Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip

Background

Tunisian local cattle populations are at risk of extinction as they were massively crossed with imported breeds. Preservation of indigenous livestock populations is important because each of them comprises a unique set of genes resulting from a local environment-driven selection that occurred over hundreds of years. The diversity and genetic structure of Tunisian local cattle populations are poorly understood. However, such information is crucial to the conservation and sustainable use of genetic resources.In addition, comparing the genomic structure of population sets from different parts of the world could help yield insight into their origin and history.In the present study, we provide a detailed assessment of the population structure of the three Tunisian local cattle populations using various methods, and we highlight their origin and history by investigating approximately ~38,000 SNPs in a broad panel of 878 individuals from 37 worldwide cattle breeds representative of African, European and indicine populations.

Results

Our study revealed a low level of divergence and high genetic diversity in Tunisian local cattle reflecting low levels of genetic drift. A Comparison with the worldwide cattle panel pinpointed the admixed origin of the genome of the three Tunisian populations with the two main European and African ancestries. Our results were in agreement with previous historical and archaeological reports about the past gene flow that existed between North African and South European breeds, in particular with Iberian cattle. We also detected a low-level indicine introgression in the three Tunisian populations and we inferred that indicine ancestry was inherited via African ancestors.

Conclusions

Our results represent the first study providing genetic evidence about the origin and history of Tunisian local cattle. The information provided by the fine-scale genetic characterization of our study will enhance the establishment of a national conservation strategy for these populations. These results may enable the identification of genetic variants involved in adaptation to harsh environmental conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1638-6) contains supplementary material, which is available to authorized users.     

Fine mapping of quantitative trait loci affecting female fertility in dairy cattle on BTA03 using a dense single-nucleotide polymorphism map

Fertility quantitative trait loci (QTL) are of high interest in dairy cattle since insemination failure has dramatically increased in some breeds such as Holstein. High-throughput SNP analysis and SNP microarrays give the opportunity to genotype many animals for hundreds SNPs per chromosome. In this study, due to these techniques a dense SNP marker map was used to fine map a QTL underlying nonreturn rate measured 90 days after artificial insemination previously detected with a low-density microsatellite marker map. A granddaughter design with 17 Holstein half-sib families (926 offspring) was genotyped for a set of 437 SNPs mapping to BTA3. Linkage analysis was performed by both regression and variance components analysis. An additional analysis combining both linkage analysis and linkage-disequilibrium information was applied. This method first estimated identity-by-descent probabilities among base haplotypes. These probabilities were then used to group the base haplotypes in different clusters. A QTL explaining 14% of the genetic variance was found with high significance (P < 0.001) at position 19 cM with the linkage analysis and four sires were estimated to be heterozygous (P < 0.05). Addition of linkage-disequilibrium information refined the QTL position to a set of narrow peaks. The use of the haplotypes of heterozygous sires offered the possibility to give confidence in some peaks while others could be discarded. Two peaks with high likelihood-ratio test values in the region of which heterozygous sires shared a common haplotype appeared particularly interesting. Despite the fact that the analysis did not fine map the QTL in a unique narrow region, the method proved to be able to handle efficiently and automatically a large amount of information and to refine the QTL position to a small set of narrow intervals. In addition, the QTL identified was confirmed to have a large effect (explaining 13.8% of the genetic variance) on dairy cow fertility as estimated by nonreturn rate at 90 days.     

Inclusion complexes of N-sulfamoyloxazolidinones with beta-cyclodextrin

A study of inclusion complexes of six N-sulfamoyloxazolidinone derivatives with beta-cyclodextrin is described. The inclusion complexes were prepared in solution and in solid state with stoichiometry host-guest 1:1, and characterized. In solution, the complexation was carried out by spectrophotometric measurements at 25 degrees C. The stoichiometries and stability constants of complexes at various pHs have been determined using second-derivative spectrophotometry UV-vis. Hydrophobic properties of N-sulfamoyloxazolidinones are improved following their inclusion into beta-CD.     

