The LOFAR pilot surveys for pulsars and fast radio transients

We have conducted two pilot surveys for radio pulsars and fast transients with the Low-Frequency Array (LOFAR) around 140 MHz and here report on the first low-frequency fast-radio burst limit and the discovery of two new pulsars. The first survey, the LOFAR Pilot Pulsar Survey (LPPS), observed a large fraction of the northern sky, ~1.4 x 10^4 sq. deg, with 1-hr dwell times. Each observation covered ~75 sq. deg using 7 independent fields formed by incoherently summing the high-band antenna fields. The second pilot survey, the LOFAR Tied-Array Survey (LOTAS), spanned ~600 sq. deg, with roughly a 5-fold increase in sensitivity compared with LPPS. Using a coherent sum of the 6 LOFAR "Superterp" stations, we formed 19 tied-array beams, together covering 4 sq. deg per pointing. From LPPS we derive a limit on the occurrence, at 142 MHz, of dispersed radio bursts of 107 Jy for the narrowest searched burst duration of 0.66 ms. In LPPS, we re-detected 65 previously known pulsars. LOTAS discovered two pulsars, the first with LOFAR or any digital aperture array. LOTAS also re-detected 27 previously known pulsars. These pilot studies show that LOFAR can efficiently carry out all-sky surveys for pulsars and fast transients, and they set the stage for further surveying efforts using LOFAR and the planned low-frequency component of the Square Kilometer Array.Comment: 18 pages, 10 figures, accepted for A&

An image-based miRNA screen identifies miRNA-135s as regulators of CNS axon growth and regeneration by targeting krüppel-like factor 4

During embryonic development, axons extend over long distances to establish functional connections. In contrast, axon regeneration in the adult mammalian CNS is limited in part by a reduced intrinsic capacity for axon growth. Therefore, insight into the intrinsic control of axon growth may provide new avenues for enhancing CNS regeneration. Here, we performed one of the first miRNome-wide functional miRNA screens to identify miRNAs with robust effects on axon growth. High-content screening identified miR-135a and miR-135b as potent stimulators of axon growth and cortical neuron migration in vitro and in vivo in male and female mice. Intriguingly, both of these developmental effects of miR-135s relied in part on silencing of Krüppel-like factor 4 (KLF4), a well known intrinsic inhibitor of axon growth and regeneration. These results prompted us to test the effect of miR-135s on axon regeneration after injury. Our results show that intravitreal application of miR-135s facilitates retinal ganglion cell (RGC) axon regeneration after optic nerve injury in adult mice in part by repressing KLF4. In contrast, depletion of miR-135s further reduced RGC axon regeneration. Together, these data identify a novel neuronal role for miR-135s and the miR-135–KLF4 pathway and highlight the potential of miRNAs as tools for enhancing CNS axon regeneration

A functional screen identifies specific microRNAs capable of inhibiting human melanoma cell viability

Malignant melanoma is an aggressive form of skin cancer with poor prognosis. Despite improvements in awareness and prevention of this disease, its incidence is rapidly increasing. MicroRNAs (miRNAs) are a class of small RNA molecules that regulate cellular processes by repressing messenger RNAs (mRNAs) with partially complementary target sites. Several miRNAs have already been shown to attenuate cancer phenotypes, by limiting proliferation, invasiveness, tumor angiogenesis, and stemness. Here, we employed a genome-scale lentiviral human miRNA expression library to systematically survey which miRNAs are able to decrease A375 melanoma cell viability. We highlight the strongest inhibitors of melanoma cell proliferation, including the miR-15/16, miR-141/200a and miR-96/182 families of miRNAs and miR-203. Ectopic expression of these miRNAs resulted in long-term inhibition of melanoma cell expansion, both in vitro and in vivo. We show specifically miR-16, miR-497, miR-96 and miR-182 are efficient effectors when introduced as synthetic miRNAs in several melanoma cell lines. Our study provides a comprehensive interrogation of miRNAs that interfere with melanoma cell proliferation and viability, and offers a selection of miRNAs that are especially promising candidates for application in melanoma therapy

A genome-wide screen for miRNAs that inhibit A375 melanoma cell growth.

