METHOD OF SEMEN COLLECTION AND ARTIFICIAL INSEMINATION IN SNAKES

This study focuses on the method for sperm extraction and artificial insemination in snakes. Ten adult healthy snakes (4.6) were included in the study (Pantherophis guttatus 1.3; Hydrodynastes gigas 1.1; Corallus hortulanus 1.1; and Sanzinia madagascariesis 1.1). Massage of the ventral aspect of the caudal third of the male snake body for 2 to 3 minutes was performed successfully for the semen collection. Both female and male P. guttatus and H. gigas were placed in brumation, with the female snakes being assessed for ovarian activity after emerging from dormancy. Only females showing ultrasonographic evidence of vitellogenic follicles were included in the study. S. madagascariensis and C. hortulanus were maintained at the same temperature through the year, and the ovarian activity was assessed ultrasonographically prior to artificially inseminating the animal. With the aid of a rigid endoscope, fresh semen was delivered through the cloaca and into the females’ oviducts using a catheter connected to the syringe. The technique failed in female S. madagascariensis and H. gigas. Two female P. guttatus laid eggs 2 months after artificial insemination, with hatchlings emerging following 2 months of development within the eggs. The third female corn snake did not lay an egg. The female C. hortulans produced eggs 4 months after insemination. The manual massage method of sperm collection in male snakes and endoscopy-assisted insemination in female snakes may be useful for conservation programs.     

“Noisy beets”: impact of phenotyping errors on genomic predictions for binary traits in <Emphasis Type="Italic">Beta vulgaris</Emphasis>

Background

Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding.

Results

In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours—KNN, random forest—RF, ridge logistic regression—LR, and support vector machines with linear or radial basis function kernels) was investigated. A sugar beet population of 123 plants phenotyped for a binary trait and genotyped for 192 SNP (single nucleotide polymorphism) markers was used. Labels (0/1 phenotype) were randomly sampled to generate noise. From the base scenario without errors in the labels, increasing proportions of noisy labels—up to 50 %—were generated and introduced in the data.

Conclusions

Local classification methods—KNN and RF—showed higher tolerance to noisy labels compared to methods that leverage global data properties—LR and the two SVM models. In particular, KNN outperformed all other classifiers with AUC (area under the ROC curve) higher than 0.95 up to 20 % noisy labels. The runner-up method, RF, had an AUC of 0.941 with 20 % noise.

     

Filtering of visual information in the tectum by an identified neural circuit

The optic tectum of zebrafish is involved in behavioral responses that require the detection of small objects. The superficial layers of the tectal neuropil receive input from retinal axons, while its deeper layers convey the processed information to premotor areas. Imaging with a genetically encoded calcium indicator revealed that the deep layers, as well as the dendrites of single tectal neurons, are preferentially activated by small visual stimuli. This spatial filtering relies on GABAergic interneurons (using the neurotransmitter γ-aminobutyric acid) that are located in the superficial input layer and respond only to large visual stimuli. Photo-ablation of these cells with KillerRed, or silencing of their synaptic transmission, eliminates the size tuning of deeper layers and impairs the capture of prey.     

Hoxa2- and rhombomere-dependent development of the mouse facial somatosensory map

In the mouse trigeminal pathway, sensory inputs from distinct facial structures, such as whiskers or lower jaw and lip, are topographically mapped onto the somatosensory cortex through relay stations in the thalamus and hindbrain. In the developing hindbrain, the mechanisms generating such maps remain elusive. We found that in the principal sensory nucleus, the whisker-related map is contributed by rhombomere 3-derived neurons, whereas the rhombomere 2-derived progeny supply the lower jaw and lip representation. Moreover, early Hoxa2 expression in neuroepithelium prevents the trigeminal nerve from ectopically projecting to the cerebellum, whereas late expression in the principal sensory nucleus promotes selective arborization of whisker-related afferents and topographic connectivity to the thalamus. Hoxa2 inactivation further results in the absence of whisker-related maps in the postnatal brain. Thus, Hoxa2- and rhombomere 3-dependent cues determine the whisker area map and are required for the assembly of the whisker-to-barrel somatosensory circuit.     

Structures from anomalous diffraction of native biological macromolecules

Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.     

Resistance of postharvest biocontrol yeasts to oxidative stress: a possible new mechanism of action

ABSTRACT We detected the generation of the reactive oxygen species (ROS) superoxide anion ( O.(-) (2)) and hydrogen peroxide (H(2)O(2)) in apple wounds 2 immediately after wounding, and assessed the relationships between (i) timely colonization of apple wounds by biocontrol yeasts, (ii) resistance of these microorganisms to oxidative stress caused by ROS, and (iii) their antagonism against postharvest wound pathogens. We analyzed a model system consisting of two yeasts with higher (Cryptococcus laurentii LS-28) or lower (Rhodotorula glutinis LS-11) antagonistic activity against the postharvest pathogens Botrytis cinerea and Penicillium expansum. LS-28 exhibited faster and greater colonization of wounds than LS-11. In contrast to LS-28, the number of LS-11 cells dropped 1 and 2 h after application, and then increased only later. In vitro, LS-28 was more resistant to ROS-generated oxidative stress. The combined application of biocontrol yeasts and ROS-deactivating enzymes in apple wounds prevented the decrease in number of LS-11 cells mentioned above, and enhanced colonization and antagonistic activity of both biocontrol yeasts against B. cinerea and P. expansum. Polar lipids of LS-11 contained the more unsaturated and oxidizable alpha-linolenic acid, which was absent in LS-28. Resistance to oxidative stress could be a key mechanism of biocontrol yeasts antagonism against postharvest wound pathogens.     

Monitoring and Analysis of Volatile Organic Compounds Around an Oil Refinery

Valle Galeria, a location in the outskirts of Rome, was selected as a case study to assess the pollution release from the industrial facilities operating in this area. For this purpose, an intensive field campaign was conducted during summer, where volatile organic compounds VOC (including benzene, toluene and xylenes) were sampled and analyzed at two different sites. A strong modulation of VOC concentrations was observed between daytime and nighttime, and alkane fraction was found to be the most abundant group, indicating the oil refinery as the major source of atmospheric hydrocarbons. Surface turbulence and upper air SODAR data were processed to investigate the relationships between meteorology and VOC levels and patterns. Atmospheric turbulence was found to be responsible for the daily modulation of VOC. In particular, the highest BTX pollution episode observed during nighttime was found to be correlated with a very strong atmospheric stability and a surface based inversion layer. The analysis of BTX ratios resulted effective in recognizing the relationship between the pollutants and their co-variance, as well as the dispersion and reaction patterns occurring during the transport across the two sites.