Proximal Soil Sensing – A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS) provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils

A two-armed probe for in-cell DEER measurements on proteins

The application of double electron-electron resonance (DEER) with site-directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin-label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two-armed GdIII complexes, GdIII-CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites

The role of 18F-FDG PET in the differentiation between lung metastases and synchronous second primary lung tumours

Contains fulltext : 87717.pdf (publisher's version ) (Closed access)PURPOSE: In lung cancer patients with multiple lesions, the differentiation between metastases and second primary tumours has significant therapeutic and prognostic implications. The aim of this retrospective study was to investigate the potential of (18)F-FDG PET to discriminate metastatic disease from second primary lung tumours. METHODS: Of 1,396 patients evaluated by the thoracic oncology group between January 2004 and April 2009 at the Radboud University Nijmegen Medical Centre, patients with a synchronous second primary lung cancer were selected. Patients with metastatic disease involving the lungs served as the control group. Maximum standardized uptake values (SUVs) measured with (18)F-FDG PET were determined for two tumours in each patient. The relative difference between the SUVs of these tumours (SUV) was determined and compared between the second primary group and metastatic disease group. Receiver-operating characteristic (ROC) curve analysis was performed to determine the sensitivity and specificity of the SUV for an optimal cut-off value. RESULTS: A total of 37 patients (21 metastatic disease, 16 second primary cancer) were included for analysis. The SUV was significantly higher in patients with second primary cancer than in those with metastatic disease (58 vs 28%, respectively, p < 0.001). The area under the ROC curve was 0.81 and the odds ratio for the optimal cut-off was 18.4. CONCLUSION: SUVs from (18)F-FDG PET images can be helpful in differentiating metastatic disease from second primary tumours in patients with synchronous pulmonary lesions. Further studies are warranted to confirm the consistency of these results.1 november 201

Corrigendum: a two-armed probe for in-cell DEER measurements on proteins (vol 26, pg 17128, 2020)

CORRIGENDUM Q. Miao, E. Zurlo, D. de Bruin, J. A. J. Wondergem, S. P. Skinner, M. Timmer, A. Blok, D. Heinrich, M. Overhand, M. Huber,* M. Ubbink* 17128–17133 A Two-Armed Probe for In-Cell DEER Measurements on Proteins Chem. Eur. J., 2020, 26 DOI: 10.1002/chem.202002743 All authors have agreed that Dr. Simon P. Skinner has made a significant contribution to this work by performing experiments and analyzing data and that his name should have been included in the list of authors. The corrected list of authors therefore reads: Dr. Qing Miao, Dr. Enrico Zurlo, Donny de Bruin, Joeri A. J. Wondergem, Dr. Simon P. Skinner, Monika Timmer, Anneloes Blok, Prof. Dr. Doris Heinrich, Dr. Mark Overhand, Dr. Martina Huber, Prof. Dr. Marcellus Ubbink The relevant affiliations for Dr. Skinner are (1) Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC Leiden, The Netherlands and (2) School of Molecular and Cellular Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, UK. The Acknowledgement section should not contain the sentence “and Dr. Simon Skinner for CLaNP5 labeled T4lys NMR data.Macromolecular Biochemistr

Methyl group assignment using pseudocontact shifts with PARAssign

Macromolecular Biochemistr

β-Lactamase of Mycobacterium tuberculosis shows dynamics in the active site that increase upon inhibitor binding

The Mycobacterium tuberculosis β-lactamase BlaC is a broad-spectrum β-lactamase that can convert a range of β-lactam antibiotics. Enzymes with low specificity are expected to exhibit active site flexibility. To probe the motions in BlaC, we studied the dynamic behavior in solution using NMR spectroscopy. 15N relaxation experiments show that BlaC is mostly rigid on the pico- to nanosecond time scale. Saturation transfer experiments indicate that also on the high millisecond time scale BlaC is not dynamic. Using relaxation dispersion experiments, clear evidence was obtained for dynamics in the low millisecond range, with an exchange rate of ca. 860 s-1 The dynamic amide groups are localized in the active site. Upon formation of an adduct with the inhibitor avibactam, extensive line broadening occurs, indicating an increase in magnitude of the active site dynamics. Furthermore, the rate of the motions increases significantly. Upon reaction with the inhibitor clavulanic acid, similar line broadening is accompanied by duplication of NMR signals, indicative of at least one additional, slower exchange process (kex < 100 s-1), while for this inhibitor also loss of pico- to nanosecond time scale rigidity is observed for some amides in the α-domain. Possible sources of the observed dynamics, such as motions in the omega loop and rearrangements of active site residues, are discussed. The increase in dynamics upon ligand binding argues against a model of inhibitor binding through conformational selection. Rather, the induced dynamics may serve to maximize the likelihood of sampling the optimal conformation for hydrolysis of the bound ligand

