Remote Photoacoustic Sensing Using Single Speckle Analysis by an Ultra-Fast Four Quadrant Photo-Detector.

The need for tissue contact makes photoacoustic imaging not applicable for special medical applications like wound imaging, endoscopy, or laser surgery. An easy, stable, and contact-free sensing technique might thus help to broaden the applications of the medical imaging modality. In this work, it is demonstrated for the first time that remote photoacoustic sensing by speckle analysis can be performed in the MHz sampling range by tracking a single speckle using a four quadrant photo-detector. A single speckle, which is created by self-interference of surface back-reflection, is temporally analyzed using this photo-detector. Phantoms and skin samples are measured in transmission and reflection mode. The potential for miniaturization for endoscopic application is demonstrated by fiber bundle measurements. In addition, sensing parameters are discussed. Photoacoustic sensing in the MHz sampling range by single speckle analysis with the four quadrant detector is successfully demonstrated. Furthermore, the endoscopic applicability is proven, and the sensing parameters are convenient for photoacoustic sensing. It can be concluded that a single speckle contains all the relevant information for remote photoacoustic signal detection. Single speckle sensing is therefore an easy, robust, contact-free photoacoustic detection technique and holds the potential for economical, ultra-fast photoacoustic sensing. The new detection technique might thus help to broaden the field of photoacoustic imaging applications in the future.

Strontium substitution of gelatin modified calcium hydrogen phosphates as porous hard tissue substitutes.

Aiming at the generation of a high strontium-containing degradable bone substitute, the exchange of calcium with strontium in gelatin-modified brushite was investigated. The ion substitution showed two mineral groups, the high-calcium containing minerals with a maximum measured molar Ca/Sr ratio of 80%/20% (mass ratio 63%/37%) and the high-strontium containing ones with a maximum measured molar Ca/Sr ratio of 21%/79% (mass ratio 10%/90%). In contrast to the high-strontium mineral phases, a high mass loss was observed for the calcium-based minerals during incubation in cell culture medium (alpha-MEM), but also an increase in strength owing to dissolution and re-precipitation. This resulted for the former in a decrease of cation concentration (Ca + Sr) in the medium, while the pH value decreased and the phosphate ion concentration rose significantly. The latter group of materials, the high-strontium containing ones, showed only a moderate change in mass and a decrease in strength, but the Ca + Sr concentration remained permanently above the initial calcium concentration in the medium. This might be advantageous for a future planned application by supporting bone regeneration on the cellular level.

Unraveling the Formation Mechanism of Solid-Liquid Electrolyte Interphases on LiPON Thin Films.

Most commercial lithium-ion batteries and other types of batteries rely on liquid electrolytes, which are preferred because of their high ionic conductivity, and facilitate fast charge-transfer kinetics at the electrodes. On the other hand, hybrid battery concepts that combine solid and liquid electrolytes might be needed to suppress unwanted shuttle effects in liquid electrolyte-only systems, in particular if mobile redox systems are involved in the cell chemistry. However, at the then newly introduced interface between liquid and solid electrolytes, a solid-liquid electrolyte interphase forms. In this study, we analyze the formation of such an interphase between the solid electrolyte lithium phosphorous oxide nitride (Li xPO yN z, "LiPON") and various liquid electrolytes using in situ neutron reflectometry, quartz crystal microbalance, and atomic force microscopy measurements. Our results show that the interphase consists of two layers: a nonconducting layer directly in contact with "LiPON" and a lithium-rich outer layer. Initially, a fast growth of the solid-liquid electrolyte interphase is observed, which slows down significantly afterward, resulting in a thickness of about 20 nm eventually. Here, a formation mechanism is proposed, which describes the solid-liquid electrolyte interphase growth as the fast deposition of a film, which mostly covers the "LiPON", with only a little degree of remaining porosity. The residual void space is then slowly filled, thus blocking the remaining channels for ionic conduction, which leads to increasing resistance of the interphase. The results obtained imply that hybrid battery concepts with liquid electrolyte and solid electrolyte can be hampered by highly resistive interphases, whose formation cannot be simply slowed down or suppressed. Further research is required regarding possible countermeasures.

Ionic Conductivity of the NASICON-Related Thiophosphate Na1+x Ti2-x Gax (PS4 )3.

