Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density

Stable isotope probing (SIP) of nucleic acids is a powerful tool that can identify the functional capabilities of noncultivated microorganisms as they occur in microbial communities. While it has been suggested previously that nucleic acid SIP can be performed with ¹⁵N, nearly all applications of this technique to date have used ¹³C. Successful application of SIP using ¹⁵N-DNA (¹⁵N-DNA-SIP) has been limited, because the maximum shift in buoyant density that can be achieved in CsCl gradients is approximately 0.016 g ml⁻¹ for ¹⁵N-labeled DNA, relative to 0.036 g ml⁻¹ for ¹³C-labeled DNA. In contrast, variation in genome G+C content between microorganisms can result in DNA samples that vary in buoyant density by as much as 0.05 g ml⁻¹. Thus, natural variation in genome G+C content in complex communities prevents the effective separation of ¹⁵N-labeled DNA from unlabeled DNA. We describe a method which disentangles the effects of isotope incorporation and genome G+C content on DNA buoyant density and makes it possible to isolate ¹⁵N-labeled DNA from heterogeneous mixtures of DNA. This method relies on recovery of “heavy” DNA from primary CsCl density gradients followed by purification of ¹⁵N-labeled DNA from unlabeled high-G+C-content DNA in secondary CsCl density gradients containing bis-benzimide. This technique, by providing a means to enhance separation of isotopically labeled DNA from unlabeled DNA, makes it possible to use ¹⁵N-labeled compounds effectively in DNA-SIP experiments and also will be effective for removing unlabeled DNA from isotopically labeled DNA in ¹³C-DNA-SIP applications.     

Diabetes induces sex-dependent changes in neuronal nitric oxide synthase dimerization and function in the rat gastric antrum

Diabetic gastroparesis is a disorder that predominantly affects women. However, the biological basis of this sex bias remains completely unknown. In this study we tested the hypothesis that a component of this effect may be mediated by the nitrergic inhibitory system of the enteric nervous system. Age-matched male and female Sprague-Dawley rats were studied 8 or 12 wk after streptozotocin (55 mg/kg body wt ip)-induced sustained hyperglycemia and compared with controls. Solid gastric emptying (GE) studies were performed in all the groups. Changes in gastric antrum neuronal nitric oxide synthase (nNOS) mRNA and protein levels were analyzed by real-time PCR and Western immunoblotting, respectively. nNOS dimerization studies were performed using low-temperature SDS-PAGE. In vitro nitrergic relaxation (area under curve/mg tissue wt) was studied after the application of electric field stimulation in an organ bath. Changes in intragastric pressure (mmHg.s) in freely moving rats in the presence or absence of N(G)-nitro-l-arginine methyl ester (nitric oxide synthase inhibitor) were examined by an ambulatory telemetric method. After diabetes induction, GE is delayed in both male and female rats. However, diabetic females exhibited significant delayed GE than in diabetic males. Compared with male controls, gastric nNOS expression and nitrergic relaxation were substantially elevated in healthy female control rats, accompanied by significantly reduced intragastric pressure. The active dimeric form and dimer-to-monomer ratio of nNOSalpha were also higher in healthy females compared with male rats (P < 0.05). Diabetic females, but not males, showed significant (P < 0.05) impairment in both gastric nNOSalpha dimerization and nitrergic relaxation, accompanied by an increase in intragastric pressure. Our data provide evidence that females may have a greater dependency on the nitrergic mechanisms in health. Furthermore, diabetes seems to affect the nitrergic system to a greater extent in females than in males. Together, these changes may account for the greater vulnerability of females to diabetic gastric dysfunction.     

Shaking alone, without concurrent aeration, affects the growth characteristics of Escherichia coli

AIMS: This study investigated the effects of linear vibration on cultures grown in both hard- and soft-sided containers to determine whether vibration alone affected the growth rate. METHODS AND RESULTS: Cultures of Escherichia coli were exposed to vibrational acceleration with and without access to additional oxygen. Vibrated cultures grown in hard-sided containers exited lag phase earlier and had a higher final yield than identical unshaken cultures, whether or not the cultures had access to ambient air. Cultures grown in soft-sided containers showed no response to vibration. CONCLUSIONS: Vibration in hard-sided containers decreases the length of the lag phase and increases final OD in E. coli, with or without increased oxygenation. Increased mixing and improved suspension, which result from vibration of cultures in hard-sided containers, are the most likely physical mechanisms for the more favorable culture conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This paper demonstrates that growth enhancement of shaken cultures is a function of the rigidity of the vessel even without aeration of the medium.     

