Bridging structural and cell biology with cryo-electron microscopy

Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.

MEGA-PRESS of GABA+: Influences of acquisition parameters

γ-aminobutyric acid (GABA) was the first molecule that was edited with MEGA-PRESS. GABA edited spectroscopy is challenged by limited selectivity of editing pulses. Coediting of resonances from macromolecules (MM) is the greatest single limitation of GABA edited spectroscopy. In this contribution, relative signal contributions from GABA, MM and homocarnosine to the total MEGA-PRESS edited signal at ~3 ppm, i.e., GABA+, are simulated at 3 tesla using several acquisition schemes. The base scheme is modeled after those currently supplied by vendors: it uses typical pulse shapes and lengths, it minimizes the first echo time (TE), and the delay between the editing pulses is kept at TE/2. Edited spectra are simulated for imperfect acquisition parameters such as incorrect frequency, larger chemical shift displacement, incorrect transmit B₁ -field calibration for localization and editing pulses, and longer TE. An alternative timing scheme and longer editing pulses are also considered. Additional simulations are performed for symmetric editing around the MM frequency to suppress the MM signal. The relative influences of these acquisition parameters on the constituents of GABA+ are examined from the perspective of modern experimental designs for investigating brain GABA concentration differences in healthy and diseased humans. Other factors that influence signal contributions, such as T₁ and T₂ relaxation times are also considered.

Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations

Once an MRS dataset has been acquired, several important steps must be taken to obtain the desired metabolite concentration measures. First, the data must be preprocessed to prepare them for analysis. Next, the intensity of the metabolite signal(s) of interest must be estimated. Finally, the measured metabolite signal intensities must be converted into scaled concentration units employing a quantitative reference signal to allow meaningful interpretation. In this paper, we review these three main steps in the post-acquisition workflow of a single-voxel MRS experiment (preprocessing, analysis and quantification) and provide recommendations for best practices at each step.

Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding

Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.

Carnivory in the larvae of Drosophila melanogaster and other Drosophila species

Drosophila melanogaster is widely used as a model organism for biological investigations, and food is a major aspect of its ecology and evolutionary biology. Previous studies have shown that this insect can use fruits, yeasts and insect carcasses as its food sources. In this study, we demonstrate that this species is an omnivore, that its larvae can exploit not only fruits and yeast but also foods of animal origin (FAOs), and that larvae consume adult carcasses regularly. FAO-fed larvae develop into adulthood within a normal developmental time frame without the help of microbes. Yeast foods are better for Drosophila development than are foods of plant origin (FPOs) or FAO because in yeast foods, more eggs complete their life cycle, and the body size of emerged flies is much greater. Flies can use a mixture of yeast-FAO, which significantly boosts female fertility. Larvae digest FAOs externally. Larval D. virilis, D. hydei, and D. simulans are also omnivorous and demonstrate the same feeding habits as larval D. melanogaster. These findings prompt us to reconsider previous conclusions about the original adaptations of D. melanogaster and other Drosophila species and have direct implications for diet-related studies using Drosophila as a model organism.

Locating macromolecules and determining structures inside bacterial cells using electron cryotomography

Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.

Biological Applications at the Cutting Edge of Cryo-Electron Microscopy

Cryo-electron microscopy (cryo-EM) is a powerful tool for macromolecular to near-atomic resolution structure determination in the biological sciences. The specimen is maintained in a near-native environment within a thin film of vitreous ice and imaged in a transmission electron microscope. The images can then be processed by a number of computational methods to produce three-dimensional information. Recent advances in sample preparation, imaging, and data processing have led to tremendous growth in the field of cryo-EM by providing higher resolution structures and the ability to investigate macromolecules within the context of the cell. Here, we review developments in sample preparation methods and substrates, detectors, phase plates, and cryo-correlative light and electron microscopy that have contributed to this expansion. We also have included specific biological applications.

Dual-frequency irradiation CEST-MRI of endogenous bulk mobile proteins

A novel MRI contrast is proposed which enables the selective detection of endogenous bulk mobile proteins in vivo. Such a non-invasive imaging technique may be of particular interest for many diseases associated with pathological alterations of protein expression, such as cancer and neurodegenerative disorders. Specificity to mobile proteins was achieved by the selective measurement of intramolecular spin diffusion and the removal of semi-solid macromolecular signal components by a correction procedure. For this purpose, the approach of chemical exchange saturation transfer (CEST) was extended to a radiofrequency (RF) irradiation scheme at two different frequency offsets (dualCEST). Using protein model solutions, it was demonstrated that the dualCEST technique allows the calculation of an image contrast which is exclusively sensitive to changes in concentration, molecular size and the folding state of mobile proteins. With respect to application in humans, dualCEST overcomes the selectivity limitations at relatively low magnetic field strengths, and thus enables examinations on clinical MR scanners. The feasibility of dualCEST examinations in humans was verified by a proof-of-principle examination of a brain tumor patient at 3 T. With its specificity for the mobile fraction of the proteome, its comparable sensitivity to conventional water proton MRI and its applicability to clinical MR scanners, this technique represents a further step towards the non-invasive imaging of proteomic changes in humans.