Inspired by the recent interest in fast ionic conducting solids for electrolytes, the ionic conductivity of a novel ionic conductor Na1+x Ti2-x Gax (PS4 )3 has been investigated. Using X-ray diffraction and impedance spectroscopy the sodium ionic conductivity in this compound was demonstrated, in which bond valence sum analysis suggests a tunnel diffusion for Na+ . Substitution with Ga3+ leads to an increasing Na+ content, an expansion of the lattice and an increasing conductivity with increasing x in Na1+x Ti2-x Gax (PS4 )3 . Given the relation to the NASICON family, upon replacement of the phosphate by a thiophosphate group, a rich structural chemistry can be expected in this class of materials. This work demonstrates the potential for making NaTi2 (PS4 )3 an ideal system to study structure-property relationships in ionic conductors.

The human phosphatase CDC14A modulates primary cilium length by regulating centrosomal actin nucleation.

CDC14A codes for a conserved proline-directed phosphatase, and mutations in the gene are associated with autosomal-recessive severe to profound deafness, due to defective kinocilia. A role of CDC14A in cilia formation has also been described in other organisms. However, how human CDC14A impacts on cilia formation remains unclear. Here, we show that human RPE1 hCDC14APD cells, encoding a phosphatase dead version of hCDC14A, have longer cilia than wild-type cells, while hCDC14A overexpression reduces cilia formation. Phospho-proteome analysis of ciliated RPE1 cells identified actin-associated and microtubule binding proteins regulating cilia length as hCDC14A substrates, including the actin-binding protein drebrin. Indeed, we find that hCDC14A counteracts the CDK5-dependent phosphorylation of drebrin at S142 during ciliogenesis. Further, we show that drebrin and hCDC14A regulate the recruitment of the actin organizer Arp2 to centrosomes. In addition, during ciliogenesis hCDC14A also regulates endocytosis and targeting of myosin Va vesicles to the basal body in a drebrin-independent manner, indicating that it impacts primary cilia formation in a multilayered manner.

Correlating Transport and Structural Properties in Li1+ xAl xGe2- x(PO4)3 (LAGP) Prepared from Aqueous Solution.

Li1+ xAl xGe2- x(PO4)3 (LAGP) is a solid lithium-ion conductor belonging to the NASICON family, representing the solid solution of LiGe2(PO4)3 and AlPO4. The typical syntheses of LAGP either involve high-temperature melt-quenching, which is complicated and expensive, or a sol-gel process requiring costly organic germanium precursors. In this work, we report a simple method based on aqueous solutions without the need of ethoxide precursors. Using synchrotron and neutron diffraction, the crystal structure, the occupancies for Al and Ge, and the distribution of lithium were determined. Substitution of germanium by aluminum allows for an increased Li+ incorporation in the material and the actual Li+ content in the sample increases with the nominal Li+ content and a solubility limit is observed for higher aluminum content. By means of impedance spectroscopy, an increase in the ionic conductivity with increasing lithium content is observed. Whereas the lithium ionic conductivity improves, due to the increasing carrier density, the bulk activation energy increases. This correlation suggests that changes in the transport mechanism and correlated motion may be at play in the Li1+ xAl xGe2- x(PO4)3 solid solution.

RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.

MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

The HUPO initiative on Model Organism Proteomes, iMOP.

The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was approved at the HUPO Ninth Annual World Congress in Sydney, 2010. iMOP will seek to stimulate scientific exchange and disseminate HUPO best practices. The needs of model organism researchers for central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases. Full details of iMOP activities, members, tools and resources can be found at our website http://www.imop.uzh.ch/ and new members are invited to join us.

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans.

Efficient experimental strategies are needed to validate computationally predicted microRNA (miRNA) target genes. Here we present a large-scale targeted proteomics approach to validate predicted miRNA targets in Caenorhabditis elegans. Using selected reaction monitoring (SRM), we quantified 161 proteins of interest in extracts from wild-type and let-7 mutant worms. We demonstrate by independent experimental downstream analyses such as genetic interaction, as well as polysomal profiling and luciferase assays, that validation by targeted proteomics substantially enriched for biologically relevant let-7 interactors. For example, we found that the zinc finger protein ZTF-7 was a bona fide let-7 miRNA target. We also validated predicted miR-58 targets, demonstrating that this approach is adaptable to other miRNAs. We propose that targeted mass spectrometry can be applied generally to validate candidate lists generated by computational methods or in large-scale experiments, and that the described strategy should be readily adaptable to other organisms.

Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes.

The development of multicellular organisms is controlled by differential gene expression whereby cells adopt distinct fates. A spatially resolved view of gene expression allows the elucidation of transcriptional networks that are linked to cellular identity and function. The haploid female gametophyte of flowering plants is a highly reduced organism: at maturity, it often consists of as few as three cell types derived from a common precursor [1, 2]. However, because of its inaccessibility and small size, we know little about the molecular basis of cell specification and differentiation in the female gametophyte. Here we report expression profiles of all cell types in the mature Arabidopsis female gametophyte. Differentially expressed posttranscriptional regulatory modules and metabolic pathways characterize the distinct cell types. Several transcription factor families are overrepresented in the female gametophyte in comparison to other plant tissues, e.g., type I MADS domain, RWP-RK, and reproductive meristem transcription factors. PAZ/Piwi-domain encoding genes are upregulated in the egg, indicating a role of epigenetic regulation through small RNA pathways-a feature paralleled in the germline of animals [3]. A comparison of human and Arabidopsis egg cells for enrichment of functional groups identified several similarities that may represent a consequence of coevolution or ancestral gametic features.

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.

Genome-wide, absolute quantification of expressed proteins is not yet within reach for most eukaryotes. However, large numbers of MS-based protein identifications have been deposited in databases, together with information on the observation frequencies of each peptide spectrum ("spectral counts"). We have conducted a meta-analysis using several million peptide observations from five model eukaryotes, establishing a consistent, semi-quantitative analysis pipeline. By inferring and comparing protein abundances across orthologs, we observe: (i) the accuracy of spectral counting predictions increases with sampling depth and can rival that of direct biochemical measurements, (ii) the quantitative makeup of the consistently observed core proteome in eukaryotes is remarkably stable, with abundance correlations exceeding R(S)=0.7 at an evolutionary distance greater than 1000 million years, and (iii) some groups of proteins are more constrained than others. We argue that our observations reveal stabilizing selection: central parts of the eukaryotic proteome appear to be expressed at well-balanced, near-optimal abundance levels. This is consistent with our further observations that essential proteins show lower abundance variations than non-essential proteins, and that gene families that tend to undergo gene duplications are less well constrained than families that keep a single-copy status.

Responsiveness to distracting stimuli, though increased in Parkinson's disease, is decreased in asymptomatic PINK1 and Parkin mutation carriers.

Patients with Parkinson's disease (PD) are more sensitive than healthy controls to response-triggering by irrelevant flanking stimuli in speeded choice-response tasks. This increased responsiveness may either indicate a lack of executive control or reflect compensatory efforts to cope with the reduced internal motor drive. Of interest in this context is whether responsiveness is already enhanced in the presymptomatic stage of PD. To address these questions, we studied a group of non-manifesting carriers of heterozygous Parkin and PINK1 mutations while they performed a choice-response task with response-compatible or incompatible flankers. These mutation carriers may be considered a model for pre-clinical PD because the mutant allele leads to a latent nigrostriatal dysfunction and may increase the risk for PD. For comparison, we studied groups of medicated patients with idiopathic PD and of healthy persons age-matched to the mutation carriers and to the patients. Measurements of reaction time, error rate, and the lateralized readiness potential of the EEG provided converging evidence that the mutation carriers were less responsive to distracting flankers than their healthy control group. In contrast, PD patients were more distractible by flankers than their control group, which replicated previous results. Mutation carriers also showed a smaller N2 component of the event-related EEG potential in trials with incompatible flankers relative to their control group, which might indicate reduced inhibitory control. We hypothesize that faulty executive control is the primary deficit, reflected by the reduced N2 component in the mutation carriers. To compensate for this deficit, mutation carriers change their strategy of speed-accuracy trade-off, in order to dampen the excitability of their lateral motor system. Disease progression might prevent symptomatic PD patients from using this compensatory mechanism, leading to increased disinhibition of their lateral motor system.

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.

The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.