Exploring the property space of periodic cellular structures based on crystal networks.

The properties of periodic cellular structures strongly depend on the regular spatial arrangement of their constituent base materials and can be controlled by changing the topology and geometry of the repeating unit cell. Recent advances in three-dimensional (3D) fabrication technologies more and more expand the limits of fabricable real-world architected materials and strengthen the need of novel microstructural topologies for applications across all length scales and fields in both fundamental science and engineering practice. Here, we systematically explore, interpret, and analyze publicly available crystallographic network topologies from a structural point of view and provide a ready-to-use unit cell catalog with more than 17,000 unique entries in total. We show that molecular crystal networks with atoms connected by chemical bonds can be interpreted as cellular structures with nodes connected by mechanical bars. By this, we identify new structures with extremal properties as well as known structures such as the octet-truss or the Kelvin cell and show how crystallographic symmetries are related to the mechanical properties of the structures. Our work provides inspiration for the discovery of novel cellular structures and paves the way for computational methods to explore and design microstructures with unprecedented properties, bridging the gap between microscopic crystal chemistry and macroscopic structural engineering.

Simulation of subcellular structures.

Advances in molecular dynamics simulations have led to large increases across spatial and complexity scales, providing valuable molecular level insight into processes occurring on the subcellular level. An increasing repertoire of methods to assemble and analyse complex membrane simulations, alongside advances in structural biology methods for membrane proteins, have contributed to our increased understanding of the roles of specific lipid interactions for multiple membrane protein systems. Large scale simulations of crowded protein solutions have provided a model describing the biophysical basis for experimentally observed diffusion properties. In this review we discuss recent approaches that pave the way towards linking molecular level detail to the cellular level.

Assessing sub-cellular resolution in spatial proteomics experiments.

The sub-cellular localisation of a protein is vital in defining its function, and a protein's mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions, including high profile mass spectrometry-based efforts. Here, we present a meta-analysis assessing and comparing the sub-cellular resolution of 29 such mass spectrometry-based spatial proteomics experiments using a newly developed tool termed QSep. Our goal is to provide a simple quantitative report of how well spatial proteomics resolve the sub-cellular niches they describe to inform and guide developers and users of such methods.

Understanding molecular mechanisms of disease through spatial proteomics.

Mammalian cells are organized into different compartments that separate and facilitate physiological processes by providing specialized local environments and allowing different, otherwise incompatible biological processes to be carried out simultaneously. Proteins are targeted to these subcellular locations where they fulfill specialized, compartment-specific functions. Spatial proteomics aims to localize and quantify proteins within subcellular structures.

Methodologies and approaches for the analysis of cell-nanoparticle interactions.

How to study nanoparticle-cell interactions is the key question that puzzles researchers in the fields of nanomedicine as well as in nanotoxicology. In nanotoxicology, the amount of nanoparticles internalized by the cells or bound to the external surfaces of cells determines the toxic profile of those particles. In medical applications, cellular uptake and binding of medically effective nanoparticles decides their efficacy. Despite the importance of understanding the extent and mode of nanoparticle-cell interactions, these processes are underinvestigated, mainly due to the lack of suitable user-friendly methodologies. Here we discuss the advantages and limitations of currently available (and most advanced) microscopic, spectroscopic, and other bioanalytical methods that could be used to assess cell-nanoparticle interactions either qualitatively or quantitatively. Special emphasis is given to the methods that enable analysis and identification of nanoparticles at single-cell level, and allow intracellular localization and speciation analysis of nanoparticles. This article is categorized under: Nanotechnology Approaches to Biology > Cells at the Nanoscale Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.

Construction of fluorescent polymeric nano-thermometers for intracellular temperature imaging: A review.

Multitudinous biochemical reactions occur in living cells, creating and releasing free energy to impel numerous cellular activities. Surplus energy is expelled as heat and resulted in elevated temperature, which induce control of gene expression, tumour metabolism and etc. Sensitive measurement of temperature on nanoscale in cells with ideal fluorescent probes is a great challenge in many areas. By taking the advantages of polymers in tunable critical solution temperature range and good biocompatibility, fluorescent polymeric thermometers (FPT) have drawn extensive attention because they are capable of accurate monitoring temperature with high spatial resolution at cellular level. This review offers a general overview of recent examples of FPT working in cells. The strategy for design and synthesis of the FPT has been highlighted. Furthermore, the applications of the constructed FPT for intracellular temperature variations under normal and external stimuli conditions have been discussed. Deep understanding of these aspects would lead to improvement in designing of unique FPT with real function and applications for intracellular temperature sensing. It will pave a new way not only for the study of intrinsic relationship between temperature and organelle function, but also provide the possibility for deep understanding of intracellular biological processes.

Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning.

MOTIVATION: There is a long-term interest in the challenging task of finding translocated and mislocated cancer biomarker proteins. Bioimages of subcellular protein distribution are new data sources which have attracted much attention in recent years because of their intuitive and detailed descriptions of protein distribution. However, automated methods in large-scale biomarker screening suffer significantly from the lack of subcellular location annotations for bioimages from cancer tissues. The transfer prediction idea of applying models trained on normal tissue proteins to predict the subcellular locations of cancerous ones is arbitrary because the protein distribution patterns may differ in normal and cancerous states. RESULTS: We developed a new semi-supervised protocol that can use unlabeled cancer protein data in model construction by an iterative and incremental training strategy. Our approach enables us to selectively use the low-quality images in normal states to expand the training sample space and provides a general way for dealing with the small size of annotated images used together with large unannotated ones. Experiments demonstrate that the new semi-supervised protocol can result in improved accuracy and sensitivity of subcellular location difference detection. AVAILABILITY AND IMPLEMENTATION: The data and code are available at: www.csbio.sjtu.edu.cn/bioinf/SemiBiomarker/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Label-free route to rapid, nanoscale characterization of cellular structure and dynamics through opaque media.

We report a novel technique for label-free, rapid visualization of structure and dynamics of live cells with nanoscale sensitivity through traditionally opaque media. Specifically, by combining principles of near-infrared (NIR) spectroscopy and quantitative phase imaging, functional characterization of cellular structure and dynamics through silicon substrates is realized in our study. We demonstrate the efficacy of the new approach by full-field imaging of erythrocyte morphology in their native states with a nm path length sensitivity. Additionally, we observe dynamic variations of human embryonic kidney cells, through a silicon substrate, in response to hypotonic stimulation with ms temporal resolution that also provides unique insight into the underlying biophysical changes. The proposed technology is fundamentally suited for high-performance investigations of biological specimens and significantly expands the options for visualization in complex microfluidic devices fabricated on silicon.

APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein.

Apoptotic proteins play key roles in understanding the mechanism of programmed cell death. Knowledge about the subcellular localization of apoptotic protein is constructive in understanding the mechanism of programmed cell death, determining the functional characterization of the protein, screening candidates in drug design, and selecting protein for relevant studies. It is also proclaimed that the information required for determining the subcellular localization of protein resides in their corresponding amino acid sequence. In this work, a new biological feature, class pattern frequency of physiochemical descriptor, was effectively used in accordance with the amino acid composition, protein similarity measure, CTD (composition, translation, and distribution) of physiochemical descriptors, and sequence similarity to predict the subcellular localization of apoptosis protein. AdaBoost with the weak learner as Random-Forest was designed for the five modules and prediction is made based on the weighted voting system. Bench mark dataset of 317 apoptosis proteins were subjected to prediction by our system and the accuracy was found to be 100.0 and 92.4 %, and 90.1 % for self-consistency test, jack-knife test, and tenfold cross validation test respectively, which is 0.9 % higher than that of other existing methods. Beside this, the independent data (N151 and ZW98) set prediction resulted in the accuracy of 90.7 and 87.7 %, respectively. These results show that the protein feature represented by a combined feature vector along with AdaBoost algorithm holds well in effective prediction of subcellular localization of apoptosis proteins. The user friendly web interface "APSLAP" has been constructed, which is freely available at http://apslap.bicpu.edu.in and it is anticipated that this tool will play a significant role in determining the specific role of apoptosis proteins with reliability.

Applications of biochromatography in the screening of bioactive natural products.

Searching for bioactive compounds from natural resources such as plant materials has become a focus for study. Several models, such as animal (biofluid, organ and tissue) and cellular (several kinds of cell lines), have traditionally been used for this purpose. As a fast, economic and effective way to identify or predict bioactive compounds in complex matrices, biochromatography has developed rapidly during the past years. Combing the properties of traditional chromatography and biomaterials, biochromatographic analysis possesses features of simultaneous screening, separation and structural identification for active compounds in a complex matrix. According to the process, biochromatography can be divided into offline and online approaches. For offline bioextraction, the biomaterials are used as the extraction phase and followed by routine chromatographic analysis. For online biochromatography, the biomaterials are directly used as the stationary phase for chromatographic analysis. This paper reviews the applications of offline bioextraction followed by chromatographic analysis and online biochromatography, including molecular, cell membrane and cell, and artificial biomembrane chromatography in the screening or predicting active compounds from natural sources.

