X-ray nanodiffraction analysis of stress oscillations in a W thin film on through-silicon via

X-ray nanodiffraction is used to evaluate axial and tangential residual stress distributions in a W thin film deposited on the scalloped inner wall of a through-silicon via. The results reveal oscillatory stress distributions which correlate well with the scallop wavelength and morphology.

Synchrotron X-ray nanodiffraction is used to analyse residual stress distributions in a 200 nm-thick W film deposited on the scalloped inner wall of a through-silicon via. The diffraction data are evaluated using a novel dedicated methodology which allows the quantification of axial and tangential stress components under the condition that radial stresses are negligible. The results reveal oscillatory axial stresses in the range of ∼445–885 MPa, with a distribution that correlates well with the scallop wavelength and morphology, as well as nearly constant tangential stresses of ∼800 MPa. The discrepancy with larger stress values obtained from a finite-element model, as well as from a blanket W film, is attributed to the morphology and microstructural nature of the W film in the via.

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.

Calcium dynamics in microbialite-forming exopolymer-rich mats on the atoll of Kiritimati, Republic of Kiribati, Central Pacific

Microbialite-forming microbial mats in a hypersaline lake on the atoll of Kiritimati were investigated with respect to microgradients, bulk water chemistry, and microbial community composition. O2, H2S, and pH microgradients show patterns as commonly observed for phototrophic mats with cyanobacteria-dominated primary production in upper layers, an intermediate purple layer with sulfide oxidation, and anaerobic bottom layers with sulfate reduction. Ca(2+) profiles, however, measured in daylight showed an increase of Ca(2+) with depth in the oxic zone, followed by a sharp decline and low concentrations in anaerobic mat layers. In contrast, dark measurements show a constant Ca(2+) concentration throughout the entire measured depth. This is explained by an oxygen-dependent heterotrophic decomposition of Ca(2+)-binding exopolymers. Strikingly, the daylight maximum in Ca(2+) and subsequent drop coincides with a major zone of aragonite and gypsum precipitation at the transition from the cyanobacterial layer to the purple sulfur bacterial layer. Therefore, we suggest that Ca(2+) binding exopolymers function as Ca(2+) shuttle by their passive downward transport through compression, triggering aragonite precipitation in the mats upon their aerobic microbial decomposition and secondary Ca(2+) release. This precipitation is mediated by phototrophic sulfide oxidizers whose action additionally leads to the precipitation of part of the available Ca(2+) as gypsum.

Complementary ab initio and X-ray nanodiffraction studies of Ta2O5

The complex structure of Ta₂O₅ led to the development of various structural models. Among them, superstructures represent the most stable configurations. However, their formation requires kinetic activity and long-range ordering processes, which are hardly present during physical vapor deposition. Based on nano-beam X-ray diffraction and concomitant ab initio studies, a new metastable orthorhombic basic structure is introduced for Ta₂O₅ with lattice parameters a = 6.425 Å, b = 3.769 Å and c = 7.706 Å. The unit cell containing only 14 atoms, i.e. two formula unit blocks in the c direction, is characterized by periodically alternating the occupied oxygen site between two possible positions in succeeding 002-planes. This structure can be described by the space group 53 (Pncm) with four Wyckoff positions, and exhibits an energy of formation of -3.209 eV atom^-1. Among all the reported basic structures, its energy of formation is closest to those of superstructures. Furthermore, this model exhibits a 2.5 eV band gap, which is closer to experimental data than the band gap of any other basic-structure model. The sputtered Ta₂O₅ films develop only a superstructure if annealed at temperatures >800 °C in air or vacuum. Based on these results and the conveniently small unit cell size, it is proposed that the basic-structure model described here is an ideal candidate for both structure and electronic state descriptions of orthorhombic Ta₂O₅ materials.

MALDI-TOF MS and ESI-LTQ-Orbitrap tandem mass spectrometry reveal specific porphyranase activity from a Pseudoalteromonas atlantica bacterial extract

Mass spectrometry analysis highlighted an unprecedented β-methyl-porphyranase activity in protein extract fromPseudoalteromonas atlantica, which can accommodate the methylated building blocks of porphyran.

