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Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

The gram-positive soil bacterium, Arthrobacter nicotianae, uses multiple organic acid functional groups to adsorb lanthanides onto its cell surface. At relevant soil pH conditions of 4.0-6.0, many of these functional groups are de-protonated and available for cation sorption and metal immobilization. However, among the plethora of naturally occurring site types, A. nicotianae is shown to possess high-affinity amide and phosphate sites that disproportionately affect lanthanide adsorption to the cell wall. We quantify neodymium (Nd)-selective site types, reporting an amide-Nd stability constant of log 10 K = 6.41 ± 0.23 that is comparable to sorption via phosphate-based moieties. These sites are two to three orders of magnitude more selective for Nd than the adsorption of divalent metals to ubiquitous carboxyl-based moieties. This implies the importance of lanthanide biosorption in the context of metal transport in subsurface systems despite trace concentrations of lanthanides found in the natural environment., (© 2023 The Authors. Environmental Microbiology Reports published by Applied Microbiology International and John Wiley & Sons Ltd.)

A total of 24 chromosome-specific fluorescence in situ hybridization probes for interphase nucleus analysis were developed to determine the chromosomal content of individual human invasive cytotrophoblasts derived from in vitro cultured assays. At least 75% of invasive cytotrophoblasts were hyperdiploid and the total number of chromosomes ranged from 47 to 61. The results also demonstrated that these hyperdiploid invasive cytotrophoblasts showed significant heterogeneity. The most copy number gains were observed for chromosomes 13, 14, 15, 19, 21, and 22 with average copy number greater than 2.3. A parallel study using primary invasive cytotrophoblasts also showed a similar trend of copy number changes. Conclusively, 24-chromosome analysis of human non-proliferating cytotrophoblasts (interphase nuclei) was achieved. Hyperdiploidy and chromosomal heterogeneity without endoduplication in invasive cytotrophoblasts may suggest a selective advantage for invasion and short lifespan during normal placental development., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Weier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Systems biology research spans a range of biological scales and science domains, and often requires a collaborative effort to collect and share data so that integration is possible. However, sharing data effectively is a challenging task that requires effort and alignment between collaborative partners, as well as coordination between organizations, repositories, and journals. As a community of systems biology researchers, we must get better at efficiently sharing data, and ensuring that shared data comes with the recognition and citations it deserves.

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into 'iVirus' on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus's functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy's Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as "live" protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems., (© 2021. The Author(s).)

Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven't been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making 'omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended., Competing Interests: BH holds concurrent appointments as an Associate Professor of Biosystems Engineering at the University Arizona and as an Amazon Scholar. This publication describes work performed at the University Arizona and is not associated with Amazon. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Blumberg, Ponsero, Bomhoff, Wood-Charlson, DeLong and Hurwitz.)

The observation of replica bands by angle-resolved photoemission spectroscopy has ignited interest in the study of electron-phonon coupling at low carrier densities, particularly in monolayer FeSe/SrTiO_{3}, where the appearance of replica bands has motivated theoretical work suggesting that the interfacial coupling of electrons in the FeSe layer to optical phonons in the SrTiO_{3} substrate might contribute to the enhanced superconducting pairing temperature. Alternatively, it has also been recently proposed that such replica bands might instead originate from extrinsic final state losses associated with the photoemission process. Here, we perform a quantitative examination of replica bands in monolayer FeSe/SrTiO_{3}, where we are able to conclusively demonstrate that the replica bands are indeed signatures of intrinsic electron-boson coupling, and not associated with final state effects. A detailed analysis of the energy splittings and relative peak intensities between the higher-order replicas, as well as other self-energy effects, allows us to determine that the interfacial electron-phonon coupling in the system corresponds to a value of λ=0.19±0.02, providing valuable insights into the enhancement of superconductivity in monolayer FeSe/SrTiO_{3}. The methodology employed here can also serve as a new and general approach for making more rigorous and quantitative comparisons to theoretical calculations of electron-phonon interactions and coupling constants.

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community., Findings: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP)., Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform., (© The Author(s) 2019. Published by Oxford University Press.)