STED microscopy and its applications: new insights into cellular processes on the nanoscale.

For about a decade, superresolution fluorescence microscopy has been advancing steadily, maturing from the proof-of-principle stage to routine application. Of the various techniques, STED (stimulated emission depletion) microscopy was the first to break the diffraction barrier. Today, it is a prominent and versatile form of superresolution light microscopy. STED microscopy has shed a sharper light on numerous topics in cell biology, but also in material sciences. Both disciplines extend into the nanometer range, making detailed studies of structural and functional relationships difficult or even impossible to achieve using diffraction-limited microscopy. With recent advancements like spectral multiplexing or live-cell imaging, STED microscopy makes nanoscale materials and components of the cell accessible for fluorescence-based investigations. With multicolor superresolution imaging, even the interactions between biological and engineered nanostructures can be studied in detail. This review gives an introduction into the working principle of STED microscopy, provides a detailed overview of recent advancements and new techniques implemented for use with STED microscopy and shows how these have been applied in the life sciences and nanotechnologies.

Fifty years of structural glycoproteins.

During decades preceding and following the last war, a favourite subject of biochemists was to study glycoproteins. One class of these substances, found in connective tissues were characterised as polysaccharides, most of them found to be linked to proteins, designated later as glycosaminoglycans and proteoglycans. Another family of glycoconjugates represented epithelial mucins as found in the gastro-intestinal and respiratory tracts and conduits. A third family of glycoconjugates is represented by circulating glycoproteins isolated from the blood plasma, mostly studied by medical biochemists in relation to pathological conditions comprising those increasing during the inflammatory reaction: acute phase glycoproteins. Their study suggested that they might be derived from connective tissues. Although inflammatory glycoproteins derive mostly from the liver, the possibility of connective tissue origin of glycoproteins remained open. Using cornea, an avascular tissue, we could show that connective tissues also synthesize glycoproteins. We proposed to designate them "structural glycoproteins" (SGP-s) to distinguish them from circulating, blood-born glycoproteins coming from the liver. They play locally "structural" roles in connective tissues where they are synthesized. Soon after fibronectin was identified and shown to mediate cell-matrix interactions. A large family of glycoproteins were then isolated from a variety of sources, cells, tissues others than liver, confirming our original hypothesis. The first experiments on these glycoproteins were published from 1961/1962 giving the opportunity to recapitulate this biochemical adventure 50 years later, together with the celebration of the foundation of the first connective tissue society in Europe, as described in the first article in this issue.

Hydrogen peroxide probes directed to different cellular compartments.

BACKGROUND: Controlled generation and removal of hydrogen peroxide play important roles in cellular redox homeostasis and signaling. We used a hydrogen peroxide biosensor HyPer, targeted to different compartments, to examine these processes in mammalian cells. PRINCIPAL FINDINGS: Reversible responses were observed to various redox perturbations and signaling events. HyPer expressed in HEK 293 cells was found to sense low micromolar levels of hydrogen peroxide. When targeted to various cellular compartments, HyPer occurred in the reduced state in the nucleus, cytosol, peroxisomes, mitochondrial intermembrane space and mitochondrial matrix, but low levels of the oxidized form of the biosensor were also observed in each of these compartments, consistent with a low peroxide tone in mammalian cells. In contrast, HyPer was mostly oxidized in the endoplasmic reticulum. Using this system, we characterized control of hydrogen peroxide in various cell systems, such as cells deficient in thioredoxin reductase, sulfhydryl oxidases or subjected to selenium deficiency. Generation of hydrogen peroxide could also be monitored in various compartments following signaling events. CONCLUSIONS: We found that HyPer can be used as a valuable tool to monitor hydrogen peroxide generated in different cellular compartments. The data also show that hydrogen peroxide generated in one compartment could translocate to other compartments. Our data provide information on compartmentalization, dynamics and homeostatic control of hydrogen peroxide in mammalian cells.

Prostasomes as potential modulators of tyrosine phosphorylation in human spermatozoa.

