Alternative SNP weighting for multi-step and single-step genomic BLUP in the presence of causative variants.

The accuracy of genetic selection in dairy can be increased by the adoption of new technologies, such as the inclusion of sequence data. In simulation studies, assigning different weights to causative single-nucleotide polymorphism (SNP) markers led to better predictions depending on the genomic prediction method used. However, it is still not clear how the weights should be calculated. Our objective was to evaluate the accuracy of a multi-step method (GBLUP) and single-step GBLUP with simulated data using regular SNP, causatives variants (QTN) and the combination of both. Additionally, we compared the accuracies of all previous scenarios using alternatives for SNP weighting. The data were simulated assuming a single trait with a heritability of 0.3. The effective population size (Ne) was approximately 200. The pedigree contained 440,000 animals, and approximately 16,800 individuals were genotyped. A total of 49,974 SNP markers were evenly placed throughout the genome, and 100, 1000 and 2000 causative QTN were simulated. Both GBLUP and ssGBLUP were used in this study. We evaluated quadratic and nonlinear SNP weights in addition to the unweighted G. The inclusion of QTN to panels led to significant accuracy gains. Nonlinear A was demonstrated to be superior to quadratic weighting and unweighted approaches; however, results from Nonlinear A were dependent on the equation parameters. The unweighted approach was more suitable for less polygenic scenarios. Finally, SNP weighting might help elucidate trait architecture features based on changes in the accuracy of genomic prediction.

Alternative co-initiators for photocurable dental resins: Polymerisation, quantum yield of conversion and cytotoxicity.

OBJECTIVE: Cyclic acetals such as are naturally occurring compounds capable of acting as co-initiators during free-radical polymerisation, and potentially serve to offer non-allergic and biologically less toxic alternatives to conventional (tertiary) amines. The current study aimed to evaluate the polymerisation efficiency and potential toxicity of cyclic acetals compared with conventional photoinitiator systems in photocurable dental resins. METHODS: Both, 1,3 benzodioxole (BZD) and piperonyl alcohol (PA) were used in 0.5, 1.0, 1.5, 2.0, 3.0, 4.0 and 6.0 mol% concentrations. Whereas, N-phenyl glycine (NPG) was utilised in 0.5, 1.0, 1.5, 2.0, 3.0, 4.0 mol% concentrations for photopolymerisation of an unfilled model resin system, BisGMA and TEGDMA (1:1 mass %), involving three separate camphorquinone (CQ) concentrations of 0.5 (Low), 1.0 (Intermediate) and 1.5 (High) mol%. Conventional tertiary amines; ethyl-4-dimethyamino benzoate (EDMAB) and dimethylaminoethyl methacrylate (DMAEMA) were utilised for comparison. Real-time degree of conversion (DC, %) was evaluated using Fourier transform near-infra-red spectroscopy and quantum yield of conversion of CQ was calculated using UV-Vis spectroscopy. Cytotoxicity of NPG and cyclic acetals were assessed using MTT to determine metabolic activity of human dental pulp cells (HDPCs). RESULTS: The cyclic acetals were capable of facilitating free radical polymerisation as co-initiators at all three CQ concentrations. Furthermore, the use of NPG as a co-initiator resulted in post-irradiation DC (%) that were comparable to both EDMAB and DMAEMA for all CQ concentrations. Alternative compounds facilitated the hydrogen abstraction process, which provided high conversion of CQ molecules. Quantum yield increased from 0.009 ± 0.0001 (0.5 mol%) to 0.03 ± 0.006 (6.0 mol%), and 0.01 ± 0.0003 (0.5 mol%) to 0.04 ± 0.001 (6.0 mol%), for respective BZD and PA formulations involving 1.0 mol% CQ. The use of NPG led to relatively higher quantum yield values (Up to 0.09 ± 0.007 at 4.0 mol%), though it exhibited competitive effects in absorbing blue light, which might be attributed to the photolytic degradation of NPG and the formation of N-methylaniline. MTT assay indicated alternative co-initiators to be comparatively less cytotoxic than EDMAB and CQ. Relative metablic activity of HDPCs treated with BZD, PA, and NPG eluates were 58.3 ± 15.7, 57.5 ± 17.4 and 64.6 ± 12.2 %, when compared with untreated HDPCs group (Control), respectively. Exposure to DMAEMA-based eluate led to relative metabolic activity (60.0 ± 0.5 %) that was comparable to that of cyclic acetals. Treatment with neat model resin eluate displayed the highest relative reduction in metabolic activity (28.9 ± 22.4) (P < 0.05), suggesting bisGMA and TEGDMA monomers played significant role in the overall cytotoxicity of photocurable systems involving HDPCs. SIGNIFICANCE: Cyclic acetals were capable of facilitating photo-induced free radical polymerisation reactions with relatively less cytotoxicity compared with their amine counterparts, which might realise reduced cytotoxicity of photocurable materials used for dentistry and biomaterial applications.

