dataesr/scientific-paragraphs-categorization huggingface dataset:
| Data collection We quantified biovolume production and energy fluxes for 10 days, corresponding to approximately 10 generations  (Laws, 2013). Data were collected each day for the first five days and at alternate days afterwards for a total of eight sampling times (day 0, 1,  2, 3, 4, 6, 8 and 10). One millilitre sample from each replicate culture was fixed with Lugol's solution (1%) to quantify the abundance and cell size of each species as described above. The total biovolume of the culture was calculated as the sum of individual species biovolumes for pairs and communities. On the same day, we measured oxygen evolution rates (net photosynthesis, post-illumination and dark metabolism) from a 5 ml sample of each culture. Oxygen evolution rates were calculated from change in percentage oxygen saturation using 24-channel sensor dish readers (SDR; PreSens Precision Sensing GmbH) following established protocols  (Ghedini, Loreau, et al.
ACK N OWLED G EM ENTS We thank  Jiaye Qin  and  Mia Wansbrough  for laboratory assistance and  Dr Martino Malerba  for statistical advice. G. G. was supported by the  Australian Research Council  ( DE190100660 ), D. J. M. by the  Centre for Geometric Biology at Monash University  and M. L. by the  TULIP Laboratory of Excellence  ( ANR-10-LABX-41 ).
, 2012; Heide and Wittig, 2013). By this, migration profiles are obtained for hundreds of proteins and proteins with similar migration profiles are likely present in common protein complexes. This technique has been applied to several photosynthetic organisms, including Arabidopsis thaliana, Physcomitrella patens, Chlamydomonas reinhardtii, and five cyanobacterial species resulting in the Protein Co-Migration Database for photosynthetic organisms (PCoM)  (Takabayashi et al. , 2017). In this study we have identified the Chlamydomonas homolog of LPA2 and employed the complexome profiling technique to thylakoids isolated from wild type and a lpa2 mutant to get new insights into the function of LPA2 in PSII biogenesis. The distinct migration profiles of PSII core subunits in wild type and lpa2 mutant allowed the identification of novel proteins potentially associated with PSII based on their co-migration with the PSII core subunits.
Results The lpa2 mutant accumulates hardly any PSII supercomplexes, shows impaired growth and is sensitive to high light intensities  Ma et al. stated  that there is no gene encoding LPA2 in cyanobacteria and Chlamydomonas  (Ma et al. , 2007; RETRACTION, 2016). To test this, we performed database searches and could confirm the absence of genes encoding LPA2 homologs in cyanobacteria but could find a gene encoding a putative LPA2 homolog in Chlamydomonas. We analyzed LPA2 homologs from land plants, moss and green algae and found that they all share properties such as a chloroplast transit peptide followed by a sequence with a twin-arginine motif, and a highly conserved region with two predicted transmembrane domains (Figure  1A ). To test, whether the Chlamydomonas protein is a bona-fide LPA2 homolog, we ordered a mutant from the Chlamydomonas library project (CLiP)  (Li et al.
However, BN-PAGE analysis showed an abolished accumulation of PSII complexes, particularly of PSII supercomplexes, in the mutant compared to the wild type (Figure  2D ). To ensure that the observed phenotypes in the mutant were caused by the inactivation of the putative LPA2 locus, we generated two constructs based on the LPA2 cDNA and genetic parts from the Modular Cloning toolbox  (Crozet et al. , 2018)  for complementation. The cDNA was driven by the HSP70A-RBCS2 fusion promoter, terminated by the RPL23 terminator, and translationally fused with parts encoding either multiple stop codons or a 3xHA epitope (Figure  1B ). The two resulting level 1 modules were combined with an aadA cassette, transformed into the mutant, and resulting spectinomycin resistant transformants were screened for restored accumulation of the D1 protein (multi-stop construct) or accumulation of HA-tagged LPA2 protein (Supplemental Figure  3 ).
Thylakoid membranes were solubilized with n-Dodecyl -D-maltoside (-DDM) and protein complexes separated on a 4-15 % BN gel (Supplemental Figure  4 ). Each gel lane was cut into 36 slices and the resulting 216 slices were subjected to tryptic in-gel digestion and LC-MS/MS analysis. In total, 1734 proteins were identified. Extracted ion chromatograms were used for protein quantification followed by normalization based on total ion intensities per lane (although equal amounts of protein were loaded, there are differences between the replicates that make normalization necessary (Supplemental Figure  4 )). Ion intensity profiles for each protein along the BN gel run can be displayed from the Excel table in Supplemental Dataset 1. The migration profiles of all identified proteins of wild type and lpa2 mutant, clustered according to their migration behavior, are shown in Supplemental Dataset 2 as heat maps.
