scholarly journals Identification of Some Errors in the Genome Assembly of Bovidae by FISH

2020 ◽  
Vol 160 (2) ◽  
pp. 85-93
Author(s):  
Lisa De Lorenzi ◽  
Pietro Parma
Keyword(s):  
Bos Taurus ◽  
Unintended Consequences ◽  
Point Of View ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Free Access ◽  
Similar Species ◽  
Economic Point ◽  
Starting Point ◽  
Genome Assemblies

From an economic point of view, Bovidae represent the most important family of the Ruminantia suborder. Thus, the mitochondrial and nuclear genomes of Bos taurus were among the first genomes to be sequenced after the sequencing of the human genomes. Over the millennia, the evolution of the genomes of the 3 main species belonging to the Bovidae family - B. taurus (BTA), Ovis aries (OAR), and Capra hircus (CHI) - has led to few chromosome rearrangements. Certainly, the availability and free access to the animal genomes significantly contributed to the improvement of animal genetics; however, some errors may exist due to the high automation in the genomic assembly construction process. In this work, some differences between the genomes of cattle, goat, and sheep highlighted by bioinformatics analysis have been verified by FISH, confirming that some errors persist even in the most recent genome assemblies. This type of approach has allowed us to detect a misassembly of a region belonging to BTA16 and to the homologues OAR12 and CHI16, a misassembly of a short tract in BTA22, OAR19, and CHI22, an incorrect mapping of a region of BTA21 and of CHI27 and OAR26, a discrepancy in the BTA26, OAR22, and CHI26 assemblies, a missed inversion in CHI1 compared to BTA1 and OAR1, and the exact assembly of a region of about 7 Mb in OAR10 and CHI12. Incorrect positioning of genomic tracts can cause unintended consequences in genetic analyses, especially when the data represent a starting point for the construction of genetic tools. In the new genomic assemblies published after the conclusion of our experiments, however, the accuracy in the construction of animal assemblies has been much improved, even if the new assemblies present more extended unmapped portions than the previous versions. The gap could be filled by comparative analyses between similar species or FISH.

Antibodies against Salmonella is associated with reduced reproductive success in female alpine chamois (Rupicapra rupicapra)

2008 ◽  
Vol 86 (10) ◽  
pp. 1111-1120 ◽  
Author(s):  
Maryline Pioz ◽  
Anne Loison ◽  
Philippe Gibert ◽  
Jean-Michel Jullien ◽  
Marc Artois ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Bos Taurus ◽  
Q Fever ◽  
High Titer ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Wild Ungulates ◽  
Rupicapra Rupicapra ◽  
Domestic Ruminants ◽  
Microbial Infections

Microbial infections that affect reproduction are poorly studied in wildlife because reproductive disorders usually go unnoticed. However, such infections are a major concern in domestic ungulates, which raises the question of their influence on reproductive success and population dynamics of wild ungulates. Three bacterial abortive infections are frequent in domestic ruminants: salmonellosis caused by Salmonella enterica serovar Abortusovis, enzootic abortion caused by Chlamydophila abortus , and Q fever caused by Coxiella burnetii . They induce abortions and neonatal mortality in sheep ( Ovis aries L., 1758), goat ( Capra hircus L., 1758), and cattle ( Bos taurus L., 1758). However, little information is known about these bacteria in wild ungulates, particularly in mountain ungulates that may share alpine pastures with infected domestic ruminants. We investigated the relationship between female serological status against Salmonella, Chlamydophila, and Coxiella and her reproductive success. From 1986 to 2003, the reproductive and serological statuses of 125 female chamois ( Rupicapra rupicapra (L., 1758)) aged 2–10 years were available. Reproductive success was the lowest for 2-year-old females and for females born at the highest density. Moreover, we showed for the first time in a wild ungulate population that females with high titer in antibodies against Salmonella experienced a decrease in their reproductive success. Titers in antibodies against Chlamydophila and Coxiella were not related to the reproductive success of female chamois.

scholarly journals OSTEOLOGICAL MATERIALS FROM CARAVANSERAI SHENGELDY

2020 ◽  
Vol 64 (1) ◽  
Author(s):  
T. Savelyeva ◽  
◽  
М. Shagirbayev ◽  
Keyword(s):  
Species Composition ◽  
Bos Taurus ◽  
Domestic Animals ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Geometric Morphometric ◽  
Equus Hemionus ◽  
Morphological Differences ◽  
Bone Remains ◽  
Degree Of Fragmentation