HIV Epidemic in Libya: Identifying Gaps.

BACKGROUND: HIV (human immunodeficiency virus) and AIDS (acquired immunodeficiency syndrome) became a public issue in Libya after the infection of 400 children in El-Fatih Hospital in 1988. Due to the civil war, social and religious barriers, HIV prevalence is hard to establish, but it is generally believed to be increasing. OBJECTIVE: This review (a) assesses the size and scope of the available literature on the HIV epidemic in Libya; and, (b) identifies the nature and extent of research conducted to date. METHODS: A comprehensive search was performed using PubMed, Medline, Web of Science, ScienceDirect, Scopus, Academic Search Ultimate, Cochrane Library and Google Scholar. Primary research studies and official reports that are exclusively on Libya published during 1988-2021 were considered. RESULTS: In total 25 studies were included: Ten primary research studies, four online news articles, six Government reports, one letter to the editor, one manuscript, three online databases. CONCLUSION: Despite the low-quality data, the literature suggests there is an increase in HIV infection rates in Libya. Culturally sensitive research on sexual activities, women, HIV preventative methods and attitudes of the Libyan public will assist in developing an effective National AIDS Programme, reducing HIV stigma, supporting People Living with HIV (PLHIV) and decreasing infection rates.

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford.

The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes' ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle.

Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

Erratum: Canle, M., et al. Improved Photocatalyzed Degradation of Phenol, as a Model Pollutant, over Metal-Impregnated Nanosized TiO2. Nanomaterials 2020, 10, 996.

The authors wish to make the following corrections to this paper: [...].

Improved Photocatalyzed Degradation of Phenol, as a Model Pollutant, over Metal-Impregnated Nanosized TiO2.

Photocatalyzed degradation of phenol in aqueous solution over surface impregnated TiO2 (M = Cu, Cr, V) under UV-Vis (366 nm) and UV (254 nm) irradiation is described. Nanosized photocatalyts were prepared from TiO2-P25 by wet impregnation, and characterized by X-ray diffraction, X-ray fluorescence, transmission electron microscopy, UV-Vis diffuse reflectance spectroscopy, Raman spectroscopy, and adsorption studies. No oxide phases of the metal dopants were found, although their presence in the TiO2-P25 lattice induces tensile strain in Cu-impregnated TiO2-P25, whereas compressive strain in Cr- and V-impregnated TiO2-P25. Experimental evidences support chemical and mechanical stability of the photocatalysts. Type IV N2 adsorption-desorption isotherms, with a small H3 loop near the maximum relative pressure were observed. Metal surface impregnated photocatalysts are mesoporous with a similar surface roughness, and a narrow pore distribution around ca. 25 Å. They were chemically stable, showing no metal lixiviation. Their photocatalytic activity was followed by UV-Vis spectroscopy and HPLC-UV. A first order kinetic model appropriately fitted the experimental data. The fastest phenol degradation was obtained with M (0.1%)/TiO2-P25, the reactivity order being Cu > V >> Cr > TiO2-P25 under 366 nm irradiation, while TiO2-P25 > Cu > V > Cr, when using 254 nm radiation. TOC removal under 366 nm irradiation for 300 min showed almost quantitative mineralization for all tested materials, while 254 nm irradiation for 60 min led to maximal TOC removal (ca. 30%). Photoproducts and intermediate photoproducts were identified by HPLC-MS, and appropriate reaction pathways are proposed. The energy efficiency of the process was analysed, showing UV lamps are superior to UVA lamps, and that the efficiency of the surface impregnated catalyst varies in the order Cu > V > Cr.

Genomic predictions combining SNP markers and copy number variations in Nellore cattle.