Aneuploidy seems to play not only a decisive role in embryonal development but also in tumorigenesis where chromosomal and genomic instability reflect a universal feature of malignant tumors. The cost of whole genome sequencing has fallen significantly, but it is still prohibitive for many institutions and clinical settings. No applied, cost-effective, and efficient technique has been introduced yet aiming at research to assess the ploidy status of all 24 different human chromosomes in interphases simultaneously, especially in single cells. Here, we present the selection of human probe DNA and a technique using multistep fluorescence in situ hybridization (FISH) employing four sets of six labeled FISH probes able to delineate all 24 human chromosomes in interphase cells. This full karyotype analysis approach will provide additional diagnostic potential for single cell analysis. The use of spectral imaging (SIm) has enabled the use of up to eight different fluorochrome labels simultaneously. Thus, scoring can be easily assessed by visual inspection, because SIm permits computer-assigned and distinguishable pseudo-colors to each probe during image processing. This enables full karyotype analysis by FISH of single-cell interphase nuclei.

This analysis integrates regional models of power system reliability, output from atmosphere-ocean general circulation models, and results from the Interruption Cost Estimate (ICE) Calculator to project long-run costs to electric utility customers from power interruptions under different future severe weather and electricity system scenarios. We discuss the challenges when attempting to model long-run costs to utility customers including the use of imperfect metrics to measure severe weather. Despite these challenges, initial findings show that discounted cumulative customer costs, through the middle of the century, could range from $1.5-$3.4 trillion ($2015) without aggressive undergrounding of the power system and increased utility operations and maintenance (O&M) spending and $1.5-$2.5 trillion with aggressive undergrounding and increased spending. By the end of the century, cumulative customer costs could range from $1.9-$5.6 trillion (without aggressive undergrounding and increased spending) and $2.0-$3.6 trillion (with aggressive undergrounding and increased spending). We find that, in some scenarios, aggressive undergrounding of distribution lines and increased O&M spending is not always cost-effective. We conclude by identifying important topics for follow-on research, which have the potential to improve the cost estimates of this model.

The ability to probe symmetry-breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in atomic-scale lines of charge and spin density. Although phonon anomalies and periodic distortions attest the importance of electron-phonon coupling in the formation of stripe phases, a direct time-domain view of vibrational symmetry breaking is lacking. We report experiments that track the transient multi-terahertz response of the model stripe compound La 1.75 Sr 0.25 NiO 4 , yielding novel insight into its electronic and structural dynamics following an ultrafast optical quench. We find that although electronic carriers are immediately delocalized, the crystal symmetry remains initially frozen-as witnessed by time-delayed suppression of zone-folded Ni-O bending modes acting as a fingerprint of lattice symmetry. Longitudinal and transverse vibrations react with different speeds, indicating a strong directionality and an important role of polar interactions. The hidden complexity of electronic and structural coupling during stripe melting and formation, captured here within a single terahertz spectrum, opens new paths to understanding symmetry-breaking dynamics in solids.

The duration of the hypercrosslinking reaction has been used to control the extent of small pores formation in polymer-based monolithic stationary phases. Segments of five columns hypercrosslinked for 30-360 min were coupled via zero-volume unions to prepare columns with segmented porosity gradients. The steepness of the porosity gradient affected column efficiency, mass transfer resistance, and separation of both small-molecule alkylbenzenes and high-molar-mass polystyrene standards. In addition, the segmented column with the steepest porosity gradient was prepared as a single column with a continuous porosity gradient. The steepness of porosity gradient in this type column was tuned. Compared to a completely hypercrosslinked column, the column with the shallower gradient produced comparable size-exclusion separation of polystyrene standards but allowed higher column permeability. The completely hypercrosslinked column and the column with porosity gradient were successfully coupled in online two-dimensional liquid chromatography of polymers., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms., Competing Interests: The authors have declared that no competing interests exist.