Empirical Factors Affecting the Quality of Non-Negative Matrix Factorization of Mammalian Cell Raman Spectra

Mammalian cells contain various macromolecules that can be investigated non-invasively with Raman spectroscopy. The particular mixture of major macromolecules present in a cell being probed are reflected in the measured Raman spectra. Determining macromolecular identities and estimating their concentrations from these mixture Raman spectra can distinguish cell types and otherwise enable biological research. However, the application of canonical multivariate methods, such as principal component analysis (PCA), to perform spectral unmixing yields mathematical solutions that can be difficult to interpret. Non-negative matrix factorization (NNMF) improves the interpretability of unmixed macromolecular components, but can be difficult to apply because ambiguities produced by overlapping Raman bands permit multiple solutions. Furthermore, theoretically sound methods can be difficult to implement in practice. Here we examined the effects of a number of empirical approaches on the quality of NNMF results. These approaches were evaluated on simulated mammalian cell Raman hyperspectra and the results were used to develop an enhanced procedure for implementing NNMF. We demonstrated the utility of this procedure using a Raman hyperspectral data set measured from human islet cells to recover the spectra of insulin and glucagon. This was compared to the relatively inferior PCA of these data.

Optical second-harmonic images of sacran megamolecule aggregates

We have detected a second-order nonlinear optical response from aggregates of the ampholytic megamolecular polysaccharide sacran extracted from cyanobacterial biomaterials by using optical second-harmonic-generation (SHG) microscopy. The SHG images of sacran cotton-like lump, fibers, and cast films showed SHG intensity microspots of several tens of micrometers in size. The dependence of the SHG spot intensity on an excitation light polarization angle was observed to illustrate sacran molecular orientation in these microdomains. We also observed SHG signals around a special region of the cast film edges of sacran. These results show that sacran megamolecules aggregate in several different ways.

Brain γ-aminobutyric acid (GABA) detection in vivo with the J-editing (1) H MRS technique: a comprehensive methodological evaluation of sensitivity enhancement, macromolecule contamination and test-retest reliability

Abnormalities in brain γ-aminobutyric acid (GABA) have been implicated in various neuropsychiatric and neurological disorders. However, in vivo GABA detection by (1) H MRS presents significant challenges arising from the low brain concentration, overlap by much stronger resonances and contamination by mobile macromolecule (MM) signals. This study addresses these impediments to reliable brain GABA detection with the J-editing difference technique on a 3-T MR system in healthy human subjects by: (i) assessing the sensitivity gains attainable with an eight-channel phased-array head coil; (ii) determining the magnitude and anatomic variation of the contamination of GABA by MM; and (iii) estimating the test-retest reliability of the measurement of GABA with this method. Sensitivity gains and test-retest reliability were examined in the dorsolateral prefrontal cortex (DLPFC), whereas MM levels were compared across three cortical regions: DLPFC, the medial prefrontal cortex (MPFC) and the occipital cortex (OCC). A three-fold higher GABA detection sensitivity was attained with the eight-channel head coil compared with the standard single-channel head coil in DLPFC. Despite significant anatomical variation in GABA + MM and MM across the three brain regions (p < 0.05), the contribution of MM to GABA + MM was relatively stable across the three voxels, ranging from 41% to 49%, a non-significant regional variation (p = 0.58). The test-retest reliability of GABA measurement, expressed as either the ratio to voxel tissue water (W) or to total creatine, was found to be very high for both the single-channel coil and the eight-channel phased-array coil. For the eight-channel coil, for example, Pearson's correlation coefficient of test vs. retest for GABA/W was 0.98 (R(2)  = 0.96, p = 0.0007), the percentage coefficient of variation (CV) was 1.25% and the intraclass correlation coefficient (ICC) was 0.98. Similar reliability was also found for the co-edited resonance of combined glutamate and glutamine (Glx) for both coils. Copyright © 2016 John Wiley & Sons, Ltd.

Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules

Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.

