The importance of reporting small details and making well-informed decisions about which information to include for each experimental parameter/factor in scientific publications can be demonstrated by the following example:
Lipopolysaccharide (LPS) is the major component of the cell wall surface of gram-negative bacteria. It is an amphipathic glycoconjugate and consists of a core oligosaccharide region that is anchored in the outer bacterial membrane by a specific carbohydrate lipid moiety termed lipid A (Alexander and Rietschel, 2001). Lipid A is the primary immunostimulatory center of LPS and can trigger innate immune responses through Toll-like receptor (TLR) 4 and its co-receptor MD2 (also known as LY96). LPS is also responsible for endotoxic shock, an often fatal complication of sepsis. TLR4 and MD2/LY96 knockout mice do not respond to LPS and are resistant to endotoxic shock, confirming the crucial roles of TLR4 and MD2/LY96 in LPS signaling (Akira et al., 2006; Nagai et al., 2002). The cellular outcome of TLR4 engagement can differ, depending upon the recruitment of the adaptor proteins myeloid differentiation primary response gene 88 (MyD88) or toll-interleukin-1 receptor domain-containing adapter inducing IFN-b (TRIF). Whereas MyD88 is required for rapid activation of the transcription factor nuclear factor-κB (NF-κB) and the NF-κB-induced production of pro-inflammatory cytokines such as tumor necrosis factor (TNF), the TRIF-dependent pathway leads to sustained NF-κB activity but also activates interferon regulatory factor 3 (IRF-3) (Yamamoto et al., 2003). How the selective recruitment of either MyD88 or TRIF to TLR4 is achieved is currently unknown.
Importantly, however, during the last decades structural studies have shown a high variability of LPS structures within and among bacterial species and strains regarding carbohydrate backbone, degree of phosphorylation, and fatty acid acylation patterns (Gaekwad et al., 2010). Even an increase in temperature during microbial growth has been demonstrated to cause changes in the concentration of carbohydrates in LPS, which modifies their composition (Tso and Dooley, 1995, J. Med. Microbiol. 42:32–8). These differences can result in very different host responses to LPS in vivo and in vitro and can influence the immune response control of bacterial infections. For example, Monophosphoryl Lipid A from Salmonella enteric (subsp. enterica serovar Minnesota), activates LPS receptor signaling very weakly compared with fully phosphorylated lipid A from its parent LPS molecule (Mata-Haro et al., 2007). Furthermore, certain bacteria strains have the ability to modify the structure of Lipid A and thereby influence its detection by the host: isolates of Pseudomonas aeruginosa are capable of modifying the structure of Lipid A into a penta-acylated moiety, which does not activate the TLR4 signaling cascade and therefore does not trigger an immune response (Miller et al., 2005).
For scientists to understand, analyze and replicate published experiments, it is crucial that all available information and details regarding the source, strain and structure of LPS are given, as LPS batches obtained from different vendors can differ significantly in terms of its biological activities and the potency of cytokine responses induced by LPS. In this context, the studies of Mata-Haro et al. have indicated that LPS or lipooligosaccharide (LOS) isolated from particular bacterial strains can preferentially induce either MyD88- or TRIF-dependent cytokine production (Mata-Haro et al., 2007), demonstrating the complex relationships between LPS structure and biological responses. Thus, due to the lack of information reported in the scientific literature regarding the source of LPS used in stimulation experiments (e.g. vendor, source, ordering number, strain, and structure), this situation can further complicate our understanding of LPS biology as replication efforts can lead to confusing and puzzling results.
To be able to unambiguously identify critical research tools, PAASP supports the Resource Identification Initiative, with the aim of promoting unique, persistent identification and tracking of key biological resources, including antibodies, cell lines, model organisms and tools. We encourage authors to include in all manuscripts, unique Research Resource Identifiers (RRIDs) provided by the Resource Identification Portal . More information on how to include listed RRIDs or generate new RRIDs can be found on the Resource Identification Portal.