The migration patterns of only few known PSII auxiliary factors differ between lpa2 mutant and wild type We reasoned that changes between the migration patterns of known auxiliary factors involved in PSII biogenesis, repair, and the regulation of PSII complex dynamics might reveal deeper insights into LPA2 function. Therefore, we started from a list of auxiliary factors compiled by  Lu (2016)  for Arabidopsis and searched for Chlamydomonas homologs that were detected in at least two replicates of mutant or wild type in the complexome profiling dataset (Supplemental Table  1 ). The migration profiles of the resulting 37 factors are displayed in the heat map shown in Figure  3B. Most of the factors were found to migrate in the low molecular mass region below LHCII trimers. Here, LPA2 and LPA19 (CGL54), a factor involved in the C-terminal processing of D1 during assembly  (Wei et al.
Identification of novel proteins potentially associated with PSI and PSII We reasoned that the characteristic, distinct migration profiles of PSII and PSI subunits in wild type and lpa2 mutant might enable the identification of novel proteins interacting with the photosystems. We therefore searched among the 1734 proteins identified in our complexome profiling dataset for proteins that meet the following four criteria: 1. Exhibit a migration profile resembling that of canonical PSI or PSII subunits in wild type and lpa2 mutant. 2. Identified in at least two of the three replicates in wild type or mutant. 3. Contain a putative chloroplast transit peptide. 4. Are conserved in photosynthetic organisms. MBI1 met all four criteria to qualify as a protein potentially interacting with PSI. It co-migrated with PSI core subunits in wild type and lpa2 mutant (Figure  3A ).
MBI1 is an OPR protein that functions as a maturation factor of the psbI transcript and appears to be conserved only in the Chlamydomonadales  (Wang et al. , 2015). Although MBI1 is a large protein (~138 kDa), we identified only a single peptide (AEAEAQRRLGLGLR) with a comparably low identification score but good ion intensity (Supplemental Dataset 3). We therefore cannot rule out that the underlying fragmentation spectrum derives from a modified peptide of a PSI core subunit that is isobaric with the assigned MBI1 peptide and produces similar fragment ions. Hence, this finding should be taken with greatest care. The gene product of Cre01. g042200 met all four criteria to qualify as a protein potentially interacting with PSII (Figure  3A , Figure  4 ). It co-migrated with PSII supercomplexes, dimers, RC47 and, most pronounced, with monomers.
Its abundance in these complexes was reduced in the lpa2 mutant compared to the wild type, while its unassembled form was more abundant in the mutant. The protein encoded by Cre01. g042200 contains 99 amino acids of which the N-terminal 36 were predicted to represent a chloroplast transit peptide (Figure  5A ). The mature 63-amino acid protein has a molecular mass of 6. 4 kDa and contains a predicted transmembrane helix. Two peptides were identified with high identification scores and good ion intensities (Supplemental Dataset 3). We found homologs only in members of the green algae, brown algae, diatoms, and Eustigmatophytes (Figure  5A ). We named this protein PBA1 (putatively Photosystem B Associated 1). The accumulation of the PSII assembly intermediate RC47 to ~6-fold higher levels in the lpa2 mutant compared to the wild type (Table  2 ) opened the possibility to also identify novel auxiliary factors in PSII assembly that specifically interact with RC47.
To this end, we searched in the complexome profiling dataset for proteins that accumulated in band 17 of the lpa2 mutant at much higher levels than in the wild type and met criteria 2-4 introduced above. Three proteins met all criteria. The first is PSB28, which accumulated in band 15 (PSII monomers) and 17 (RC47) only in the lpa2 mutant, and as free protein in mutant and wild type (Figures  3B  and 4 ). The second protein, encoded by Cre03. g151200 (CGLD16), co-migrated with PSII monomers and RC47. In the lpa2 mutant, less of this protein was present in the monomer band and more in the RC47 band compared to the wild type. CGLD16 is conserved in the green lineage and diatoms. The N-terminal 36 of the overall 110 amino-acids were predicted to form a chloroplast transit peptide, leaving a mature protein of 7.