There is a substantial interest in the heterostructures of semiconducting transition metal dichalcogenides (TMDCs) among each other or with arbitrary materials, through which the control of the chemical, structural, electronic, spintronic, and optical properties can lead to a change in device paradigms. A critical need is to understand the interface between TMDCs and insulating substrates, for example, high-κ dielectrics, which can strongly impact the electronic properties such as the optical gap. Here, we show that the chemical and electronic properties of the single-layer (SL) TMDC, WS 2 , can be transferred onto high-κ transition metal oxide substrates TiO 2 and SrTiO 3 . The resulting samples are much more suitable for measuring their electronic and chemical structures with angle-resolved photoemission than their native-grown SiO 2 substrates. We probe the WS 2 on the micron scale across 100 μm flakes and find that the occupied electronic structure is exactly as predicted for free-standing SL WS 2 with a strong spin-orbit splitting of 420 meV and a direct band gap at the valence band maximum. Our results suggest that TMDCs can be combined with arbitrary multifunctional oxides, which may introduce alternative means of controlling the optoelectronic properties of such materials.

The discovery of new families of exfoliatable 2D crystals that have diverse sets of electronic, optical, and spin-orbit coupling properties enables the realization of unique physical phenomena in these few-atom-thick building blocks and in proximity to other materials. Herein, using NaSn 2 As 2 as a model system, we demonstrate that layered Zintl phases having the stoichiometry ATt 2 Pn 2 (A = group 1 or 2 element, Tt = group 14 tetrel element, and Pn = group 15 pnictogen element) and feature networks separated by van der Waals gaps can be readily exfoliated with both mechanical and liquid-phase methods. We identified the symmetries of the Raman-active modes of the bulk crystals via polarized Raman spectroscopy. The bulk and mechanically exfoliated NaSn 2 As 2 samples are resistant toward oxidation, with only the top surface oxidizing in ambient conditions over a couple of days, while the liquid-exfoliated samples oxidize much more quickly in ambient conditions. Employing angle-resolved photoemission spectroscopy, density functional theory, and transport on bulk and exfoliated samples, we show that NaSn 2 As 2 is a highly conducting 2D semimetal, with resistivities on the order of 10 -6 Ω·m. Due to peculiarities in the band structure, the dominating p-type carriers at low temperature are nearly compensated by the opening of n-type conduction channels as temperature increases. This work further expands the family of exfoliatable 2D materials to layered van der Waals Zintl phases, opening up opportunities in electronics and spintronics.

We use uranium (U) isotope ratios to detect and quantify the extent of natural U reduction in groundwater across a roll front redox gradient. Our study was conducted at the Smith Ranch-Highland in situ recovery (ISR) U mine in eastern Wyoming, USA, where economic U deposits occur in the Paleocene Fort Union formation. To evaluate the fate of aqueous U in and adjacent to the ore body, we investigated the chemical composition and isotope ratios of groundwater samples from the roll-front type ore body and surrounding monitoring wells of a previously mined area. The (238)U/(235)U of groundwater varies by approximately 3‰ and is correlated with U concentrations. Fluid samples down-gradient of the ore zone are the most depleted in (238)U and have the lowest U concentrations. Activity ratios of (234)U/(238)U are ∼5.5 up-gradient of the ore zone, ∼1.0 in the ore zone, and between 2.3 and 3.7 in the down-gradient monitoring wells. High-precision measurements of (234)U/(238)U and (238)U/(235)U allow for development of a conceptual model that evaluates both the migration of U from the ore body and the extent of natural attenuation due to reduction. We find that the premining migration of U down-gradient of the delineated ore body is minimal along eight transects due to reduction in or adjacent to the ore body, whereas two other transects show little or no sign of reduction in the down-gradient region. These results suggest that characterization of U isotopic ratios at the mine planning stage, in conjunction with routine geochemical analyses, can be used to identify where more or less postmining remediation will be necessary.

Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth., (© 2015 The Authors.)

