Perspectives on the genetic architecture of divergence in body shape in sticklebacks

The body shape of fishes encompasses a number of morphological traits that are intrinsically linked to functional systems and affect various measures of performance, including swimming, feeding, and avoiding predators. Changes in shape can allow a species to exploit a new ecological niche and can lead to ecological speciation. Body shape results from the integration of morphological, behavioral and physiological traits. It has been well established that functional interdependency among traits plays a large role in constraining the evolution of shape, affecting both the speed and the repeated evolution of particular body shapes. However, it is less clear what role genetic or developmental constraints might play in biasing the rate or direction of the evolution of body shape. Here, we suggest that the threespine stickleback (Gasterosteus aculeatus) is a powerful model system in which to address the extent to which genetic or developmental constraints play a role in the evolution of body shape in fishes. We review the existing data that begins to address these issues in sticklebacks and provide suggestions for future areas of research that will be particularly fruitful for illuminating the mechanisms that contribute to the evolution of body shape in fishes.     

Neurobehavioral Abnormalities in the HIV-1 Transgenic Rat Do Not Correspond to Neuronal Hypometabolism on 18F-FDG-PET

Motor and behavioral abnormalities are common presentations among individuals with HIV-1 associated neurocognitive disorders (HAND). We investigated whether longitudinal motor and behavioral performance in the HIV-1 transgenic rat (Tg), a commonly used neuro-HIV model, corresponded to in vivo neuronal death/dysfunction, by using rotarod and open field testing in parallel to [¹⁸F] 2-fluoro-2-deoxy-D-glucose (FDG) positron emission tomography (PET). We demonstrated that age-matched non-Tg wild type (WT) rats outperformed the HIV-1 Tg rats at most time points on rotarod testing. Habituation to rotarod occurred at 8 weeks of age (fifth weekly testing session) in the WT rats but it never occurred in the Tg rats, suggesting deficits in motor learning. Similarly, in open field testing, WT rats outperformed the Tg rats at most time points, suggesting defective exploratory/motor behavior and increased emotionality in the Tg rat. Despite the neurobehavioral abnormalities, there were no concomitant deficits in ¹⁸F-FDG uptake in Tg rats on PET compared to age-matched WT rats and no significant longitudinal loss of FDG uptake in either group. The negative PET findings were confirmed using ¹⁴C- Deoxy-D-glucose autoradiography in 32 week-old Tg and WT rats. We believe that the neuropathology in the HIV-1 Tg rat is more likely a consequence of neuronal dysfunction rather than overt neurodegeneration/neuronal cell death, similar to what is seen in HIV-positive patients in the post-ART era.     

Biodiversity,Nitrogen Deposition,and CO<Subscript>2</Subscript> Affect Grassland Soil Carbon Cycling but not Storage

Grasslands are globally widespread and capable of storing large amounts of carbon (C) in soils, and are generally experiencing increasing atmospheric CO₂, nitrogen (N) deposition, and biodiversity losses. To better understand whether grasslands will act as C sources or sinks in the future we measured microbial respiration in long-term laboratory incubations of soils collected from a grassland field experiment after 9 years of factorial treatment of atmospheric CO₂, N deposition, and plant species richness on a deep and uniformly sandy soil. We fit microbial soil respiration rates to three-pool models of soil C cycling to separate treatment effects on decomposition and pool sizes of fast, slow, and resistant C pools. Elevated CO₂ decreased the mean residence time (MRT) of slow C pools without affecting their pool size. Decreasing diversity reduced the size and MRT of fast C pools (comparing monocultures to plots planted with 16 species), but increased the slow pool MRT. N additions increased the size of the resistant pool. These effects of CO₂, N, and species-richness treatments were largely due to plant biomass differences between the treatments. We found no significant interactions among treatments. These results suggest that C sequestration in sandy grassland soils may not be strongly influenced by elevated CO₂ or species losses. However, high N deposition may increase the amount of resistant C in these grasslands, which could contribute to increased C sequestration.     