Treatment with CRH-1 antagonist antalarmin reduces behavioral and endocrine responses to social stressors in marmosets (Callithrix kuhlii)

Corticotropin-releasing hormone (CRH) has multiple roles in coordinating the behavioral and endocrine responses to a host of environmental challenges, including social stressors. In the present study we evaluated the role of CRH in mediating responses to a moderate social stressor in Wied's black tufted-eared marmosets (Callithrix kuhlii). Male and female marmosets (n=14) were administered antalarmin (a selective CRH-1 receptor antagonist; 50 microg/kg, p.o.) or vehicle in a blind, counterbalanced, crossover design. One hr after treatment, marmosets were separated from long-term pairmates and then housed alone in a novel enclosure for 7 hr. Behavior was recorded during separation and upon reunion with the partner, and urine samples for cortisol assay collected before, during, and after the intervention. Separation from partners elevated urinary cortisol concentrations over baseline for both conditions, but antalarmin treatment reduced the magnitude of the elevation. Antalarmin also lowered rates of behavioral patterns associated with arousal (alarm and "e-e" vocalizations, object manipulate/chew), but had no effect on contact calls, locomotory activity or alertness. Although most patterns of social behavior upon reunion with the partner were not affected by antalarmin, antalarmin-treated marmosets displayed more sexual behavior (mounts and copulations) upon reunion. These data indicate that antagonism of the CRH-1 receptor acts to reduce the magnitude of both endocrine and behavioral responses to a moderate social stressor without causing any overall reduction in alertness or general activity. This supports the hypothesis that CRH, acting through its type 1 receptor, is involved in coordinating the responses to anxiety-producing events. These results further suggest that the marmoset is a useful model for exploration of the role of CRH in mediating the behavioral and neuroendocrine responses to psychosocial stressors, particularly in the context of heterosexual social relationships.     

Optimizing selection for function-valued traits

We consider a function-valued trait z(t) whose pre-selection distribution is Gaussian, and a fitness function W that models optimizing selection, subject to certain natural assumptions. We show that the post-selection distribution of z(t) is also Gaussian, compute the selection differential, and derive an equation that expresses the selection gradient in terms of the parameters of W and of the pre-selection distribution. We make no assumptions on the nature of the “time” parameter t.      

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool

Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able to show that there are two types of positional artifacts in microarray data introducing spurious correlations between genes. First, we find that genes that are close on the microarray chips tend to have higher correlations between their expression profiles. We call this the 'chip artifact'. Our calculations suggest that the carry-over during the printing process is one of the major sources of this type of artifact, which is later confirmed by our experiments. Based on our experiments, the measured intensity of a microarray spot contains 0.1% (for fully-hybridized spots) to 93% (for un-hybridized ones) of noise resulting from this artifact. Secondly, we, for the first time, show that genes that are close on the microtiter plates in microarray experiments also tend to have higher correlations. We call this the 'plate artifact'. Both types of artifacts exist with different severity in all cDNA microarray experiments that we analyzed. Therefore, we develop an automated web tool-COP (COrrelations by Positional artifacts) to detect these artifacts in microarray experiments. COP has been integrated with the microarray data normalization tool, ExpressYourself, which is available at http://bioinfo.mbb.yale.edu/ExpressYourself/. Together, the two can eliminate most of the common noises in microarray data.     

