A genome-wide RNAi screen identifies factors required for distinct stages of C-elegans piRNA biogenesis

In animals, piRNAs and their associated Piwi proteins guard germ cell genomes against mobile genetic elements via an RNAi-like mechanism. In Caenorhabditis elegans, 21U-RNAs comprise the piRNA class, and these collaborate with 22G RNAs via unclear mechanisms to discriminate self from nonself and selectively and heritably silence the latter. Recent work indicates that 21U-RNAs are post-transcriptional processing products of individual transcription units that produce similar to 26-nucleotide capped precursors. However, nothing is known of how the expression of precursors is controlled or how primary transcripts give rise to mature small RNAs. We conducted a genome-wide RNAi screen to identify components of the 21U biogenesis machinery. Screening by direct, quantitative PCR (qPCR)-based measurements of mature 21U-RNA levels, we identified 22 genes important for 21U-RNA production, termed TOFUs (Twenty-One-u Fouled Ups). We also identified seven genes that normally repress 21U production. By measuring mature 21U-RNA and precursor levels for the seven strongest hits from the screen, we assigned factors to discrete stages of 21U-RNA production. Our work identifies for the first time factors separately required for the transcription of 21U precursors and the processing of these precursors into mature 21U-RNAs, thereby providing a resource for studying the biogenesis of this important small RNA class

Rendering volumetric haptic shapes in mid-air using ultrasound

We present a method for creating three-dimensional haptic shapes in mid-air using focused ultrasound. This approach applies the principles of acoustic radiation force, whereby the non-linear effects of sound produce forces on the skin which are strong enough to generate tactile sensations. This mid-air haptic feedback eliminates the need for any attachment of actuators or contact with physical devices. The user perceives a discernible haptic shape when the corresponding acoustic interference pattern is generated above a precisely controlled two-dimensional phased array of ultrasound transducers. In this paper, we outline our algorithm for controlling the volumetric distribution of the acoustic radiation force field in the form of a three-dimensional shape. We demonstrate how we create this acoustic radiation force field and how we interact with it. We then describe our implementation of the system and provide evidence from both visual and technical evaluations of its ability to render different shapes. We conclude with a subjective user evaluation to examine users’ performance for different shapes

Evolution of spectral function in a doped Mott insulator : surface vs. bulk contributions

We study the evolution of the spectral function with progressive hole doping in a Mott insulator, $La_{1-x}Ca_xVO_3$ with $x$ = 0.0 - 0.5. The spectral features indicate a bulk-to-surface metal-insulator transition in this system. Doping dependent changes in the bulk electronic structure are shown to be incompatible with existing theoretical predictions. An empirical description based on the single parameter, $U/W$, is shown to describe consistently the spectral evolution.Comment: Revtex, 4 pages, 3 postscript figures. To appear in Phys. Rev. Let

Concomitant CIS on TURBT does not impact oncological outcomes in patients treated with neoadjuvant or induction chemotherapy followed by radical cystectomy

© Springer-Verlag GmbH Germany, part of Springer Nature 2018Background: Cisplatin-based neoadjuvant chemotherapy (NAC) for muscle invasive bladder cancer improves all-cause and cancer specific survival. We aimed to evaluate whether the detection of carcinoma in situ (CIS) at the time of initial transurethral resection of bladder tumor (TURBT) has an oncological impact on the response to NAC prior to radical cystectomy. Patients and methods: Patients were identified retrospectively from 19 centers who received at least three cycles of NAC or induction chemotherapy for cT2-T4aN0-3M0 urothelial carcinoma of the bladder followed by radical cystectomy between 2000 and 2013. The primary and secondary outcomes were pathological response and overall survival, respectively. Multivariable analysis was performed to determine the independent predictive value of CIS on these outcomes. Results: Of 1213 patients included in the analysis, 21.8% had concomitant CIS. Baseline clinical and pathologic characteristics of the ‘CIS’ versus ‘no-CIS’ groups were similar. The pathological response did not differ between the two arms when response was defined as pT0N0 (17.9% with CIS vs 21.9% without CIS; p = 0.16) which may indicate that patients with CIS may be less sensitive to NAC or ≤ pT1N0 (42.8% with CIS vs 37.8% without CIS; p = 0.15). On Cox regression model for overall survival for the cN0 cohort, the presence of CIS was not associated with survival (HR 0.86 (95% CI 0.63–1.18; p = 0.35). The presence of LVI (HR 1.41, 95% CI 1.01–1.96; p = 0.04), hydronephrosis (HR 1.63, 95% CI 1.23–2.16; p = 0.001) and use of chemotherapy other than ddMVAC (HR 0.57, 95% CI 0.34–0.94; p = 0.03) were associated with shorter overall survival. For the whole cohort, the presence of CIS was also not associated with survival (HR 1.05 (95% CI 0.82–1.35; p = 0.70). Conclusion: In this multicenter, real-world cohort, CIS status at TURBT did not affect pathologic response to neoadjuvant or induction chemotherapy. This study is limited by its retrospective nature as well as variability in chemotherapy regimens and surveillance regimens.Peer reviewedFinal Accepted Versio