The article discusses osteological material from the excavations of the Shengeldy caravanserai. In the descriptions of the representatives of the fauna from the medieval caravanserai of Shengeldy and in table 1, the majority of bone remains are identified to a species. Examination of the species composition of the fauna shows their not rich species composition, although as a result of the study all species of domestic ungulates are found. Bone remains were determined by species, skeleton elements and degree of fragmentation. Bones found: horses (Equus caballus), cattle (Bos taurus), sheep (Ovis aries), goats (Capra hircus) and camel (Camelus bactrianus); wild animals - kulan (Equus hemionus), saiga (Saiga tatarica) and turtles (Testudines). Among domestic animals, the bones of horses and small cattle prevail. Cattle ranks third in number. One camel bone was found. Of the bones of domestic animals, 23.4% were intact and 76.6% were fragmented. Among the departments of the skeleton of domestic ungulates, carcass bones (scapula, vertebrae, ribs) and upper legs (femurs and tibia) predominate. Several fragments of human bones were found. Morphometric studies of the bones of horses, sheep, goats and cattle were carried out. Geometric morphometric methods have revealed morphological differences and similarities between species.

scholarly journals Experimental Study on the Mechanical Properties of Biomass Briquettes from a Mixture of Rice Husk and Pine Sawdust

Energies ◽  
2020 ◽  
Vol 13 (5) ◽  
pp. 1060 ◽  
Author(s):  
Andrés Niño ◽  
Nelson Arzola ◽  
Oscar Araque
Keyword(s):  
Mechanical Properties ◽  
Rice Husk ◽  
Industrial Process ◽  
Point Of View ◽  
Total Biomass ◽  
Economic Point ◽  
Pine Sawdust ◽  
Starting Point ◽  
Mechanical Durability ◽  
Compaction Time

In search of guaranteeing global energy requirements, waste from different agricultural, forestry and industrial sources is presented as a renewable and sustainable energy source. The manufacture of solid fuels from biomass based on the densification of this to improve its mechanical and energy properties is one of the mechanisms of viable energy production from the technical-economic point of view. The biomass mixture is one of the topics currently researched, in which various factors can affect the final behavior of the briquettes. In this research the influence on the mechanical properties of briquettes obtained from the mixture between two biomasses is studied: rice husk and pine sawdust. A mixed factorial experimental factorial design is used, in which the process temperature, the proportion of the rice husk biomass over the total mass, and the compaction time are defined as experimental factors. Experimental statistical models are obtained that partially explain the behavior of several responses that characterize the mechanical properties of the briquettes based on the selected independent parameters. It was found that the mechanical durability of the briquettes is higher than 97.5%, meets the existing standards, like German Institute for Standardization (DIN) 51731, Theological Institute Batista Ebenézer (ITEBE) SS187120 or International Organization for Standardization (ISO) 17225-2, for a compaction temperature of 110 °C and a proportion of rice husk that does not exceed 60% of the total biomass mixture in the briquette. The compaction time was also statistically significant to achieve a briquettes density and an appropriate elasticity modulus in the briquettes. The results of this research are of interest and can serve as a starting point for the design of the industrial process of densification of these two mixed biomasses.

PCR Identification of Beef, Sheep, Goat, and Pork in Raw and Heat-Treated Meat Mixtures

2004 ◽  
Vol 67 (1) ◽  
pp. 172-177 ◽  
Author(s):  
MIGUEL A. RODRÍGUEZ ◽  
TERESA GARCÍA ◽  
ISABEL GONZÁLEZ ◽  
LUIS ASENSIO ◽  
PABLO E. HERNÁNDEZ ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Bos Taurus ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Accurate Identification ◽  
Qualitative Detection ◽  
Heat Treated ◽  
Sus Scrofa Domesticus ◽  
Species Specific ◽  
Identification Analysis

A PCR assay has been developed for the specific and qualitative detection of pork ( Sus scrofa domesticus), beef ( Bos taurus), sheep ( Ovis aries), and goat ( Capra hircus) in raw and heat-treated meat mixtures. A forward common primer was designed on a conserved DNA sequence in the mitochondrial 12S ribosomal RNA gene (rRNA), and reverse primers were designed to hybridize on species-specific DNA sequences of each species considered. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear species identification. Analysis of experimental meat mixtures demonstrated that the detection limit of the assay was 1% (wt/wt) for each species analyzed. This assay can be useful for the accurate identification of these species, avoiding mislabeling or fraudulent species substitution in meat mixtures.

PCR-RFLP Authentication of Meats from Red Deer (Cervus elaphus), Fallow Deer (Dama dama),Roe Deer (Capreolus capreolus), Cattle (Bos taurus), Sheep (Ovis aries), and Goat (Capra hircus)

2006 ◽  
Vol 54 (4) ◽  
pp. 1144-1150 ◽  
Author(s):  
Violeta Fajardo ◽  
Isabel González ◽  
Inés López-Calleja ◽  
Irene Martín ◽  
Pablo E. Hernández ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Roe Deer ◽  
Bos Taurus ◽  
Capreolus Capreolus ◽  
Fallow Deer ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Dama Dama ◽  
Pcr Rflp

scholarly journals Variation of Meiotic Recombination Rates and MLH1 Foci Distribution in Spermatocytes of Cattle, Sheep and Goats