Loss of Electrostatic Interactions Causes Increase of Dynamics within the Plastocyanin–Cytochrome <i>f</i> Complex

Recent studies on the electron transfer complex formed by cytochrome <i>f</i> and plastocyanin from <i>Nostoc</i> revealed that both hydrophobic and electrostatic interactions play a role in the process of complex formation. To study the balance between these two types of interactions in the encounter and the final state, the complex between plastocyanin from <i>Phormidium laminosum</i> and cytochrome <i>f</i> from <i>Nostoc</i> sp. PCC 7119 was investigated using NMR spectroscopy and Monte Carlo docking. Cytochrome <i>f</i> has a highly negative charge. <i>Phormidium</i> plastocyanin is similar to that from <i>Nostoc</i>, but the net charge of the protein is negative rather than positive. NMR titrations of Zn-substituted <i>Phormidium</i> plastocyanin and <i>Nostoc</i> cytochrome <i>f</i> indicated that a complex with an affinity intermediate between those of the <i>Nostoc</i> and <i>Phormidium</i> complexes is formed. Plastocyanin was found in a head-on orientation, as determined using pseudocontact shifts, similar to that in the <i>Phormidium</i> complex, in which the hydrophobic patch represents the main site of interaction on plastocyanin. However, the interaction in the cross-complex is dependent on electrostatics, similar to that in the <i>Nostoc</i> complex. The negative charge of plastocyanin decreases, but not abolishes, the attraction to cytochrome <i>f</i>, resulting in the formation of a more diffuse encounter complex than in the <i>Nostoc</i> case, as could be determined using paramagnetic relaxation spectroscopy. This work illustrates the subtle interplay of electrostatic and hydrophobic interactions in the formation of transient protein complexes. The results are discussed in the context of a model for association on the basis of hydrophobic contacts in the encounter state

Discordance and Conversion Rates of Progesterone-, Estrogen-, and HER2/neu-Receptor Status in Primary Breast Cancer and Brain Metastasis Mainly Triggered by Hormone Therapy

Background/Aim: Knowing the molecular footprint of tumors is a precondition for personalized medicine. For breast cancer, targeted therapies are frequently based on the molecular status of the tissue gained from the primary tumor operation. However, it is unclear whether metastases in different organs maintain the same status. Patients and Methods: We compared the estrogen-(ER), progesterone-(PgR) and HER2/neu receptor status of the primary tumor with brain metastases in a series of 24 consecutive breast cancer patients. Results: 62.5-75% of patients exhibited a constant receptor status between the primary tumor and the brain metastasis, whereas discordance rates of 25-37.5% were found, depending on the receptor. The rate of ER and PgR expression was each 41.6% in the primary tumors and decreased to 12.5% and 16.6% in the brain metastases. In contrast, the rate for Her2+ tumors increased from 41.6% in primary breast cancer to 65.2% in the respective brain metastases. The Ki-67 proliferation index increased significantly from a mean of 21% at the primary tumor site to 60% in brain metastases (p<0.001). All anti-estrogen treated breast tumors lost the estrogen receptor expression in the brain metastases, whereas no Her2/neu conversions occurred after treatment with trastuzumab. Conclusion: In summary, receptor conversion is frequent during disease progression. Therefore, the receptor status of the primary tumor is invalid for planning a therapy targeted against brain metastases, especially after hormone-therapy. In these cases, new tissue collection by biopsy or resection is mandatory for the selection of adequate therapeutic targets and accurate decision-making for systemic therapies