A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Calcium and phosphorus contents of body parts of some domestic animals used as meat source in Nigeria

Objective:To investigate the calcium and phosphorus contents of four domestic animals used as sources of meat in Nigeria.Methods:The calcium contents of the body parts of the animals were determined using atomic absorption spectrometer.Their phosphorus contents were determined colorimetrically using the molybdenum blue method.Results:The calcium and phosphorus contents were significantly higher in the bone samples than in the other animal parts investigated (P【0.05).The calcium contents of all the edible parts were higher in chicken than in the other animals.High calcium and phosphorus contents were detected in the faeces of chicken and goat, and that of cattle and goat,respectively.Low calcium and phosphorus contents were detected in the urine samples.Calcium:phosphorus ratios calculated for the bones of chicken,cattle and goat were satisfactory.Conclusions:In conclusion,calcium and phosphorus contents of the animal parts vary significantly and their relative contents may be related to the animal’s diet.Chicken parts may be the preferred dietary source of these minerals.This study highlights the need for routine investigation of the mineral contents of food,which is necessary for proper nutritional guidelines.

Management practices and technologies for efficient biological sample collection from domestic animals with special reference to Indian field conditions

Management strategies and the use of advanced technologies are equally important for determining the sample number and sampling frame for successful field sampling for animal disease prevalence studies.The quality of the biological samples collected in the field has a direct bearing on the integrity of the data generated,prevalence estimates and subsequent policy decisions on disease control.Hence,compromising the quality of biological samples collected in the field could potentially undermine the priority setting principles in disease control strategies.Biological samples collected from domestic animals in the field are precious materials and require meticulous planning for sample collection,sample storage in the field,transportation,and storage in the laboratory.Poorly managed field sampling has a significant detrimental impact on the sample quality and quantity and directly affects the accuracy of disease prevalence data.A bad choice of sampling tools,containers,storage and transport all have a negative impact on the integrity of the sample and consequently have an impact on the outcome.Over the last two years,as part of our one health animal sampling work in ndia,we have observed challenges and opportunities in the field sampling of animals for disease prevalence studies.This paper aims to provide information on management practices and technologies for efficient biological sample collection from the field and ensure that good quality samples are available fortesting.

Sero-Prevalence of Toxoplasmosis in Domestic Animals in Benadir Region, Somalia

A sero-prevalence survey of Toxoplasmosis in domestic animals (camels, cattle, sheep and goats) was conducted in the Benadir region of Somalia from January to July 2014 to determine the status of the disease. A total of 151 sera were tested, 64 camels;28 cattle;29 sheep and 30 goats, for the presence of Toxoplasma gondii antibodies using Latex Agglutination Test (LAT). Totally about 15.9% (24/151) of studied animals showed sero-positive. The sero-prevalence was found in 6.3% of 64 camels, 7.1% of 28 cattle, 34.5% of 29 sheep and 26.7% of 30 goats. The antibody titres to T. gondii positive sera were 2 (8.3%), 9 (37.5%), 4 (16.7%), 4 (16.7%), 4 (16.7%), 1 (4.2%) and 0 (0%) by dilution of 1:2, 1:4, 1:8, 1:16, 1:32, 1:64 and 1:128 respectively. Out of 151 domestic animals (45 male and 106 female), 8 (5.3%) males and 16 (10.6%) females were infected with T. gondii. The study recommends the need for further researches in the whole country using different serological tests and to determine the impact of these findings on the human population. It would be important to increase public awareness on zoonotic potential of Toxoplasmosis.

Immunoglobulin genes and diversity: what we have learned from domestic animals

This review focuses on the diversity of immunoglobulin （Ig） genes and Ig isotypes that are expressed in domestic animals. Four livestock species--cattle, sheep, pigs, and horses--express a full range of Ig heavy chains （IgHs）, including t J, 6, y, c, and a. Two poultry species （chickens and ducks） express three IgH isotypes, la, u, and a, but not （5. The K and X light chains are both utilized in the four livestock species, but only the X chain is expressed in poultry. V（D）J recombination, somatic hypermutation （SHM）, and gene conversion （GC） are three distinct mechanisms by which immunoglobulin variable region diversity is generated. Different domestic animals may use distinct means to diversifyrearrancled variable reqions of la aenes.

