Bovine TWINKLE and mitochondrial ribosomal protein L43 genes are regulated by an evolutionary conserved bidirectional promoter

TWINKLE is a mitochondrial DNA helicase playing an important role in mitochondrial DNA replication. In human, mutations in this gene cause progressive external ophtalmoplegia and mitochondrial DNA depletion syndrome-7. TWINKLE is well conserved among multicellular eukaryotes and is believed to be a key regulator of mitochondrial DNA copy number in mammals.     

Helicobacter pylori Genotypes Associated with Gastric Histo-Pathological Damages in a Moroccan Population

H. pylori persistent infection induces chronic gastritis and is associated with peptic ulcer disease and gastric carcinoma development. The severity of these diseases is related to human’s genetic diversity, H. pylori genetic variability and environmental factors. To identify the prevalence of histo-pathological damages caused by H. pylori infection in Moroccan population, and to determine their association to H. pylori genotypes, a prospective study has been conducted during 3 years on patients attending the gastroenterology department of Hassan II University Hospital (CHU) of Fez, Morocco. A total of 801 Moroccan adults’ patients were recruited; H. pylori was diagnosed and genotyped by PCR in biopsy specimens and histological exam was performed. We found a high rate of glandular atrophy. Chronic inflammation, neutrophil activity and glandular atrophy showed statistically significant association with H. pylori infection. However, intestinal metaplasia was inversely associated to this infection and no association was observed with gastric cancer cases. A statistically significant association was found between intestinal metaplasia and vacAs1 and vac Am1 genotypes in patients aged 50 years and more but not in younger. This last genotype is also associated to gastric cancer. In this study, gastric cancer showed no significant association with H. pylori. Further studies are warranted to determine the role of other etiological agents such as Epstein-Barr virus, human papillomavirus and possibly environmental and dietetic factors in the occurrence of this pathology.     

A Second Generation Integrated Map of the Rainbow Trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) Genome: Analysis of Conserved Synteny with Model Fish Genomes

DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.     

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated F_ST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing F_ST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the F_ST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.     

Effect of Ramadan fasting on feelings,dietary intake,rating of perceived exertion and repeated high intensity short-term maximal performance

The present study was designed to investigate the effect of Ramadan fasting on feelings, dietary intake, rating of perceived exertion (RPE) and repeated high-intensity short-term maximal performance. Thirteen physically active men (age: 21.2 ± 2.9 years, height: 175.6 ± 5.6 cm, body-mass: 72.4 ± 8.6 kg) performed a 5-m shuttle run test (6 × 30-s + 35-s of recovery in-between) during five experimental periods: fifteen days before Ramadan (BR), the first ten days of Ramadan (FR), the last ten days of Ramadan (ER), ten days after Ramadan (AR10) and 20 days after Ramadan (AR20). The study was carried out in Tunisia during the 2016 Ramadan month. During the 5-m shuttle run test, higher distance (HD), total distance (TD) and fatigue index (FI) were recorded. RPE was determined after a 5-min warm-up and after each repetition of the 5-m shuttle run test (the mean RPE score during the test was calculated). Moreover, a feelings scale (FS) was used after the warm-up and after the end of the 5-m shuttle run test. During the five experimental periods, dietary intake was assessed. The results showed that HD, TD and FI during the 5-m shuttle run test were not affected by Ramadan observance (p > 0.05). Likewise, FS scores recorded after the warm-up and the 5-m shuttle run test were not affected by Ramadan fasting (p > 0.05). However, mean RPE scores during the 5-m shuttle run test were significantly lower at ER (4.06 UA), AR10 (3.86 UA) and AR20 (3.71 UA) in comparison to BR (4.51 UA) (p < 0.05). The results showed also that Ramadan fasting has no adverse effect on energy intake, protein (g and %), fat (g and %) and carbohydrate (g). However, the fractional contribution of carbohydrate was significantly higher AR10 than FR (53.1% vs. 45.8%) and ER (53.1% vs. 46.5%) and AR20 than FR (5.92% vs. 45.8%) (p < 0.05). In conclusion, Ramadan fasting has no adverse effect on feelings, dietary intake, and short-term maximal performance. However, the RPE during repeated high intensity short-term maximal exercise was reduced AR20 in comparison to ER.

Abbreviations:

AR: After Ramadan; AR10: Ten days after Ramadan; AR20: Twenty days after Ramadan; BR: Fifteen days before Ramadan; ER: Last ten days of Ramadan; FI: Fatigue index; FR: First ten days of Ramadan; FS: Feelings scale; HD: Higher distance; PSQI: The Pittsburgh Sleep Quality Index; RPE: Rating of Perceived Exertion Scale; TD: Total distance     

Diversity of lactic acid bacteria associated with fish and the fish farm environment, established by amplified rRNA gene restriction analysis

Lactic acid bacteria have become a major source of concern for aquaculture in recent decades. In addition to true pathogenic species of worldwide significance, such as Streptococcus iniae and Lactococcus garvieae, several species have been reported to produce occasional fish mortalities in limited geographic areas, and many unidentifiable or ill-defined isolates are regularly isolated from fish or fish products. To clarify the nature and prevalence of different fish-associated bacteria belonging to the lactic acid bacterium group, a collection of 57 isolates of different origins was studied and compared with a set of 22 type strains, using amplified rRNA gene restriction analysis (ARDRA). Twelve distinct clusters were delineated on the basis of ARDRA profiles and were confirmed by sequencing of sodA and 16S rRNA genes. These clusters included the following: Lactococcus raffinolactis, L. garvieae, Lactococcus l., S. iniae, S. dysgalactiae, S. parauberis, S. agalactiae, Carnobacterium spp., the Enterococcus "faecium" group, a heterogeneous Enterococcus-like cluster comprising indiscernible representatives of Vagococcus fluvialis or the recently recognized V. carniphilus, V. salmoninarum, and Aerococcus spp. Interestingly, the L. lactis and L. raffinolactis clusters appeared to include many commensals of fish, so opportunistic infections caused by these species cannot be disregarded. The significance for fish populations and fish food processing of three or four genetic clusters of uncertain or complex definition, namely, Aerococcus and Enterococcus clusters, should be established more accurately.     

Posters Part 2

The effects of different CdCl₂ concentrations on the growth and on certain biochemical parameters of almond seedlings (Prunus dulcis) were studied under controlled conditions in the nutrient solutions containing increasing CdCl₂ concentrations ranging from 0 to 150 μM CdCl₂. Under Cd stress conditions, damage was variable. Cadmium reduced dry matter production in leaves and roots. While chlorophyll content was severely decreased, that of leaf sugars appeared to be increased. Furthermore, leaf nutritional status seemed to be more altered than that of roots. Both in roots and leaves, there was an increase in MDA content as metal concentration increased. It may be suggested from the present study that toxic concentrations of Cd cause oxidative damage as shown by the increase of lipid peroxidation.     

A physical map of the bovine genome

Background

Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.

Results

A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.

Conclusion

Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.     

Changes in water relations,photosynthetic activity and proline accumulation in one-year-old olive trees (<Emphasis Type="Italic">Olea europaea</Emphasis> L. cv. Chemlali) in response to NaCl salinity

The comparative responses of young olive trees (Olea europaea L. cv “Chemlali”) to different NaCl salinity levels were investigated over 11 months. One-year-old own rooted plants were grown in 10-L pots containing sand and perlite mixture (1:3 v/v). Trees were subjected to three irrigation treatments: CP (control plants that were irrigated with fresh water); SS1 (salt stressed plants irrigated with water containing 100 mM NaCl) and SS2 plants (salt stressed plants irrigated with water containing 200 mM NaCl). Shoot elongation rate, relative water content, leaf water potential and net carbon dioxide exchange rates decreased significantly with increased NaCl salinity level. Under stressed conditions, the increase of Na⁺ and Cl⁻ ions in both leaves and roots was accompanied with that of proline and soluble sugars. The above results show that the accumulation of proline and sugars under stressed conditions could play a role in salt tolerance. The absence of toxicity symptoms under both stress treatments and the superior photosynthetic activity recorded in SS1-treated plants suggest that cv Chemlali is better able to acclimatize to 100 mM NaCl than at 200 mM NaCl. Our findings indicate that saline water containing 100 mM NaCl, the most available water in arid region in Tunisia, can be recommended for the irrigation of cv Chemlali in the arid south of Tunisia.     

Genetic differences between Tunisian camel and sheep strains of the cestode Echinococcus granulosus revealed by SSCP

Ovine and dromedary Echinococcus granulosus isolates from Tunisia were identified as G1 and G6 strains based on polymorphism of the mitochondrial cytochrome C oxydase CO1. Single strand conformation polymorphism (SSCP) was used in order to examine the genetic variation within and between Tunisian G1 and G6 strains and to estimate the extent of selfing. The dromedary isolates are genetically distinct from sheep isolates (high value of genetic variation between populations: Fst= 0.46). No significant deficiency in heterozygotes was found in sheep isolates, whereas heterozygote deficiency (suggesting selfing) was found in a limited number of camel isolates.