Sunflecks in the upper canopy : dynamics of light-use efficiency in sun and shade leaves of Fagus sylvatica

Sunflecks are transient patches of direct radiation that provide a substantial proportion of the daily irradiance to leaves in the lower canopy. In this position, faster photosynthetic induction would allow for higher sunfleck-use efficiency, as is commonly reported in the literature. Yet, when sunflecks are too few and far between, it may be more beneficial for shade leaves to prioritize efficient photosynthesis under shade. We investigated the temporal dynamics of photosynthetic induction, recovery under shade, and stomatal movement during a sunfleck, in sun and shade leaves of Fagus sylvatica from three provenances of contrasting origin. We found that shade leaves complete full induction in a shorter time than sun leaves, but that sun leaves respond faster than shade leaves due to their much larger amplitude of induction. The core-range provenance achieved faster stomatal opening in shade leaves, which may allow for better sunfleck-use efficiency in denser canopies and lower canopy positions. Our findings represent a paradigm shift for future research into light fluctuations in canopies, drawing attention to the ubiquitous importance of sunflecks for photosynthesis, not only in lower-canopy leaves where shade is prevalent, but particularly in the upper canopy where longer sunflecks are more common due to canopy openness.Peer reviewe

Sunflecks in the upper canopy: dynamics of light-use efficiency in sun and shade leaves of Fagus sylvatica

Sunflecks are transient patches of direct radiation that provide a substantial proportion of the daily irradiance to leaves in the lower canopy. In this position, faster photosynthetic induction would allow for higher sunfleck-use efficiency, as is commonly reported in the literature. Yet, when sunflecks are too few and far between, it may be more beneficial for shade leaves to prioritize efficient photosynthesis under shade. We investigated the temporal dynamics of photosynthetic induction, recovery under shade, and stomatal movement during a sunfleck, in sun and shade leaves of Fagus sylvatica from three provenances of contrasting origin. We found that shade leaves complete full induction in a shorter time than sun leaves, but that sun leaves respond faster than shade leaves due to their much larger amplitude of induction. The core-range provenance achieved faster stomatal opening in shade leaves, which may allow for better sunfleck-use efficiency in denser canopies and lower canopy positions. Our findings represent a paradigm shift for future research into light fluctuations in canopies, drawing attention to the ubiquitous importance of sunflecks for photosynthesis, not only in lower-canopy leaves where shade is prevalent, but particularly in the upper canopy where longer sunflecks are more common due to canopy openness

Natalizumab alters the TCR repertoire after one year of treatment in four MS patients

International audiencen.

Peculiar Velocities into the Next Generation: Cosmological Parameters From Large Surveys without Bias from Nonlinear Structure

We investigate methods to best estimate the normalisation of the mass density fluctuation power spectrum (sigma_8) using peculiar velocity data from a survey like the Six degree Field Galaxy Velocity Survey (6dFGSv). We focus on two potential problems (i) biases from nonlinear growth of structure and (ii) the large number of velocities in the survey. Simulations of LambdaCDM-like models are used to test the methods. We calculate the likelihood from a full covariance matrix of velocities averaged in grid cells. This simultaneously reduces the number of data points and smooths out nonlinearities which tend to dominate on small scales. We show how the averaging can be taken into account in the predictions in a practical way, and show the effect of the choice of cell size. We find that a cell size can be chosen that significantly reduces the nonlinearities without significantly increasing the error bars on cosmological parameters. We compare our results with those from a principal components analysis following Watkins et al (2002) and Feldman et al (2003) to select a set of optimal moments constructed from linear combinations of the peculiar velocities that are least sensitive to the nonlinear scales. We conclude that averaging in grid cells performs equally well. We find that for a survey such as 6dFGSv we can estimate sigma_8 with less than 3% bias from nonlinearities. The expected error on sigma_8 after marginalising over Omega_m is approximately 16 percent.Comment: Accepted for publication in MNRAS, 12 pages, 5 figures. V2 Discussion clarified, 1 figure added, improvements to the text and figures; V3 Figure 5 Plotting error corrected, SN1a contours smalle

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

A “Coiled-Coil” Motif Is Important for Oligomerization and DNA Binding Properties of Human Cytomegalovirus Protein UL77

Human cytomegalovirus (HCMV) UL77 gene encodes the essential protein UL77, its function is characterized in the present study. Immunoprecipitation identified monomeric and oligomeric pUL77 in HCMV infected cells. Immunostaining of purified virions and subviral fractions showed that pUL77 is a structural protein associated with capsids. In silico analysis revealed the presence of a coiled-coil motif (CCM) at the N-terminus of pUL77. Chemical cross-linking of either wild-type pUL77 or CCM deletion mutant (pUL77ΔCCM) implicated that CCM is critical for oligomerization of pUL77. Furthermore, co-immunoprecipitations of infected and transfected cells demonstrated that pUL77 interacts with the capsid-associated DNA packaging motor components, pUL56 and pUL104, as well as the major capsid protein. The ability of pUL77 to bind dsDNA was shown by an in vitro assay. Binding to certain DNA was further confirmed by an assay using biotinylated 36-, 250-, 500-, 1000-meric dsDNA and 966-meric HCMV-specific dsDNA designed for this study. The binding efficiency (BE) was determined by image processing program defining values above 1.0 as positive. While the BE of the pUL56 binding to the 36-mer bio-pac1 containing a packaging signal was 10.0±0.63, the one for pUL77 was only 0.2±0.03. In contrast to this observation the BE of pUL77 binding to bio-500 bp or bio-1000 bp was 2.2±0.41 and 4.9±0.71, respectively. By using pUL77ΔCCM it was demonstrated that this protein could not bind to dsDNA. These data indicated that pUL77 (i) could form homodimers, (ii) CCM of pUL77 is crucial for oligomerization and (iii) could bind to dsDNA in a sequence independent manner

The Incidence of AIDS-Defining Illnesses at a Current CD4 Count ≥200 Cells/µL in the Post-Combination Antiretroviral Therapy Era

The incidence of AIDS was higher in patients with a current CD4 count of 500-749 cells/µL compared to 750-999 cells/µL, but did not decrease further at higher CD4 levels. Results were similar in those virologically suppressed on combination antiretroviral therapy, suggesting immune reconstitution is incomplete until CD4 >750/µ

Health, education, and social care provision after diagnosis of childhood visual disability

Aim: To investigate the health, education, and social care provision for children newly diagnosed with visual disability.Method: This was a national prospective study, the British Childhood Visual Impairment and Blindness Study 2 (BCVIS2), ascertaining new diagnoses of visual impairment or severe visual impairment and blindness (SVIBL), or equivalent vi-sion. Data collection was performed by managing clinicians up to 1-year follow-up, and included health and developmental needs, and health, education, and social care provision.Results: BCVIS2 identified 784 children newly diagnosed with visual impairment/SVIBL (313 with visual impairment, 471 with SVIBL). Most children had associated systemic disorders (559 [71%], 167 [54%] with visual impairment, and 392 [84%] with SVIBL). Care from multidisciplinary teams was provided for 549 children (70%). Two-thirds (515) had not received an Education, Health, and Care Plan (EHCP). Fewer children with visual impairment had seen a specialist teacher (SVIBL 35%, visual impairment 28%, χ2p < 0.001), or had an EHCP (11% vs 7%, χ2p < 0 . 01).Interpretation: Families need additional support from managing clinicians to access recommended complex interventions such as the use of multidisciplinary teams and educational support. This need is pressing, as the population of children with visual impairment/SVIBL is expected to grow in size and complexity.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707