Zooplankton distribution in four ponds of different salinity: a seasonal study in the solar salterns of Sfax (Tunisia)

The seasonal distribution of metazooplankton and large-sized ciliates was studied in four ponds of different salinity in the solar salterns of Sfax (Tunisia). Total zooplankton abundance varied from 1 × 10³ to 4.7 × 10⁶ ind m^–3. Salinity had a negative effect on the abundance of copepods and rotifers which were absent in the pond with the highest salt concentration (180) in which the number of taxa was low and Artemia or the ciliate Fabrea largely dominated the zooplankton community. Temperature and the presence of Dunaliella salina as prey appeared as key factors in controlling the abundance of Artemia, while organic detritus appeared as important in the diet of Fabrea. Change in zooplankton species composition along the hypersaline gradient (40–90) was primarily related to salinity. However, our data suggest the importance of both the abundance and composition of food in the spatial and temporal variations of some zooplankton species.     

Persistence of Microbial Contamination on Transvaginal Ultrasound Probes despite Low-Level Disinfection Procedure

Aim of the Study

In many countries, Low Level Disinfection (LLD) of covered transvaginal ultrasound probes is recommended between patients'' examinations. The aim of this study was to evaluate the antimicrobial efficacy of LLD under routine conditions on a range of microorganisms.

Materials and Methods

Samples were taken over a six month period in a private French Radiology Center. 300 specimens derived from endovaginal ultrasound probes were analyzed after disinfection of the probe with wipes impregnated with a quaternary ammonium compound and chlorhexidine. Human papillomavirus (HPV) was sought in the first set of s100 samples, Chlamydia trachomatis and mycoplasmas were searched in the second set of 100 samples, bacteria and fungi in the third 100 set samples. HPV, C. trachomatis and mycoplasmas were detected by PCR amplification. PCR positive samples were subjected to a nuclease treatment before an additional PCR assay to assess the likely viable microorganisms. Bacteria and fungi were investigated by conventional methods.

Results

A substantial persistence of microorganisms was observed on the disinfected probes: HPV DNA was found on 13% of the samples and 7% in nuclease-resistant form. C. trachomatis DNA was detected on 20% of the probes by primary PCR but only 2% after nuclease treatment, while mycoplasma DNA was amplified in 8% and 4%, respectively. Commensal and/or environmental bacterial flora was present on 86% of the probes, occasionally in mixed culture, and at various levels (10->3000 CFU/probe); Staphylococcus aureus was cultured from 4% of the probes (10-560 CFU/probe). No fungi were isolated.

Conclusion

Our findings raise concerns about the efficacy of impregnated towels as a sole mean for disinfection of ultrasound probes. Although the ultrasound probes are used with disposable covers, our results highlight the potential risk of cross contamination between patients during ultrasound examination and emphasize the need for reviewing the disinfection procedure.     

Optimization of β-mannanase production by Bacillus subtilis US191 using economical agricultural substrates

The Bacillus subtilis US191 strain producing highly thermostable β-mannanase was previously selected as potential probiotic candidate for application as feed supplement in poultry industry. Initially, the level of extracellular β-mannanase production by this strain was 1.48 U ml⁻¹. To improve this enzyme titer, the present study was undertaken to optimize the fermentation conditions through experimental designs and valorization of agro-industrial byproducts. Using the Plackett–Burman design, in submerged fermentation, a set of 14 culture variables was evaluated in terms of their effects on β-mannanase production. Locust bean gum (LBG), soymeal, temperature, and inoculum size were subsequently optimized by response surface methodology using Box–Behnken design. Under optimized conditions (1 g L⁻¹ LBG, 8 g L⁻¹ soymeal, temperature of 30°C and inoculum size of 10¹⁰ CFU ml⁻¹), a 2.59-fold enhancement in β-mannanase titer was achieved. Next, to decrease the enzyme production cost, the effect of partial substitution of LBG (1 g L⁻¹) by agro-industrial byproducts was investigated, and a Taguchi design was applied. This allowed the attaining of a β-mannanase production level of 8.75 U ml⁻¹ in presence of 0.25 g L⁻¹ LBG, 5 g L⁻¹ of coffee residue powder, 5 g L⁻¹ of date seeds powder, and 5 g L⁻¹ of prickly pear seeds powder as mannans sources. Overall, a 5.91-fold improvement in β-mannanase production by B. subtilis US191 was achieved.     

