Absence of DICER in Monocytes and Its Regulation by HIV-1

MicroRNAs (miRNAs) are a class of small RNA molecules that function to control gene expression and restrict viral replication in host cells. The production of miRNAs is believed to be dependent upon the DICER enzyme. Available evidence suggests that in T lymphocytes, HIV-1 can both suppress and co-opt the host''s miRNA pathway for its own benefit. In this study, we examined the state of miRNA production in monocytes and macrophages as well as the consequences of viral infection upon the production of miRNA. Monocytes in general express low amounts of miRNA-related proteins, and DICER in particular could not be detected until after monocytes were differentiated into macrophages. In the case where HIV-1 was present prior to differentiation, the expression of DICER was suppressed. MicroRNA chip results for RNA isolated from transfected and treated cells indicated that a drop in miRNA production coincided with DICER protein suppression in macrophages. We found that the expression of DICER in monocytes is restricted by miR-106a, but HIV-1 suppressed DICER expression via the viral gene Vpr. Additionally, analysis of miRNA expression in monocytes and macrophages revealed evidence that some miRNAs can be processed by both DICER and PIWIL4. Results presented here have implications for both the pathology of viral infections in macrophages and the biogenesis of miRNAs. First, HIV-1 suppresses the expression and function of DICER in macrophages via a previously unknown mechanism. Second, the presence of miRNAs in monocytes lacking DICER indicates that some miRNAs can be generated by proteins other than DICER.     

Steady-state,Pre-steady-state,and Single-turnover Kinetic Measurement for DNA Glycosylase Activity

Human 8-oxoguanine DNA glycosylase (OGG1) excises the mutagenic oxidative DNA lesion 8-oxo-7,8-dihydroguanine (8-oxoG) from DNA. Kinetic characterization of OGG1 is undertaken to measure the rates of 8-oxoG excision and product release. When the OGG1 concentration is lower than substrate DNA, time courses of product formation are biphasic; a rapid exponential phase (i.e. burst) of product formation is followed by a linear steady-state phase. The initial burst of product formation corresponds to the concentration of enzyme properly engaged on the substrate, and the burst amplitude depends on the concentration of enzyme. The first-order rate constant of the burst corresponds to the intrinsic rate of 8-oxoG excision and the slower steady-state rate measures the rate of product release (product DNA dissociation rate constant, k_off). Here, we describe steady-state, pre-steady-state, and single-turnover approaches to isolate and measure specific steps during OGG1 catalytic cycling. A fluorescent labeled lesion-containing oligonucleotide and purified OGG1 are used to facilitate precise kinetic measurements. Since low enzyme concentrations are used to make steady-state measurements, manual mixing of reagents and quenching of the reaction can be performed to ascertain the steady-state rate (k_off). Additionally, extrapolation of the steady-state rate to a point on the ordinate at zero time indicates that a burst of product formation occurred during the first turnover (i.e. y-intercept is positive). The first-order rate constant of the exponential burst phase can be measured using a rapid mixing and quenching technique that examines the amount of product formed at short time intervals (<1 sec) before the steady-state phase and corresponds to the rate of 8-oxoG excision (i.e. chemistry). The chemical step can also be measured using a single-turnover approach where catalytic cycling is prevented by saturating substrate DNA with enzyme (E>S). These approaches can measure elementary rate constants that influence the efficiency of removal of a DNA lesion.     

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations,dog introgression,and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.     

What we (don't) know about global plant diversity

The era of big biodiversity data has led to rapid, exciting advances in the theoretical and applied biological, ecological and conservation sciences. While large genetic, geographic and trait databases are available, these are neither complete nor random samples of the globe. Gaps and biases in these databases reduce our inferential and predictive power, and this incompleteness is even more worrisome because we are ignorant of both its kind and magnitude. We performed a comprehensive examination of the taxonomic and spatial sampling in the most complete current databases for plant genes, locations and functional traits. To do this, we downloaded data from The Plant List (taxonomy), the Global Biodiversity Information Facility (locations), TRY (traits) and GenBank (genes). Only 17.7% of the world's described and accepted land plant species feature in all three databases, meaning that more than 82% of known plant biodiversity lacks representation in at least one database. Species coverage is highest for location data and lowest for genetic data. Bryophytes and orchids stand out taxonomically and the equatorial region stands out spatially as poorly represented in all databases. We have highlighted a number of clades and regions about which we know little functionally, spatially and genetically, on which we should set research targets. The scientific community should recognize and reward the significant value, both for biodiversity science and conservation, of filling in these gaps in our knowledge of the plant tree of life.     

