Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα) and FOXA1 binding in their proximal promoter regions.

Low cost, LoRa based river water level data acquisition system.

In recent years, climate change and catchment degradation have negatively affected stage patterns in rivers which in turn have affected the availability of enough water for various ecosystems. To realize and quantify the effects of climate change and catchment degradation on rivers, water level monitoring is essential. Various effective infrastructures for river water level monitoring that have been developed and deployed in developing countries over the years, are often bulky, complex and expensive to build and maintain. Additionally, most are not equipped with communication hardware components which can enable wireless data transmission. This paper presents a river water level data acquisition system that improves on the effectiveness, size, deployment design and data transmission capabilities of systems being utilized. The main component of the system is a river water level sensor node. The node is based on the MultiTech mDot - an ARM-Mbed programmable, low power RF module - interfaced with an ultrasonic sensor for data acquisition. The data is transmitted via LoRaWAN and stored on servers. The quality of the stored raw data is controlled using various outlier detection and prediction machine learning models. Simplified firmware and easy to connect hardware make the sensor node design easy to develop. The developed sensor nodes were deployed along River Muringato in Nyeri, Kenya for a period of 18 months for continuous data collection. The results obtained showed that the developed system can practically and accurately obtain data that can be useful for analysis of river catchment areas.

DSAIL power management board: Powering the Raspberry Pi autonomously off the grid.

The Raspberry Pi is a credit card sized single board computer that finds its use in very diverse projects. Being a computer it runs on a full operating system and can be interfaced with a wide range of hardware. Its ability to collect and store data and its superior processing capabilities gives it an edge over other microprocessors. When used to collect data away from the grid, alternative methods of powering the Raspberry Pi have to be used. An ideal powering system should be autonomous, allowing the Raspberry Pi to be deployed indefinitely without the need to check on the system due to power shortcomings. In this paper we introduce the DSAIL Power Management Board that is used to power the Raspberry Pi autonomously. We have developed a prototype and used it to collect ecological data from a conservancy in Central Kenya.

A Bioacoustic Record of a Conservancy in the Mount Kenya Ecosystem.

BACKGROUND: Environmental degradation is a major threat facing ecosystems around the world. In order to determine ecosystems in need of conservation interventions, we must monitor the biodiversity of these ecosystems effectively. Bioacoustic approaches offer a means to monitor ecosystems of interest in a sustainable manner. In this work we show how a bioacoustic record from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, was obtained in a cost effective manner. A subset of the dataset was annotated with the identities of bird species present since they serve as useful indicator species. These data reveal the spatial distribution of species within the conservancy and also point to the effects of major highways on bird populations. This dataset will provide data to train automatic species recognition systems for birds found within the Mount Kenya ecosystem. Such systems are necessary if bioacoustic approaches are to be employed at the large scales necessary to influence wildlife conservation measures. NEW INFORMATION: We provide acoustic recordings from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, obtained using a low cost acoustic recorder. A total of 2701 minute long recordings are provided including both daytime and nighttime recordings. We present an annotation of a subset of the daytime recordings indicating the bird species present in the recordings. The dataset contains recordings of at least 36 bird species. In addition, the presence of a few nocturnal species within the conservancy is also confirmed.