9 kDa that contains a predicted transmembrane domain at its C-terminus (Figure  5B ). Only one peptide was identified for CGLD16 with high identification score and good ion intensity (Supplemental Dataset 3). The last protein, encoded by Cre06. g278245 (PAO5), comigrated only with RC47 and only in the lpa2 mutant. It contains a predicted chloroplast transit peptide, a Rieske [2Fe-S2] domain, and a pheophorbide a oxygenase (PAO) domain (Figure  5C ). The mature protein has a molecular mass of 52 kDa. Three independent peptides were identified for PAO5 with rather low identification scores presumably due to the low precursor ion intensities (Supplemental Dataset 3). PAO5 is a member of a gene family with eight members in Chlamydomonas, while there are only three family members in Arabidopsis thaliana (Supplemental Figure  5 ).
Accordingly, there is no processing of this sequence, as judged from the identification of two tryptic peptides in this sequence by mass spectrometry (Figure  1A ; Supplemental Dataset 3). The twin-arginine motif might potentially aid in directing the protein to the thylakoid membrane for insertion. The Chlamydomonas lpa2 mutant shares many phenotypes with the Arabidopsis lpa2 mutant  (Ma et al. , 2007; RETRACTION, 2016) : both display slower growth (Figures  1E  and 1F ) and PSII maximum quantum efficiency is reduced to ~65% of wild-type levels (Figure  1D ). Both mutants accumulate slightly more ATP synthase (29% more in Chlamydomonas) (Table  1 ). Both accumulate PSII core subunits D1, D2, CP47, and CP43 to only ~30% of wild-type levels, while subunits of the oxygen-evolving complex were more mildly reduced (Figure  2A ; Table  1 ).
, 2007; RETRACTION, 2016)  (Figure  2B ). Since the Chlamydomonas lpa2 mutant contained the mutagenesis cassette in the second intron of the LPA2 gene (Figure  1B ), it appears possible that this finding is due to residual LPA2 protein in the mutant. However, while LPA2 was detected with three peptides and good ion intensities in all replicates of the wild type, it was not detected in any of the replicates of the mutant (Supplemental Dataset 3). Hence, the unaffected synthesis rate and stability of newly made CP43 in the Chlamydomonas lpa2 mutant argues against the previously proposed role of LPA2 in mediating efficient synthesis or stability of newly made CP43  (Ma et al. , 2007; RETRACTION, 2016). Although such a role seems to be supported by the observed ~6-fold increased accumulation of the RC47 intermediate in the lpa2 mutant compared to the wild type (Figure  4 ; Table  2 ), there are more arguments against it: first, a block of PSII assembly at the level of RC47 would be expected to result in the accumulation of early assembly intermediates, i.
, 2015). And in Synechocystis the absence of PsbI resulted in a destabilization of CP43 binding within PSII monomers and dimers  (Dobakova et al. , 2007). PsbJ also appeared an attractive candidate, as it was the only PSII core subunit identified that accumulated to higher levels in the lpa2 mutant than in the wild type (Table  1 ; Figure  4 ). However, we could detect PsbJ in monomers, dimers and supercomplexes in the mutant (Table  2 ). Unfortunately, mass spectrometry was blind for all other small PSII core subunits. Another possibility is that the lpa2 mutant is impaired in the C-terminal processing of D1 because the absence of LPA2 came along with the absence of LPA19 (Figure  3B ), which facilitates this step in Arabidopsis  (Wei et al. , 2010). LPA19 was detected with three peptides with average identification scores and low ion intensities in all three wild-type replicates (Supplemental Dataset 3), therefore it appears unlikely that we simply missed the protein in the mutant.
Novel proteins that potentially interact with PSII Complexome profiling allowed us to identify three novel proteins potentially interacting with PSII. One of them, PBA1, was found to co-migrate with PSII core subunits. Here, the distinct migration profiles exhibited by the core subunits in wild type and lpa2 mutant increased the confidence of true co-migration and the detection of two peptides the confidence of its identification (Figures  3A  and 4 ; Supplemental Dataset 3). The protein is conserved only in green algae, diatoms, Eustigmatophytes, and brown algae (Figure  5A ), which might explain why it has not been detected so far. Its small size (6. 4 kDa) and the predicted transmembrane helix are typical features of small PSII core subunits  (Pagliano et al. , 2013). CGLD16 also is a small protein (7.
