Three-dimensional petrographical investigations on borehole rock samples: a comparison between X-ray computed- and neutron tomography

Technical difficulties associated with excavation works in tectonized geological settings are frequent. They comprise instantaneous and/or delayed convergence, sudden collapse of gallery roof and/or walls, outpouring of fault-filling materials and water inflows. These phenomena have a negative impact on construction sites and their safety. In order to optimize project success, preliminary studies on the reliability of rock material found on site are needed. This implies in situ investigations (surface mapping, prospective drilling, waterflow survey, etc.) as well as laboratory investigations on rock samples (permeability determination, moisture and water content, mineralogy, petrography, geochemistry, mechanical deformation tests, etc.). A set of multiple parameters are then recorded which permit better insight on site conditions and probable behavior during excavation. Because rock formations are by nature heterogeneous, many uncertainties remain when extrapolating large-scale behavior of the rock mass from analyses of samples order of magnitudes smaller. Indirect large-scale field investigations (e.g. geophysical prospecting) could help to better constrain the relationships between lithologies at depth. At a much smaller scale, indirect analytical methods are becoming more widely used for material investigations. We discuss in this paper X-ray computed tomography (XRCT) and neutron tomography (NT), showing promising results for 3D petrographical investigations of the internal structure of opaque materials. Both techniques record contrasts inside a sample, which can be interpreted and quantified in terms of heterogeneity. This approach has the advantage of combining genetic parameters (physico-chemical rock composition) with geometric parameters resulting from alteration or deformation processes (texture and structure). A critical analysis of such 3D analyses together with the results of mechanical tests could improve predictions of short- and long-term behavior of a rock unit. Indirect methods have the advantage of being non-destructive. However, as it is the case with large-scale geophysical surveying, XRCT and NT are affected by several error factors inherent to the interaction of a radiation modality (X-ray or neutron beam) with the atomic structure of the investigated materials. Recorded signals are therefore in particular cases not artifact-free and need to be corrected in a subsequent stage of data processin

One-Step Synthesis of N‑Heterocyclic Compounds from Carbohydrates over Tungsten-Based Catalysts

A one-step reaction system has been developed to convert glucose and other renewable carbohydrates into important N-heterocyclic compounds in ammonia solution. Under optimal conditions, 2-methyl pyrazine (MP) and 4(5)-methyl imidazole (MI) were produced within 15 min with combined yields of around 40%. While the formation of 4(5)-MI was identified as a noncatalytic process, the yield of 2-MP was highly influenced by the presence of catalysts. In particular, nearly 3-fold yield enhancement of 2-MP was achieved over several tungsten-based catalysts. Control experiments, isotope-labeling tests, ESI-MS, and NMR analysis revealed that the formation of 2-MP follows a fragmentation mechanism, while small tungsten clusters such as [HW₂O₇]⁻ and [W₄O₁₃]^2– were the catalytically active species facilitating both glucose fragmentation and the subsequent cyclization reaction to generate pyrazine rings. The work exemplifies the possibility of sustainable production of important <i>N</i>-containing, heterocyclic chemicals from woody biomass, where the identification and understanding of novel catalysts are the key

Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase

The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins. Here, we performed force spectroscopy experiments and multiscale molecular dynamics simulations to study the unfolding pathway of diacylglycerol kinase (DGK), a small trimeric multispan transmembrane enzyme. The remarkable agreement between experiments and simulations allowed precise structural assignment and interaction analysis of unfolding intermediates, bypassing existing limitations on structural mapping, and thus provided mechanistic explanations for the formation of these states. DGK unfolding was found to proceed with structural segments varying in size that do not correlate with its secondary structure. We identified intermolecular side-chain packing interactions as one of the major contributions to the stability of unfolding intermediates. Mutagenesis creating packing defects induced a dramatic decrease in the mechano-stability of corresponding intermediates and also in the thermo-stability of DGK trimer, in good agreement with predictions from simulations. Hence, the molecular determinants of the mechano- and thermo-stability of a membrane protein can be identified at residue resolution. The accurate structural assignment established and microscopic mechanism revealed in this work may substantially expand the scope of single-molecule studies of membrane proteins

In Vivo Fate of CXCR2-Overexpressing Mesenchymal Stromal/Stem Cells in Pulmonary Diseases Monitored by Near-Infrared Region 2 Imaging