Prostasomes, vesicles present in human semen, are known to play a role in male fertility. However, the mechanisms involved are still poorly understood. The present study looks at the direct influence of different concentrations of prostasomes on human sperm function in conditions supporting capacitation in vitro. Five million Percoll selected spermatozoa were incubated for 3 h at 37°C under an atmosphere of 5% CO2 in air, in 100 µl Biggers Whitten Whittingham's medium (BWW) containing polyvinyl alcohol (PVA, 1 mg/ml) and bovine serum albumin (BSA; 3 mg/ml) in the absence or presence of increasing concentrations of prostasomes (expressed in terms of their cholesterol content: 15; 30; 45 nmoles per 100 µL of incubation medium). After in vitro exposure of spermatozoa to prostasomes, our data indicate that i) tyrosine phosphorylation intensity of the 107 KDa protein band was dose dependently lower and ii) the percentage of viable and progressive motile spermatozoa was unchanged and the percentage of non-progressive motility decreased. In addition, the incubation of prostasomes with spermatozoa resulted in an enrichment of their lipid content. Our experiments suggest that adhesion of prostasomes to spermatozoa could be responsible for the decrease in Tyrosine phosphorylation and the alteration of the mean curvilinear velocity (VCL) and the average path velocity (VAP).

Micellar electrokinetic chromatographic analysis for in vitro accumulation of anthracyclines enhanced by inhibitors of cell membrane transporter-proteins in cancer cells.

Cell membrane transporter-proteins have been partly implicated in lowering the accumulation of drugs in cancer cells, leading to multidrug resistance (MDR). Two cancer cell lines, A549 and RDES, were continuously exposed to subclinical concentration (250 nM) of anthracyclines and micellar electrokinetic chromatography was used to investigate their in vitro accumulation after treatment with inhibitors of membrane transporter-proteins. The four anthracylines [doxorubicin (DOX), epirubicin (EPI), daunorubicin (DNR), and idarubicin (IDA)] were separated within a short analysis time of less than 15 min in borate buffer (80 mM, pH 9.22) containing sodium taurodeoxycholate (35 mM), 2-hydroxypropyl-γ-cyclodextrin (3.5% wt/v), and sodium dodecylsulfate (20 mM). Laser-induced fluorescence was used for detection of the anthracyclines. Three inhibitors, verapamil, cyclosporine A and probenecid, were examined by adding each inhibitor independently or two inhibitors simultaneously to the culture medium. It was found that independent use of each inhibitor leads to more efficient accumulation than combined use of verapamil and probenecid. In addition, the results show that effect of inhibitors on the accumulation of anthracyclines depended on type of cell: in RDES, inhibitors enhanced accumulation of all four anthracyclines, while in A549, inhibitors showed different accumulation behavior for each anthracycline. Generally higher accumulation of anthracyclines was observed in RDES cells than A549, as evidenced by dead cells (7-16%) after 24 h of continuous exposure to subclinical concentration.

An inventory of the bacterial macromolecular components and their spatial organization.

Formerly regarded as small 'bags' of nucleic acids with randomly diffusing enzymes, bacteria are organized by a sophisticated and tightly regulated molecular machinery. Here, we review qualitative and quantitative data on the intracellular organization of bacteria and provide a detailed inventory of macromolecular structures such as the divisome, the degradosome and the bacterial 'nucleolus'. We discuss how these metabolically active structures manage the spatial organization of the cell and how macromolecular crowding influences them. We present for the first time a visualization program, lifeexplorer, that can be used to study the interplay between metabolism and spatial organization of a prokaryotic cell.

Engineering the extracellular environment: Strategies for building 2D and 3D cellular structures.

Cell fate is regulated by extracellular environmental signals. Receptor specific interaction of the cell with proteins, glycans, soluble factors as well as neighboring cells can steer cells towards proliferation, differentiation, apoptosis or migration. In this review, approaches to build cellular structures by engineering aspects of the extracellular environment are described. These methods include non-specific modifications to control the wettability and stiffness of surfaces using self-assembled monolayers (SAMs) and polyelectrolyte multilayers (PEMs) as well as methods where the temporal activation and spatial distribution of adhesion ligands is controlled. Building on these techniques, construction of two-dimensional cell sheets using temperature sensitive polymers or electrochemical dissolution is described together with current applications of these grafts in the clinical arena. Finally, methods to pattern cells in three-dimensions as well as to functionalize the 3D environment with biologic motifs take us one step closer to being able to engineer multicellular tissues and organs.