Human reproduction is a tightly controlled process of stepwise evolution with multiple, mostly yet unknown milestones and checkpoints. Healthy halpoid gametes have to be produced by the parents, which will fuse to form the diploid zygote that implants in the female uterus and grows to become first an embryo, then a fetus and finally matures into a newborn. There are several known risk factors that interfere with normal production of gametes, spermatocytes or oocytes, and often cause embryonic mortality and fetal demise at an early stage. Yet some embryos with chomosomal abnormalities can develop beyond the critical first trimester of pregnancy and, while those with supernumary chromosomes in their hyperdiploid cells will be spontaneously aborted, a small fraction of fetuses with an extra chromosome continues to grow to term and will be delivered as a liveborn baby. While minor clinical symptoms displayed by children with trisomies are manageable for many parents, the burden of caring for a child with numerical chromosome abnormalities can be overwhelming to partners or individual families. It also poses a significant financial burden to the society and poses ethical dilemma. In this communication, we will review the progress that has been made in the development of molecular techniques to test individual fetal cells for chromosomal imbalances. We will focus our discussion on the direct visualization of chromosome-specific DNA sequences in live or fixed specimens using fluorescence in situ hybridization (FISH) and, more specifically, talk about the groundbreaking progress that in recent years has been achieved towards an improved diagnosis with novel, chromosome-specific DNA probes.

A new approach has been developed for the preparation of mixed-mode stationary phases to separate proteins. The pore surface of monolithic poly(glycidyl methacrylate-co-ethylene dimethacrylate) capillary columns was functionalized with thiols and coated with gold nanoparticles. The final mixed mode surface chemistry was formed by attaching, in a single step, alkanethiols, mercaptoalkanoic acids, and their mixtures on the free surface of attached gold nanoparticles. Use of these mixtures allowed fine tuning of the hydrophobic/hydrophilic balance. The amount of attached gold nanoparticles according to thermal gravimetric analysis was 44.8 wt.%. This value together with results of frontal elution enabled calculation of surface coverage with the alkanethiol and mercaptoalkanoic acid ligands. Interestingly, alkanethiols coverage in a range of 4.46-4.51 molecules/nm(2) significantly exceeded that of mercaptoalkanoic acids with 2.39-2.45 molecules/nm(2). The mixed mode character of these monolithic stationary phases was for the first time demonstrated in the separations of proteins that could be achieved in the same column using gradient elution conditions typical of reverse phase (using gradient of acetonitrile in water) and ion exchange chromatographic modes (applying gradient of salt in water), respectively.

This paper demonstrates the significant utility of deploying non-traditional biological techniques to harness available volatiles and waste resources on manned missions to explore the Moon and Mars. Compared with anticipated non-biological approaches, it is determined that for 916 day Martian missions: 205 days of high-quality methane and oxygen Mars bioproduction with Methanobacterium thermoautotrophicum can reduce the mass of a Martian fuel-manufacture plant by 56%; 496 days of biomass generation with Arthrospira platensis and Arthrospira maxima on Mars can decrease the shipped wet-food mixed-menu mass for a Mars stay and a one-way voyage by 38%; 202 days of Mars polyhydroxybutyrate synthesis with Cupriavidus necator can lower the shipped mass to three-dimensional print a 120 m(3) six-person habitat by 85% and a few days of acetaminophen production with engineered Synechocystis sp. PCC 6803 can completely replenish expired or irradiated stocks of the pharmaceutical, thereby providing independence from unmanned resupply spacecraft that take up to 210 days to arrive. Analogous outcomes are included for lunar missions. Because of the benign assumptions involved, the results provide a glimpse of the intriguing potential of 'space synthetic biology', and help focus related efforts for immediate, near-term impact.

The macroporous structure of poly(styrene-co-divinylbenzene) monolithic capillary columns has been optimized for the gradient separation of peptides. To exploit monolithic supports with porosity exceeding 70%, the thermodynamic properties of the polymerization mixture were carefully tailored to yield homogeneous monolithic materials featuring macropore and polymer microglobule sizes in the range of 50–200 nm. The effects of (i) initiator content, (ii) composition of porogenic mixture, comprising tetrahydrofuran and 1-decanol, (iii) percentage of divinylbenzene crosslinker, and (iv) monomers to porogen ratio on the morphology was investigated. The resulting column structures were investigated using scanning electron microscopy and the prepared monolithic columns were tested for the separation of a tryptic digest of cytochrome c while applying a fixed flow rate and gradient time. To obtain a better understanding of the effects of macropore and microglobule size, and structure homogeneity on the separation performance in gradient elution, both in terms of peak capacity and gradient plate height, separations were also carried out at different flow rates while maintaining a constant gradient steepness. Furthermore, performance limits were determined applying ultra-high pressure conditions up to the maximum system pressure of 80 MPa. The potential of monolithic nanostructured columns is demonstrated for the separation of tryptic digests of cytochrome c and bovine serum albumin.