Diagnosis of Rabies via RT-PCR on Skin Samples of Wild and Domestic Animals

In developing countries, brain tissues from rabies suspect animals are not always available for diagnosis for a variety of reasons, such as lack of transport to submit a carcass or the difficulty of removing an animal’s head or brain under field conditions. To enable diagnosis in such cases, there is a need for a reliable method, using an alternative non-neural tissue, which can be removed and submitted to the diagnostic laboratory without special training or equipment. In human medicine, skin is used successfully for the detection of rabies virus antigen using RT-PCR technology. Little work has been done in animals using RT-PCR on skin or extracted hair follicles. The current study was conducted in Grenada on skin from 36 wild and domestic animals, in which rabies virus infection had been confirmed in brain tissue via the direct fluorescent antibody (DFA) test, and in 31 negative control animals. RT-PCR on skin yielded a sensitivity of 97.2% (35/36) and a specificity of 100% (31/31). It is concluded that the examination of skin samples via RT-PCR provides a valuable diagnostic alternative in those cases where brain tissue is not readily available.

Presence of Virulence-Associated Genes and Ability to Form Biofilm among Clinical Isolates of <i>Escherichia coli</i>Causing Urinary Infection in Domestic Animals

Background: Urinary tract infection caused by Escherichia coli is a frequently observed condition both in humans and animals. Uropathogenic E. coli (UPEC) has been shown to have a pathogenicity island that enables them to infect the urinary tract. Because there is little information about the presence of UPEC-associated virulent genes in animal isolates this work was carried out with the intent to enhance the understanding about the strains of E.coli that cause infections in animals. Results: We screened 21 E. coli strains isolated causing urinary tract infection in domestic animals. Primers were designed to amplify urinary infection-associated genes. Nine genes, papA, tcpC, fyuA, tpbA, Lma, hylA, picU, tonB, and flicC were then amplified and sequenced. Different from the human isolate CFT073, all the animals E. coli lack some of the pathogenesis-associated genes. Genes encoding for proteins used to scavenge iron appear not to be so necessary during animal infections as they are in human infection. In further investigation of phenotypic properties, it was observed that animal UPECs have significantly more impaired ability to form biofilms than human UPEC strain. Conclusions: This study identified significant differences between human and animal UPECs. This may have its roots in the fact that it is difficult to determine if an animal has symptoms. Future studies will focus on some of the observations.

Effect of Micro-electrolysis and Micro-nano Bubbles Coupled with Peroxymonosulfate Treatment of Rural Domestic Sewage

With the continuous deepening of rural revitalization strategy and the increasingly strict sewage discharge standards,rural domestic sewage treatment technology is facing higher challenges and requirements.The combined process of micro-electrolysis+micro-nano bubbles coupled with peroxymonosulfate was constructed in this study,and the treatment effect and application value of this technology were explored with the actual rural domestic sewage as the treatment object.The experimental results showed that under the conditions of HRT of 120 min,PMS dosage of 0.15 mmol/L,pH=7,MBs air intake of 15 ml/min,current intensity of 15 A,and Fe/C mass ratio of 1:1,the removal rates of COD,ammonia nitrogen and total phosphorus can reach 88.55%,77.18%and 74.67%,respectively.Under the condition that the pH value of sewage was not adjusted,the non-biochemical simultaneous decarbonization,denitrification and phosphorus removal of rural domestic sewage can be achieved by micro-electrolysis and micro-nano bubbles coupled with peroxymonosulfate.The concentrations of effluent COD,ammonia nitrogen and total phosphorus met the requirements of the first level standard of the Discharge Standard of Water Pollutants for Rural Domestic Sewage Treatment Facilities(DB45T2413-2021).And the comprehensive operating cost was about 1.15 yuan/m 3.

Analysis of the Effect and Influencing Factors of Rural Domestic Sewage Treatment Based on A^(2)O-MBBR Integrated Process

[Objectives] This study was conducted to solve the prominent problems in the treatment of domestic sewage in southern rural areas of China. [Methods] An integrated process treatment mode of anaerobic/anoxic/aerobic moving bed biofilm reactor (A 2O-MBBR) was proposed to analyze and study its operating effect and influencing factors. [Results] The A^(2)O-MBBR mode had good COD removal efficiency and nitrogen and phosphorus removal performance, and the water quality index of the effluent met the Class A standard of GB181918-2002. This mode is suitable for treating rural domestic sewage, and has high treatment effects in different operating periods. In spring, the average removal rates of COD, NH_(4)^(+)-N, TN, TP and SS reached (83.53 ± 2.15)%, (89.44 ± 4.97)%, (67.36±18.53)%, (88.22±11.21)% and (91.73±2.25)%, respectively;In the autumn period, the average removal rates of COD, NH_(4)^(+)-N, TN, TP and SS were (83.49±2.64)%, (89.26±9.19)%, (66.05±17.00)%, (87.48±9.68)%, and (91.13±2.35)%. [Conclusions] This study provides theoretical reference and technical support for the popularization and application of A^(2)O-MBBR integrated process.

A Train Adventure of Wild Animals

An empty goods train was speedingthrough a jungle. Up front, in the engire,was the driver and at the back, in the lastcompartment, was the guard, Apart fromthem, the entire train was empty.A goods train carries goods like logs ofwood, or boxes of chocolate and even carsand jeeps. But this train had been carryingcoal, After unloading all the coal, the emptytrain was going back to get more coal.

Efficiency and effectiveness of systems for the treatment of domestic wastewater based on subsurface flow constructed wetlands in Jarabacoa, Dominican Republic

Constructed wetlands(CwW)are well known nature-based systems for water treatment.This study evaluated the efficiency and effectiveness of seven domestic wastewater treatment systems based on horizontal flow CWs in Jarabacoa,the Dominican Republic.The results showed that the CWs were efficient in reducing the degree of contamination of wastewater to levels below the Dominican wastewater discharge standards for parameters such as the 5-day biochemical oxygen demand(BOD5)and chemical oxygen demand,but not for the removal of phosphorus and fecal coliforms.In addition,a horizontal flow subsurface wetland in the peri-urban area El Dorado was evaluated in terms of the performance of wastewater treatment in tropical climatic conditions.The concentrations of heavy metals,such as zinc,copper,chromium,and iron,were found to decrease in the effluent of the wetland,and the concentrations for nickel and manganese tended to increase.The levels of heavy metals in the effluent were lower than the limit values of the Dominican wastewater discharge standards.The construction cost of these facilities was around 200 USD per population equivalent,similar to the cost in other countries in the same region.This study suggested some solutions to the improved performance of CWs:selection of a microbial flora that guarantees the reduction of nitrates and nitrites to molecular nitrogen,use of endemic plants that bioaccumulate heavy metals,combination of constructed wetlands with filtration on activated carbon,and inclusion of water purification processes that allow to evaluate the reuse of treated water.

Occurrence of microcystins in water,sediment,and aquatic animals in Dau Tieng Reservoir,Vietnam

