Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests

Background  

Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems.     

N-Acetylsuccinimidylglutamate, a Cyclic Imide Form of the Peptide N-Acetylaspartylglutamate, Is Present in Low Micromolar Concentrations in Murine and Bovine CNS

Abstract: N -Acetylsuccinimidylglutamate [(asu)NAAG], a cyclic form of the peptide N -acetylaspartylglutamate (NAAG) in which the aspartyl residue is linked to glutamate via the α- and β-carboxylates, was identified and quantified by HPLC in the murine and bovine CNS. In the rat, the highest concentrations of (asu)NAAG were detected in the spinal cord (1.83 ± 0.15 pmol/mg of wet tissue weight) and brainstem (1.16 ± 0.08 pmol/mg wet weight), whereas the levels were below the limit of detection in cerebellum, hippocampus, and cerebral cortex. (Asu)NAAG was also detected in significant amounts in the superior colliculus and lateral genicutale nucleus (1.17 ± 0.05 and 0.82 ± 0.13 pmol/mg wet weight, respectively). Although the tissue content of (asu)NAAG was about three orders of magnitude lower than that of NAAG, levels of both peptides were positively correlated among different CNS regions ( r = 0.74, p < 0.003). In the rat spinal cord, (asu)NAAG levels progressively increased from week 2 to month 12 after birth. In bovine spinal cord, the contents of (asu)NAAG and NAAG were comparable in gray and white matter as well as in the dorsal and ventral horns. These results suggest that NAAG and (asu)-NAAG are closely related metabolically and raise the question of the physiological significance of such a cyclic peptide.     

Presynaptic regulation of dopaminergic transmission in the striatum

1. In vitro studies have indicated that several transmitters present in the striatum can regulate presynaptically the release of dopamine (DA) from nerve terminals of the nigrostriatal DA neurons. 2. The receptors involved in these local regulatory processes are located or not located on DA nerve terminals. 3. Recent in vivo investigations have demonstrated that the corticostriatal glutamatergic neurons facilitate presynaptically the release of DA and have allowed the analysis of the respective roles of presynaptic events and nerve activity in the control of DA transmission.     

Microbiological Evaluation of a Large-Volume Air Incinerator

Two semiportable metal air incinerators, each with a capacity of 1,000 to 2,200 standard ft(3) of air per min, were constructed to sterilize infectious aerosols created for investigative work in a microbiological laboratory. Each unit has about the same air-handling capacity as a conventional air incinerator with a brick stack but costs only about one-third as much. The units are unique in that the burner housing and combustion chamber are air-tight and utilize a portion of the contaminated air stream to support combustion of fuel oil. Operation is continuous. Aerosols of liquid and dry suspensions of Bacillus subtilis var. niger spores and dry vegetative cells of Serratia marcescens were disseminated into the two incinerators to determine the conditions required for sterilization of contaminated air. With the latter organisms (concentration 2.03 x 10(7) cells/ft(3) of air), a temperature of 525 F (274 C), measured at the firebox in front of the heat exchanger, was sufficient for sterilization. To sterilize 1.74 x 10(7) and 1.74 x 10(9) wet spores of B. subtilis per ft(3), the required temperature ranged from 525 to 675 F (274 to 357 C) and 625 to 700 F (329 to 371 C), respectively. Air-sterilization temperature varied with each incinerator. This was because of innate differences of fabrication, different spore concentrations, and use of one or two burners With dry B. subtilis spores (1.86 x 10(8)/ft(3)), a temperature of 700 F was required for sterilization. With dry spores, no difference was noted in the sterilization temperature for the two incinerators.     