Simple devices for the adsorption and preconcentration of metal ions comprising various monolithic polymers have been prepared by in situ polymerization within the 5.5cm long and 5.6mm i.d. polypropylene syringes. Poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith was modified with ethylenediamine to obtain the chelating material. The poly(butyl methacrylate-co-ethylene dimethacrylate) and poly(lauryl methacrylate-co-ethylene dimethacrylate) monoliths were first photografted with glycidyl methacrylate prior to functionalization with ethylenediamine. Alternatively, other chelating functionalities including poly(ethylene imines) varying in molecular weight and shape (linear and branched) as well as lysozyme were also attached to the monolithic supports. We found that the poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith functionalized with ethylenediamine exhibited the best chelating properties characterized with rapid adsorption and a capacity of 111.2mg/g (537μmol/g) for Pb(2+), 38.1mg/g (649μmol/g) for Ni(2+), 69.9mg/g (1100μmol/g) for Cu(2+), and 188.9mg/g (3633μmol/g) for Cr(3+). The very fast desorption was then achieved using 1.0mol/L HNO3 as the eluent. An enrichment factor of 300 was observed for metal ions adsorbed from solutions containing 2ppb of the metal., (Copyright © 2014 Elsevier B.V. All rights reserved.)

A new approach to the preparation of porous polymer monoliths possessing both large surface area and functional groups has been developed. The chloromethyl groups of poly(styrene-co-4-acetoxystyrene-co-vinylbenzyl chloride-co-divinylbenzene) monolith enable post-polymerization hypercrosslinking catalyzed by ferric chloride in dichloroethane leading to a multitude of small pores thus enhancing the surface area. The acetoxy functionalities are easily deprotected using hydrazine to produce polar phenolic hydroxyl groups, which would be difficult to obtain by direct copolymerization of hydroxyl-containing monomers. The hypercrosslinking and deprotection reactions as well as their sequence were studied in detail with bulk polymer monoliths containing up to 50% 4-acetoxystyrene and its progress monitored by infrared spectrometry and nitrogen adsorption/desorption measurements. No significant difference was found for both possible successions. All monoliths were also prepared in a capillary column format, then deprotected and hypercrosslinked. Capillary columns were tested for the separation of small molecules using reversed phase and normal phase chromatographic modes. For polymer monoliths containing 50% deprotected 4-acetoxystyrene, column efficiencies of 40,000 plates/m for benzene in reversed phase mode and 31,800 plates/m for nitrobenzene in normal phase mode, were obtained. The percentage of hydroxyl groups in the monoliths enables modulation of polarity of the stationary phase. They also represent functionalities that are potentially suitable for further modifications and formation of new types of stationary phases for liquid chromatography., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Regular special issues concerning monoliths have always been a stronghold of the Journal of Separation Science. Typically, we issued a call for papers, collected and processed the submitted manuscripts, and all of them were then printed in a single issue of the journal. This approach worked to a certain limit quite acceptably but there was always a longer waiting time between the early submissions and publication. This is why we decided to do it this year differently. I claimed in my 2013 New Years Editorial: "We are living in the electronic era! Why not to make an advantage of that?" And we do. As a result, all manuscript submitted for publication in the special issue Monoliths have already been published in regular issues as soon as they were accepted. The first page of these papers includes a footnote: "This paper is included in the virtual special issue Monoliths available at the Journal of Separation Science website." All papers published with this footnote were collected in a virtual special issue accessible through the internet. This concept ruled out possible delays in publication of contributions submitted early. Since we did not have any real "special issue", there was no need for any hard deadline for submission. We just collected manuscripts submitted for the special issue Monoliths published from January to July 2013 and included them in the virtual special issue. This new approach worked very well and we published 22 excellent papers that are included in the issue available now at this website: http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1615-9314/homepage/virtual_special_issue__monoliths.htm., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Many human tumors show significant changes in their signal transduction pathways and, thus, the way the cells interact with their environment. Often caused by chromosomal rearrangements, including gene amplifications, translocations or deletions, the altered levels of gene expression may provide a tumor-specific signature that can be exploited for diagnostic or therapeutic purposes. We investigated the utility of multiplexed fluorescence in situ hybridization (FISH) using non-isotopically labeled cDNA probes detected by Spectral Imaging as a sensitive and rapid procedure to measure tumor-specific gene expression signatures. We used a commercially available system to acquire and analyze multicolor FISH images. Initial investigations used panels of fluorescent calibration standards to evaluate the system. These experiments were followed by hybridization of five-to-six differently labeled cDNA probes, which target the transcripts of tyrosine kinase genes known to be differently expressed in normal cells and tumors of the breast or thyroid gland. The relatively simple, yet efficient, molecular cytogenetic method presented here may find many applications in characterization of solid tumors or disseminated tumor cells. Addressing tumor heterogeneity by means of multi-parameter single cell analyses is expected to enable a wide range of investigations in the areas of tumor stem cells, tumor clonality and disease progression.

