Ten simple rules for providing effective bioinformatics research support.

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support.

The Kinetics of the Humoral and Interferon-Gamma Immune Responses to Experimental Mycobacterium bovis Infection in the White Rhinoceros (Ceratotherium simum).

Mycobacterium bovis is the cause of tuberculosis (TB) in a wide range of species, including white rhinoceroses (Ceratotherium simum). Control of the disease relies on the indirect detection of infection by measuring pathogen-specific responses of the host. These are poorly described in the white rhinoceros and this study aimed to characterize the kinetics of immune responses to M. bovis infection in this species. Three white rhinoceroses were infected with M. bovis and their immune sensitization to this pathogen was measured monthly for 20 months. Cell-mediated immunity was characterized in whole blood samples as the differential release of interferon-gamma in response to bovine purified protein derivative (PPDb) and avian PPD (PPDa) as well as the release of this cytokine in response to the M. bovis proteins 6 kDa early secretory antigenic target (ESAT-6)/10 kDa culture filtrate protein (CFP-10). Humoral immunity was quantified as the occurrence or the magnitude of antibody responses to the proteins ESAT-6/CFP-10, MPB83, MPB83/MPB70, and PPDb. The magnitude and duration of immune reactivity varied between individuals; however, peak responses to these antigens were detected in all animals circa 5-9 months postinfection. Hereafter, they gradually declined to low or undetectable levels. This pattern was associated with limited TB-like pathology at postmortem examination and appeared to reflect the control of M. bovis infection following the development of the adaptive immune response. Measurement of these markers could prove useful for assessing the disease status or treatment of naturally infected animals. Moreover, immune responses identified in this study might be used to detect infection; however, further studies are required to confirm their diagnostic utility.