Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq.

One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in eight prioritized tissues collected as part of the FAANG equine biobank from two thoroughbred mares. Data were generated according to optimized experimental parameters developed during quality control testing. To ensure that we obtained sufficient ChIP and successful peak-calling, data and peak-calls were assessed using six quality metrics, replicate comparisons, and site-specific evaluations. Tissue specificity was explored by identifying binding motifs within unique active regions, and motifs were further characterized by gene ontology (GO) and protein-protein interaction analyses. The histone marks identified in this study represent some of the first resources for tissue-specific regulation within the equine genome. As such, these publicly available annotation data can be used to advance equine studies investigating health, performance, reproduction, and other traits of economic interest in the horse

Optimization of multi-gigabit transceivers for high speed data communication links in HEP Experiments

The scheme of the data acquisition (DAQ) architecture in High Energy Physics (HEP) experiments consist of data transport from the front-end electronics (FEE) of the online detectors to the readout units (RU), which perform online processing of the data, and then to the data storage for offline analysis. With major upgrades of the Large Hadron Collider (LHC) experiments at CERN, the data transmission rates in the DAQ systems are expected to reach a few TB/sec within the next few years. These high rates are normally associated with the increase in the high-frequency losses, which lead to distortion in the detected signal and degradation of signal integrity. To address this, we have developed an optimization technique of the multi-gigabit transceiver (MGT) and implemented it on the state-of-the-art 20nm Arria-10 FPGA manufactured by Intel Inc. The setup has been validated for three available high-speed data transmission protocols, namely, GBT, TTC-PON and 10 Gbps Ethernet. The improvement in the signal integrity is gauged by two metrics, the Bit Error Rate (BER) and the Eye Diagram. It is observed that the technique improves the signal integrity and reduces BER. The test results and the improvements in the metrics of signal integrity for different link speeds are presented and discussed

Interference and Bandwidth Adjusted (ETX) in Wireless Multi-hop Networks

In this paper, we propose a new quality link metric, interference and bandwidth adjusted ETX (IBETX) for wireless multi-hop networks. As MAC layer affects the link performance and consequently the route quality, the metric therefore, tackles the issue by achieving twofold MAC-awareness. Firstly, interference is calculated using cross-layered approach by sending probes to MAC layer. Secondly, the nominal bit rate information is provided to all nodes in the same contention domain by considering the bandwidth sharing mechanism of 802.11. Like ETX, our metric also calculates link delivery ratios that directly affect throughput and selects those routes that bypass dense regions in the network. Simulation results by NS-2 show that IBETX gives 19% higher throughput than ETX and 10% higher than Expected Throughput (ETP). Our metric also succeeds to reduce average end-to-end delay up to 16% less than Expected Link Performance (ELP) and 24% less than ETX

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

BAckground: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results: We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion: We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material