The separations of small molecules using columns containing porous polymer monoliths invented two decades ago went a long way from the very modest beginnings to the current capillary columns with efficiencies approaching those featured by their silica-based counterparts. This review article presents a variety of techniques that have been used to form capillary formats of monolithic columns with enhanced separation performance in isocratic elutions. The following text first describes the traditional approaches used for the preparation of efficient monoliths comprising variations in polymerization conditions including temperature as well as composition of monomers and porogenic solvents. Encouraging results of these experiments fueled research of completely new preparation methods such as polymerization to an incomplete conversion, use of single crosslinker, hypercrosslinking, and incorporation of carbon nanotubes that are described in the second part of the text., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Field ionization as a means to create ions for compact and rugged neutron sources is pursued. Arrays of carbon nano-fibers promise the high field-enhancement factors required for efficient field ionization. We report on the fabrication of arrays of field emitters with a density up to 10(6) tips∕cm(2) and measure their performance characteristics using electron field emission. The critical issue of uniformity is discussed, as are efforts towards coating the nano-fibers to enhance their lifetime and surface properties.

Recurrent translocations are well known hallmarks of many human solid tumors and hematological disorders, where patient- and breakpoint-specific information may facilitate prognostication and individualized therapy. In thyroid carcinomas, the proto-oncogenes RET and NTRK1 are often found to be activated through chromosomal rearrangements. However, many sporadic tumors and papillary thyroid carcinomas (PTCs) arising in patients with a history of exposure to elevated levels of ionizing irradiation do not carry these known abnormalities. We developed a rapid scheme to screen tumor cell metaphase spreads and identify candidate genes of tumorigenesis and neoplastic progression for subsequent functional studies. Using a series of overnight fluorescence in situ hybridization (FISH) experiments with pools comprised of bacterial artificial chromosome (BAC) clones, it now becomes possible to rapidly refine breakpoint maps and, within one week, progress from the low resolution Spectral Karyotyping (SKY) maps or Giemsa-banding (G-banding) karyotypes to fully integrated, high resolution physical maps including a list of candiate genes in the critical regions.

Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'- end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners.We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabasepair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of breakpoints in papillary thyroid cancer (PTC).

Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

Structural chromosome aberrations are known hallmarks of many solid tumors. In the papillary form of thyroid cancer (PTC), for example, activation of the receptor tyrosine kinase (RTK) genes, ret or the neurotrophic tyrosine kinase receptor type I (NTRK1) by intra- or interchromosomal rearrangements have been suggested as a cause of the disease. The 1986 accident at the nuclear power plant in Chernobyl, Ukraine, led to the uncontrolled release of high levels of radioisotopes. Ten years later, the incidence of childhood papillary thyroid cancer (chPTC) near Chernobyl had risen by two orders of magnitude. Tumors removed from some of these patients showed aberrant expression of the ret RTK gene due to a ret/PTC1 or ret/PTC3 rearrangement involving chromosome 10. However, many cultured chPTC cells show a normal G-banded karyotype and no ret rearrangement. We hypothesize that the "ret-negative" tumors inappropriately express a different oncogene or have lost function of a tumor suppressor as a result of chromosomal rearrangements, and decided to apply molecular and cytogenetic methods to search for potentially oncogenic chromosomal rearrangements in Chernobyl chPTC cases. Knowledge of the kind of genetic alterations may facilitate the early detection and staging of chPTC as well as provide guidance for therapeutic intervention.

Structural chromosome aberrations are known hallmarks of many solid tumors. In the papillary form of thyroid cancer (PTC), for example, activation of the receptor tyrosine kinase (RTK) genes, RET and neurotrophic tyrosine kinase receptor type I (NTRK1) by intra- and interchromosomal rearrangements has been suggested as a cause of the disease. However, many phenotypically similar tumors do not carry an activated RET or NTRK-1 gene or express abnormal ret or NTRK-1 transcripts. Thus, we hypothesize that other cellular RTK-type genes are aberrantly expressed in these tumors. Using fluorescence in situ hybridization-based methods, we are studying karyotype changes in a relatively rare subgroup of PTCs, i.e., tumors that arose in children following the 1986 nuclear accident in Chernobyl, Ukraine. Here, we report our technical developments and progress in deciphering complex chromosome aberrations in case S48TK, an aggressively growing PTC cell line, which shows an unusual high number of unbalanced translocations.

This overview is presented to celebrate the birthday of one of the luminaries of the separation science and my friend - Stellan Hjertén. He made significant contributions to a variety of areas in separation science such as electrophoresis, LC, and CEC to name just a few. Since the scope of his work was enormous, this review will focus only on a single aspect of his scientific activities, the design and applications of monolithic materials. During the years starting from 1989, Stellan Hjertén published many excellent papers concerning the preparation of acrylamide chemistry-based monoliths and their use in both micro-HPLC and CEC. The following text details his works in the field.

Supported Pd clusters catalyze methanol oxidation to methyl formate with high turnover rates and >90% selectivity at near ambient temperatures (313 K). Metal clusters are much more reactive than PdO clusters and rates are inhibited by the reactant O(2). These data suggest that ensembles of Pd metal atoms on surfaces nearly saturated with chemisorbed oxygen are required for kinetically-relevant C-H bond activation in chemisorbed methoxide intermediates. Pd metal surfaces become more reactive with increasing metal particle size. The higher coordination of surface atoms on larger clusters leads to more weakly-bound chemisorbed species and to a larger number of Pd metal ensembles available during steady-state catalysis. Chemisorbed oxygen removes H-atoms formed in C-H bond activation steps and inhibits methoxide decomposition and CO(2) formation, two functions essential for the high turnover rates and methyl formate selectivities reported here.

Monolithic materials are finding their place in a variety of fields. While liquid chromatography is the most emphasized use of this new category of porous media, some other just as important applications are eclipsed by the success of monolithic columns. This review article describes all current facets of use of monoliths in preconcentration and solid-phase extraction. In addition to the typical off line use that does not seem to be the main stream application for the monolithic materials, in-line connection of the preconcentration with HPLC, electrochromatography, electrophoresis, enzymatic digestion, as well as its applications in microfluidics are presented.

