Intrinsic Circadian Clock of the Mammalian Retina: Importance for Retinal Processing of Visual Information

SummaryCircadian clocks are widely distributed in mammalian tissues, but little is known about the physiological functions of clocks outside the suprachiasmatic nucleus of the brain. The retina has an intrinsic circadian clock, but its importance for vision is unknown. Here we show that mice lacking Bmal1, a gene required for clock function, had abnormal retinal transcriptional responses to light and defective inner retinal electrical responses to light, but normal photoreceptor responses to light and retinas that appeared structurally normal by light and electron microscopy. We generated mice with a retina-specific genetic deletion of Bmal1, and they had defects of retinal visual physiology essentially identical to those of mice lacking Bmal1 in all tissues and lacked a circadian rhythm of inner retinal electrical responses to light. Our findings indicate that the intrinsic circadian clock of the retina regulates retinal visual processing in vivo

Valley Splitting Theory of SiGe/Si/SiGe Quantum Wells

We present an effective mass theory for SiGe/Si/SiGe quantum wells, with an emphasis on calculating the valley splitting. The theory introduces a valley coupling parameter, $v_v$, which encapsulates the physics of the quantum well interface. The new effective mass parameter is computed by means of a tight binding theory. The resulting formalism provides rather simple analytical results for several geometries of interest, including a finite square well, a quantum well in an electric field, and a modulation doped two-dimensional electron gas. Of particular importance is the problem of a quantum well in a magnetic field, grown on a miscut substrate. The latter may pose a numerical challenge for atomistic techniques like tight-binding, because of its two-dimensional nature. In the effective mass theory, however, the results are straightforward and analytical. We compare our effective mass results with those of the tight binding theory, obtaining excellent agreement.Comment: 13 pages, 7 figures. Version submitted to PR

Aeolian features on Venus: Preliminary Magellan results

Magellan synthetic aperture radar data reveal numerous surface features that are attributed to aeolian, or wind processes. Wind streaks are the most common aeolian feature. They consist of radar backscatter patterns that are high, low, or mixed in relation to the surface on which they occur. A data base of more than 3400 wind streaks shows that low backscatter linear forms (long, narrow streaks) are the most common and that most streaks occur between 17°S to 30°S and 5°N to 53°N on smooth plains. Moreover, most streaks are associated with deposits from certain impact craters and some tectonically deformed terrains. We infer that both of these geological settings provide fine particulate material that can be entrained by the low-velocity winds on Venus. Turbulence and wind patterns generated by the topographic features with which many streaks are associated can account for differences in particle distributions and in the patterns of the wind streaks. Thus, some high backscatter streaks are considered to be zones that are swept free of sedimentary particles to expose rough bedrock; other high backscatter streaks may be lag deposits of dense materials from which low-density grains have been removed (dense materials such as ilmenite or pyrite have dielectric properties that would produce high backscatter patterns). Wind streaks generally occur on slopes < 2° and tend to be oriented toward the equator, consistent with the Hadley model of atmospheric circulation. In addition to wind streaks, other aeolian features on Venus include yardangs(?) and dune fields. The Aglaonice dune field, centered at 25°S, 340°E, covers ∼1290 km^2 and is located in an ejecta flow channel from the Aglaonice impact crater. The Meshkenet dune field, located at 67°N, 90°E, covers ∼17,120 km^2 in a valley between Ishtar Terra and Meshkenet Tessera. Wind streaks associated with both dune fields suggest that the dunes are of transverse forms in which the dune crests are perpendicular to the prevailing winds. Dunes on Venus signal the presence of sand-size (∼60 to 2,000 μm) grains. The possible yardangs are found at 9°N, 60.5°E, about 300 km southeast of the crater Mead. Although most aeolian features are concentrated in smooth plains near the equator, the occurrence of wind streaks is widespread, and some have been found at all latitudes and elevations. They demonstrate that aeolian processes operate widely on Venus. The intensity of wind erosion and deposits, however, varies with locality and is dependent on the wind regime and supply of particles

Brain-Specific Phosphorylation of MeCP2 Regulates Activity-Dependent Bdnf Transcription, Dendritic Growth, and Spine Maturation

Mutations or duplications in MECP2 cause Rett and Rett-like syndromes, neurodevelopmental disorders characterized by mental retardation, motor dysfunction, and autistic behaviors. MeCP2 is expressed in many mammalian tissues and functions as a global repressor of transcription; however, the molecular mechanisms by which MeCP2 dysfunction leads to the neural-specific phenotypes of RTT remain poorly understood. Here, we show that neuronal activity and subsequent calcium influx trigger the de novo phosphorylation of MeCP2 at serine 421 (S421) by a CaMKII-dependent mechanism. MeCP2 S421 phosphorylation is induced selectively in the brain in response to physiological stimuli. Significantly, we find that S421 phosphorylation controls the ability of MeCP2 to regulate dendritic patterning, spine morphogenesis, and the activity-dependent induction of Bdnf transcription. These findings suggest that, by triggering MeCP2 phosphorylation, neuronal activity regulates a program of gene expression that mediates nervous system maturation and that disruption of this process in individuals with mutations in MeCP2 may underlie the neural-specific pathology of RTT

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p<0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so

Surface processes recorded by rocks and soils on Meridiani Planum, Mars: Microscopic Imager observations during Opportunity's first three extended missions

The Microscopic Imager (MI) on the Mars Exploration Rover Opportunity has returned images of Mars with higher resolution than any previous camera system, allowing detailed petrographic and sedimentological studies of the rocks and soils at the Meridiani Planum landing site. Designed to simulate a geologist's hand lens, the MI is mounted on Opportunity's instrument arm and can resolve objects 0.1 mm across or larger. This paper provides an overview of MI operations, data calibration, and analysis of MI data returned during the first 900 sols (Mars days) of the Opportunity landed mission. Analyses of Opportunity MI data have helped to resolve major questions about the origin of observed textures and features. These studies support eolian sediment transport, rather than impact surge processes, as the dominant depositional mechanism for Burns formation strata. MI stereo observations of a rock outcrop near the rim of Erebus Crater support the previous interpretation of similar sedimentary structures in Eagle Crater as being formed by surficial flow of liquid water. Well-sorted spherules dominate ripple surfaces on the Meridiani plains, and the size of spherules between ripples decreases by about 1 mm from north to south along Opportunity's traverse between Endurance and Erebus craters

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

Proteomic and Physiological Responses of Kineococcus radiotolerans to Copper

Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0–1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R2 = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration