“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.

     

Genome scan for the possibility of identifying candidate resistance genes for goat lentiviral infections in the Italian Garfagnina goat breed

Tropical Animal Health and Production - Small ruminant lentiviruses (SRLVs) are a heterogeneous group of viruses of sheep, goat, and wild ruminants responsible of lifelong persistent infection...     

The potential for mitigation of methane emissions in ruminants through the application of metagenomics,metabolomics, and other -OMICS technologies

Ruminant supply chains contribute 5.7 gigatons of CO_2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH₄), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH₄ production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH₄ yield in ruminants indicates that genomic selection for reduced CH₄ emissions is possible. Although the microbiology of CH₄ production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH₄ production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH₄ emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH₄ production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH₄ emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH₄ production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.     

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.     

Chemical composition of volatiles in Sardinian myrtle (Myrtus communis L.) alcoholic extracts and essential oils

The chemical composition of the volatile fraction of myrtle (Myrtus communis L.) alcoholic extracts and essential oils from leaves and berries collected in different places in Sardinia (Italy) was studied. A simple and rapid liquid-liquid extraction method was used to isolate volatile compounds from myrtle alcoholic extracts followed by GC and GC-MS analysis allowing the detection of 24 compounds. The volatile fraction was characterized by the terpenes fraction corresponding to that of the essential oils and by a fatty acid ethyl esters fraction. The variation during extraction of the volatile fraction in alcoholic extracts of berries and leaves was evaluated. Essential oils were obtained by hydrodistillation, and the yields were on average 0.52 +/- 0.03% (v/w dried weight) and 0.02 +/- 0.00% for leaves and berries, respectively. The essential oils were analyzed by GC and GC-MS, and a total of 27 components were detected, accounting for 90.6-98.7% of the total essential oil composition. Strong chemical variability depending on the origin of the samples was observed. The major compounds in the essential oils were alpha-pinene (30.0 and 28.5%), 1,8-cineole (28.8 and 15.3%), and limonene (17.5 and 24.1%) in leaves and berries, respectively, and were characterized by the lack of myrtenyl acetate.     

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.     

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.     

Yield Potential and Ecophysiological Traits of the Altamurano Linseed (Linum usitatissimum L.), a Landrace of Southern Italy

Altamurano is a linseed landrace of southern Italy. Its area of origin is characterised by typical Mediterranean climate. Traditionally, Altamurano is spring sown, and mainly used as a feed integrator for animals. This landrace was evaluated during 2 years within varietal (16 modern varieties) and sowing date (15 sowings, from October to April, with ‘Antares’ as a control) trials. Growth analysis was carried out on two sowings. Seed yield was slightly lower than modern varieties, with advantages in late sowings. Reproductive efficiency, mean seed weight, harvest index and oil percentage were often higher than in modern cultivars. Altamurano was also characterised by early flowering, low vegetative growth, long leaf area duration, high light use efficiency during early grain filling phase, and relatively long grain filling period. All these features are connected with its adaptation to spring sowings in Mediterranean areas, characterised by early spring drought. Despite the decrease of its cultivation area from about 400 to less than 100 ha in the last 10 years, Altamurano is still present in the more traditional farms of the area as a heritage of past growing systems and historical adaptation to the environment.     

Electrochemotherapy in treatment of canine oral non‐tonsillar squamous cell carcinoma. A case series report

Non‐tonsillar squamous cell carcinoma (ntSCC) is a common and locally aggressive oral tumour in dogs. The treatments of choice are currently surgery and radiotherapy. Electrochemotherapy (ECT) is a local ablative anti‐tumour technique using electric pulses to enhance the intracellular diffusion of cytotoxic drugs. The aim was to retrospectively evaluate the outcome of patients with oral ntSCC treated with ECT. Twelve dogs with ntSCC were retrospectively enrolled. ECT was combined with IV bleomycin (15 000 UI/m²) alone in 11 cases and post‐surgery in 1. Parameters considered were: tumour site and size, electroporation parameters, response rate (complete remission [CR], partial remission [PR]), median survival time (MST), recurrence rate (RR), median disease‐free interval (DFI) and treatment toxicity (6‐point scale). Median tumour size was 1.65 cm (range 0.3‐8.0 cm) and the response rate was 90.9% (10/11; 8 CR and 2 PR). Two dogs underwent a second ECT. MST for dogs dead with tumour (n = 2) was 110 days and for dogs dead without tumour (n = 3) was 831 days. Among five surviving dogs, one experienced tumour recurrence and four were in CR. Results from two dogs were analysed separately. Overall RR was 27.3%. DFI and MST for dogs with recurrence were 50 and 115 days, respectively. Treatment toxicity was very low. We noticed that all dogs with tumours smaller than 1‐2 cm achieved CR without recurrence suggesting a favourable prognosis when using ECT. ECT for canine ntSCC could be considered a valid treatment option especially for smaller tumours, but a larger caseload would be needed to confirm this statement.