Reproductive biology and mating system estimates of two Andean melocacti, Melocactus schatzlii and M. andinus (Cactaceae)

BACKGROUND AND AIMS: The genus Melocactus comprises 36 species of globose cacti with the most derived traits in the Cereeae tribe. It is the proper study system to examine what are the most derived reproductive strategies within that tribe. This study aims to characterize the reproductive biology and to estimate the mating system parameters of two Andean melocacti, Melocactus schatzlii and M. andinus. METHODS: The reproductive attributes of the two species were described, including floral morphology, anthesis patterns, floral rewards, floral visitors and visitation patterns. Levels of self-compatibility and autonomous self-pollination were estimated by hand-pollination experiments. Mating system estimates were obtained by conducting progeny array analyses using isozymes. KEY RESULTS: The flowers of the two species present the typical hummingbird-pollination syndrome. Despite their morphological resemblance, the two species differ in flower size, pollen and ovule production and anthesis pattern. Their main pollinator agents are hummingbirds, four species in M. schatzlii and one species in M. andinus. Both cacti are self-compatible and capable of self-pollination without the aid of pollen vectors. Population-level outcrossing rate was higher for M. schatzlii (t(m)=0.9) than for M. andinus (t(m)=0.4). At the family level, outcrossing rates for most mothers of M. schatzlii were higher (t(m)>0.8) than for M. andinus (t(m)<0.5). CONCLUSIONS: Although the two cacti are capable of selfing, M. schatzlii is a predominantly outcrossing species, while M. andinus behaves as a mixed-mating cactus. Hummingbirds are the only pollinators responsible for outcrossing and gene flow events in these species. In their absence, both melocacti set seeds by selfing. Based on its low population size, restricted distribution in Venezuela, low rates of floral visits, and high levels of inbreeding, M. andinus is considered to be an endangered species deserving further study to define its conservation status.     

A comparison of substrate dynamics in human CYP2E1 and CYP2A6

Considering the dynamic nature of CYPs, methods that reveal information about substrate and enzyme dynamics are necessary to generate predictive models. To compare substrate dynamics in CYP2E1 and CYP2A6, intramolecular isotope effect experiments were conducted, using deuterium labeled substrates: o-xylene, m-xylene, p-xylene, 2,6-dimethylnaphthalene, and 4,4'-dimethylbiphenyl. Competitive intermolecular experiments were also conducted using d(0)- and d(6)-labeled p-xylene. Both CYP2E1 and CYP2A6 displayed full isotope effect expression for o-xylene oxidation and almost complete suppression for dimethylbiphenyl. Interestingly, (k(H)/k(D))(obs) for d(3)-p-xylene oxidation ((k(H)/k(D))(obs)=6.04 and (k(H)/k(D))(obs)=5.53 for CYP2E1 and CYP2A6, respectively) was only slightly higher than (k(H)/k(D))(obs) for d(3)-dimethylnaphthalene ((k(H)/k(D))(obs)=5.50 and (k(H)/k(D))(obs)=4.96, respectively). One explanation is that in some instances (k(H)/k(D))(obs) values are generated by the presence of two substrates-bound simultaneously to the CYP. Speculatively, if this explanation is valid, then intramolecular isotope effect experiments should be useful in the mechanistic investigation of P450 cooperativity.     

Contribution of triglyceride-rich lipoproteins to plasma free fatty acids.

Free fatty acids are the major lipid fuel of the body. Dysregulation of adipose tissue lipolysis results in increased plasma free fatty acid concentrations, and via that mechanism contributes to insulin resistance in obesity and type 2 diabetes mellitus. Adipose tissue hormone sensitive lipase is thought to be responsible for the production of the majority of free fatty acids. However, a separate contribution comes from the action of endothelial lipases, especially lipoprotein lipase, on triglyceride-rich lipoproteins via a process known as spillover. The primary substrate for spillover appears to be chylomicrons derived from dietary fat. The spillover of fatty acids into the free fatty acid pool varies from one tissue to another. For example, spillover is low ( approximately 14%) in the forearm of healthy volunteers, suggesting that triglyceride fatty acid storage is relatively efficient in skeletal muscle. In contrast, spillover appears to be higher in adipose tissue and may also be higher in the splanchnic bed, based on preliminary data. If systemic spillover is increased in insulin resistant states such as diabetes, this could represent a mechanism contributing to the abnormal increases in plasma concentrations of free fatty acids in that condition.