Growth phenology and water potential patterns of Periploca angustifolia in relation to water availability

Periploca angustifoliaLabill., is a multipurpose shrub also used to rehabilitate drylands. It is essential to understand its phenological patterns under arid conditions. In order to understand how plants manage extreme drought, this study investigates the relationship between phenological traits of P. angustifolia Labill., water potential and climatic conditions. During two successive growing seasons (Sep 2009–Augst 2011) phenological patterns, soil water content and water potentials were measured monthly for plants of Periploca angustifoliaLabill growing under rain-fed conditions (Annual rainfall = 168 mm) at the pastoretum of the Arid Regions Institute in southern Tunisia. The Ψmd decreased progressively and concomitantly with increasing seasonal drought, reaching the lowest values in late summer (down to –3 MPa). Water potentials of P. angustifoliaLabill were affected by spatial and temporal variations in soil water content. The increased diurnal amplitude values (∆ψ > −1.3 MPa) explained the especially high biological activity of this species during the dry season. Our results clearly demonstrate that P. angustifolia Labill is a drought-tolerant species reaching low water potentials during the driest months of summer. These characteristics make this shrub as promising for rehabilitating degraded arid ecosystems.     

Loss of Function of Glucocerebrosidase GBA2 Is Responsible for Motor Neuron Defects in Hereditary Spastic Paraplegia

Spastic paraplegia 46 refers to a locus mapped to chromosome 9 that accounts for a complicated autosomal-recessive form of hereditary spastic paraplegia (HSP). With next-generation sequencing in three independent families, we identified four different mutations in GBA2 (three truncating variants and one missense variant), which were found to cosegregate with the disease and were absent in controls. GBA2 encodes a microsomal nonlysosomal glucosylceramidase that catalyzes the conversion of glucosylceramide to free glucose and ceramide and the hydrolysis of bile acid 3-O-glucosides. The missense variant was also found at the homozygous state in a simplex subject in whom no residual glucocerebrosidase activity of GBA2 could be evidenced in blood cells, opening the way to a possible measurement of this enzyme activity in clinical practice. The overall phenotype was a complex HSP with mental impairment, cataract, and hypogonadism in males associated with various degrees of corpus callosum and cerebellar atrophy on brain imaging. Antisense morpholino oligonucleotides targeting the zebrafish GBA2 orthologous gene led to abnormal motor behavior and axonal shortening/branching of motoneurons that were rescued by the human wild-type mRNA but not by applying the same mRNA containing the missense mutation. This study highlights the role of ceramide metabolism in HSP pathology.     

A sampling design and model for estimating abundance of Nile crocodiles while accounting for heterogeneity of detectability of multiple observers

As part of the development of a management program for Nile crocodiles in Lake Nasser, Egypt, we used a dependent double-observer sampling protocol with multiple observers to compute estimates of population size. To analyze the data, we developed a hierarchical model that allowed us to assess variation in detection probabilities among observers and survey dates, as well as account for variation in crocodile abundance among sites and habitats. We conducted surveys from July 2008–June 2009 in 15 areas of Lake Nasser that were representative of 3 main habitat categories. During these surveys, we sampled 1,086 km of lake shore wherein we detected 386 crocodiles. Analysis of the data revealed significant variability in both inter- and intra-observer detection probabilities. Our raw encounter rate was 0.355 crocodiles/km. When we accounted for observer effects and habitat, we estimated a surface population abundance of 2,581 (2,239–2,987, 95% credible intervals) crocodiles in Lake Nasser. Our results underscore the importance of well-trained, experienced monitoring personnel in order to decrease heterogeneity in intra-observer detection probability and to better detect changes in the population based on survey indices. This study will assist the Egyptian government establish a monitoring program as an integral part of future crocodile harvest activities in Lake Nasser. © 2012 The Wildlife Society.