The CP43 Proximal Antenna Complex of Higher Plant Photosystem II Revisited: Modeling and Hole Burning Study. I

The final version is available at: http://pubs.acs.org/journal/jpcbfkThe CP43 core antenna complex of photosystem II is known to possess two quasi-degenerate “red”-trap states (Jankowiak, R. et al. J. Phys. Chem. B 2000, 104, 11805). It has been suggested recently ( Zazubovich, V.; Jankowiak, R. J. Lumin. 2007, 127, 245) that the site distribution functions of the red states (A and B) are uncorrelated and that narrow holes are burned in the subpopulations of chlorophylls (Chls) from states A and B that are the lowest-energy Chl in their complex and previously thought not to transfer energy. This model of uncorrelated excitation energy transfer (EET) between the quasidegenerate bands is expanded by taking into account both electron−phonon and vibrational coupling. The model is applied to fit simultaneously absorption, emission, zero-phonon action, and transient hole burned (HB) spectra obtained for the CP43 complex with minimized contribution from aggregation. It is demonstrated that the above listed spectra can be well-fitted using the uncorrelated EET model, providing strong evidence for the existence of efficient energy transfer between the two lowest energy states, A and B (either from A to B or from B to A), in CP43. Possible candidate Chls for the low-energy A and B states are discussed, providing a link between CP43 structure and spectroscopy. Finally, we propose that persistent holes originate from regular NPHB accompanied by the redistribution of oscillator strength due to excitonic interactions, rather than photoconversion involving Chl−protein hydrogen bonding, as suggested before (Hughes J. L. et al. Biochemistry 2006, 45, 12345). In the accompanying paper ( Reppert, M.; Zazubovich, V.; Dang, N. C.; Seibert, M.; Jankowiak, R. J. Phys. Chem. B 2008, 9934), it is demonstrated that the model discussed in this manuscript is consistent with excitonic calculations, which also provide very good fits to both transient and persistent HB spectra obtained under non-line-narrowing conditions.This work was supported by the start-up funding at the Department of Chemistry, Kansas State University (RJ, NCD, MR and BN), and in part by the U.S. Department of Energy (DOE) EPSCoR grant (RJ), Energy Biosciences Program, Basic Energy Sciences, DOE (MS and NCD) and BFU2005-07422-CO2-01; Spain (RP). VZ acknowledges support by NSERC.Peer reviewe

Transcriptional Landscape of the Prenatal Human Brain

Summary The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development

Associations of Underlying Health Conditions With Anxiety and Depression Among Outpatients: Modification Effects of Suspected COVID-19 Symptoms, Health-Related and Preventive Behaviors

Objectives: We explored the association of underlying health conditions (UHC) with depression and anxiety, and examined the modification effects of suspected COVID-19 symptoms (S-COVID-19-S), health-related behaviors (HB), and preventive behaviors (PB).Methods: A cross-sectional study was conducted on 8,291 outpatients aged 18–85 years, in 18 hospitals and health centers across Vietnam from 14th February to May 31, 2020. We collected the data regarding participant's characteristics, UHC, HB, PB, depression, and anxiety.Results: People with UHC had higher odds of depression (OR = 2.11; p < 0.001) and anxiety (OR = 2.86; p < 0.001) than those without UHC. The odds of depression and anxiety were significantly higher for those with UHC and S-COVID-19-S (p < 0.001); and were significantly lower for those had UHC and interacted with “unchanged/more” physical activity (p < 0.001), or “unchanged/more” drinking (p < 0.001 for only anxiety), or “unchanged/healthier” eating (p < 0.001), and high PB score (p < 0.001), as compared to those without UHC and without S-COVID-19-S, “never/stopped/less” physical activity, drinking, “less healthy” eating, and low PB score, respectively.Conclusion: S-COVID-19-S worsen psychological health in patients with UHC. Physical activity, drinking, healthier eating, and high PB score were protective factors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Diffusion of Squalene in <i>n</i>‑Alkanes and Squalane

Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six methyl groups and six isolated double bonds. Capillary flow techniques have been used to determine its translational diffusion constant, <i>D</i>, at room temperature in squalane, <i>n</i>-C₁₆, and three <i>n</i>-C₈–squalane mixtures. The <i>D</i> values have a weaker dependence on viscosity, η, than predicted by the Stokes–Einstein relation, <i>D</i> = <i>k</i>_B<i>T</i>/(6πη<i>r</i>). A fit to the modified relation, <i>D</i>/<i>T</i> = <i>A</i>_SE/η^<i>p</i>, gives <i>p</i> = 0.820 ± 0.028; <i>p</i> = 1 for the Stokes–Einstein limit. The translational motion of squalene appears to be much like that of <i>n</i>-alkane solutes with comparable chain lengths; their <i>D</i> values show similar deviations from the Stokes–Einstein model. The <i>n</i>-alkane with the same carbon chain length as squalene, <i>n</i>-C₂₄, has a near-equal <i>p</i> value of 0.844 ± 0.018 in <i>n</i>-alkane solvents. The values of the hydrodynamic radius, <i>r</i>, for <i>n</i>-C₂₄, squalene, and other <i>n</i>-alkane solutes decrease as the viscosity increases and have a common dependence on the van der Waals volumes of the solute and solvent. The possibility of studying squalene in lipid droplets and membranes is discussed