This study investigates the variations of microcystins(MCs)in water,cyanobacterial blooms,sediment,and aquatic organisms collected from the Dau Tieng Reservoir(DTR).Vietnam.Highperformance liquid chromatography(HPLC)was employed to measure MC concentrations in various target samples.Results indicate that Microcystis spp.dominates as the primary MC producer in the DTR.The average concentrations of analyzed MCs in surface water ranged from 1.10 to 5.54μg/L,temporally and spatially.In sediment,average concentrations varied from 0.15 to 1.13μg/g wet weight(WW)temporally and from 0.41 to 0.72μg/g WW spatially.MCs were detected in different organs of fish species(Oreochromis sp.and Labiobarbus sp.)and in the entire soft tissues of bivalve(Corbicula sp.)and gastropod(Assiminea sp.).The highest observed MC concentration in July was 0.83±0.22μg/g WW in the intestines of fish Oreochromis sp.The presence of MCs in grass shrimp Palaemonetes sp.was observed solely in June,reaching a concentration of 0.28±0.19μg/g WW.This is the first report of MC accumulation in the grass shrimp Palaemonetes sp.during field collection.For the bivalve Corbicula sp.,the presence of analyzed MCs was consistent throughout the study period,except for March and September,with the highest concentrations in July at 0.77±0.1μg/g WW.Pearson correlation analysis revealed significant positive correlations between MCs in water and sediment with MC concentrations in aquatic animals,indicating the potential transfer of MCs across different trophic levels.The estimated daily intake values for analyzed MCs indicate that fish collected from the DTR are considered safe for consumption,as long as only the edible organs,such as the muscle,are consumed.However,bivalves or gastropods collected from the DTR are not safe for human consumption.This study underscored the importance of monitoring MC accumulation in aquatic animals used as food to mitigate adverse effects on human health.

Lead, Zinc and Iron Pollutants Load Assessment in Selected Rivers in Southern Nigeria: Implications for Domestic Uses

The aim of the study is to comparatively assess the concentrations of lead, zinc and iron in Rivers Ase, Warri and Ethiope, in Nigeria. Monthly water samples were collected from six randomly selected sites along the rivers course. 72 water samples were collected from each river at 0 - 15 cm depths. Samples were analysed based on the standard methods recommended by the WHO for testing lead, zinc and iron. The assessment of the water quality was done using the Water Quality Index (WQI) of the Canadian Council of Ministers of the Environment (CCME-WQI). While hypotheses were tested using ANOVA. Findings indicated that CCME-WQI values were 47.3, 66.52 and 78.7. This meant that the water quality of River Ase is impaired and departed from desirable levels, while that of Warri and Ethiope were considered to occasionally be impaired and depart from desirable levels. The ANOVA model showed that there is a significant variation in heavy metal load in the selected rivers at P < 0.05. River water was put to domestic uses such as drinking (20.5%) preparing food (17.8%), bathing (19.8%), washing clothes and dishes (21.3%), brushing teeth (13.3%), and catering for domestic animals (7.5%). Poverty (49.5%) was the major reason for the use of river water for domestic purposes. The locals highlighted that they usually suffer from cholera (26.8%), diarrhoea (25.8%), dysentery (24%) and typhoid (23.5%) as a result of using the river water. The study recommended routine monitoring of anthropogenic and geologic activities, testing of the water regularly amongst others.

Finding biomarkers of experience in animals

At a time when there is a growing public interest in animal welfare,it is critical to have objective means to assess the way that an animal experiences a situation.Objectivity is critical to ensure appropriate animal welfare outcomes.Existing behavioural,physiological,and neurobiological indicators that are used to assess animal welfare can verify the absence of extremely negative outcomes.But welfare is more than an absence of negative outcomes and an appropriate indicator should reflect the full spectrum of experience of an animal,from negative to positive.In this review,we draw from the knowledge of human biomedical science to propose a list of candidate biological markers(biomarkers)that should reflect the experiential state of non-human animals.The proposed biomarkers can be classified on their main function as endocrine,oxidative stress,non-coding molecular,and thermobiological markers.We also discuss practical challenges that must be addressed before any of these biomarkers can become useful to assess the experience of an animal in real-life.