Containment of Microbial Aerosols in a Microbiological Safety Cabinet

A microbiological safety cabinet was evaluated to determine conditions under which microorganisms might escape. Tests were conducted under three cabinet-closure conditions, various airflow velocities, and different laboratory operations, with 10(5), 1.1 x 10(5), and 10(6) microorganisms per cubic foot of cabinet space released per min for 5 min. The data revealed that (i) escape of a human infectious dose is possible when the cabinet is used with the glove panel off; (ii) the number of organisms that escaped from the cabinet increased with a decrease in air velocity; and (iii) an increase in the number of laboratory operations resulted in an increase in the number of organisms that escaped. Thus, when the glove panel was off, the cabinet was only safe for operations that released a small number of microorganisms into the cabinet, whereas the cabinet was safe for operations of significantly greater hazard when used with the glove panel on but with the gloves unattached.     

Peroxynitrite-Induced Cytotoxicity in PC12 Cells: Evidence for an Apoptotic Mechanism Differentially Modulated by Neurotrophic Factors

Abstract: Peroxynitrite is a powerful oxidant formed by the near-diffusion-limited reaction of nitric oxide with superoxide. Large doses of peroxynitrite (>2 m M ) resulted in rapid cell swelling and necrosis of undifferentiated PC12 cells. However, brief exposure to lower concentrations of peroxynitrite (EC₅₀ = 850 µ M ) initially (3–4 h) caused minimal damage to low-density cultures. By 8 h, cytoplasmic shrinkage with nuclear condensation and fragmentation became increasingly evident. After 24 h, 36% of peroxynitrite-treated cells demonstrated these features associated with apoptosis. In addition, 46% of peroxynitrite-treated cells demonstrated DNA fragmentation (by terminal-deoxynucleotide transferase-mediated dUTP-digoxigenin nick end-labeling) after 7 h, which was inhibited by posttreatment with the endonuclease inhibitor aurintricarboxylic acid. Serum starvation also resulted in apoptosis in control cells (23%), the percentage of which was not altered significantly by peroxynitrite treatment. Although peroxynitrite is known to be toxic to cells, the present study provides a first indication that peroxynitrite induces apoptosis. Furthermore, pretreatment of cells with nerve growth factor or insulin, but not epidermal growth factor, was protective against peroxynitrite-induced apoptosis. However, both acidic and basic fibroblast growth factors greatly increased peroxynitrite-initiated apoptosis, to 63 and 70%, respectively. Thus, specific trophic factors demonstrate differential regulation of peroxynitrite-induced apoptosis in vitro.     

N-Acetyl-aspartylglutamate (NAAG) in human cerebrospinal fluid: Determination by high performance liquid chromatography,and influence of biological variables

Summary NAAG is one of the neuropeptides found in highest concentrations in the CNS. The presence of micromolar concentrations of NAAG in human CSF was demonstrated by using two different and complementary analytical approaches: 1) isocratic separation of endogenous NAAG by reverse-phase high performance liquid chromatography (HPLC) with dual wavelength detection and 2) derivatization of endogenous NAAG with acidic methanol and subsequent HPLC analysis of the derivative NAAG-trimethyl ester. The NAAG concentration was between 0.44µmol/l and 7.16µmol/l (mean of 2.19 ± 1.53µmol/l) in CSF samples from forty neuropsychiatric patients. Endogenous NAAG or [³H]NAAG added to CSF samples were not significantly degraded when the CSF was incubated at 37°C during one hour, suggesting that the peptide is a highly stable metabolite in the subarachnoid space. In addition, evidence is provided that NAAG does not present a concentration gradient along the lower subarachnoid space.     

Biohazards Assessment in Large-Scale Zonal Centrifugation

A study was conducted to determine the biohazards associated with use of the large-scale zonal centrifuge for purification of moderate risk oncogenic viruses. To safely and conveniently assess the hazard, coliphage T₃ was substituted for the virus in a typical processing procedure performed in a National Cancer Institute contract laboratory. Risk of personnel exposure was found to be minimal during optimal operation but definite potential for virus release from a number of centrifuge components during mechanical malfunction was shown by assay of surface, liquid, and air samples collected during the processing. High concentration of phage was detected in the turbine air exhaust and the seal coolant system when faulty seals were employed. The simulant virus was also found on both centrifuge chamber interior and rotor surfaces.     

Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture

Background

The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped.

Methods

Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets.

Results

Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams.

Conclusions

Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.     

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.