2015 ◽  
Vol 146 (3) ◽  
pp. 211-221 ◽  
Author(s):  
Jan Fröhlich ◽  
Miluse Vozdova ◽  
Svatava Kubickova ◽  
Halina Cernohorska ◽  
Hana Sebestova ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Individual Variability ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Evolutionary Divergence ◽  
Recombination Rates ◽  
Crossover Interference ◽  
The Family ◽  
Frequency Position ◽  
Mlh1 Foci

Despite similar genome sizes, a great variability in recombination rates is observed in mammals. We used antibodies against SYCP3, MLH1 and centromeres to compare crossover frequency, position along chromosome arms and the effect of crossover interference in spermatocytes of 4 species from the family Bovidae (Bos taurus, 2n = 60, tribe Bovini; Ovis aries, 2n = 54, Capra hircus, 2n = 60 and Ammotragus lervia, 2n = 58, tribe Caprini). Despite significant individual variability, our results also show significant differences in both recombination rates and the total length of autosomal synaptonemal complexes (SC) between cattle (47.53 MLH1 foci/cell, 244.59 µm) and members of the tribe Caprini (61.83 MLH1 foci, 296.19 µm) which can be explained by the length of time that has passed since their evolutionary divergence. Sheep displayed the highest number of MLH1 foci per cell and recombination density, although they have a lower diploid chromosome number caused by centric fusions corresponding to cattle chromosomes 1;3, 2;8 and 5;11. However, the proportion of MLH1 foci observed on the fused chromosomes in sheep (26.14%) was significantly lower than on the orthologous acrocentrics in cattle (27.6%) and goats (28.2%), and their distribution along the SC arms differed significantly. The reduced recombination rate in metacentrics is probably caused by interference acting across the centromere.

scholarly journals Forest without prey: livestock sustain a leopard Panthera pardus population in Pakistan

Oryx ◽  
2014 ◽  
Vol 49 (2) ◽  
pp. 248-253 ◽  
Author(s):  
Wasim Shehzad ◽  
Muhammad Ali Nawaz ◽  
François Pompanon ◽  
Eric Coissac ◽  
Tiayyba Riaz ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Human Life ◽  
Domestic Animals ◽  
Ovis Aries ◽  
Diet Analysis ◽  
Domestic Dog ◽  
Capra Hircus ◽  
Generalist Predator ◽  
Panthera Pardus ◽  
Canis Lupus Familiaris

AbstractHuman–carnivore conflict is one of the major challenges in the management of populations of large carnivores. Concerns include the increasing human population; habitat loss as a result of degradation and fragmentation of forest; and livestock predation as a result of a lack of natural prey, leading to retaliatory killings of wild carnivores. Conflicts may be further aggravated by occasional attacks that result in injury and loss of human life. The level of consumption of prey species by a predator is a benchmark to evaluate the scale of this conflict. We used a newly developed DNA-based diet analysis to study the prey profile of common leopards Panthera pardus in Ayubia National Park, Pakistan. The results suggest that the common leopard is a generalist predator, subsisting mainly on domestic animals. Based on the frequency of occurrence of prey items in 57 faecal samples, the diet of the leopard is dominated by domestic goat Capra hircus (64.9%), followed by domestic dog Canis lupus familiaris (17.5%) and cow Bos taurus (12.3%). Domestic animals (goat, dog, cow, water buffalo Bubalus bubalis, horse Equus caballus and sheep Ovis aries) occurred in 54 (95%) of the 57 samples. We recommend a two-step strategy to mitigate this conflict: (1) introducing incentives for increased acceptance of leopards among local communities in the vicinity of the protected area and (2) increasing the availability of wild prey. We hope that the results of this study will contribute to the survival of the leopard in Pakistan.

Comparative micelle structure: II. Structure and composition of casein micelles in ovine and caprine milk as compared with those in bovine milk

1974 ◽  
Vol 41 (2) ◽  
pp. 239-247 ◽  
Author(s):  
B. C. Richardson ◽  
L. K. Creamer ◽  
K. N. Pearce ◽  
R. E. Munford
Keyword(s):  
Bos Taurus ◽  
Bovine Milk ◽  
Chemical Properties ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Casein Micelles ◽  
Mineral Contents ◽  
Caprine Milk ◽  
Micelle Size ◽  
Physical And Chemical

SummaryThe casein micelles of sheep (Ovis aries), goat (Capra hircus) and cow (Bos taurus) milks have been examined by electron microscopy. The ovine micelles were smaller than bovine micelles, most being below 80 nm diam. The caprine micelles were either large (c. 200 nm diam.), easily sedimented and electron-dense, or small (below 80 nm) and similar to the ovine micelles. Examination of the micelles using the freeze-etch technique showed, however, that they were all composed of subunits of similar dimensions (10–15 nm diam.).Electrophoresis of the caseins showed that there were differences between them, with the caprine casein containing a smaller proportion of its protein in the more mobile components. The mineral contents of the milks were also different, but these were apparently related to the different pH and casein contents of the milks. It is likely that the diiferences in micelle size distribution are determined by the physical and chemical properties of the casein components.

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