ProbeInterface: a unified framework for probe handling in extracellular electrophysiology

Recording neuronal activity with penetrating extracellular multi-channel electrode arrays, more commonly known as neural probes, is one of the most widespread approaches to probe neuronal activity. Despite a plethora of available extracellular probe designs, the time-consuming process of mapping of electrode channel order and relative geometries, as required by spike-sorting software is invariably left to the end-user. Consequently, this manual process is prone to mis-mapping mistakes, which in turn lead to undesirable spike-sorting errors and inefficiencies.Here we introduce ProbeInterface, an open-source project that aims to unify neural probe metadata descriptions by removing the manual step of probe mapping prior to spike-sorting for the analysis of extracellular neural recordings. ProbeInterface is first of all a Python API, which enables users to create and visualize probes and probe groups at any required complexity level. Second, ProbeInterface facilitates the generation of comprehensive wiring description ina reproducible fashion for any specific data-acquisition setup, which usually involves the use of a recording probe, a headstage, adapters, and an acquisition system. Third, we collaborate with probe manufacturers to compile an open library of available probes, which can be downloaded at run time using our Python API. Finally, with ProbeInterface we define a file format for probe handling which includes all necessary information for a FAIR probe description and is compatiblewith and complementary to other open standards in neuroscience.

Ets-2 Protein Is a Transcriptional Repressor Of The HIV-1 Virus and Acts Through Binding To The HIV-LTR-RATS Element

HIV-1 is transcriptionally active in activated CD4+ T (Th) cells, and inactive in naive Th cells. Our previous work has shown that Ets-2 is a candidate transcriptional repressor of HIV-1 in naive Th cells, because the -279 to -250 upstream region of HIV-1-LTR (RATS, Repressor Activator Target Sequence), that participates in HIV-1-LTR transcriptional silencing, encompasses the AAGGAG Ets-2 binding site. In this proof of concept study, we investigated whether Ets-2 represses the expression of HIV-1. We measured the levels of ets-2 mRNA in peripheral blood T-cells, Jurkat cells and 10 other human leukemic T, B and monocytic cell lines, before and after activation of the cells with the mitogens PMA and ionomycin (P/I). Ets-2 mRNA was synthesized in T-cells, Jurkat cells and in most cell lines tested when cultured in plain culture medium (CM), but its synthesis was severely reduced upon cell activation. To directly assess whether Ets-2 can silence HIV-1 activation acting through the RATS sequence, we transfected Jurkat cells with (i) the plasmids HIV-1-LTR-CAT (carries the whole LTR sequence of the HIV-1 virus) or 2xRATS-CAT (carries 2 copies of the RATS sequence) or 2xmutantRATS-CAT (carries a point mutation in the Ets-2 binding site) or CMV-CAT (control), (ii) pCDNA3-ets-2 (for ets-2 overexpression) and (iii) ets-2 shRNA (to silence ets-2 expression in the cells). When Jurkat cells were transfected with HIV-1-LTR-CAT, 2xRATS-CAT or CMV-CAT, there was no transcriptional activity of the genes in CM. After activation of the cells, the expression of the transfected genes increased, except of CMV-CAT. Co-transfection of Jurkat cells with increasing amounts of pCDNA3-ets-2, led to a gradual reduction of HIV-1-LTR-CAT and 2xRATS-CAT activities upon cell stimulation, but not of CMV-CAT. No transcriptional response was observed for the 2xmutantRATS-CAT gene. Co-transfection experiments with HIV-1-LTR-CAT, 2xRATS-CAT and ets-2 shRNA, led to an increase in the activity of both reporter genes, but had no effect on the activities of 2xmutantRATS-CAT and CMV-CAT. To assess whether Ets-2 binds to HIV-1 LTR directly in vivo, Jurkat cells were transfected with the plasmid HIV-1-LTR-CAT, left in CM for 24h, and then in CM±P/I for a further 12h. The cells were then attached to slides and stained for the Ets-2 protein and the HIV-1-LTR sequence by combining immunofluorescence and FISH techniques respectively. In CM condition, Ets-2 protein bound to the HIV-1-LTR sequence (Fig. 1A), whereas after P/I activation of the cells Figure 1 Figure 1 Jurkat cells were transfected with the HIV-1-LTR-CAT plasmid, and were then stained for the Ets-2 protein (green spots) and HIV-LTR (red spots), and counterstained with DAPI (blue). A. Jurkat cells in CM condition. Ets-2 and HIV-LTR co-localize inside the nucleus (yellow spots). B. Jurkat cells activated with P/I for 12h. Ets-2 no more co-localizes with the HIV-1-LTR sequence. Figure 1. Figure 1 Jurkat cells were transfected with the HIV-1-LTR-CAT plasmid, and were then stained for the Ets-2 protein (green spots) and HIV-LTR (red spots), and counterstained with DAPI (blue). A. Jurkat cells in CM condition. Ets-2 and HIV-LTR co-localize inside the nucleus (yellow spots). B. Jurkat cells activated with P/I for 12h. Ets-2 no more co-localizes with the HIV-1-LTR sequence. Figure 2 EMSA with Ets-2 protein eluted from cord blood-derived naive T-cells and an oligonucleotide probe mapping the RATS sequence. a-e represent points with decreasing amounts of protein eluates. Figure 2. EMSA with Ets-2 protein eluted from cord blood-derived naive T-cells and an oligonucleotide probe mapping the RATS sequence. a-e represent points with decreasing amounts of protein eluates. Disclosures: No relevant conflicts of interest to declare.

Mapping Affymetrix Microarray Probes to the Rat Genome via a Persistent Index

A probe mapping technique using a novel implementation of a persistent q-gram index was developed. It guarantees to find all matches that meet certain definitions. These include exact matching of the central 19 bases of 25 base probes, matching the central 19 bases with at most one or three mismatches and exact matching of any 16 bases. In comparison with BLAST and BLAT, the new methods were either significantly faster or identified matches missed by the heuristics. The 16 bp method was used to map the 342,410 perfect match probes from the Affymetrix GeneChip Rat Genome 230 2.0 Array to the genome. When compared with the mapping from Ensembl, the new mapping included over seven million novel matches, providing additional evidence for researchers wishing to further investigate the sources of signals measured in microarray experiments. The results demonstrate the practicality of the index, which could support other q-gram based algorithms.