Crop utilization and fixation of added ammonium in soils of the West Indies

NH₄ ⁺-fixation by inorganic and organic soil components and crop utilization of fertilier nitrogen was studied in a number of Carbbean soils using¹⁵N fertilizers. At moderate rates of nitrogen application, NH₄ ⁺-fixation by clays during several-week laboratory incubations was rapid and highly vaiable, ranging from less than 10% to over 70% of the NH₄ ⁺ added. The 2: 1 lattice types were the most reactive, and the process were almost complete by one week after fertilization. Fixation increased with rate of NH₄ ⁺-N application and was higher at elevated temperatures in soils that were allowed to air-dry during incubation. NH₄ ⁺-N fixation was more active in the fulvic fractions of the soil organic matter than in the humuc fractions (25–69%vs0–3% of the added NH₄ ⁺ was fixed in each, respectively). There was little incorporation of fertilizer-N by the N-containing fractions of soil organic matter. Plant uptake of added NH₄ ⁺-N in greenhouse pot experiments showed that a greater percentalte of fertilizer-N was taken up by Sudan grass (Sourghum sudanese) at a fertilizer rate of 40 kg NH₄ ⁺-N ha^?1 than at a rate of 200n kg NH₄ ⁺N ha^?1. howver, the recovery was low, ranging from 10 to 25 percent of that applied. In field experiments with maize (Zea mays), urea-N was rapidly lost when applied to soils in a wet tropical environment. At normal rates of application (100 kg urea-N ha^?1) only about half of the fertilizer was utilized by the crop. Mulches did not significantly affect the fate of added nitrogen; however, mulching did result in increased yields for dry-season cropping, due probably to water conservation effects. There is good indication that for conditions in Trinidad, NH₄ ⁺-N is better utilzed and less subject to unidentified losses than is urea. Addition of fertilizer-N resulted in crop uptake of important quantities of native soil nitrogen. The Caribbean Andepts were outstanding in that the showed very little NH₄ ⁺-fixation under all experimental conditions and very little tendency for apparent nitrification of added NH₄ ⁺-N.     

Reliability of genetic bottleneck tests for detecting recent population declines

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.     

More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing

In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery et al. 2012, Molecular Ecology, 21 , 3403–3418), Hoban et al. (2013, Molecular Ecology, in press) conducted population genetic simulations to show that the statistical power of genetic bottleneck tests can be increased substantially by sampling large numbers of microsatellite loci, as they suggest is now possible in the age of genomics. While we agree with Hoban and co‐workers in principle, sampling large numbers of microsatellite loci can dramatically increase the probability of committing type 1 errors (i.e. detecting a bottleneck in a stable population) when the mutation model is incorrectly assumed. Using conservative values for mutation model parameters can reduce the probability of committing type 1 errors, but doing so can result in significant losses in statistical power. Moreover, we believe that practical limitations associated with developing large numbers of high‐quality microsatellite loci continue to constrain sample sizes, a belief supported by a literature review of recent studies using next generation sequencing methods to develop microsatellite libraries. conclusion, we maintain that researchers employing genetic bottleneck tests should proceed with caution and carefully assess both statistical power and type 1 error rates associated with their study design.     

Determining Glomerular Filtration Rate in Homozygous Sickle Cell Disease: Utility of Serum Creatinine Based Estimating Equations

Background

Various estimating equations have been developed to estimate glomerular filtration rate (GFR) for use in clinical practice. However, the unique renal physiological and pathological processes that occur in sickle cell disease (SCD) may invalidate these estimates in this patient population. This study aims to compare GFR estimated using common existing GFR predictive equations to actual measured GFR in persons with homozygous SCD. If the existing equations perform poorly, we propose to develop a new estimating equation for use in persons with SCD.

Methods

98 patients with the homozygous SS disease (55 females: 43 males; mean age 34±2.3 years) had serum measurements of creatinine, as well as had GFR measured using ^99mTc-DTPA nuclear renal scan. GFR was estimated using the Modification of Diet in Renal Disease (MDRD), Cockcroft-Gault (CG), and the serum creatinine based CKD-EPI equations. The Bland-Altman limit of agreement method was used to determine agreement between measured and estimated GFR values. A SCD-specific estimating equation for GFR (JSCCS-GFR equation) was generated by means of multiple regression via backward elimination.

Results

The mean measured GFR±SD was 94.9±27.4 mls/min/1.73 m² BSA, with a range of 6.4–159.0 mls/min/1.73 m². The MDRD and CG equations both overestimated GFR, with the agreement worsening with higher GFR values. The serum creatinine based CKD-EPI equation performed relatively well, but with a systematic bias of about 45 mls/min. The new equation developed resulted in a better fit to our sickle cell disease data than the MDRD equation.

Conclusion

Current estimating equations, other than the CKD-EPI equation, do not perform very accurately in persons with homozygous SS disease. A fairly accurate estimating equation, suitable for persons with GFR >60 mls/min/1.73 m² has been developed from our dataset and validated within a simulated dataset.     