9 kDa) containing a predicted transmembrane helix. It co-migrated only with PSII monomers and RC47 and, as expected, more with monomers in the wild type, and more with RC47 in the lpa2 mutant (Figures  3A  and 4 ). Although its detection was based on a single peptide, this was with a high identification score (Supplemental Dataset 3). This protein is conserved in the green lineage and diatoms (Figure  5B ) and could potentially represent a novel factor involved in PSII assembly or the regulation of PSII complex dynamics. The small size of PBA1 and CGLD16 justified that their potential interaction with the different PSII assembly states did not change their migration properties. This is different for the third protein found to potentially interact only with RC47 and only in the lpa2 mutant, PAO5, which has a predicted molecular mass of 52 kDa and was identified with three peptides of low ion intensity (Supplemental Dataset 3).
Clearly, its direct interaction partners need to be identified by coimmunoprecipitation or related approaches. In this study, we analyzed our complexome profiling dataset with a focus on the major photosynthetic complexes in the thylakoid membranes. However, the dataset is so rich that proteins involved in many other aspects can be investigated, such as complexes of the mitochondrial respiration chain or complexes formed by TCA cycle enzymes  (Rugen et al. , 2020). These are in the dataset, because tubular mitochondria are closely connected with chloroplasts in Chlamydomonas  (Niemeyer et al. , 2020)  and contaminate thylakoid preparations.
Evaluation of MS data The analysis of MS runs was performed using MaxQuant version 1. 6. 0. 1  (Cox and Mann, 2008). Library generation for peptide spectrum matching was based on Chlamydomonas reinhardtii genome release 5. 5  (Merchant et al. , 2007)  including chloroplast and mitochondrial proteins. Oxidation of methionine and acetylation of the N-terminus were considered as peptide modifications. Maximal missed cleavages were set to 3 and peptide length to 6 amino acids, the maximal mass to 6000 Da. Thresholds for peptide spectrum matching and protein identification were set by a false discovery rate (FDR) of 0. 01. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier XXX (in work). Total protein group intensities varied between samples.
The distance of the average migration profiles for every protein was calculated as the Euclidean distance between wild type and mutant. To adjust for amplitude-introduced bias, each distance was divided by the maximal average intensity of wild type or mutant, respectively. Data normalization and analysis were performed using FSharp. Stats (https://github. com/CSBiology/FSharp. Stats). The migration profiles were visualized using Plotly. NET (https://github. com/muehlhaus/FSharp. Plotly) and the NOVA software  (Giese et al. , 2014).
The chosen configurations for the modulator (M), analyzer (A) and polarizer (P) positions were: M = 0 • and A = 45 • ; the incidence angle was AOI = 70 •. The experimental data were fitted by modelling using the Delta Psi 2 software from Horiba Jobin Yvon (Horiba Jobin Yvon, Longjumeau, France). The optimization of the models was done by following the procedure described in  [17]. The electrical conductivity measurements were done using four-point method in planar geometry at room temperature using a Keithley 2600 source Metter (RS Components Ltd. , Northants, UK), by measuring the total (sheet) resistance of the multilayer structure. The distance between the probe tips was 0. 635 mm. The electrical conductivity was calculated using the estimated value of thickness obtained by ellipsometry for the three-layer structure.
lyzer (A) and polarizer (P) positions were: M = 0° and A = 45°; the incidence angle was AOI = 70°. The experimental data were fitted by modelling using the Delta Psi 2 software from Horiba Jobin Yvon (Horiba Jobin Yvon, Longjumeau, France). The optimization of the models was done by following the procedure described in  [17]. The electrical conductivity measurements were done using four-point method in planar geometry at room temperature using a Keithley 2600 source Metter (RS Components Ltd. , Northants, UK), by measuring the total (sheet) resistance of the multilayer structure. The distance between the probe tips was 0. 635 mm. The electrical conductivity was calculated using the estimated value of thickness obtained by ellipsometry for the three-layer structure.
For TiO 2 films and TiO 2 /Ag/TiO 2 films on glass and plastic substrates, the contact angles decreased after exposure to UV, indicating that the surfaces became more hydrophilic. This is in agreement with the classical behavior of TiO 2 films  [36]. For TiO 2 :Nb/Ag/TiO 2 :Nb and NiO/Ag/NiO, the influence of UV radiation was quite slight. Refractive index and film thickness were determined by spectroscopic ellipsometry. Thickness for single layers and the individual thicknesses in multilayer structures were determined by fitting the experimental ellipsometric spectra with those which resulted from theoretical models. For the numerical simulations and modeling, we used the Delta Psi2 software from Horiba Jobin Yvon. The global refractive indices of structures were measured and modelled using the following dispersion formulas: the new amorphous dispersion formula for TiO 2 and TiO 2 :Nb; the Tauc-Lorentz formula for NiO; and the Drude and Tauc-Lorentz formulae for Ag.