Calcium Deposits in the Crayfish, Cherax quadricarinatus: Microstructure Versus Elemental Distribution

The crayfish Cherax quadricarinatus stores calcium ions, easily mobilizable after molting, for calcifying parts of the new exoskeleton. They are chiefly stored as amorphous calcium carbonate (ACC) during each premolt in a pair of gastroliths synthesized in the stomach wall. How calcium carbonate is stabilized in the amorphous state in such a biocomposite remains speculative. The knowledge of the microstructure at the nanometer level obtained by field emission scanning electron microscopy and atomic force microscopy combined with scanning electron microscopy energy-dispersive X-ray spectroscopy, micro-Raman and X-ray absorption near edge structure spectroscopy gave relevant information on the elaboration of such an ACC-stabilized biomineral. We observed nanogranules distributed along chitin-protein fibers and the aggregation of granules in thin layers. AFM confirmed the nanolevel structure, showing granules probably surrounded by an organic layer and also revealing a second level of aggregation as described for other crystalline biominerals. Raman analyses showed the presence of ACC, amorphous calcium phosphate, and calcite. Elemental analyses confirmed the presence of elements like Fe, Na, Mg, P, and S. P and S are heterogeneously distributed. P is present in both the mineral and organic phases of gastroliths. S seems present as sulfate (probably as sulfated sugars), sulfonate, sulfite, and sulfoxide groups and, in a lesser extent, as sulfur-containing amino acids.

Contribution of Macromolecular Antioxidants to Dietary Antioxidant Capacity: A Study in the Spanish Mediterranean Diet

Epidemiological and clinical studies show that diets with a high antioxidant capacity, such us those rich in plant food and beverages, are associated with significant decreases in the overall risk of cardiovascular disease or colorectal cancer. Current studies on dietary antioxidants and dietary antioxidant capacity focus exclusively on low molecular weight or soluble antioxidants (vitamins C and E, phenolic compounds and carotenoids), ignoring macromolecular antioxidants. These are polymeric phenolic compounds or polyphenols and carotenoids linked to plant food macromolecules that yield bioavailable metabolites by the action of the microbiota with significant effects either local and/or systemic after absorption. This study determined the antioxidant capacity of the Spanish Mediterranean diet including for the first time both soluble and macromolecular antioxidants. Antioxidant capacity and consumption data of the 54 most consumed plant foods and beverages were used. Results showed that macromolecular antioxidants are the major dietary antioxidants, contributing a 61% to the diet antioxidant capacity (8000 μmol Trolox, determined by ABTS method). The antioxidant capacity data for foods and beverages provided here may be used to estimate the dietary antioxidant capacity in different populations, where similar contributions of macromolecular antioxidants may be expected, and also to design antioxidant-rich diets. Including macromolecular antioxidants in mechanistic, intervention and observational studies on dietary antioxidants may contribute to a better understanding of the role of antioxidants in nutrition and health.

Probing structures of large protein complexes using zero-length cross-linking

Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed.

The influence of frame alignment with dose compensation on the quality of single particle reconstructions

As direct electron detection devices in cryo-electron microscopy become ubiquitous, the field is now ripe for new developments in image analysis techniques that take advantage of their increased SNR coupled with their high-throughput frame collection abilities. In approaching atomic resolution of native-like biomolecules, the accurate extraction of structural locations and orientations of side-chains from frames depends not only on the electron dose that a sample receives but also on the ability to accurately estimate the CTF. Here we use a new 2.8Å resolution structure of a recombinant gene therapy virus, AAV-DJ with Arixtra, imaged on an FEI Titan Krios with a DE-20 direct electron detector to probe new metrics including relative side-chain density and ResLog analysis for optimizing the compensation of electron beam damage and to characterize the factors that are limiting the resolution of the reconstruction. The influence of dose compensation on the accuracy of CTF estimation and particle classifiability are also presented. We show that rigorous dose compensation allows for better particle classifiability and greater recovery of structural information from negatively charged, electron-sensitive side-chains, resulting in a more accurate macromolecular model.

The MORPHEUS II protein crystallization screen

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

Optimization of crystallization conditions for biological macromolecules

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Large molecule run acceptance: Recommendation for best practices and harmonization from the Global Bioanalysis Consortium Harmonization Team

The L1 Global Harmonization Team provides recommendations specifically for run acceptance of ligand binding methods used in bioanalysis of macromolecules in support of pharmacokinetics. The team focused on standard curve calibrators and quality controls for use in both pre-study validation and in-study sample analysis, including their preparation and acceptance criteria. The team also considered standard curve editing and the concept of total error.

Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy

Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.

Unedited in vivo detection and quantification of γ-aminobutyric acid in the occipital cortex using short-TE MRS at 3 T

Short-TE MRS has been proposed recently as a method for the in vivo detection and quantification of γ-aminobutyric acid (GABA) in the human brain at 3 T. In this study, we investigated the accuracy and reproducibility of short-TE MRS measurements of GABA at 3 T using both simulations and experiments. LCModel analysis was performed on a large number of simulated spectra with known metabolite input concentrations. Simulated spectra were generated using a range of spectral linewidths and signal-to-noise ratios to investigate the effect of varying experimental conditions, and analyses were performed using two different baseline models to investigate the effect of an inaccurate baseline model on GABA quantification. The results of these analyses indicated that, under experimental conditions corresponding to those typically observed in the occipital cortex, GABA concentration estimates are reproducible (mean reproducibility error, <20%), even when an incorrect baseline model is used. However, simulations indicate that the accuracy of GABA concentration estimates depends strongly on the experimental conditions (linewidth and signal-to-noise ratio). In addition to simulations, in vivo GABA measurements were performed using both spectral editing and short-TE MRS in the occipital cortex of 14 healthy volunteers. Short-TE MRS measurements of GABA exhibited a significant positive correlation with edited GABA measurements (R = 0.58, p < 0.05), suggesting that short-TE measurements of GABA correspond well with measurements made using spectral editing techniques. Finally, within-session reproducibility was assessed in the same 14 subjects using four consecutive short-TE GABA measurements in the occipital cortex. Across all subjects, the average coefficient of variation of these four GABA measurements was 8.7 ± 4.9%. This study demonstrates that, under some experimental conditions, short-TE MRS can be employed for the reproducible detection of GABA at 3 T, but that the technique should be used with caution, as the results are dependent on the experimental conditions.

Matrix-algebra-based calculations of the time evolution of the binary spin-bath model for magnetization transfer

Quantification of magnetization-transfer (MT) experiments are typically based on the assumption of the binary spin-bath model. This model allows for the extraction of up to six parameters (relative pool sizes, relaxation times, and exchange rate constants) for the characterization of macromolecules, which are coupled via exchange processes to the water in tissues. Here, an approach is presented for estimating MT parameters acquired with arbitrary saturation schemes and imaging pulse sequences. It uses matrix algebra to solve the Bloch-McConnell equations without unwarranted simplifications, such as assuming steady-state conditions for pulsed saturation schemes or neglecting imaging pulses. The algorithm achieves sufficient efficiency for voxel-by-voxel MT parameter estimations by using a polynomial interpolation technique. Simulations, as well as experiments in agar gels with continuous-wave and pulsed MT preparation, were performed for validation and for assessing approximations in previous modeling approaches. In vivo experiments in the normal human brain yielded results that were consistent with published data.

Cr(VI) reduction capability of humic acid extracted from the organic component of municipal solid waste

The capacity of humic acid extracted from organic waste (HAw) to reduce Cr(VI) was tested at pH 2.5, 4 and 6 and compared with coal-derived humic acid (HAc). HAw was more effective than HAc in reducing Cr(VI). The kinetics of Cr(VI) reductions depended strongly on pH. The calculation of the apparent rate coefficients indicated that HAw was more efficient at reducing Cr(VI) than HAc, but was also more efficient than HAs from soil and peat. The reduction capability of HAs depends on the type of functional groups (i.e., thiols and phenols) present, rather than the free radicals. HAw was more efficient at reducing Cr(VI) than HAc because more reactive phenols were present, i.e., methoxy- and methyl-phenols.

Influence of temperature and macromolecular mobility on sorption of TCE on humic acid coated mineral surfaces

This study demonstrates differences in sorptive capacity of volatile organic compound (VOC) trichloroethylene (TCE) onto natural organic matter (NOM) coated and uncoated mineral surfaces above and below the NOM glass transition temperature. TCE sorption isotherms for dry NOM-mineral systems below the NOM glass transition temperature (T(g)) demonstrated sorption behavior characteristic of micropore filling, with sorption capacities reduced relative to uncoated mineral matrices. Such differences were not entirely associated with differences in surface areas of the coated and uncoated mineral matrices, but were likely associated with either a blockage of pore space available to the VOC or a kinetic limitation that does not allow the VOC access to the internal porosity of the model soil within the time periods of the experiment. TCE sorption in dry NOM-mineral matrices above the T(g), however, was described in terms of sorption within a more fluid, macromolecular dissolution medium that does not hinder access to mineral surfaces. Such observations have potential important implications for modeling the fate and transport of VOCs in soils and sediment systems.