Abstract A57: Differential tumor cell expression of VEGF isoforms impacts on the tumor microenvironment, metastasis and radiation response in a mouse fibrosarcoma model

We aimed to determine the influence of differential tumor cell expression of vascular endothelial growth factor A (VEGF) isoforms on lung metastasis and response to radiotherapy. We hypothesized that vascular and other adaptations of the tumor microenvironment, in response to tumor cell expression of individual VEGF isoforms, would impact on tumor progression and treatment response.

Mouse fibrosarcoma cells that exclusively express either VEGF120, 164 or 188 (fs120, fs164 and fs188 cells respectively) and cells expressing all three isoforms (fsWT) were grown as sub-cutaneous implants in SCID mice. Tumor sections were stained for vascularity (CD31), oxygenation status (pimonidazole protein adducts), activated fibroblasts/pericytes (FAPalpha/alpha-sma), necrosis (H&E), apoptosis (TUNEL) and extra-cellular matrix proteins (collagen-1, laminin, fibronectin). Interstitial fluid pressure (IFP) was measured by the ‘wick-in-needle’ technique. Parallel single VEGF isoform-expressing cell lines were generated to stably express luciferase2 and mStrawberry (LS) for analysis of lung metastasis from sub-cutaneous implants. Luminescence was measured in lung tissue lysates, using an IVIS Lumina II optical imaging system. Sub-cutaneous tumors were irradiated with a single or fractionated 20 Gy dose of X-rays and tumor volume response measured.

All tumors were well-vascularized but IFP was lower in untreated fs188 tumors than in fs120 tumors, consistent with a lower vascular permeability, as previously reported. Fs188 tumors were also significantly less hypoxic (P < 0.05) than fs120 tumors (approximately 20 versus 30% pimonidazole staining). Perivascular alpha-SMA was most prevalent in fs188 and fsWT tumors. FAPalpha was lowest in fs120 tumours. Lungs from fs120-LS and fs164-LS but not fs188-LS and fsWT-LS tumor-bearing mice were significantly more luminescent than control lungs (910 ± 283 and 1107 ± 401 versus 8 ± 3 luminescence units respectively). Laminin staining was significantly greater in the more metastatic tumor types (fs120 and fs164) but no other matrix protein showed any correlation. Fs188 tumors were significantly more sensitive to both single and fractionated radiotherapy (growth and necrosis end-points) than fs120 tumors, despite similar radio-sensitivities of the cells irradiated in vitro. However, TUNEL staining in CD31+ cells was greater in fs120 tumors than in fs188 tumors, suggesting that fs120-associated vasculature was more radio-sensitive than fs188-associated vasculature.

Results showed that tumor cell expression of individual VEGF isoforms had a profound effect on the tumor microenvironment. The more metastatic fs120 tumors had relatively high IFP and hypoxia, factors known to influence tumor progression. Less pericyte investiture in fs120 and fs164 tumors could also facilitate tumor cell escape into the circulation for these more metastatic types, which may also relate to high levels of laminin in the extra-cellular matrix. The radio-sensitivity of fs188 tumors is most likely explained by relatively low hypoxia, as oxygen is a classic radio-sensitizer. The fact that blood vessels in the fs120 tumors were actually more sensitive that those in fs188 tumors suggests that the response of blood vessels has only a minor influence on the overall tumor response to radio-therapy. These results suggest the potential for differential VEGF isoform expression (or down-stream consequences of expression) as prognostic and predictive tumor bio-markers.

This work was supported by a Programme Grant from Cancer Research UK.

