustering of relic neutrinos and implications for their detection

We study the gravitational clustering of big bang relic neutrinos onto existing cold dark matter (CDM) and baryonic structures within the flat $\Lambda$CDM model, using both numerical simulations and a semi-analytical linear technique, with the aim of understanding the neutrinos' clustering properties for direct detection purposes. In a comparative analysis, we find that the linear technique systematically underestimates the amount of clustering for a wide range of CDM halo and neutrino masses. This invalidates earlier claims of the technique's applicability. We then compute the exact phase space distribution of relic neutrinos in our neighbourhood at Earth, and estimate the large scale neutrino density contrasts within the local Greisen--Zatsepin--Kuzmin zone. With these findings, we discuss the implications of gravitational neutrino clustering for scattering-based detection methods, ranging from flux detection via Cavendish-type torsion balances, to target detection using accelerator beams and cosmic rays. For emission spectroscopy via resonant annihilation of extremely energetic cosmic neutrinos on the relic neutrino background, we give new estimates for the expected enhancement in the event rates in the direction of the Virgo cluster.Comment: 38 pages, 8 embedded figures, iopart.cls; v2: references added, minor changes in text, to appear in JCA