Unlabelled: Currently, 2 types of phantoms (physical and computer generated) are used for testing and comparing tomographic reconstruction methods. Data from physical phantoms include all physical effects associated with the detection of radiation. However, with physical phantoms it is difficult to control the number of detected counts, simulate the dynamics of uptake and washout, or create multiple noise realizations of an acquisition. Computer-generated phantoms can overcome some of the disadvantages of physical phantoms, but simulation of all factors affecting the detection of radiation is extremely complex and in some cases impossible. To overcome the problems with both types of phantoms, we developed a physical and computer-generated hybrid phantom that allows the creation of multiple noise realizations of tomographic datasets of the dynamic uptake governed by kinetic models., Methods: The method is phantom and camera specific. We applied it to an anthropomorphic torso phantom with a cardiac insert, using a SPECT system with attenuation correction. First, real data were acquired. For each compartment (heart, blood pool, liver, and background) of the physical phantom, large numbers of short tomographic projections were acquired separately for each angle. Sinograms were built from a database of projections by summing the projections of each compartment of the phantom. The amount of activity in each phantom compartment was regulated by the number of added projections. Sinograms corresponding to various projection times, configurations and numbers of detector heads, numbers of noise realizations, numbers of phantom compartments, and compartment-specific time-activity curves in MBq/cm3 were assembled from the database., Results: The acquisition produced a database of 120 projection angles ranging over 360 degrees . For each angle, 300 projections of 0.5 s each were stored in 128 x 128 matrices for easy access. The acquired database was successful in the generation of static and dynamic sinograms for which the myocardial uptake and washout was governed by a compartment kinetic model., Conclusion: A method has been developed that allows creation of sinograms of physical phantoms with the capacity to control the number of noise realizations, the level of noise, the dynamics of uptake in the phantom compartments, and the acquisition parameters and acquisition modes.

We report the first observation of stimulated emission of terahertz radiation from internal transitions of excitons. The far-infrared electromagnetic response of Cu2O is monitored via broadband terahertz pulses after ultrafast resonant excitation of three-dimensional 3p excitons. Stimulated emission from the 3p to the energetically lower 2s bound level occurs at a photon energy of 6.6 meV, with a cross section of approximately 10(-14) cm2. Simultaneous excitation of both exciton levels, in turn, drives quantum beats, which lead to efficient terahertz emission sharply peaked at the difference frequency.

The incidence of papillary thyroid carcinoma (PTC) increases significantly after exposure of the head and neck region to ionizing radiation, yet we know neither the steps involved in malignant transformation of thyroid epithelium nor the specific carcinogenic mode of action of radiation. Such increased tumor frequency became most evident in children after the 1986 nuclear accident in Chernobyl, Ukraine. In the eight years following the accident, the average incidence of childhood PTCs (chPTC) increased 70-fold in Belarus, 200-fold in Gomel, 10-fold in the Ukraine and 50-fold in Tschnigov, Kiev, Rovno, Shitomyr and Tscherkassy compared to the rate of about 1 tumor incidence per 106 children per year prior to 1986 (Likhtarev et al., 1995; Sobolev et al., 1997; Jacob et al., 1998). To study the etiology of radiation-induced thyroid cancer, we formed an international consortium to investigate chromosomal changes and altered gene expression in cases of post-Chernobyl chPTC. Our approach is based on karyotyping of primary cultures established from chPTC specimens, establishment of cell lines and studies of genotype-phenotype relationships through high resolution chromosome analysis, DNA/cDNA micro-array studies, and mouse xenografts that test for tumorigenicity. Here, we report the application of fluorescence in situ hybridization (FISH)-based techniques for the molecular cytogenetic characterization of a highly tumorigenic chPTC cell line, S48TK, and its subclones. Using chromosome 9 rearrangements as an example, we describe a new approach termed 'BAC-FISH' to rapidly delineate chromosomal breakpoints, an important step towards a better understanding of the formation of translocations and their functional consequences., (Copyright 2006 S. Karger AG, Basel.)

Full-field soft X-ray microscopy in combination with X-ray magnetic circular dichroism as contrast mechanism is a powerful technique to image with elemental specificity magnetic nanostructures and multilayered thin films at high lateral resolution down to 15nm by using Fresnel zone plates as X-ray optical elements. Magnetization reversal phenomena on a microscopic level are studied by recording the images in varying external magnetic fields. Local spin dynamics at a time resolution below 100ps can be addressed by engaging a stroboscopic pump-and-probe scheme taking into account the time pattern of synchrotron storage rings. Characteristic features of magnetic soft X-ray microscopy are reviewed and an outlook into future perspectives with regard to increased lateral and temporal resolution is given.