BACKGROUND: Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not sufficient to predict these traits due to the missing heritability caused by other genetic variations such as microsatellite and copy number variation (CNV), which have been shown to affect disease and complex traits in humans and other species. RESULTS: In this study, CNVs were included in a SNP based genomic selection framework. A Nellore cattle dataset consisting of 2230 animals genotyped on BovineHD SNP array was used, and 9 weight and carcass traits were analyzed. A total of six models were implemented and compared based on their prediction accuracy. For comparison, three models including only SNPs were implemented: 1) BayesA model, 2) Bayesian mixture model (BayesB), and 3) a GBLUP model without polygenic effects. The other three models incorporating both SNP and CNV included 4) a Bayesian model similar to BayesA (BayesA+CNV), 5) a Bayesian mixture model (BayesB+CNV), and 6) GBLUP with CNVs modeled as a covariable (GBLUP+CNV). Prediction accuracies were assessed based on Pearson's correlation between de-regressed EBVs (dEBVs) and direct genomic values (DGVs) in the validation dataset. For BayesA, BayesB and GBLUP, accuracy ranged from 0.12 to 0.62 across the nine traits. A minimal increase in prediction accuracy for some traits was noticed when including CNVs in the model (BayesA+CNV, BayesB+CNV, GBLUP+CNV). CONCLUSIONS: This study presents the first genomic prediction study integrating CNVs and SNPs in livestock. Combining CNV and SNP marker information proved to be beneficial for genomic prediction of some traits in Nellore cattle.

Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis.

BACKGROUND: Running multiple-chain Markov Chain Monte Carlo (MCMC) provides an efficient parallel computing method for complex Bayesian models, although the efficiency of the approach critically depends on the length of the non-parallelizable burn-in period, for which all simulated data are discarded. In practice, this burn-in period is set arbitrarily and often leads to the performance of far more iterations than required. In addition, the accuracy of genomic predictions does not improve after the MCMC reaches equilibrium. RESULTS: Automatic tuning of the burn-in length for running multiple-chain MCMC was proposed in the context of genomic predictions using BayesA and BayesCπ models. The performance of parallel computing versus sequential computing and tunable burn-in MCMC versus fixed burn-in MCMC was assessed using simulation data sets as well by applying these methods to genomic predictions of a Chinese Simmental beef cattle population. The results showed that tunable burn-in parallel MCMC had greater speedups than fixed burn-in parallel MCMC, and both had greater speedups relative to sequential (single-chain) MCMC. Nevertheless, genomic estimated breeding values (GEBVs) and genomic prediction accuracies were highly comparable between the various computing approaches. When applied to the genomic predictions of four quantitative traits in a Chinese Simmental population of 1217 beef cattle genotyped by an Illumina Bovine 770 K SNP BeadChip, tunable burn-in multiple-chain BayesCπ (TBM-BayesCπ) outperformed tunable burn-in multiple-chain BayesCπ (TBM-BayesA) and Genomic Best Linear Unbiased Prediction (GBLUP) in terms of the prediction accuracy, although the differences were not necessarily caused by computational factors and could have been intrinsic to the statistical models per se. CONCLUSIONS: Automatically tunable burn-in multiple-chain MCMC provides an accurate and cost-effective tool for high-performance computing of Bayesian genomic prediction models, and this algorithm is generally applicable to high-performance computing of any complex Bayesian statistical model.

The impact of socio-cultural factors on transmission of Taenia spp. and Echinococcus granulosus in Kosovo.

Echinococcus granulosus sensu latu (s.l.) and Taenia hydatigena are common parasites of ruminant intermediate hosts in the Balkans. Transmission is linked mainly to home slaughtering and the feeding of infected organs to dogs. In Kosovo, many old sheep are slaughtered particularly during Eid al-Adha (Feast of Sacrifice). To determine whether this tradition could affect parasite transmission, we compared the probability of 504 dogs to contract taenid infections after deworming during one period before Eid al-Adha and a similar period beginning with this event. Initially, taeniid eggs were detected in 6·2% (CI 4·2-8·6) of the dogs. The prevalence before Eid al-Adha was significantly lower (1·2%, CI 0·4-2·6) as compared with the prevalence after the event (4·3%, CI 2·6-6·3). A comparable trend was apparent at species level for T. hydatigena and E. granulosus. These results indicate that the pronounced increase of taeniid infections, including E. granulosus s.l., after Eid al-Adha is linked to traditional home slaughtering that occurs during this celebration. This particular epidemiological situation provides an opportunity for implementing focussed control activities.

CNV Analysis of Host Responses to Porcine Reproductive and Respiratory Syndrome Virus Infection.

Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i.e. viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain (WG42 from 0 to 42 days post infection). To investigate the effects of CNVs on differential host responses to PRRS, we compared groups of animals with extreme high and low estimated breeding values (EBVs) for both traits using a case-control study design. For VL, we identified 163 CNVRs (84 Mb) from the high group and 159 CNVRs (76 Mb) from the low group. For WG42, we detected 126 (68 Mb) and 156 (79 Mb) CNVRs for high and low groups, respectively. Based on gene annotation within group-specific CNVRs, we performed network analyses and observed some potential candidate genes. Our results revealed these group-specific genes are involved in regulating innate and acquired immune response pathways. Specifically, molecules like interferons and interleukins are closely related to host responses to PRRS virus infection.

Vitamin D status and insulin sensitivity are novel predictors of resting metabolic rate: a cross-sectional analysis in Australian adults.

PURPOSE: Resting metabolic rate (RMR) accounts for two-thirds of the total energy expenditure in sedentary individuals. After accounting for traditional factors, there still remains a considerable unexplained variance in RMR. There is a pandemic of obesity and metabolic syndrome (MetS) which coexists with a high prevalence of vitamin D insufficiency. The aim of this study was to evaluate the potential effects of vitamin D status, insulin sensitivity (IS) and the metabolic syndrome (MetS) on RMR in Australian adults. METHODS: RMR, respiratory quotient (RQ), McAuley's insulin sensitivity index, fat mass (FM), fat-free mass (FFM) and vitamin D status were assessed in Australian adults. The presence of MetS was evaluated by current standard criteria. Predictors of RMR were examined through multiple linear regression based on stepwise and backward regression approaches with attention to multi-collinearity. All analyses were conducted on SPSS version 21. RESULTS: One hundred and twenty-seven participants (45 men, 82 women), aged 53.4 ± 11.7 years and BMI 31.9 ± 5.2 kg/m(2), were included. Forty-one subjects were insufficient in vitamin D status (<50 nmol/L), and 75 participants had the MetS. A parsimonious regression model explained 85.8 % of RMR and was given by: RMR (kJ/d) = 1931 + 83.5 × FFM (kg) + 29.5 × FM (kg) + 5.65 × 25(OH)D (nmol/L) - 17.6 × age (years) - 57.51 × IS. CONCLUSION: Vitamin D status and IS are novel independent predictors of RMR in adults. Future studies could validate a causal role for these factors in human energy metabolism.

Isolation and Identification of Brucella melitensis Biovar 3 from Vaccinated Small Ruminants: A Public Health Threat in Kosovo.

In 2011, a human brucellosis case with severe clinical symptoms was reported at the University Clinic for Infectious Diseases in Prishtina, Kosovo. A trace-back investigation was conducted to find the source of human infection. A total of 49 blood samples and 15 corresponding milk samples from sheep and goats raised on the patient's farm were taken for serological and molecular analysis. Serology using RBT and CFT revealed 11 positive animals. Twelve milk samples were PCR positive. A Brucella strain isolated from a goat's milk sample was classified as Brucella melitensis biovar 3, indicating the first ever isolation and report in Kosovo. The use of the Bruce-ladder PCR provided differentiation between the field strain and the vaccine strain. Hence, the accidental transmission of the vaccine strain Rev 1 that was previously used for the vaccination of the farm animals could be excluded. The findings of this study show that brucellosis is still a public health threat in Kosovo despite control measures.

Quantification of water as a potential risk factor for cross-contamination with Salmonella, Campylobacter and Listeria in a poultry abattoir.

Water used in a modern poultry processing line was tested from October 2005 to June 2006 to determine the level of bacteria in an abattoir in Germany. A total of 420 water samples were taken from 14 processing sites (PSs), at 10 times, and from three different hours of the working shift at three sampling hours (SHs) at 5:00 a.m. (SH 1), 9:00 a.m. (SH 2) and 12:00 a.m. (SH 3). Each sample was assessed for the aerobic plate count (APC) and the prevalence of Salmonella, Campylobacter, Listeria and Yersinia over 30 sampling weeks. The APC numbers of each PS from three SHs were compared, and the prevalence of Salmonella, Campylobacter, Listeria and Yersinia from each PS of three SHs was determined as well as change from the initial PS to the end of the processing line. A total of 46 water samples were positive for Salmonella, 120 positive for Campylobacter and 4 positive for Listeria. None of the water samples was found to be positive for Yersinia. During the course of the day, the APC increased. Salmonella was mostly found during SH 1 (5 a.m.) in water from all PSs. A high number of Campylobacter were observed at SH 2 (9 a.m.) and SH 3 (12 a.m.) from all PSs. The results show that water, which is still used in substantial amounts in present poultry processing technology, can serve as a carrier for Salmonella and Campylobacter. The findings indicate that birds might progressively contaminate the equipment and become contaminated via the same equipment, that water at every processing position of the line constitutes a risk and that more attention should be paid to effective water management in the processing plan.

