Effects of photoperiod extension on clock gene and neuropeptide RNA expression in the SCN of the Soay sheep

In mammals, changing daylength (photoperiod) is the main synchronizer of seasonal functions. The photoperiodic information is transmitted through the retino-hypothalamic tract to the suprachiasmatic nuclei (SCN), site of the master circadian clock. To investigate effects of day length change on the sheep SCN, we used in-situ hybridization to assess the daily temporal organization of expression of circadian clock genes (Per1, Per2, Bmal1 and Fbxl21) and neuropeptides (Vip, Grp and Avp) in animals acclimated to a short photoperiod (SP; 8h of light) and at 3 or 15 days following transfer to a long photoperiod (LP3, LP15, respectively; 16h of light), achieved by an acute 8-h delay of lights off. We found that waveforms of SCN gene expression conformed to those previously seen in LP acclimated animals within 3 days of transfer to LP. Mean levels of expression for Per1-2 and Fbxl21 were nearly 2-fold higher in the LP15 than in the SP group. The expression of Vip was arrhythmic and unaffected by photoperiod, while, in contrast to rodents, Grp expression was not detectable within the sheep SCN. Expression of the circadian output gene Avp cycled robustly in all photoperiod groups with no detectable change in phasing. Overall these data suggest that synchronizing effects of light on SCN circadian organisation proceed similarly in ungulates and in rodents, despite differences in neuropeptide gene expression

Timing as a sexually selected trait: the right mate at the right moment

Sexual selection favours the expression of traits in one sex that attract members of the opposite sex for mating. The nature of sexually selected traits such as vocalization, colour and ornamentation, their fitness benefits as well as their costs have received ample attention in field and laboratory studies. However, sexually selected traits may not always be expressed: coloration and ornaments often follow a seasonal pattern and behaviours may be displayed only at specific times of the day. Despite the widely recognized differences in the daily and seasonal timing of traits and their consequences for reproductive success, the actions of sexual selection on the temporal organization of traits has received only scant attention. Drawing on selected examples from bird and mammal studies, here we summarize the current evidence for the daily and seasonal timing of traits. We highlight that molecular advances in chronobiology have opened exciting new opportunities for identifying the genetic targets that sexual selection may act on to shape the timing of trait expression. Furthermore, known genetic links between daily and seasonal timing mechanisms lead to the hypothesis that selection on one timescale may simultaneously also affect the other. We emphasize that studies on the timing of sexual displays of both males and females from wild populations will be invaluable for understanding the nature of sexual selection and its potential to act on differences within and between the sexes in timing. Molecular approaches will be important for pinpointing genetic components of biological rhythms that are targeted by sexual selection, and to clarify whether these represent core or peripheral components of endogenous clocks. Finally, we call for a renewed integration of the fields of evolution, behavioural ecology and chronobiology to tackle the exciting question of how sexual selection contributes to the evolution of biological clocks.This article is part of the themed issue 'Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'

Prospects for constraining the shape of non-Gaussianity with the scale-dependent bias

We consider whether the non-Gaussian scale-dependent halo bias can be used not only to constrain the local form of non-Gaussianity but also to distinguish among different shapes. In particular, we ask whether it can constrain the behavior of the primordial three-point function in the squeezed limit where one of the momenta is much smaller than the other two. This is potentially interesting since the observation of a three-point function with a squeezed limit that does not go like the local nor equilateral templates would be a signal of non-trivial dynamics during inflation. To this end we use the quasi-single field inflation model of Chen and Wang as a representative two-parameter model, where one parameter governs the amplitude of non-Gaussianity and the other the shape. We also perform a model-independent analysis by parametrizing the scale-dependent bias as a power-law on large scales, where the power is to be constrained from observations. We find that proposed large-scale structure surveys (with characteristics similar to the dark energy task force stage IV surveys) have the potential to distinguish among the squeezed limit behavior of different bispectrum shapes for a wide range of fiducial model parameters. Thus the halo bias can help discriminate between different models of inflation.Comment: 12 pages, 3 figures, v2. minor corrections to the text, matches JCAP published versio

Complex refractive indices in the ultraviolet and visible spectral region for highly absorbing non-spherical biomass burning aerosol

Biomass burning aerosol is a major source of PM2.5, and significantly affects Earth's radiative budget. The magnitude of its radiative effect is poorly quantified due to uncertainty in the optical properties of aerosol formed from biomass burning. Using a broadband cavity-enhanced spectrometer with a recently increased spectral range (360&ndash;720&thinsp;nm) coupled to a size-selecting aerosol inlet, we retrieve complex refractive indices of aerosol throughout the near-ultraviolet and visible spectral region. We demonstrate refractive index retrievals for two standard aerosol samples: polystyrene latex spheres and ammonium sulfate. We then retrieve refractive indices for biomass burning aerosol from 13 controlled fires during the 2016 Missoula Fire Science Laboratory Study. We demonstrate that the technique is highly sensitive to the accuracy of the aerosol size distribution method and find that while we can constrain the optical properties of brown carbon aerosol for many fires, fresh smoke dominated by fractal-like black carbon aerosol presents unique challenges and is not well-represented by Mie theory. For the 13 fires, we show that the accuracy of Mie theory retrievals decreases as the fraction of black carbon mass increases. At 475&thinsp;nm, the average refractive index is 1.635 (&plusmn;0.056) +0.06 (&plusmn;0.12)i, and at 365&thinsp;nm, the average refractive index is 1.605 (&plusmn;0.041) +0.038 (&plusmn;0.074)i. &nbsp;</p

