Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale

BACKGROUND

Rodent models are invaluable for studying biological processes in the context of whole organisms. The reproducibility of such research is based on an assumption of metabolic similarity between experimental animals, controlled for by breeding and housing strategies that minimise genetic and environmental variation. Here, we set out to demonstrate the effect of experimental uraemia on the rat urinary metabolome and gut microbiome but found instead that the effect of vendor shipment batch was larger in both areas than that of uraemia.

RESULTS

Twenty four Wistar rats obtained from the same commercial supplier in two separate shipment batches underwent either subtotal nephrectomy or sham procedures. All animals undergoing subtotal nephrectomy developed an expected uraemic phenotype. The urinary metabolome was studied using ¹H-NMR spectroscopy and found to vary significantly between animals from different batches, with substantial differences in concentrations of a broad range of substances including lactate, acetate, glucose, amino acids, amines and benzoate derivatives. In animals from one batch, there was a complete absence of the microbiome-associated urinary metabolite hippurate, which was present in significant concentrations in animals from the other batch. These differences were so prominent that we would have drawn quite different conclusions about the effect of uraemia on urinary phenotype depending on which batch of animals we had used. Corresponding differences were seen in the gut microbiota between animals in different batches when assessed by the sequencing of 16S rRNA gene amplicons, with higher alpha diversity and different distributions of Proteobacteria subtaxa and short-chain fatty acid producing bacteria in the second batch compared to the first. Whilst we also demonstrated differences in both the urinary metabolome and gut microbiota associated with uraemia, these effects were smaller in size than those associated with shipment batch.

CONCLUSIONS

These results challenge the assumption that experimental animals obtained from the same supplier are metabolically comparable, and provide metabolomic evidence that batch-to-batch variations in the microbiome of experimental animals are significant confounders in an experimental study. We discuss strategies for reducing such variability and the need for transparency in research publications about the supply of experimental animals.

Acute kidney injury among HIV-infected patients admitted to the intensive care unit

We describe the incidence, associations and outcomes of acute kidney injury (AKI) among HIV-infected patients admitted to the intensive care unit (ICU). We retrospectively analysed 223 admissions to an inner-London, University-affiliated ICU between 1999 and 2012, and identified those with AKI and performed multivariate analysis to determine associations with AKI. Of all admissions, 66% were affected by AKI of any severity and 35% developed stage 3 AKI. In multivariate analysis, AKI was associated with chronic kidney disease (odds ratio [OR] = 3.19; p = 0.014), a previous AIDS-defining illness (OR = 1.93; p = 0.039) and the Acute Physiology and Chronic Health Evaluation (APACHE) II score, (OR = 3.49; p = 0.018, if > 30). No associations were demonstrated with use of anti-retroviral medication (including tenofovir), or an individual's HIV viral load or CD4 count. AKI was associated with higher inpatient mortality and longer duration of ICU admission. Among patients with stage 3 AKI, only 41% were alive 90 days after ICU admission. Among survivors, 74% regained good renal function, the remainder were dependent on renal replacement therapy or were left with significant ongoing renal dysfunction. Of note, many patients had baseline serum creatinine concentrations well below published reference ranges. AKI among HIV-infected patients admitted to ICU carries a poor prognosis.

Electronic structure contributions to electron transfer in blue Cu and Cu(A)

The experimentally determined electronic structures of mononuclear blue Cu and binuclear Cu(A) centers are summarized and their relation to intra- and inter-protein electron transfer (ET) kinetics are described. Specific contributions of the electronic structures of these two broad classes of Cu ET proteins to H(AB), lambda, and deltaE degrees are discussed. Also, the role of the protein structure in determining key geometric features which define the electronic structures of the metal sites in these proteins is considered.

Hydrogen bonding, solvent exchange, and coupled proton and electron transfer in the oxidation and reduction of redox-active tyrosine Y(Z) in Mn-depleted core complexes of photosystem II

