Hidden in the Middle : Culture, Value and Reward in Bioinformatics

Bioinformatics - the so-called shotgun marriage between biology and computer science - is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised 'outputs' in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinary cultures with their own distinct ways of working. Perceived problems of interdisciplinarity include difficulties of making explicit knowledge that is practical, theoretical, or cognitive. But successful interdisciplinary research also depends on an understanding of disciplinary cultures and value systems, often only tacitly understood by members of the communities in question. In bioinformatics, the 'parent' disciplines have different value systems; for example, what is considered worthwhile research by computer scientists can be thought of as trivial by biologists, and vice versa. This paper concentrates on the problems of reward and recognition described by scientists working in academic bioinformatics in the United Kingdom. We highlight problems that are a consequence of its cross-cultural make-up, recognising that the mismatches in knowledge in this borderland take place not just at the level of the practical, theoretical, or epistemological, but also at the cultural level too. The trend in big, interdisciplinary science is towards multiple authors on a single paper; in bioinformatics this has created hybrid or fractional scientists who find they are being positioned not just in-between established disciplines but also in-between as middle authors or, worse still, left off papers altogether

Corporate reputation past and future: a review and integration of existing literature and a framework for future research

The concept of corporate reputation is steadily growing in interest among management researchers and practitioners. In this article, we trace key milestones in the development of reputation literature over the past six decades to suggest important research gaps as well as to provide contextual background for a subsequent integration of approaches and future outlook. In particular we explore the need for better categorised outcomes; a wider range of causes; and a deeper understanding of contingencies and moderators to advance the field beyond its current state while also taking account of developments in the macro business environment. The article concludes by presenting a novel reputation framework that integrates insights from reputation theory and studies, outlines gaps in knowledge and offers directions for future research

Specific BK Channel Activator NS11021 Protects Rat Renal Proximal Tubular Cells from Cold Storage—Induced Mitochondrial Injury In Vitro

Kidneys from deceased donors used for transplantation are placed in cold storage (CS) solution during the search for a matched recipient. However, CS causes mitochondrial injury, which may exacerbate renal graft dysfunction. Here, we explored whether adding NS11021, an activator of the mitochondrial big-conductance calcium-activated K+ (mitoBK) channel, to CS solution can mitigate CS-induced mitochondrial injury. We used normal rat kidney proximal tubular epithelial (NRK) cells as an in vitro model of renal cold storage (18 h) and rewarming (2 h) (CS + RW). Western blots detected the pore-forming α subunit of the BK channel in mitochondrial fractions from NRK cells. The fluorescent K+-binding probe, PBFI-AM, revealed that isolated mitochondria from NRK cells exhibited mitoBK-mediated K+ uptake, which was impaired ~70% in NRK cells subjected to CS + RW compared to control NRK cells maintained at 37 °C. Importantly, the addition of 1 μM NS11021 to CS solution prevented CS + RW-induced impairment of mitoBK-mediated K+ uptake. The NS11021–treated NRK cells also exhibited less cell death and mitochondrial injury after CS + RW, including mitigated mitochondrial respiratory dysfunction, depolarization, and superoxide production. In summary, these new data show for the first time that mitoBK channels may represent a therapeutic target to prevent renal CS-induced injury

The Mitochondrial BK Channel as a Novel Therapeutic Target During Renal Cold Storage and Transplantation: Its Role as a Mitochondrial-Protective Factor

Last year ~34% of donor kidneys were discarded due in part to injury that occurs during cold storage (CS), leading to a high mortality of patients waiting for transplantation. Deceased donor kidneys exposed to CS are five-fold more likely to fail than those from living donors (without CS). Thus, there is a critical need to investigate mechanisms involved with CS-induced renal injury, which will help advance the development of novel therapeutic interventions to improve transplant outcomes. Our laboratory and others have shown that CS ‘alone’ induces renal mitochondrial dysfunction and oxidative injury. However, the extent of injury when CS is combined with transplantation (CS+Tx) as well as the identity of specific mitochondrial targets remain elusive. Exploring these questions was the primary goal of this dissertation project. First, using a novel rat renal transplant model, we demonstrated that even short-term (4h) CS exacerbates mitochondrial and renal injury after Tx compared to Tx alone (without CS). Next, we speculated that the mitochondrial large-conductance Ca2+-activated K+ channel (mitoBK) was a potential therapeutic target since its activation has been shown to be mitochondrial-protective during warm ischemic injury. The hypothesis to be tested is CS-induced mitochondrial ROS impair mitoBK channel function, which contributes to renal and mitochondrial injury. Addition of BK activators during CS protects against mitochondrial and renal injury following transplantation. Using our rat renal cell line (NRK), we identified, for the first time, the presence of an active mitoBK channel. Cells exposed to CS followed by rewarming (CS+RW) significantly reduced mitoBK function. Excitingly, addition of the specific BK activator, NS11021 (1 μM), during CS restored mitoBK function and mitigated CS+RW-induced mitochondrial and cell injury. Finally, using our preclinical rat model of CS+Tx, NS11021 (3 μM) partially mitigated mitochondrial dysfunction and cell injury, but not renal dysfunction. Overall, these studies support our hypothesis and identify the mitoBK channel as a promising pharmacotherapeutic target for preventing CS-induced mitochondrial injury and renal injury. Future studies are warranted to better characterize mitoBK’s mitochondrial-protective role and to optimize this therapeutic approach, which is a clinically attractive strategy that avoids systemic drug exposure in the transplant recipient