<p>(A) Inhibition of melanoma growth was measured by means of cell viability and cell count. For each sample a B-score was calculated and B-scores from both assays are plotted against each other. There is a strong correlation between both assays. The B-scores for one miRNA, miR-518b, fell outside the range of the graph: they were −6 for cell count and −12 for cell viability. (B) A comparison with a normal distribution shows that the cell viability screen is sensitive for identifying growth-inhibitory miRNAs. A concomitant estimate of the false discovery rate is shown in grey fill (secondary axis). (C) 55 potential inhibitory miRNAs were tested in a confirmation screen against 11 empty vector samples and a population of 28 miRNAs with small or no effects in the primary screen. Box plots show values between 25^th and 75^th percentile in boxes, and the outermost values as whiskers. 20 of 55 inhibitory miRNAs scored better than any of the control miRNAs (below dashed line). *p = 6.8*10⁻⁵, **p = 1.6*10⁻⁶, ***p = 5.4*10⁻¹⁰. (D) Individual hits selected for follow-up, and their relative effect on cell viability. A virus containing a short-hairpin construct targeting BRAF was used as a positive control. Error bars represent standard deviation of three samples.</p

Transcriptome analysis after miR-203 transfection.

<p>(A) A375 cells were transfected with either miR-203 or scrambled control and the transcriptome was quantified by RNA-Seq. All differentially expressed genes are plotted in the left graph, while only the differentially expressed genes containing miR-203 target sites are plotted in the right graph. Genes with miR-203 target sites are much more likely to be downregulated after miR-203 overexpression, and downregulated genes are highly enriched for genes with miR-203 target sites (p<0.0001). (B) One of the differentially expressed genes after miR-203 transfection is BIRC5. Repression was examined at both the mRNA and the protein level by qPCR (left) and Western blot (right) respectively. The BIRC5 transcript and its protein product survivin are both reduced after miR-203 transfection, but also after siBRAF transfection.</p

Effect of introduction of synthetic miRNAs on A375 viability.

<p>A375 cells were transfected with a range of concentrations of different miRNAs, and 72 hours after transfection viability was measured by means of MTS assay. Effects are compared to a scrambled control and a pool of 4 siRNAs against BRAF (siBRAF) as a positive control for A375 growth inhibition. Specific effects of miRNAs are best observed at concentrations of 10 nM. Each panel shows a different subset of miRNA mimics, although miRNAs were assessed in the same experiment. Error bars represent standard deviation of three samples. A representative of three experiments is shown.</p

Comparison of miRNA-induced effects in several melanoma cell lines.

<p>Cells were transfected with 10 nM (A375 and A2058) or 30 nM (SK-MEL-28 and SK-MEL-173) RNA and cell viability was measured 72 hours after transfection. Data are plotted relative to a mock-infected control. Error bars represent standard deviation of three samples.</p

Endogenous miRNA expression and expression after lentiviral transduction in A375 cells.

<p>qPCR data are relative to U6 small RNA. Endogenous: empty vector-transduced, ectopic: miRNA-transduced.</p

The Apertif Radio Transient System (ARTS): Design, commissioning, data release, and detection of the first five fast radio bursts

Fast radio bursts (FRBs) must be powered by uniquely energetic emission mechanisms. This requirement has eliminated a number of possible source types, but several remain. Identifying the physical nature of FRB emitters arguably requires good localisation of more detections, as well as broad-band studies enabled by real-time alerting. In this paper, we present the Apertif Radio Transient System (ARTS), a supercomputing radio-telescope instrument that performs real-time FRB detection and localisation on the Westerbork Synthesis Radio Telescope (WSRT) interferometer. It reaches coherent-addition sensitivity over the entire field of the view of the primary-dish beam. After commissioning results verified that the system performed as planned, we initiated the Apertif FRB survey (ALERT). Over the first 5 weeks we observed at design sensitivity in 2019, we detected five new FRBs, and interferometrically localised each of them to 0.4–10 sq. arcmin. All detections are broad band, very narrow, of the order of 1 ms in duration, and unscattered. Dispersion measures are generally high. Only through the very high time and frequency resolution of ARTS are these hard-to-find FRBs detected, producing an unbiased view of the intrinsic population properties. Most localisation regions are small enough to rule out the presence of associated persistent radio sources. Three FRBs cut through the halos of M31 and M33. We demonstrate that Apertif can localise one-off FRBs with an accuracy that maps magneto-ionic material along well-defined lines of sight. The rate of one every ~7 days ensures a considerable number of new sources are detected for such a study. The combination of the detection rate and localisation accuracy exemplified by the first five ARTS FRBs thus marks a new phase in which a growing number of bursts can be used to probe our Universe