Virtual navigation in humans: the impact of age, sex, and hormones on place learning

Certain cognitive processes, including spatial ability, decline with normal aging. Spatial ability is also a cognitive domain with robust sex differences typically favoring males. However, tests of spatial ability do not seem to measure a homogeneous class of processes. For many, mentally matching rotated three-dimensional images is the gold standard for measuring spatial cognition in humans, while the Morris water task (MWT) is a preferred method in the domain of nonhuman animal research. The MWT is sensitive to hippocampal damage, a structure critical for normal learning and memory and often implicated in age-related cognitive decline. A computerized (virtual) version of the MWT (VMWT) appears to require and engage human hippocampal circuitry, and has proven useful in studying sex differences and testing spatial learning theories. In Experiment 1, we tested participants (20-90 years of age) in the VMWT and compared their performance to that on the Vandenberg Mental Rotation Test. We report an age-related deficit in performance on both tasks. In Experiment 2, we tested young (age 20-39) and elderly (age >60) participants in the VMWT and correlated their performance to the circulating levels of testosterone and cortisol. Our findings indicate that the persistence of male spatial advantage may be related to circulating testosterone, but not cortisol levels, and independent of generalized age-related cognitive decline.     

Variation in alpha-L-fucosidase properties among 28 inbred mouse strains: Six strains have high enzyme activity and heat-stabile enzyme with a variant pH-activity curve; twenty-two strains have low activity and heat-labile enzyme

Alpha-L-fucosidase in tissues of 28 inbred mouse strains varied with respect to three properties: high or low heat stability, a pH-activity curve with high or low relative activity at pH 2.8, and high or low activity. Alpha-L-fucosidase from six strains (A/J, BDP/J, LP/J, P/J, SEA/GNJ, and 129/J) had high heat stability, high pH 2.8 relative activity, and high activity, whereas the other 22 strains all had low heat stability, low pH 2.8 relative activity, and low activity. The heat-stability difference was seen in all organs tested (brain, liver, kidney, spleen, heart, skeletal muscle, lung, and testis) for two heat-stabile strains (P/J and 129/J) and four heat-labile strains (C57 BL/6J, C3H/HeJ, DBA/2J, and BALB/cJ) studied in detail. The findings suggested that two structural variants of alpha-L-fucosidase, probably genetically determined, exist in these 28 inbred mouse strains, although the presence of linkage disequilibrium between alleles of tightly linked structural and regulatory genes could not be excluded.This work was supported by grants from the National Institutes of Health (NS-15281 and NS-11766), the Muscular Dystrophy Association (H. Houston Merritt Clinical Center for Muscular Dystrophy and Related Diseases), the March of Dimes Birth Defects Foundation, and a generous gift from the Alexander Rapaport Foundation.     

Anti-bat tiger moth sounds: Form and function

The night sky is the venue of an ancient acoustic battle between echolocating bats and their insect prey. Many tiger moths (Lepidoptera: Arctiidae) answer the attack calls of bats with a barrage of high frequency clicks. Some moth species use these clicks for acoustic aposematism and mimicry, and others for sonar jamming, however, most of the work on these defensive functions has been done on individual moth species. We here analyze the diversity of structure in tiger moth sounds from 26 spe-cies collected at three locations in North and South America. A principal components analysis of the anti-bat tiger moth sounds reveals that they vary markedly along three axes: (1) frequency, (2) duty cycle (sound production per unit time) and frequency modulation, and (3) modulation cycle (clicks produced during flexion and relaxation of the sound producing tymbal) structure. Tiger moth species appear to cluster into two distinct groups: one with low duty cycle and few clicks per modulation cycle that supports an acoustic aposematism function, and a second with high duty cycle and many clicks per modulation cycle that is con-sistent with a sonar jamming function. This is the first evidence from a community-level analysis to support multiple functions for tiger moth sounds. We also provide evidence supporting an evolutionary history for the development of these strategies. Further-more, cross-correlation and spectrogram correlation measurements failed to support a "phantom echo" mechanism underlying sonar jamming, and instead point towards echo interference.     

A multi-scale perspective of water pulses in dryland ecosystems: climatology and ecohydrology of the western USA

In dryland ecosystems, the timing and magnitude of precipitation pulses drive many key ecological processes, notably soil water availability for plants and soil microbiota. Plant available water has frequently been viewed simply as incoming precipitation, yet processes at larger scales drive precipitation pulses, and the subsequent transformation of precipitation pulses to plant available water are complex. We provide an overview of the factors that influence the spatial and temporal availability of water to plants and soil biota using examples from western USA drylands. Large spatial- and temporal-scale drivers of regional precipitation patterns include the position of the jet streams and frontal boundaries, the North American Monsoon, El Niño Southern Oscillation events, and the Pacific Decadal Oscillation. Topography and orography modify the patterns set up by the larger-scale drivers, resulting in regional patterns (10²–10⁶ km²) of precipitation magnitude, timing, and variation. Together, the large-scale and regional drivers impose important pulsed patterns on long-term precipitation trends at landscape scales, in which most site precipitation is received as small events (<5 mm) and with most of the intervals between events being short (<10 days). The drivers also influence the translation of precipitation events into available water via linkages between soil water content and components of the water budget, including interception, infiltration and runoff, soil evaporation, plant water use and hydraulic redistribution, and seepage below the rooting zone. Soil water content varies not only vertically with depth but also horizontally beneath versus between plants and/or soil crusts in ways that are ecologically important to different plant and crust types. We highlight the importance of considering larger-scale drivers, and their effects on regional patterns; small, frequent precipitation events; and spatio-temporal heterogeneity in soil water content in translating from climatology to precipitation pulses to the dryland ecohydrology of water availability for plants and soil biota.