Lessons learned during the development and transfer of technology related to a new Hib conjugate vaccine to emerging vaccine manufacturers.

The incidence of Haemophilus Influenzae type b (Hib) disease in developed countries has decreased since the introduction of Hib conjugate vaccines in their National Immunization Programs (NIP). In countries where Hib vaccination is not applied routinely, due to limited availability and high cost of the vaccines, invasive Hib disease is still a cause of mortality. Through the development of a production process for a Hib conjugate vaccine and related quality control tests and the transfer of this technology to emerging vaccine manufacturers in developing countries, a substantial contribution was made to the availability and affordability of Hib conjugate vaccines in these countries. Technology transfer is considered to be one of the fastest ways to get access to the technology needed for the production of vaccines. The first Hib conjugate vaccine based on the transferred technology was licensed in 2007, since then more Hib vaccines based on this technology were licensed. This paper describes the successful development and transfer of Hib conjugate vaccine technology to vaccine manufacturers in India, China and Indonesia. By describing the lessons learned in this process, it is hoped that other technology transfer projects can benefit from the knowledge and experience gained.

The effect of Protexin on prevention of ileocecal infection by Mycobacterium avium subspecies paratuberculosis in dairy calves.

The objective of this study was to evaluate the effect of Protexin (Probiotics International Ltd., South Petherton, UK) in the prevention of ileocecal infection by Mycobacterium avium ssp. paratuberculosis (MAP) in dairy calves in the field situation. Forty Holstein bull calves whose dams were paratuberculosis negative (confirmed by serum ELISA test and fecal nested PCR) were randomly selected in 2 groups. All calves were fed raw milk collected from the bulk tank in a paratuberculosis-infected dairy farm, which was confirmed by PCR. The treatment group (20 calves) was given 2 g of Protexin from birth until weaning (90 d). The control group (20 calves) did not consume Protexin. The calves were culled at 12 mo of age and the ileocecal lymph nodes were sampled. The lymph nodes were tested by nested PCR to evaluate MAP infection. In the treatment group, 2 out of 20 calf (10%) ileoceca were infected by MAP, whereas in the control group, 8 out of 20 calf (40%) ileoceca were infected by MAP. A significant difference existed between ileocecal infection by MAP in treatment and control groups. Thus, Protexin showed a significant effect in decreasing the ileocecal infection by MAP.

The protection role of heat shock protein 70 (HSP-70) in the testes of cadmium-exposed rats.

Cadmium (Cd) is an environmental carcinogenic pollutant known to inactivate several proteins involved in DNA repair systems while at the same time creating an oxidative stress that can result in additional DNA lesions. The testis and the lung are the target organs for cadmium carcinogenesis. Increased production of oxidants in vivo can cause damage to intracellular macromolecules such as DNA, proteins and lipids, which in turn lead to oxidative injury. So, this investigation aimed to evaluate the protective role of L-Carnitine through up regulation of HSPs against DNA damage induced by cadmium chloride. The current study was carried out on forty adult male rats, each with average weight 220-250g., were divided into 4 equal groups. 1(st) group was received saline solution (0.5 ml/100 g body weight) and kept as control. 2(nd) group was received 500mg / kg body weight L-Carnitine intraperitoneally (IP). 3(rd) group was administered 1.2 mg cadmium chloride IP. 4(th) group was received both cadmium chloride and L-Carnitine simultaneously. The comet assay parameters showed significantly increased HSP70 and DNA damage in testis cells after 10 and 56 days in the third group. Meanwhile, HSP70 showed significantly decreased levels after 10 days and 56 days in the fourth group after L-Carnitine treatment simultaneously with cadmium chloride. The results of the present study demonstrate a damaging effect of cadmium chloride on DNA of the testis cells (with low stress response). This damaging effect increases the synthesis of HSP70 that upregulated by L-Carnitine treatment and showed ameliorative effect of the cells for recovery.