The redox-active tyrosines, Y(Z) and Y(D), of Photosystem II are oxidized by P680+ to the neutral tyrosyl radical. This oxidation thus involves the transfer of the phenolic proton as well as an electron. It has recently been proposed that tyrosine Y(Z) might replace the lost proton by abstraction of a hydrogen atom or a proton from a water molecule bound to the manganese cluster, thereby increasing the driving force for water oxidation. To compare and contrast with the intact system, we examine here, in a simplified Mn-depleted PSII core complex, isolated from a site-directed mutant of Synechocystis PCC 6803 lacking Y(D), the role of proton transfer in the oxidation and reduction of Y(Z). We show how the oxidation and reduction rates for Y(Z), the deuterium isotope effect on these rates, and the Y(Z)* - Y(Z) difference spectra all depend on pH (from 5.5 to 9.5). This simplified system allows examination of electron-transfer processes over a broader range of pH than is possible with the intact system and with more tractable rates. The kinetic isotope effect for the oxidation of P680+ by Y(Z) is maximal at pH 7.0 (3.64). It decreases to lower pH as charge recombination, which shows no deuterium isotope, starts to become competitive with Y(Z) oxidation. To higher pH, Y(Z) becomes increasingly deprotonated to form the tyrosinate, the oxidation of which at pH 9.5 becomes extremely rapid (1260 ms(-1)) and no longer limited by proton transfer. These observations point to a mechanism for the oxidation of Y(Z) in which the tyrosinate is the species from which the electron occurs even at lower pH. The kinetics of oxidation of Y(Z) show elements of rate limitation by both proton and electron transfer, with the former dominating at low pH and the latter at high pH. The proton-transfer limitation of Y(Z) oxidation at low pH is best explained by a gated mechanism in which Y(Z) and the acceptor of the phenolic proton need to form an electron/proton-transfer competent complex in competition with other hydrogen-bonding interactions that each have with neighboring residues. In contrast, the reduction of Y(Z)* appears not to be limited by proton transfer between pH 5.5 and 9.5. We also compare, in Mn-depleted Synechocystis PSII core complexes, Y(Z) and Y(D) with respect to solvent accessibility by detection of the deuterium isotope effect for Y(Z) oxidation and by 2H ESEEM measurement of hydrogen-bond exchange. Upon incubation of H2O-prepared PSII core complexes in D2O, the phenolic proton of Y(Z) is exchanged for a deuterium in less than 2 min as opposed to a t(1/2) of about 9 h for Y(D). In addition, we show that Y(D)* is coordinated by two hydrogen bonds. Y(Z)* shows more disordered hydrogen bonding, reflecting inhomogeneity at the site. With 2H ESEEM modulation comparable to that of Y(D)*, Y(Z)* would appear to be coordinated by two hydrogen bonds in a significant fraction of the centers.

Proximity of acetate, manganese, and exchangeable deuterons to tyrosine YZ. in acetate-inhibited photosystem II membranes: implications for the direct involvement of YZ. in water-splitting

The environment of the photosystem II YZ. radical, trapped in the "split-signal" form, is examined in acetate-treated PSII membranes using pulsed EPR methods. The split-signal line shape is simulated with dipolar and exchange couplings to the Mn cluster of 1260 and -28 MHz, respectively. The 1260-MHz dipolar coupling corresponds to a Mn-YZ. distance of 3.5 A in the point dipole limit. A 0.117-MHz dipolar coupling is observed between nonexchangeable deuterons of methyl-deuterated acetate and YZ.. This interaction is modeled with a 3.1-A distance between an acetate methyl group deuteron and the phenoxy oxygen of YZ*. Since acetate inhibition is competitive with Cl-, this result strongly suggests a close proximity between YZ. and the Cl- cofactor binding site. Analysis of pulsed ENDOR and ESEEM experiments investigating the proximity of deuterons exchanged into the vicinity of YZ. after incubation in 2H2O-enriched buffer demonstrates that YZ. trapped in the split-signal form participates in two hydrogen-bonding interactions, in contrast to YD*, which forms a single hydrogen bond. This result is inconsistent with a simple electron transfer role for YZ* and provides direct experimental evidence for a role for YZ* in proton or hydrogen atom transfer.

Proximity of the manganese cluster of photosystem II to the redox-active tyrosine YZ

Electron spin echo electron-nuclear double resonance (ESE-ENDOR) experiments performed on a broad radical electron paramagnetic resonance (EPR) signal observed in photosystem II particles depleted of Ca2+ indicate that this signal arises from the redox-active tyrosine YZ. The tyrosine EPR signal width is increased relative to that observed in a manganese-depleted preparation due to a magnetic interaction between the photosystem II manganese cluster and the tyrosine radical. The manganese cluster is located asymmetrically with respect to the symmetry-related tyrosines YZ and YD. The distance between the YZ tyrosine and the manganese cluster is estimated to be approximately 4.5 A. Due to this close proximity of the Mn cluster and the redox-active tyrosine YZ, we propose that this tyrosine abstracts protons from substrate water bound to the Mn cluster.