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

Global-scale evidence for the refractory nature of riverine black carbon

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Nature Geoscience 11 (2018): 584-588, doi:10.1038/s41561-018-0159-8.Wildfires and incomplete combustion of fossil fuel produce large amounts of black carbon. Black carbon production and transport are essential components of the carbon cycle. Constraining estimates of black carbon exported from land to ocean is critical, given ongoing changes in land use and climate, which affect fire occurrence and black carbon dynamics. Here, we present an inventory of the concentration and radiocarbon content (∆14C) of particulate black carbon for 18 rivers around the globe. We find that particulate black carbon accounts for about 15.8 ± 0.9% of river particulate organic carbon, and that fluxes of particulate black carbon co-vary with river-suspended sediment, indicating that particulate black carbon export is primarily controlled by erosion. River particulate black carbon is not exclusively from modern sources but is also aged in intermediate terrestrial carbon pools in several high-latitude rivers, with ages of up to 17,000 14C years. The flux-weighted 14C average age of particulate black carbon exported to oceans is 3,700 ± 400 14C years. We estimate that the annual global flux of particulate black carbon to the ocean is 0.017 to 0.037 Pg, accounting for 4 to 32% of the annually produced black carbon. When buried in marine sediments, particulate black carbon is sequestered to form a long-term sink for CO2.A.C. acknowledges financial support from the University of Zurich Forschungskredit Fellowship and the University of Zurich (grant No. STWF-18-026). M.R., S.A. and M.S. acknowledge support from the University Research Priority Projection Global Change and Biodiversity (URPP-GCB). M.Z. acknowledges support from the National Natural Science Foundation of China (No. 41521064). T.E. acknowledges support from the Swiss National Science Foundation (“CAPS-LOCK” and “CAPS-LOCK2” #200021_140850). V.G. acknowledges financial support from an Independent Study Award from the Woods Hole Oceanographic Institution

White Paper on Digital and Complex Information

Information is one of the main traits of the contemporary era. Indeed there aremany perspectives to define the present times, such as the Digital Age, the Big Dataera, the Fourth Industrial Revolution, the fourth Paradigm of science, and in all ofthem information, gathered, stored, processed and transmitted, plays a key role.Technological developments in the last decades such as powerful computers, cheaperand miniaturized solutions as smartphones, massive optical communication, or theInternet, to name few, have enabled this shift to the Information age. This shift hasdriven daily life, cultural and social deep changes, in work and personal activities,on access to knowledge, information spreading, altering interpersonal relations orthe way we interact in public and private sphere, in economy and politics, pavingthe way to globalizationPeer reviewe

Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models.

BACKGROUND: The post-2015 End TB Strategy proposes targets of 50% reduction in tuberculosis incidence and 75% reduction in mortality from tuberculosis by 2025. We aimed to assess whether these targets are feasible in three high-burden countries with contrasting epidemiology and previous programmatic achievements. METHODS: 11 independently developed mathematical models of tuberculosis transmission projected the epidemiological impact of currently available tuberculosis interventions for prevention, diagnosis, and treatment in China, India, and South Africa. Models were calibrated with data on tuberculosis incidence and mortality in 2012. Representatives from national tuberculosis programmes and the advocacy community provided distinct country-specific intervention scenarios, which included screening for symptoms, active case finding, and preventive therapy. FINDINGS: Aggressive scale-up of any single intervention scenario could not achieve the post-2015 End TB Strategy targets in any country. However, the models projected that, in the South Africa national tuberculosis programme scenario, a combination of continuous isoniazid preventive therapy for individuals on antiretroviral therapy, expanded facility-based screening for symptoms of tuberculosis at health centres, and improved tuberculosis care could achieve a 55% reduction in incidence (range 31-62%) and a 72% reduction in mortality (range 64-82%) compared with 2015 levels. For India, and particularly for China, full scale-up of all interventions in tuberculosis-programme performance fell short of the 2025 targets, despite preventing a cumulative 3·4 million cases. The advocacy scenarios illustrated the high impact of detecting and treating latent tuberculosis. INTERPRETATION: Major reductions in tuberculosis burden seem possible with current interventions. However, additional interventions, adapted to country-specific tuberculosis epidemiology and health systems, are needed to reach the post-2015 End TB Strategy targets at country level. FUNDING: Bill and Melinda Gates Foundation