Insight into the Electronic Structure of the CP47 Antenna Protein Complex of Photosystem II: Hole Burning and Fluorescence Study

16 Pag., 12 Fig.We report low temperature (T) optical spectra of the isolated CP47 antenna complex from Photosystem II (PSII) with a low-T fluorescence emission maximum near 695 nm and not, as previously reported, at 690−693 nm. The latter emission is suggested to result from three distinct bands: a lowest-state emission band near 695 nm (labeled F1) originating from the lowest-energy excitonic state A1 of intact complexes (located near 693 nm and characterized by very weak oscillator strength) as well as emission peaks near 691 nm (FT1) and 685 nm (FT2) originating from subpopulations of partly destabilized complexes. The observation of the F1 emission is in excellent agreement with the 695 nm emission observed in intact PSII cores and thylakoid membranes. We argue that the band near 684 nm previously observed in singlet-minus-triplet spectra originates from a subpopulation of partially destabilized complexes with lowest-energy traps located near 684 nm in absorption (referred to as AT2) giving rise to FT2 emission. It is demonstrated that varying contributions from the F1, FT1, and FT2 emission bands led to different maxima of fluorescence spectra reported in the literature. The fluorescence spectra are consistent with the zero-phonon hole action spectra obtained in absorption mode, the profiles of the nonresonantly burned holes as a function of fluence, as well as the fluorescence line-narrowed spectra obtained for the Qy band. The lowest Qy state in absorption band (A1) is characterized by an electron−phonon coupling with the Huang−Rhys factor S of 1 and an inhomogeneous width of 180 cm−1. The mean phonon frequency of the A1 band is 20 cm−1. In contrast to previous observations, intact isolated CP47 reveals negligible contribution from the triplet-bottleneck hole, i.e., the AT2 trap. It has been shown that Chls in intact CP47 are connected via efficient excitation energy transfer to the A1 trap near 693 nm and that the position of the fluorescence maximum depends on the burn fluence. That is, the 695 nm fluorescence maximum shifts blue with increasing fluence, in agreement with nonresonant hole burned spectra. The above findings provide important constraints and parameters for future excitonic calculations, which in turn should offer new insight into the excitonic structure and composition of low-energy absorption traps.This work was performed at K-State and was supported by a U.S. Department of Energy (US-DOE) EPSCoR grant (R.J.) (DE-FG02-08ER46504) and the supplements from the Office of Basic Energy Sciences (US-DOE) and the Kansas Technology Enterprise Corporation. Partial support was also provided by the Office of Science, US-DOE (M.S.; NREL Contract DE-AC36-08GO28308), and the PN I+D+I of Spain (R.P.; AGL2008-00377). V.Z. acknowledges support by NSERC Discovery Grant.Peer reviewe

Integrated freshwater aquaculture, crop and livestock production in the Mekong delta, Vietnam: Determinants and the role of the pond

Promotion of integrated aquaculture with agriculture, including crops and livestock (IAA-farming), requires consideration of both bio-physical and socio-economic contexts. The major factors influencing the adoption of IAA-farming by households at three sites in the Mekong delta were identified. Special attention was given to the multiple roles ponds play in IAA-farming systems. Information was collected through semi-structured interviews and discussions with focus groups and key individuals. Data were analyzed using multivariate factor analysis, analysis of variance or participatory ranking methods. Three major lAA-systems were identified: (1) low-input fish farming integrated with intensive fruit production (system 1), (2) medium-input fish farming integrated with less intensive fruit production (system 2), and (3) high-input fish farming integrated with less intensive fruit production (system 3). System I was commonly practised in a rural fruit-dominated area with fertile soils, while systems 2 and 3 were more evident ill peri-urban rice-dominated areas with less fertile soils. In the study area, only 6% of poor farmers adopted IAA-farming, while this was 42% for intermediate and 60% for rich households. Richer farmers tended to intensify fish farming and seek a more commercial orientation. The major factors why farmers did not start aquaculture were the inappropriateness of technology, insufficient land holding or poor access to extension services, limited farm management, and through a fear of conflicts associated with pesticide use on crops. The main motivations for practising IAA-farming included increased income and food for home consumption from the available farm resources while reducing environmental impacts. Further improvements to IAA-systems can be realized by strengthening nutrient recycling between different IAA-system components while enhancing farming output and safeguarding the environment