Lung-associated diseases pose a huge threat to human society. Mesenchymal stromal/stem cells (MSCs) hold great promise in the treatment of pulmonary diseases through cell transdifferentiation, paracrine factors, immune regulation, EV secretion, and drug loading. However, intravenous injection of MSCs often resulted in limited lesion tropism and apparent off-target accumulation. The IL-8-CXCR1/2 chemokine axis has been shown to be involved in progression of diseases including lung cancer and acute lung injury (ALI). Herein, we took advantage of this chemokine axis to enhance the homing of MSCs to cancerous and inflammation lesions. The in vivo distribution of MSCs was further monitored real-time by near-infrared region 2 (NIR-II) imaging owing to its outstanding performance in deep tissue imaging. Specifically, a new high-brightness D-A-D NIR-II dye, LJ-858, was synthesized and coprecipitated with a poly(d,l-lactic acid) polymer to form LJ-858 nanoparticles (NPs) with a relative quantum yield of 14.978%. LJ-858 NPs can efficiently label MSCs, and the NIR-II signal can be stable for 14 days without compromising the cell viability. Subcutaneous tracking of labeled MSCs showed no significant decline of NIR-II intensity within 24 h. The enhanced tropism of CXCR2-overexpressing MSCs to A549 tumor cells and the inflamed lung tissue was demonstrated through transwell models. The in vivo and ex vivo NIR-II imaging results further validated the significantly enhanced lesion retention of MSCCXCR2 in the lung cancer and ALI models. Taken together, this work reported a robust strategy to enhance the pulmonary disease tropism by the IL-8-CXCR1/2 chemokine axis. In addition, in vivo distribution of MSCs was successfully visualized by NIR-II imaging, which provides more insights into optimizing protocols for MSC-based therapies in the future

Protein-protein interactions of the <i>Y. pestis</i> TTSS measured byY2H.

<p>Protein-protein interactions of the <i>Y. pestis</i> TTSS measured byY2H.</p

Identification of Novel Protein-Protein Interactions of <em>Yersinia pestis</em> Type III Secretion System by Yeast Two Hybrid System

<div><p>Type III secretion system (T3SS) of the plague bacterium <em>Y. pestis</em> encodes a syringe-like structure consisting of more than 20 proteins, which can inject virulence effectors into host cells to modulate the cellular functions. Here in this report, interactions among the possible components in T3SS of <em>Yersinia pestis</em> were identified using yeast mating technique. A total of 57 genes, including all the pCD1-encoded genes except those involved in plasmid replication and partition, pseudogenes, and the putative transposase genes, were subjected to yeast mating analysis. 21 pairs of interaction proteins were identified, among which 9 pairs had been previously reported and 12 novel pairs were identified in this study. Six of them were tested by GST pull down assay, and interaction pairs of YscG-SycD, YscG-TyeA, YscI-YscF, and YopN-YpCD1.09c were successfully validated, suggesting that these interactions might play potential roles in function of <em>Yersinia</em> T3SS. Several potential new interactions among T3SS components could help to understand the assembly and regulation of <em>Yersinia</em> T3SS.</p> </div

Graphic view of the protein-protein interaction network of <i>Yersinia</i> T3SS.

<p>The graphic view of the network was drawn using Cytoscape 2.0 software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054121#pone.0054121-Shannon1" target="_blank">[47]</a>. All the functionally well characterized interactions among <i>Yersinia</i> type III secretion apparatus components and the potential novel interactions identified in this study were included. The darker colors indicate the higher centrality of a protein in this network. Red lines indicate known interactions that had been reported and functionally validated by biochemical methods. Blue and dotted lines indicate novel interactions identified by our yeast mating assays.</p

Schematic representation of <i>Yersinia</i> type III secretion apparatus and the protein-protein interactions among the different components.

<p>Symbols in dotted line indicate that interactions between these proteins have not been previously reported and were newly identified in this study.</p

Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests-0

<p><b>Copyright information:</b></p><p>Taken from "Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S62</p><p>BMC Proceedings 2007;1(Suppl 1):S62-S62.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367463.</p><p></p

Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests-1

Tus with the true RA status in the testing dataset. Each color curve represents prediction accuracy of one of the five CVs.<p><b>Copyright information:</b></p><p>Taken from "Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S62</p><p>BMC Proceedings 2007;1(Suppl 1):S62-S62.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367463.</p><p></p