Significant genomic introgression from grey junglefowl(Gallus sonneratii)to domestic chickens(Gallus gallus domesticus)

Background Chicken is one of the most numerous and widely distributed species around the world,and many studies support the multiple ancestral origins of domestic chickens.The research regarding the yellow skin phenotype in domestic chickens(regulated by BCO2)likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens.However,beyond the BCO2 gene region,much remains unknown about the introgression from the grey junglefowl into domestic chickens.Therefore,in this study,based on wholegenome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds,we explored the introgression events from the grey junglefowl to domestic chickens.Results We successfully detected introgression regions besides BCO2,including two associated with growth trait(IGFBP2 and TKT),one associated with angiogenesis(TIMP3)and two members of the heat shock protein family(HSPB2 and CRYAB).Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens.Furthermore,we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds,indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained.Additionally,our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens,possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.Conclusions In summary,our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens,laying the foundation for a deeper understanding of the genetic composition within domestic chickens,and offering new perspectives on the impact of introgression on domestic chickens.

Imprinting at the KBTBD6 locus involves species-specific m ternal methylation and monoallelic expression in livestock animals

Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting.Results Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter Cp G island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter Cp G islands were methylated in oocytes and/or allelically methyl-ated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these Cp G islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting.Conclusions In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.

Analysis on Selection of Domestic Sewage Treatment Method in Rural Area

Based on the characteristics of the domestic sewage in rural district,four sewage treatment methods were analyzed.The results found that the optimum method was to process the domestic sewage on the spot,and it should be popularized and applied in rural area.

Evaluation of the Effect of Four Levels of Shade on the Growth and Development of Desmodium adscendens with a View to Its Domestication as a Cover Crop in Côte d’Ivoire

Desmodium adscendens is a plant in the Fabaceae family that is very important to man, both agronomically and medicinally. It is an important cover crop that contributes to improving soil fertility, reducing the risks associated with crop pests and weeds. However, very little research has been carried out into its domestication for use as a cover crop in banana plantations in Côte d’Ivoire. The general objective of this study was to evaluate, under semi-controlled conditions, the effect of different levels of shade on the growth and development of Desmodium adscendens. The studies were carried out on the experimental site of the UP-Plant Physiology Laboratory. Four shading levels were evaluated: 0 (NO), 20% (N1), 40% (N2) and 60% (N3) light levels. The Desmodium adscendens cuttings used were collected from a 3-month nursery. For each treatment, 10 tubs containing sterilized soil were used, and 50 cuttings were planted. After planting, growth and development parameters were assessed weekly on 10 plants. In addition, yield and fresh and dry mass were measured. Finally, the reproductive cycle of Desmodium adscendens was determined. The results showed that plant growth and development were greatest in plants grown under the 40% shade level, followed by the 20% and 60% shade levels. In contrast, plants in full light showed poor growth and development. The 40% shade level was the most favorable for growing Desmodium adscendens cuttings, with a cycle length of 67 days. Growing Desmodium adscendens under shade with 20% and 40% light levels could be recommended to farmers.

Problem and Countermeasure of Rural Domestic Sewage Treatment

With the development of rural economy, pollutions of rural sewage are in- creasingly serious. This paper introduces the characteristics of rural domestic sewage and the rural sewage treatment situation, and according to the problems of funds, management, process selection, policy and weak awareness of environmental protection in the rural domestic sewage treatment, puts forward relevant countermea- sures to ensure long-term operation of sewage treatment system, and achieve the purpose of improving rural water environment and protect the ecological environment in rural areas.

Go-Ahead Element of Domestic Architecture:Socio-Economic and Cultural Characteristics of the Residents in Benin

The domestic architecture of a traditional settlement is greatly influenced by the socio-economic and socio-cultural characteristics of its residents.Benin City which is the focus of the paper is a case of a traditional settlement undergoing domestic architectural evolution with the changing times influenced by factors of growth and development.The paper has examined the effect of socio-economic and socio-cultural characteristics as factors that partly determine the design,style,pattern,space use,organization,location and meaning as well as land use of the domestic architecture of Benin.The study employed the use of questionnaire administered to residents across the cross-section of the city.In the end,descriptive frequency tables were used to analyse the data collected from the residential zones in Benin.The research has been able to corroborate the theory that socio-economic and socio-cultural factors are some of the determinants/elements of domestic architecture of a people.