425 research outputs found
Whole-genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype
The association between variants on TYRP1, TYRP2, MC1R, KITLG, KIT, ASIP and MITF genes and fleece color has been described for alpaca and llama (Zhu et al., 2019; Feeley et al., 2016; Chandramohan et al., 2015; Anello et al., 2022; Pallotti et al., 2020; Shah et al., 2023; Jones et al., 2019; Tan et al., 2022). In this regard, variants on KIT were associated to white and blue-eyed white phenotype in alpaca (Jones et al., 2019; Tan et al., 2022) due to its important role in melanogenesis (Roskoski, 2005). Moreover, previous segregation analysis suggested that the inheritance of white color in alpaca was due to a single gene which is completely dominant over black and brown pigmentation (Valbonesi et al., 2011).
In the present study, the segregation of KITLG, KIT and MITF genes was analyzed to find variants associated to white coat phenotype in alpaca. Six Peruvian alpacas belonging to two test-cross families were tested: white huacaya male × pigmented suri female and white suri male x pigmented huacaya female which gave birth to one white suri and one pigmented huacaya, respectively (Table 1). The animals were raised at the experimental station of the INIA (the Peruvian National Institute for Agronomic Innovation) located in Quimsachata, Peru. Sampling of the animals and genomics analysis were performed as reported in Pallotti et al. (2023). Briefly, genomic DNA extracted from skin biopsies underwent whole-genome sequencing on Illumina NovaSeq 6000 System, with a 150x2 bp mode, and an average sequencing depth of 25X. After quality control and alignment to VicPac3 reference genome, the variants were called using the standard joint-call GATK pipeline. All the variants were annotated using SNPeff and filtered according to the segregation of the white coat phenotype.
No segregating variants for white coat color were identified in KITLG and MITF. On the contrary, two different KIT variants segregated in white animals (Table 1): two white alpacas, belonging to family 1, were heterozygous (G/A) for the c.35G>A (p.Arg12His) variant, while one white alpaca, belonging to family 2, was heterozygotes (G/C) for c.982G>C (p.Val328Leu) variant. Conversely, all the pigmented animals showed a homozygous G/G genotype. The protein functional domains predicted using InterProScan (Quevillon et al., 2005) suggested that the two mutations were in the N-terminal region of the signal peptide and in the extracellular region which are essential for the binding of the appropriate ligand and consequent activation of KIT (Roskoski, 2005). In addition, such results may suggest a dominant inheritance for alpaca white color as proposed by previous segregation studies (Valbonesi et al., 2011).
Although these results must be validated on larger sample, our findings refine the current understanding of the association between gene variants and white color in alpaca and suggest new potential KIT variants as a starting point for further studies on the genetics of white color in alpaca
Psychosocial and behavioral impact of COVID-19 in autism spectrum disorder: an online parent survey
The 2019 coronavirus disease (COVID-19) outbreak could result in higher levels of psychological distress, especially among people suffering from pre-existing mental health conditions. Young individuals with autism spectrum disorders (ASD) are particularly at risk due to their vulnerability to unpredictable and complex changes. This study aimed to investigate the impact of the COVID-19 pandemic on ASD individuals, whether any pre-pandemic sociodemographic or clinical characteristics would predict a negative outcome, and to narratively characterize their needs. Parents and guardians of ASD individuals filled out an online survey consisting of 40 questions investigating socio-demographic and clinical characteristics of their children, impact of the COVID-19 outbreak on their wellbeing and needs to deal with the emergency. Data were available on 527 survey participants. The COVID-19 emergency resulted in a challenging period for 93.9% of families, increased difficulties in managing daily activities, especially free time (78.1%) and structured activities (75.7%), and, respectively, 35.5% and 41.5% of children presenting with more intense and more frequent behavior problems. Behavior problems predating the COVID-19 outbreak predicted a higher risk of more intense (odds ratio (OR) = 2.16, 95% confidence interval (CI) 1.42-3.29) and more frequent (OR = 1.67, 95% CI 1.13-2.48) disruptive behavior. Even though ASD children were receiving different types of support, also requiring specialist (19.1%) or emergency (1.5%) interventions in a relatively low proportion of cases, a number of needs emerged, including receiving more healthcare support (47.4%), especially in-home support (29.9%), as well as interventions to tackle a potentially disruptive quarantine (16.8%). The COVID-19 outbreak has undoubtedly resulted in increased difficulties among ASD individuals
Genome-wide scan for runs of homozygosity in South American Camelids
Background: Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results: A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions: The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies
inheritance of suri and huacaya type of fleece in alpaca
The inheritance of the two types of fleece, Suri and Huacaya, observed in Alpaca (Lama pacos L.) is still not clearly defined. The objective of this work is to investigate the patter of inheritance of these two phenotypes, throughout 588 Suri x Suri and 2126 Huacaya x Huacaya offspring. The single gene and the three two-phenotype epistatic models were tested in the 19 Suri x Suri segregating families. The single dominant gene hypothesis best fitted our segregation data and could be, therefore, accepted (GT=20.276, P=0.378). The gene frequency of the recessive Huacaya allele was 0.295, being the frequency of the dominant Suri allele 0.705. The frequency of heterozygotes, estimated in the whole population and among dominant individuals, was 0.416 and 0.455, respectively, with a "carrier" Suri to Huacaya ratio of 4.780. In three Huacaya families, 3 Suri were born, as a result of a new dominant mutation on some germinal lines of Huacaya animals. The direct mutation rate can be estimated at 0.0014
Statistical Approach to the EMI Modeling of Large ASICs by a Single Noise-Current Source
Large and complex ASICs are source of propagating noise inside the powerbus planes. A lumped noise source model is proposed and validated by means of a statistics based method
Quantitative variation of melanins in alpaca (Lama pacos L.)
