Photoperiodic control of the <i>Arabidopsis</i> proteome reveals a translational coincidence mechanism

Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in proteins of photosynthesis, primary and secondary metabolism, including pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates in the day than the night likely contribute to these changes, via an interaction with rhythmic changes in RNA abundance. Photoperiodic control of protein levels might be greatest only if high translation rates coincide with high transcript levels in some photoperiods. We term this proposed mechanism “translational coincidence”, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that translational coincidence contributes to seasonal control of the proteome in many phototrophic organisms. This may explain why many transcripts but not their cognate proteins exhibit diurnal rhythms

Size-selective nanoparticle growth on few-layer graphene films

We observe that gold atoms deposited by physical vapor deposition onto few layer graphenes condense upon annealing to form nanoparticles with an average diameter that is determined by the graphene film thickness. The data are well described by a theoretical model in which the electrostatic interactions arising from charge transfer between the graphene and the gold particle limit the size of the growing nanoparticles. The model predicts a nanoparticle size distribution characterized by a mean diameter D that follows a scaling law D proportional to m^(1/3), where m is the number of carbon layers in the few layer graphene film.Comment: 15 pages, 4 figure

The Impact of Implementing a Test, Treat and Retain HIV Prevention Strategy in Atlanta among Black Men Who Have Sex with Men with a History of Incarceration: A Mathematical Model

Background Annually, 10 million adults transition through prisons or jails in the United States (US) and the prevalence of HIV among entrants is three times higher than that for the country as a whole. We assessed the potential impact of increasing HIV Testing/Treatment/Retention (HIV-TTR) in the community and within the criminal justice system (CJS) facilities, coupled with sexual risk behavior change, focusing on black men-who-have-sex-with-men, 15–54 years, in Atlanta, USA. Methods We modeled the effect of a HIV-TTR strategy on the estimated cumulative number of new (acquired) infections and mortality, and on the HIV prevalence at the end of ten years. We additionally assessed the effect of increasing condom use in all settings. Results In the Status Quo scenario, at the end of 10 years, the cumulative number of new infections in the community, jail and prison was, respectively, 9246, 77 and 154 cases; HIV prevalence was 10815, 69 and 152 cases, respectively; and the cumulative number of deaths was 2585, 18 and 34 cases, respectively. By increasing HIV-TTR coverage, the cumulative number of new infections could decrease by 15% in the community, 19% in jail, and 8% in prison; HIV prevalence could decrease by 8%, 9% and 7%, respectively; mortality could decrease by 20%, 39% and 18%, respectively. Based on the model results, we have shown that limited use and access to condoms have contributed to the HIV incidence and prevalence in all settings. Conclusions Aggressive implementation of a CJS-focused HIV-TTR strategy has the potential to interrupt HIV transmission and reduce mortality, with benefit to the community at large. To maximize the impact of these interventions, retention in treatment, including during the period after jail and prison release, and increased condom use was vital for decreasing the burden of the HIV epidemic in all settings

Recommendations for economic evaluations of cell and gene therapies: a systematic literature review with critical appraisal

Objective: No consensus exists on the ideal methodology to evaluate the economic impact and value of new, potentially curative gene therapies. We aimed to identify and describe published methodologic recommendations for the economic evaluation of gene therapies and assess whether these recommendations have been applied in published evaluations. Methods: This study was conducted in three stages: a systematic literature review of methodologic recommendations for economic evaluation of gene therapies; an assessment of the appropriateness of recommendations; and a review to assess the degree to which the recommendations were applied in published evaluations. Results: A total of 2,888 references were screened, 83 articles were reviewed to assess eligibility, and 20 papers were included. Fifty recommendations were identified, and 21 reached consensus thresholds. Most evaluations were based on naive treatment comparisons and did not apply consensus recommendations. Innovative payment mechanisms for gene therapies were rarely considered. The only widely applied recommendations related to modeling choices and methods. Conclusions: Methodological recommendations for economic evaluations of gene therapies are generally not being followed. Assessing the applicability and impact of the recommendations from this study may facilitate the implementation of consensus recommendations in future evaluations

Observation of low energy dispersive modes in un- derdoped (La, Nd) 2−x Sr x CuO 4

We find excitations lower in energy than known phonon modes in underdoped La$_{2-x}$Sr$_x$CuO$_{4+\delta}$ (x=0.08), with both inelastic X-Ray scattering (IXS) and inelastic neutron scattering (INS). A non dispersive excitation at 9 meV is identified and is also seen by INS in (La,Nd)$_{2-x}$Sr$_x$CuO$_{4+\delta}$, with 40$\%$ Nd substitution. INS also identifies a still lower energy dispersive mode at low q in the Nd free sample. These modes are clearly distinct from the longitudinal acoustic phonon and correspond in energy to the Zone Centre modes measured by optical spectroscopy and associated with stripe dynamics

Relating multivariate shapes to genescapes using phenotype-biological process associations for craniofacial shape.

Realistic mappings of genes to morphology are inherently multivariate on both sides of the equation. The importance of coordinated gene effects on morphological phenotypes is clear from the intertwining of gene actions in signaling pathways, gene regulatory networks, and developmental processes underlying the development of shape and size. Yet, current approaches tend to focus on identifying and localizing the effects of individual genes and rarely leverage the information content of high-dimensional phenotypes. Here, we explicitly model the joint effects of biologically coherent collections of genes on a multivariate trait - craniofacial shape - in a sample of n = 1145 mice from the Diversity Outbred (DO) experimental line. We use biological process Gene Ontology (GO) annotations to select skeletal and facial development gene sets and solve for the axis of shape variation that maximally covaries with gene set marker variation. We use our process-centered, multivariate genotype-phenotype (process MGP) approach to determine the overall contributions to craniofacial variation of genes involved in relevant processes and how variation in different processes corresponds to multivariate axes of shape variation. Further, we compare the directions of effect in phenotype space of mutations to the primary axis of shape variation associated with broader pathways within which they are thought to function. Finally, we leverage the relationship between mutational and pathway-level effects to predict phenotypic effects beyond craniofacial shape in specific mutants. We also introduce an online application that provides users the means to customize their own process-centered craniofacial shape analyses in the DO. The process-centered approach is generally applicable to any continuously varying phenotype and thus has wide-reaching implications for complex trait genetics

Rothirschprojekt Aletsch-Goms : Abschlussbericht zum Forschungs- und Managementprojekt 2017–2021

Ab etwa Mitte des 20. Jahrhunderts kommt der Rothirsch im Wallis in nennenswerten Beständen vor. Trotz intensiver Bejagung nehmen die Bestände seither stetig zu und führen teilweise zu Konflikten, insbesondere im Wald und in der Region Aletsch-Goms. Über die Raumnutzung und das Wanderverhalten der Rothirsche in dieser Region lagen bislang einige Einschätzungen und Vermutungen, jedoch kaum gesicherte Fakten vor. Mit dem im Jahr 2017 initiierten Rothirschprojekt Aletsch-Goms wurden bedeutende Wissenslücken für einen fachlich fundierten Umgang mit dieser anspruchsvollen Wildtierart nun geschlossen