Combination of isothermal titration calorimetry and time-resolved luminescence for high affinity antibody-ligand interaction thermodynamics and kinetics

For experiments using synthetic ligands as probes for biological experiments, it is useful to determine the specificity and affinity of the ligands for their receptors. As ligands with higher affinities are developed (K(A)>10(8)M(-1); K(D)<10(-8)M), a new challenge arises: to measure these values accurately. Isothermal titration calorimetry measures heat produced or consumed during ligand binding, and also provides the equilibrium binding constant. However, as normally practiced, its range is limited. Displacement titration, where a competing weaker ligand is used to lower the apparent affinity of the stronger ligand, can be used to determine the binding affinity as well as the complete thermodynamic data for ligand-antibody complexes with very high affinity. These equilibrium data have been combined with kinetic measurements to yield the rate constants as well. We describe this methodology, using as an example antibody 2D12.5, which captures yttrium S-2-(4-aminobenzyl)-1, 4, 7, 10-tetraazacyclododecanetetraacetate.

IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure

The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a “focused electron tomography reconstruction” (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single “snapshot” molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.

Analysis of the voltage response to identify macromolecule quantities in an electrolyte

Current techniques of detecting proteins in solution can prove to be time consuming and expensive. Although low cost techniques are available, these are often slow and inaccurate. The authors propose an innovative technique for detecting the presence of proteins and other organic macromolecules in an electrolyte by analyzing the voltage waveform resulting from a biphasic, constant-current, charge-balanced electrical stimulation. Initial experiments have proven the viability of the technique. However due to the limitation of technique accuracy, further refinement of the measurement approach is required.

Influence of hesperidin on renal cell surface glycoprotein content, nucleic acids, lysosomal enzymes and macromolecules against 7, 12-dimethylbenz [a] anthracene induced experimental breast carcinoma

Therapeutic substances may reduce the risk of developing cancer by modulating the factors responsible for carcinogenesis. To evaluate these hypotheses, the present study was designed to investigate the modulatory effect of bioflavonoid "Hesperidin" against DMBA induced experimental breast cancer with reference to renal cell surface glycoproteins, nucleic acids, protein content, lipid profile and lysosomal enzymes. The female sprague-dawley rats were orally administered with single dose of 7, 12-DMBA to induce breast cancer and were treated with hesperidin [30 mg/kg/body weight] for a consecutive 45 days. The results revealed that there was a significant elevation in the levels of glycoproteins, nucleic acids, lysosomal enzymes and also significant alterations in macromolecules in renal tissues of cancer bearing animals. Interestingly, the altered levels of these parameters were remarkably reverted back to near normal in hesperidin treatment. The histopathological analysis of liver and kidney tissues were well supported the biochemical alterations and inevitably proves the protective role of hesperidin. It is proposed that, the effect of hesperidin during DMBA induced breast cancer could be due to the intervention strategies of hesperidin in the protein, nucleic acid biosynthesis, membrane stabilizing potentials on lysosomal compartment and inhibitory effect on cell surface glycoproteins and bio-fuel such as lipids.

Method for determining the absolute number concentration of nanoparticles from electrospray sources

We have developed a simple, fast, and accurate method to measure the absolute number concentration of nanoparticles in solution. The method combines electrospray differential mobility analysis (ES-DMA) with a statistical analysis of droplet-induced oligomer formation. A key feature of the method is that it allows determination of the absolute number concentration of particles by knowing only the droplet size generated from a particular ES source, thereby eliminating the need for sample-specific calibration standards or detailed analysis of transport losses. The approach was validated by comparing the total number concentration of monodispersed Au nanoparticles determined by ES-DMA with UV/vis measurements. We also show that this approach is valid for protein molecules by quantifying the absolute number concentration of Rituxan monoclonal antibody in solution. The methodology is applicable for quantification of any electrospray process coupled to an analytical tool that can distinguish monomers from higher order oligomers. The only requirement is that the droplet size distribution be evaluated. For users only interested in implementation of the theory, we provide a section that summarizes the relevant formulas. This method eliminates the need for sample-specific calibration standards or detailed analysis of transport losses.