Biopsy confirmation of metastatic sites in breast cancer patients:clinical impact and future perspectives

Determination of hormone receptor (estrogen receptor and progesterone receptor) and human epidermal growth factor receptor 2 status in the primary tumor is clinically relevant to define breast cancer subtypes, clinical outcome,and the choice of therapy. Retrospective and prospective studies suggest that there is substantial discordance in receptor status between primary and recurrent breast cancer. Despite this evidence and current recommendations,the acquisition of tissue from metastatic deposits is not routine practice. As a consequence, therapeutic decisions for treatment in the metastatic setting are based on the features of the primary tumor. Reasons for this attitude include the invasiveness of the procedure and the unreliable outcome of biopsy, in particular for biopsies of lesions at complex visceral sites. Improvements in interventional radiology techniques mean that most metastatic sites are now accessible by minimally invasive methods, including surgery. In our opinion, since biopsies are diagnostic and changes in biological features between the primary and secondary tumors can occur, the routine biopsy of metastatic disease needs to be performed. In this review, we discuss the rationale for biopsy of suspected breast cancer metastases, review issues and caveats surrounding discordance of biomarker status between primary and metastatic tumors, and provide insights for deciding when to perform biopsy of suspected metastases and which one (s) to biopsy. We also speculate on the future translational implications for biopsy of suspected metastatic lesions in the context of clinical trials and the establishment of bio-banks of biopsy material taken from metastatic sites. We believe that such bio-banks will be important for exploring mechanisms of metastasis. In the future,advances in targeted therapy will depend on the availability of metastatic tissue

Instability, Intermixing and Electronic Structure at the Epitaxial LaAlO3/SrTiO3(001) Heterojunction

The question of stability against diffusional mixing at the prototypical LaAlO3/SrTiO3(001) interface is explored using a multi-faceted experimental and theoretical approach. We combine analytical methods with a range of sensitivities to elemental concentrations and spatial separations to investigate interfaces grown using on-axis pulsed laser deposition. We also employ computational modeling based on the density function theory as well as classical force fields to explore the energetic stability of a wide variety of intermixed atomic configurations relative to the idealized, atomically abrupt model. Statistical analysis of the calculated energies for the various configurations is used to elucidate the relative thermodynamic stability of intermixed and abrupt configurations. We find that on both experimental and theoretical fronts, the tendency toward intermixing is very strong. We have also measured and calculated key electronic properties such as the presence of electric fields and the value of the valence band discontinuity at the interface. We find no measurable electric field in either the LaAlO3 or SrTiO3, and that the valence band offset is near zero, partitioning the band discontinuity almost entirely to the conduction band edge. Moreover, we find that it is not possible to account for these electronic properties theoretically without including extensive intermixing in our physical model of the interface. The atomic configurations which give the greatest electrostatic stability are those that eliminate the interface dipole by intermixing, calling into question the conventional explanation for conductivity at this interface - electronic reconstruction. Rather, evidence is presented for La indiffusion and doping of the SrTiO3 below the interface as being the cause of the observed conductivity

Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions

Frequent fluctuations in sulfate availability rendered syntrophic interactions between the sulfate reducing bacterium Desulfovibrio vulgaris (Dv) and the methanogenic archaeon Methanococcus maripaludis (Mm) unsustainable. By contrast, prolonged laboratory evolution in obligate syntrophy conditions improved the productivity of this community but at the expense of erosion of sulfate respiration (SR). Hence, we sought to understand the evolutionary trajectories that could both increase the productivity of syntrophic interactions and sustain SR. We combined a temporal and combinatorial survey of mutations accumulated over 1000 generations of 9 independently-evolved communities with analysis of the genotypic structure for one community down to the single-cell level. We discovered a high level of parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance of a rare SR+ Dv lineage within many evolution lines. An in-depth investigation revealed that synergistic epistasis across Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, allowing their co-existence as r- and K-strategists, respectively