In vitro inhibition of human influenza A virus replication by chloroquine

Inhibition of the human cytomegalovirus UL97 kinase by maribavir is thought to be responsible for the antiviral activity of this compound. Some mutations that confer resistance to maribavir map to UL97, however additional mutations that also confer resistance to the drug were mapped to UL27. These open reading frames share a low level of homology, yet the function of pUL27 remains unknown. A recombinant virus with a deletion in the UL27 open reading frame was reported previously to exhibit a slight replication deficit, but a more important function in vivo was hypothesized given its homology to the UL97 kinase. The potential for an important function in vivo was investigated by determining if these knockout viruses could replicate in human tissue implanted in SCID mice. None of the AD169 derived viruses replicated well in the implanted thymus/liver tissue, and is consistent with previous observations, although all of the viruses replicated to some degree in retinal tissue implants. Replication of the parent viruses was observed at 7 days post inoculation, whereas no replication was detected with any of the recombinant viruses with deletions in UL27. By day 14, replication was detected in two of the three knockout viruses and in all of the viruses by day 42. These data are consistent with minimal defects observed in cell culture, but are not consistent with an important role for UL27 in vivo. We conclude that UL27 is not required for viral replication in vivo.     

Activity and kinetic properties of basal aryl hydrocarbon hydroxylase during proliferation in the transformable C3H 10T12; CL8 cell line

Basal aryl hydrocarbon hydroxylase (AHH) activity and its kinetic properties were studied as a function of proliferation in C3H mouse embryo 10T$\text{1}\text{2}$ CL8 cells. Activity was low in freshly plated cells, increased during exponential growth, peaked at confluency, and then declined. The apparent K_m-values for benzo[a]pyrene (BP) and NADPH were less in proliferating (approx. 0.37 μM BP, 3.3 nM NADPH) than in confluent cells (0.74–1.39 μM BP, 33.4–53.4 nM NADPH). Cells at different growth states responded differently to benz[a]anthracene (BA) and aminophylline, an inhibitor of cyclic nucleotide phosphodiesterases. When cells were harvested at the mid log phase of growth, 12 h of exposure to aminophylline caused maximum induction, while 24 h of BA treatment were required. In contrast, at early confluence, 12 h of BA treatment gave the greatest levels of activity, while exposure to aminophylline did not induce AHH. In fact, decreases in activity were observed. These differences are indicative of different regulatory mechanisms for BA and aminophylline induction. They also suggest the regulation of basal AHH by cyclic nucleotides changes during growth. The exposure times giving maximum activity were used to determine the kinetic properties of BA-induced activity. As with basal AHH, the K_m-value for BP was less in log phase (0.2–0.4 μM BP) than in confluent cells (0.64–1.05 μM BP). Moreover, the K_m-values for BP and NADPH in control cultures at confluency (0.10–0.14 μM BP, 15.4–23.2 nM NADPH) were less than those for BA-treated cells (0.64 μM BP, 37.9–54.8 nM NADPH) under the same nutritional conditions. The finding that the K_m-value for BP is lower in rapidly dividing cells than in confluent cells may help to explain why proliferating cells are more susceptible to transforming agents.     

Inhibition of the reconstitution of the haemolytic activity of the first component of human complement by a pepsin-derived fragment of subcomponent C1q.

1. A fragment of subcomponent C1q, which contained all the collagen-like features present in the intact molecule, was isolated by pepsin digestion as described by Reid [Biochem. J. (1976) 155, 5-17]. 2. The pepsin-derived fragment of subcomponent C1q did not bind to antibody-coated erythrocytes under conditions where complete binding of sub-component C1q took place. 3. The peptic fragment blocked the reconstitution of C1 haemolytic activity by competing with intact subcomponent C1q in the utilization of a mixture of the other two subcomponents, C1r and C1s. 4. Reduction and alkylation of the interchain disulphide bonds in the pepsin fragment did not markedly affect its inhibitory effect, whereas heating at 56 degrees C for 30min completely abolished the effect. 5. Lathyritic rat skin collagen and CNBr-derived peptides of pig type II collagen showed no ability to mimic the inhibitory effect of the pepsin fragment when tested over the same concentration range as used for the peptic fragment. 6. The peptic fragment was unable to block efficiently the reconstitution of C1 haemolytic activity unless it was added to the mixture of subcomponents C1r and C1s before the attempt to reconstitute C1 haemolytic activity, in solution, or on the surface of antibody-coated erythrocytes. 7. Evidence was obtained that suggested that subcomponent C1q bound the subcomponent C1r-C1s complex more efficiently when the subcomponent C1q was bound to antibody than when it was free in solution.