Contribution of extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms to U(VI) immobilization

The goal of this study was to quantify the contribution of extracellular polymeric substances (EPS) to U(VI) immobilization by Shewanella sp. HRCR-1. Through comparison of U(VI) immobilization using cells with bound EPS (bEPS) and cells with minimal EPS, we show that (i) bEPS from Shewanella sp. HRCR-1 biofilms contribute significantly to U(VI) immobilization, especially at low initial U(VI) concentrations, through both sorption and reduction; (ii) bEPS can be considered a functional extension of the cells for U(VI) immobilization and they likely play more important roles at lower initial U(VI) concentrations; and (iii) the U(VI) reduction efficiency is dependent upon the initial U(VI) concentration and decreases at lower concentrations. To quantify the relative contributions of sorption and reduction to U(VI) immobilization by EPS fractions, we isolated loosely associated EPS (laEPS) and bEPS from Shewanella sp. HRCR-1 biofilms grown in a hollow fiber membrane biofilm reactor and tested their reactivity with U(VI). We found that, when reduced, the isolated cell-free EPS fractions could reduce U(VI). Polysaccharides in the EPS likely contributed to U(VI) sorption and dominated the reactivity of laEPS, while redox active components (e.g., outer membrane c-type cytochromes), especially in bEPS, possibly facilitated U(VI) reduction.

Assessment of the influence of thermal pre-treatment time on the macromolecular composition and anaerobic biodegradability of sewage sludge

Laboratory and pilot-scale experiments were carried out in order to evaluate the influence of thermal pre-treatment time on waste-activated sludge properties and anaerobic biodegradability. Six experimental conditions were analyzed from 0 to 30 min of hydrolysis time. Solubilization of macromolecular compounds, changes in the main sludge properties and anaerobic biodegradability of the sewage sludge were evaluated. A similar carbohydrate solubilization degree was achieved, from 53% to 70% and 59% to 75% for lab- and pilot-scale experiments, respectively. In the case of proteins, the values of solubilization were lower in the pilot-scale experiment than in the laboratory, with 31-45% and 47-70%, respectively. Ammonia and volatile fatty acid did not undergo important changes; however the sludge dewaterability enhanced at increased pre-treatment times. All the pre-treatment conditions had a positive effect with regard to anaerobic biodegradability and by fitting experimental data with a simplified mathematical model, it was concluded that the maximum biogas production rate is more influenced by the pre-treatment time than the total biogas production.

Microfluidics in macro-biomolecules analysis: macro inside in a nano world

Use of microfluidic devices in the life sciences and medicine has created the possibility of performing investigations at the molecular level. Moreover, microfluidic devices are also part of the technological framework that has enabled a new type of scientific information to be revealed, i.e. that based on intensive screening of complete sets of gene and protein sequences. A deeper bioanalytical perspective may provide quantitative and qualitative tools, enabling study of various diseases and, eventually, may offer support for the development of accurate and reliable methods for clinical assessment. This would open the way to molecule-based diagnostics, i.e. establish accurate diagnosis and disease prognosis based on identification and/or quantification of biomacromolecules, for example proteins or nucleic acids. Finally, the development of disposable and portable devices for molecule-based diagnosis would provide the perfect translation of the science behind life-science research into practical applications dedicated to patients and health practitioners. This review provides an analytical perspective of the impact of microfluidics on the detection and characterization of bio-macromolecules involved in pathological processes. The main features of molecule-based diagnostics and the specific requirements for the diagnostic devices are discussed. Further, the techniques currently used for testing bio-macromolecules for potential diagnostic purposes are identified, emphasizing the newest developments. Subsequently, the challenges of this type of application and the status of commercially available devices are highlighted, and future trends are noted.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute-solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R(free) and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 A) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

Group theory and biomolecular conformation: I. Mathematical and computational models

Biological macromolecules, and the complexes that they form, can be described in a variety of ways ranging from quantum mechanical and atomic chemical models, to coarser grained models of secondary structure and domains, to continuum models. At each of these levels, group theory can be used to describe both geometric symmetries and conformational motion. In this survey, a detailed account is provided of how group theory has been applied across computational structural biology to analyze the conformational shape and motion of macromolecules and complexes.

Progress in rational methods of cryoprotection in macromolecular crystallography

Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2-13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed.

The application of microfluidics in biology

Recent advances in the bio- and nanotechnologies have led to the development of novel microsystems for bio-particle separation and analysis. Microsystems are already revolutionising the way we do science and have led to the development of a number of ultrasensitive bioanalytical devices capable of analysing complex biological samples. These devices have application in a number of diverse areas such as pollution monitoring, clinical diagnostics, drug discovery and biohazard detection. In this chapter we give an overview of the physical principles governing the behaviour of fluids and particles at the micron scale, which are relevant to the operation of microfluidic devices. We briefly discuss some of the fabrication technologies used in the production of microfluidic systems and then present a number of examples of devices and applications relevant to the biological and life sciences.

Recent developments in phasing and structure refinement for macromolecular crystallography

Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models.

Expression dynamics and ultrastructural localization of epitope-tagged Abutilon mosaic virus nuclear shuttle and movement proteins in Nicotiana benthamiana cells

The geminivirus Abutilon mosaic virus (AbMV) encodes two proteins which are essential for viral spread within plants. The nuclear shuttle protein (NSP) transfers viral DNA between the nucleus and cytoplasm, whereas the movement protein (MP) facilitates transport between cells through plasmodesmata and long-distance via phloem. An inducible overexpression system for epitope-tagged NSP and MP in plants yielded unprecedented amounts of both proteins. Western blots revealed extensive posttranslational modification and truncation for MP, but not for NSP. Ultrastructural examination of Nicotiana benthamiana tissues showed characteristic nucleopathic alterations, including fibrillar rings, when epitope-tagged NSP and MP were simultaneously expressed in leaves locally infected with an AbMV DNA A in which the coat protein gene was replaced by a green fluorescent protein encoding gene. Immunogold labelling localized NSP in the nucleoplasm and in the fibrillar rings. MP appeared at the cell periphery, probably the plasma membrane, and plasmodesmata.

[Applications of terahertz spectroscopy and imaging techniques in food safety inspection]

With the development of ultra-fast laser technology and the further understanding of the mechanism behind the interaction of terahertz radiation and materials, THz radiation is actively developed as a new-style technology for a wide range of applications. Currently THz spectroscopy and imaging techniques show great promise in security detection, medical diagnosis, wireless communication, pharmaceutical and many other areas. Because of the growing importance of food safety issues, the detection technology of food safety is also faced with great opportunities and challenges, while THz spectroscopy and imaging techniques provide a new solution to the problem. Compared to other technologies, THz radiation with higher signal-to-noise ratio and wide dynamic range can simultaneously obtain both frequency-domain and time-domain information of the sample which relates to the information of physical structure and chemical composition of materials. Above all THz radiation features unique advantages in food safety inspection. In the present paper, the brief concept of terahertz radiation was introduced, while the properties and technical methods of THz wave were also discussed. The most recent progress in THz technology used in food safety inspection was summarized. The prospect and restricted factors of this novel technology in food industry were also discussed.

Reactive desorption electrospray ionization for rapid screening of guests for supramolecular inclusion complexes

Reactive desorption electrospray ionization (DESI), an ambient technique, has been explored as a tool for the development of a fast screening approach for supramolecular complexes capitalizing on the specificity of mass spectrometric detection. A library of twelve potential guests for inclusion by a beta-cyclodextrin host was initially screened via DESI using a spray solution incorporating the host directed toward an array of deposited guests. The steroid nortestosterone was used to verify the applicability of reactive DESI for complexation experiments with beta-cyclodextrin. Results from the DESI experiment and results from an analogous electrospray ionization (ESI) mass spectral screen were compared with solution-phase data obtained by nuclear magnetic resonance (NMR) spectroscopy. The complexes detected using DESI were identical to those determined using NMR, validating the applicability of the technique to supramolecular applications, but the ESI data exhibited significant disparities, predominantly due to the interference of nonspecific artifacts.

A lithography-free pathway for chemical microstructuring of macromolecules from aqueous solution based on wrinkling

We report on a novel lithography-free method for obtaining chemical submicron patterns of macromolecules on flat substrates. The approach is an advancement of the well-known microcontact printing scheme: While for classical microcontact printing lithographically produced masters are needed, we show that controlled wrinkling can serve as an alternative pathway to producing such masters. These can even show submicron periodicities. We expect upscaling to larger areas to be considerably simpler than that for existing techniques, as wrinkling results in a macroscopic deformation process that is not limited in terms of substrate size. Using this approach, we demonstrate successful printing of aqueous solutions of polyelectrolytes and proteins. We study the effectiveness of the stamping process and its limits in terms of periodicities and heights of the stamps' topographical features. We find that critical wavelengths are well below 355 nm and critical amplitudes are below 40 nm and clarify the failure mechanism in this regime. This will permit further optimization of the approach in the future.