The amount of melanin pigments was investigated in 95 Peruvian alpaca, representative of six different fleece colours, by means of spectrophotometric assays: SpEM (Spectrophotometric Eumelanin), SpPM (Spectrophotometric Pheomelanin), SpASM (Spectrophotometric Alkali Soluble Melanin), and SpTM (Spectrophotometric Total Melanin). It was found that these melanin pigments were suitable for identifying three homogeneous groups, each consisting of two closely related colours. A low, an intermediate, and a high amount of SpASM, SpTM, and SpPM characterize pinkish grey and light reddish brown, brown and reddish brown, dark reddish brown and black fleeces, respectively. SpEM and SpTM provide a further split within this latter group; higher concentrations of these pigments distinguish black fleece from dark reddish brown
Quantization for decentralized learning under subspace constraints
In this paper, we consider decentralized optimization problems where agents
have individual cost functions to minimize subject to subspace constraints that
require the minimizers across the network to lie in low-dimensional subspaces.
This constrained formulation includes consensus or single-task optimization as
special cases, and allows for more general task relatedness models such as
multitask smoothness and coupled optimization. In order to cope with
communication constraints, we propose and study an adaptive decentralized
strategy where the agents employ differential randomized quantizers to compress
their estimates before communicating with their neighbors. The analysis shows
that, under some general conditions on the quantization noise, and for
sufficiently small step-sizes , the strategy is stable both in terms of
mean-square error and average bit rate: by reducing , it is possible to
keep the estimation errors small (on the order of ) without increasing
indefinitely the bit rate as . Simulations illustrate the
theoretical findings and the effectiveness of the proposed approach, revealing
that decentralized learning is achievable at the expense of only a few bits
Hydrogen production from natural gas and biomethane with carbon capture and storage - A techno-environmental analysis
This study presents an integrated techno-environmental assessment of hydrogen production from natural gas and biomethane, combined with CO2 capture and storage (CCS). We have included steam methane reforming (SMR) and autothermal reforming (ATR) for syngas production. CO2 is captured from the syngas with a novel vacuum pressure swing adsorption (VPSA) process, that combines hydrogen purification and CO2 separation in one cycle. As comparison, we have included cases with conventional amine-based technology. We have extended standard attributional Life Cycle Assessment (LCA) following ISO standards with a detailed carbon balance of the biogas production process (via digestion) and its by-products. The results show that the life-cycle greenhouse gas (GHG) performance of the VPSA and amine-based CO2 capture technologies is very similar as a result of comparable energy consumption. The configuration with the highest plant-wide CO2 capture rate (almost 100% of produced CO2 captured) is autothermal reforming with a two-stage water-gas shift and VPSA CO2 capture – because the latter has an inherently high CO2 capture rate of 98% or more for the investigated syngas. Depending on the configuration, the addition of CCS to natural gas reforming-based hydrogen production reduces its life-cycle Global Warming Potential by 45–85 percent, while the other environmental life-cycle impacts slightly increase. This brings natural gas-based hydrogen on par with renewable electricity-based hydrogen regarding impacts on climate change. When biomethane is used instead of natural gas, our study shows potential for net negative greenhouse gas emissions, i.e. the net removal of CO2 over the life cycle of biowaste-based hydrogen production. In the special case where the biogas digestate is used as agricultural fertiliser, and where a substantial amount of the carbon in the digestate remains in the soil, the biowaste-based hydrogen reaches net-negative life cycle greenhouse gas emissions even without the application of CCS. Addition of CCS to biomethane-based hydrogen production leads to net-negative emissions in all investigated cases.ISSN:2398-490
Guidelines for the monitoring of Rosalia alpina
Rosalia alpina (Linnaeus, 1758) is a large longhorn beetle (Coleoptera: Cerambycidae) which is protected by the Habitats Directive and which typically inhabits beech forests characterised by the presence of mature, dead (or moribund) and sun-exposed trees. A revision of the current knowledge on systematics, ecology and conservation of R. alpina is reported. The research was carried out as part of the LIFE MIPP project which aims to find a standard monitoring method for saproxylic beetles protected in Europe. For monitoring this species, different methods were tested and compared in two areas of the Apennines, utilising wild trees, logs and tripods (artificially built with beech woods), all potentially suitable for the reproduction of the species. Even if all methods succeeded in the survey of the target species, these results showed that the use of wild trees outperformed other methods. Indeed, the use of wild trees allowed more adults to be observed and required less intensive labour. However, monitoring the rosalia longicorn on wild trees has the main disadvantage that they can hardly be considered “standard sampling units”, as each tree may be differently attractive to adults. Our results demonstrated that the most important factors influencing the attraction of single trunks were wood volume, sun-exposure and decay stage. Based on the results obtained during the project LIFE MIPP, as well as on a literature review, a standard monitoring method for R. alpina was developed
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