Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity

Multiple Dynamics in Tumor Microenvironment Under Radiotherapy.

The tumor microenvironment (TME) is an evolutionally low-level and embryonically featured tissue comprising heterogenic populations of malignant and stromal cells as well as noncellular components. Under radiotherapy (RT), the major modality for the treatment of malignant diseases [1], TME shows an adaptive response in multiple aspects that affect the efficacy of RT. With the potential clinical benefits, interests in RT combined with immunotherapy (IT) are intensified with a large scale of clinical trials underway for an array of cancer types. A better understanding of the multiple molecular aspects, especially the cross talks of RT-mediated energy reprogramming and immunoregulation in the irradiated TME (ITME), will be necessary for further enhancing the benefit of RT-IT modality. Coming studies should further reveal more mechanistic insights of radiation-induced instant or permanent consequence in tumor and stromal cells. Results from these studies will help to identify critical molecular pathways including cancer stem cell repopulation, metabolic rewiring, and specific communication between radioresistant cancer cells and the infiltrated immune active lymphocytes. In this chapter, we will focus on the following aspects: radiation-repopulated cancer stem cells (CSCs), hypoxia and re-oxygenation, reprogramming metabolism, and radiation-induced immune regulation, in which we summarize the current literature to illustrate an integrated image of the ITME. We hope that the contents in this chapter will be informative for physicians and translational researchers in cancer radiotherapy or immunotherapy