Contact Angle, WAXS, and SAXS Analysis of Poly(β-hydroxybutyrate) and Poly(ethylene glycol) Block Copolymers Obtained via Azotobacter vinelandii UWD

This study investigated and correlated physical properties and cell interactions of copolymers obtained by a poly(ethylene glycol) (PEG)-modulated fermentation of Azotobacter vinelandii UWD. PEGs with molecular weights of 400 and 3400 Da and di(ethylene glycol) (DEG) were used to modulate the bacterial synthesis of poly(beta-hydroxybutyrate) (PHB). The PHB crystallinity was determined by wide-angle X-ray scattering (WAXS). Small-angle X-ray scattering (SAXS) showed that lamellar distances decreased between the PHB and the PHB modulated with PEG or DEG. Furthermore, the contact angle of water on the PHB/PEG polymer surfaces decreased when compared to that of PHB. The significant decrease of the contact angle and corresponding increase in surface tension, as well as significant decrease in cell adhesion, suggest the presence of hydrophilic PEG and DEG within the hydrophobic surface.

Complex formation of uranium(VI) with L-phenylalanine and 3-phenylpropionic acid studied by attenuated total reflection Fourier transform infrared spectroscopy

Uranyl complexes with phenylalanine and the analogous ligand phenylpropionate were investigated in aqueous solution by attenuated total reflection (ATR) Fourier transform infrared (FT-IR) spectroscopy. The assignment of the observed bands to vibrational modes was accomplished using spectra of the pure ligands recorded at different pH values and spectra of the 15N labeled analogous compounds of the amino acid. The results presented in this work provide a detailed description of the binding states of the uranyl complexes in solution. A bidentate binding of the carboxylate group to the actinide ion was observed by the characteristic shifts of the carboxylate modes. From the spectra the presence of the protonated amino group in the actinide complex can be derived. Due to these findings, contributions of the amino group to the binding to the uranyl ion in the amino acid complex can be ruled out.

Short-TE localised 1H MRS of the human brain at 3 T: quantification of the metabolite signals using two approaches to account for macromolecular signal contributions

The goal of this study was to validate metabolite quantification at short TE, with particular focus on how to best account for the macromolecular signal contribution. A robust, short-TE PRESS protocol is presented, which allows reliable quantification, in vivo, of metabolite signals at 3 T in human brain. Water suppression was adapted to the experimental conditions at 3 T. Metabolite signal from the parietal white matter was quantified in the time domain using QUEST (jMRUI). The increased macromolecular signal contribution at short TE was dealt with by two approaches, based on either metabolite nulling or initial signal truncation. A detailed comparison of the two approaches was made. The first used a metabolite-nulled signal, measured either individually or averaged over different subjects. The second used the total signal, metabolites and macromolecules, from a single scan. The two approaches gave similar quantification results in terms of metabolite concentrations, but differed in their precision and the number of metabolites quantified reliably. With an average metabolite-nulled baseline, a set of seven metabolites could be reliably quantified in parietal white matter under these experimental conditions: N-acetylaspartate, myo-inositol, glucose, glutamate, glutathione, creatine and choline. When initial signal truncation was used, glucose was removed from this set. The short TE (10-11 ms) facilitated quantification of glutamate. The reliable quantification of N-acetylaspartyl glutamate at 3 T proved very difficult.

Rate measurements of the hydrolysis of complex organic macromolecules in cold aqueous solutions: implications for prebiotic chemistry on the early Earth and Titan

Organic macromolecules ("complex tholins") were synthesized from a 0.95 N(2)/0.05 CH(4) atmosphere in a high-voltage AC flow discharge reactor. When placed in liquid water, specific water soluble compounds in the macromolecules demonstrated Arrhenius type first order kinetics between 273 and 313 K and produced oxygenated organic species with activation energies in the range of approximately 60+/-10 kJ mol(-1). These reactions displayed half lives between 0.3 and 17 days at 273 K. Oxygen incorporation into such materials--a necessary step toward the formation of biological molecules--is therefore fast compared to processes that occur on geologic timescales, which include the freezing of impact melt pools and possible cryovolcanic sites on Saturn's organic-rich moon Titan.

Installation and testing of a focusing mirror at beamline X28C for high flux x-ray radiolysis of biological macromolecules

The NSLS X28C white-light beamline has been upgraded with a focusing mirror in order to provide increased x-ray density and a wide selection of beam shapes at the sample position. The cylindrical single crystal silicon mirror uses an Indalloy 51 liquid support bath as both a mechanism for heat transfer and a buoyant support to counter the effects of gravity and correct for minor parabolic slope errors. Calorimetric measurements were performed to verify that the calculated more than 200-fold increase in flux density is delivered by the mirror at the smallest beam spot. The properties of the focused beam relevant to radiolytic footprinting, namely, the physical dimensions of the beam, the effective hydroxyl radical dose delivered to the sample, and sample heating upon irradiation, have been studied at several mirror angles.