Renal cold storage followed by transplantation impairs expression of key mitochondrial fission and fusion proteins

<div><p>Background</p><p>The majority of transplanted kidneys are procured from deceased donors which all require exposure to cold storage (CS) for successful transplantation. Unfortunately, this CS leads to renal and mitochondrial damage but, specific mitochondrial targets affected by CS remain largely unknown. The goal of this study is to determine whether pathways involved with mitochondrial fusion or fission, are disrupted during renal CS.</p><p>Methods</p><p>Male Lewis rat kidneys were exposed to cold storage (CS) alone or cold storage combined with transplantation (CS/Tx). To compare effects induced by CS, kidney transplantation without CS exposure (autotransplantation; ATx) was also used. Mitochondrial function was assessed using high resolution respirometry. Expression of mitochondrial fusion and fission proteins were monitored using Western blot analysis.</p><p>Results</p><p>CS alone (no Tx) reduced respiratory complex I and II activities along with reduced expression of the primary mitochondrial fission protein, dynamin related protein (DRP1), induced loss of the long form of <u>O</u>ptic <u>A</u>trophy <u>P</u>rotein (OPA1), and altered the mitochondrial protease, OMA1, which regulates OPA1 processing. CS followed by Tx (CS/Tx) reduced complex I, II, and III activities, and induced a profound loss of the long and short forms of OPA1, mitofusin 1 (MFN1), and mitofusin 2 (MFN2) which all control mitochondrial fusion. In addition, expression of DRP1, along with its primary receptor protein, mitochondrial fission factor (MFF), were also reduced after CS/Tx. Interestingly, CS/Tx lead to aberrant higher molecular weight OMA1 aggregate expression.</p><p>Conclusions</p><p>Our results suggest that CS appears to involve activation of the OMA1, which could be a key player in proteolysis of the fusion and fission protein machinery following transplantation. These findings raise the possibility that impaired mitochondrial fission and fusion may be unrecognized contributors to CS induced mitochondrial injury and compromised renal graft function after transplantation.</p></div

Impact of cold storage alone, combined cold storage plus transplantation, and autotransplantation on mitochondrial fusion protein expression.

<p>Renal extracts (30 ug) were resolved on SDS-PAGE gels and immunoblotted. Representative MFN 1 and MFN2 western blots showing distinct protein bands of both MFN1/2 (~75 kDa) in Sham, ATx, and CS/Tx kidneys <b>(A)</b> as well as control and CS alone kidneys <b>(B).</b> Actin was used as a loading control. Densitometry evaluation of each blot (normalized to actin) is shown on the right panel. Representative OPA1 western blot showing long form of OPA1 (L, ~95 kDa) and short form of OPA1 (S, ~75 kDa) in Sham, ATx, and CS/Tx kidneys CS/Tx <b>(C)</b> as well as control and CS alone kidneys <b>(D).</b> Actin was used as a loading control. Densitometry evaluation of each blot (normalized to actin) is shown on the right panel. Values were expressed as Mean ± S.E.M. (n = 4). Unpaired Student’s t test was used to compare the means between control and CS kidneys. One-way ANOVA followed by Tukey’s post-hoc test for multiple group comparisons was used to compare the means between sham, ATx, and CS/Tx kidneys; * indicates means are significantly different (P < 0.05) when compared to control or sham and # indicates means are significantly different (P < 0.05) when compared to ATx.</p

Cold storage plus transplantation impairs renal function and mitochondrial morphology.

<p><b>(A)</b> Serum creatinine and blood urea nitrogen (BUN) from the sham and 18 hr CS/Tx rats were analyzed using hand-held clinical chemistry analyzer (iSTAT^TM) and Chem8⁺ cassettes as described in materials and methods. Values were expressed as Mean ± S.E.M. (n = 4). The unpaired Student’s t test was used to compare the means between sham and CS/Tx; * indicates means are significantly different from sham (P < 0.05). <b>(B)</b> Electron micrographs revealed normal mitochondria in sham kidneys (cortical region), but 18 hr CS/Tx kidneys show rounded, fragmented mitochondria with dense aggregates. Images are representative of n = 3 in each group; bar, 500 nm. TEM was performed at the Georgia Reagents TEM Core Facility.</p

Schematic of five rat surgical groups used in this study.

<p>The left panel depicts the sham surgery, in which the right kidney was removed (<b>control kidney</b>) and the rat survives with only the left native kidney (<b>sham kidney</b>). The middle panel shows transplant surgery using donor kidneys (left and right), which were harvested and exposed to cold storage solution for 18 hrs. The right kidney was saved as CS control (<b>CS kidney</b>) and the left kidney was transplanted in a new recipient rat, in which both native kidneys were removed so that the kidney function depends on the transplanted donor kidney (<b>CS/Tx kidney</b>). The right panel shows autotransplant surgery, in which both native kidneys were removed in a rat, but the left native kidney was transplanted immediately back to the same rat. This kidney was saved as autotransplanted kidney (<b>ATx kidney</b>) and served as a control transplant kidney without CS for the CS/Tx kidney.</p