For the numerical simulations and modeling, we used the Delta Psi2 software from Horiba Jobin Yvon. The global refractive indices of structures were measured and modelled using the following dispersion formulas: the new amorphous dispersion formula for TiO2 and TiO2:Nb; the Tauc-Lorentz formula for NiO; and the Drude and Tauc-Lorentz formulae for Ag. Figure  5  illustrates the optical models used for the theoretical calculations and simulations for single layers (A) and O/M/O structures (B). (A) (B) Refractive index and film thickness were determined by spectroscopic ellipsometry. Thickness for single layers and the individual thicknesses in multilayer structures were determined by fitting the experimental ellipsometric spectra with those which resulted from theoretical models. For the numerical simulations and modeling, we used the Delta Psi2 software from Horiba Jobin Yvon.
Characterization X-ray diffraction (XRD) was recorded on a PANalytical Empyrean Xray diffractometer in Bragg-Brentano configuration with the 0. 02 • step size and 1 s step time. Cu Kα radiation (40 kV and 30 mA) was used as the X-ray source. N 2 adsorption isotherms were collected by a volumetric gas adsorption analyzer (Quantachrome Instruments Autosorb-iQ-MP-AG). Typically, 50-80 mg powder sample was loaded in a mm large bulb sample cell and degassed under vacuum at 120 • C for 8 h. The BET surface area was determined using the data points in the pressure range of 0. 01 -0. 1 P/P 0 from the N 2 adsorption isotherms at Fig. 1. Scheme of the synthesis of Ru@MCM catalyst. Q. Wang et al. K. TGA was carried out by SDT Q600 (Figs. 2 3 4 5 ) in the temperature range of 25~900 • C under air/N 2 conditions.
7 eV) and 180 • double focusing hemispherical analyzer with a six-channel detector. The BE (binding energy) of the photoemission spectra was calibrated to the Si 2p peak with BE 103. 4 eV for Si containing samples and to adventitious carbon C 1s peak with BE 284. 8 eV. Small Angle Scattering experiments were done on two homebuilt instruments at the LPS (Laboratoire de Physique des Solides, Orsay, France). Solid materials were recorded on a SAXS instrument operating with a copper rotating anode X-ray source (CuKα = 0. 1542 nm) when the micellar solutions were recorded on a second instrument called MODIX operating with a molybdenum rotating anode X-ray source (MoKα = 0. 071 nm). Data reduction from 2D-image to the radially averaged intensity was done following standard procedures using the NIKA macros written for IgorPro (Wavemetrics, Oswego, USA)  [28].
Acknowledgments Vitaly Ordomsky and  Qiyan Wang  thank the  ANR (France)   Nano4 - FUT  ( ANR-16-CE06-0013 ) project for financial support. Sara Santos ,  César A. Urbina-Blanco  and  Mark Saeys  acknowledge the support from  VLAIO  with the cluster  SBO  project  CO2PERATE  (project number  HBC. 2017. 0692 )and from  UGent High-Performance Computing (HPC). The computational resources ( Stevin Supercomputer Infrastructure ) and services used in this work were provided by the  VSC (Flemish Supercomputer Center) , funded by  Ghent University, FWO  and the  Flemish Governmentdepartment EWI. César A. Urbina-Blanco  acknowledges financial support from a senior postdoctoral fellowship from the  Fund for Scientific Research Flanders (FWO). We thank the  Swiss Light Source  for providing beamtime at the SuperXAS beamline.
Catalyst Characterization XRD analysis was performed using a Phillips PW 1730 (Eindhoven, Netherlands) with 2θ ranging from 5 to 80°. The lattice parameters of the structure were refined using the Rietveld method using the software, MAUD (version 2. 93). Structural presentation was realized using the Vesta program. Raman spectra were obtained from 100 to 800 cm -1 using a Horiba Jobin-Yvon (LabRAM HR, Longjumeau, France). The morphology of the sample was visualized by field emission scanning electron microscopy (FESEM) (JEOL JSM-7610plus, Tokyo, Japan). The sample's UV-visible diffuse reflectance spectrum (DRS) was obtained from 200 to 800 cm -1 using a Cary 5000 UV-vis (Agilent, Stevens Creek Blvd, Santa Clara, USA). The photoluminescence spectra were determined using an FL3-DFX-IHR320 spectrophotometer (Horiba, Longjumeau, France) with a wavelength excitation of 342 nm.