Citation Format: William R. English, Sarah Jane Lunt, Matthew Fisher, Jack E. Hurrell, Diane V. Lefley, Debayan Mukherjee, Rachel Daniel, Scott K. Lyons, Chryso Kanthou, Gillian M. Tozer. Differential tumor cell expression of VEGF isoforms impacts on the tumor microenvironment, metastasis and radiation response in a mouse fibrosarcoma model. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr A57. doi:10.1158/1538-7445.CHTME14-A57

The consequence of an additional NADH dehydrogenase paralog on the growth of Gluconobacter oxydans DSM3504

Acetic acid bacteria such as Gluconobacter oxydans are used in several biotechnological processes due to their ability to perform rapid incomplete regio- and stereo-selective oxidations of a great variety of carbohydrates, alcohols, and related compounds by their membrane-bound dehydrogenases. In order to understand the growth physiology of industrial strains such as G. oxydans ATCC 621H that has high substrate oxidation rates but poor growth yields, we compared its genome sequence to the genome sequence of strain DSM 3504 that reaches an almost three times higher optical density. Although the genome sequences are very similar, DSM 3504 has additional copies of genes that are absent from ATCC 621H. Most importantly, strain DSM 3504 contains an additional type II NADH dehydrogenase (ndh) gene and an additional triosephosphate isomerase (tpi) gene. We deleted these additional paralogs from DSM 3504, overexpressed NADH dehydrogenase in ATCC 621H, and monitored biomass and the concentration of the representative cell components as well as O2 and CO2 transfer rates in growth experiments on mannitol. The data revealed a clear competition of membrane-bound dehydrogenases and NADH dehydrogenase for channeling electrons in the electron transport chain of Gluconobacter and an important role of the additional NADH dehydrogenase for increased growth yields. The less active the NADH dehydrogenase is, the more active is the membrane-bound polyol dehydrogenase. These results were confirmed by introducing additional ndh genes via plasmid pAJ78 in strain ATCC 621H, which leads to a marked increase of the growth rate.

A SNaPshot of next generation sequencing for forensic SNP analysis

Forensic phenotyping can provide useful intelligence regarding the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of an evidentiary sample. Currently, single nucleotide polymorphism (SNP) based inference of BGA and EVCs is performed most commonly using SNaPshot(®), a single base extension (SBE) assay. However, a single SNaPshot multiplex PCR is limited to 30-40 SNPs. Next generation sequencing (NGS) offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. The PCR multiplexes from five SNaPshot assays (SNPforID 52plex, SNPforID 34plex, Eurasiaplex, IrisPlex and an unpublished BGA assay) were applied to three different DNA template amounts (0.1, 0.2 and 0.3 ng) in three samples (9947A and 007 control DNAs and a male donor). The pooled PCR amplicons containing 136 unique SNPs were sequenced using Life Technologies' Ion Torrent™ PGM system. Approximately 72 Mb of sequence was generated from two 10 Mb Ion 314™ v1 chips. Accurate genotypes were readily obtained from all three template amounts. Of a total of 408 genotypes, 395 (97%) were fully concordant with SNaPshot across all three template amounts. Of those genotypes discordant with SNaPshot, six Ion Torrent sequences (1.5%) were fully concordant with Sanger sequencing across the three template amounts. Seven SNPs (1.7%) were either discordant between template amounts or discordant with Sanger sequencing. Sequence coverage observed in the negative control, and, allele coverage variation for heterozygous genotypes highlights the need to establish a threshold for background levels of sequence output and heterozygous balance. This preliminary study of the Ion Torrent PGM system has demonstrated considerable potential for use in forensic DNA analyses as a low to medium throughput NGS platform using established SNaPshot assays.

On-chip detection of cellular activity

The use of on-chip cellular activity monitoring for biological/chemical sensing is promising for environmental, medical and pharmaceutical applications. The miniaturization revolution in microelectronics is harnessed to provide on-chip detection of cellular activity, opening new horizons for miniature, fast, low cost and portable screening and monitoring devices. In this chapter we survey different on-chip cellular activity detection technologies based on electrochemical, bio-impedance and optical detection. Both prokaryotic and eukaryotic cell-on-chip technologies are mentioned and reviewed.