Photoreduction of the secondary Photosystem I electron acceptor vitamin K1 in intact spinach chloroplasts and Cyanobacteria in vivo

AbstractThe light-induced EPR changes in the g=2 region of intact spinach chloroplasts and of marine cyanobacteria Synechococcus PCC 7002 at room temperature have been analysed. Illumination after dark adaptation results in the well known transient oxidation of P700 and its subsequent re-reduction during the first 100 ms of the illumination, as monitored by EPR Signal I. Here we show, that after a distinct lag phase, coinciding with the re-reduction of P700, a second EPR signal is generated. This signal could be identified as the reduction signal of phylloquinone electron acceptor A1 by its asymmetric spectrum (g=2.0049, ΔHptp=1.00 mT) and by its sensitivity to conditions which suppress limitation of electron transport at the acceptor side of PS I during illumination. Since steady state reduction of A1 has to date been found only by photoaccumulation in prereduced PS I particles at cryogenic temperatures, this is the first observation of the species under physiological conditions. A1 reduction is shown to saturate with light intensity at a level of 0.5 per P700. The observation of substantial levels of reduced A1 in vivo should provide new insights into the mechanisms of energy dissipation and light regulation of the reaction centre of PS I under acceptor limited conditions

EPR kinetic studies of the S−1 state in spinach thylakoids

AbstractThe YZ decay kinetics in a formal S−1 state, regarded as a reduced state of the oxygen evolving complex, was determined using time-resolved EPR spectroscopy. This S−1 state was generated by biochemical treatment of thylakoid membranes with hydrazine. The steady-state oxygen evolution of the sample was used to optimize the biochemical procedure for performing EPR experiments. A high yield of the S−1 state was generated as judged by the two-flash delay in the first maximum of oxygen evolution in Joliot flash-type experiments. We have shown that the YZ re-reduction rate by the S−1 state is much slower than that of any other S-state transition in hydrazine-treated samples. This slow reduction rate in the S−1 to S0 transition, which is in the order of the S3 to S0 transition rate, suggests that this transition is accompanied by some structural rearrangements. Possible explanations of this unique, slow reduction rate in the S−1 to S0 transition are considered, in light of earlier observations by others on hydrazine/hydroxylamine reduced PS II samples

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Persistent spectral hole burning from oxygen-evolving Photosystem II cores from cyanobacteria and higher plants

Persistent spectral hole burning was performed on active Photosystem II (PSII) cores from spinach and Synechocystis 6803, each containing about 32 chl a molecules per core. Hole-burning action spectra are presented. The data appear inconsistent with a mechanism involving non-photochemical hole burning, as has previously been observed in isolated PSII protein-pigment fragments. A photochemical hole-burning mechanism involving charge separation in P680 accounts for the features of the spectra presented