MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads

Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next‐generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.     

The use of Aspergillus niger for the bioconversion of olive mill waste-waters

Summary Olive mill waste-water was used for protein production in small-scale experiments, using non-sterilized medium without pH control. A 14 g/1 concentration of proteins, 61% chemical oxygen demand removal and a 58% reduction in total phenolic compounds were obtained using an Aspergillus niger strain. The removal of phenolic compounds resulted in a change in the colour of the waste-water from black to brown.Offprint requests to: J. L. Garcia     

Structural organization of pLP1, a cryptic plasmid from Lactobacillus plantarum CCM 1904

To construct shuttle vectors based on an endogenous replicon, we isolated a small cryptic plasmid (pLP1) from Lactobacillus plantarum CCM 1904. The nucleotide sequence (2093 bp, 38.25 GC mol%) revealed one major open reading frame encoding for a 317 amino acid protein (Rep). Comparisons with proteins encoded by other Gram-positive bacteria plasmids strongly suggest that the protein encoded by pLP1 has a replicative role. The presence of a consensus sequence including a tyrosine residue known to be the replication protein binding site to the DNA (in phage φX174) strengthens this hypothesis. The DNA sequence contains also a sequence similar to the pC194 origin nick sequence, which initiates the plasmid replication at the plus origin, characteristic of plasmids which replicate following a rolling circle mechanism via single-stranded DNA intermediates. A set of 13 direct repeats of 17 bp could be involved in the expression of the incompatibility or in the copy number control as in the other plasmids. A promoter sequence located at the rep 5′ region has been identified and is functional in Bacillus subtilis.     

Prévalence de la pyospermie et retentissement sur la qualite du sperme chez les hommes infertiles

There are numerous controverses concerning the relationship between the presence of leukocytes in semen and male infertility. In the aim to determine the impact of pyospermia on sperm quality, we have realised a retrospective study in which we analysed and compared semen parameters and abnormalities frequencies between pyospermic and non pyospermic infertile patients. 833 spermiograms were included in this study. They were done in accord with WHO method. Leucocytes identification was performed by cyto-enzymologic method that reveals myelo-peroxydase in polymorphonuclear granulations. Pyospermia was considered when number of leucocytes was more than one million per millititre of sperm. The non pyospermic group was composed by sperm with leucocytospermia less than 50.000 per millilitre. The prevalence of pyospermia was 5.88%. There was not significative difference of semen parameters (volume, motility, morphology, number of spermatozoa and viability) between pyospermic and non pyospermic groups. In the other hand, no correlation was found between leucospermia and semen parameters. However, oligospermia was significantly more frequent in pyospermic group (40.8%) than in non pyospermic group (20,3%). Inversly, the frequence of teratospermia was significantly higher in non pyospermic group (47.2% vs 34.1%, p<0,05). These results suggest that inflammation and/or infection associated with pyospermia is complicated by reduction of spermatic ducts permeability. Although, the leucocytes would act in removing amorphous gametes by phagocytosis. No relationship was established between pyospermia and infection. In future, a prospective study would be done with exhaustive exploration of pyospermia etiology, with hopes to clarify the true link with infection and autoimmune reaction and to determine the effect of pyospermia on glandular activities in male genital tract and on functional properties of spermatozoa.     

Comparison of the effect of tromethamine and polyvinylpyrrolidone on dissolution properties and analgesic effect of nimesulide

The solubilizing and absorption enhancer properties towards nimesulide (ND) of tromethamine (Tris) and polyvinylpyrrolidone (PVP) have been investigated. Solid binary systems were prepared at various drug-polymer ratios by mixing or coprecipitation, characterized by differential scanning calorimetry, X-ray diffractometry, and Fourier transform infrared spectroscopy, and tested for dissolution behavior. Both carriers improved drug dissolution and their performance depended on concentration of the hydrophilic carrier in coprecipitates. Tris was more effective than PVP, despite the amorphizing power of PVP as revealed by solid state analyses. Complete drug amorphiztion was attained at 1∶3 (wt/wt) drug: PVP, 25% (wt/wt) ND in PVP. According to thermal behavior of ND and Tris, ND-Tris systems present a eutectic behavior. The eutectic composition was 30% ND-70% Tris at ∼129°C. Amorphous ND-PVP and eutectic ND-Tris mixtures showed an improvement of 5.55 and 6.6 times of drug dissolution efficiency, respectively. In vivo experiments in mice demonstrated that administration of 60 mg/kg of drug coprecipitated with PVP or Tris resulted, respectively, in a 50% and 94% reduction of acetic acid-induced writhings in comparison with pure drug, which, instead, was statistically ineffective as compared with the control group. Moreover, the eutectic mixture of ND-Tris demonstrated antiwrithing potency 1.88 times higher than amorphous ND-PVP coprecipitate. Thus, the solubilizing power, dissolution-enhancing effect, and analgesic effect enhancer ability toward the drug make Tris particularly suitable for developing a reduced-dose, fast-release solid oral dosage form of nimesulide. Published: August 10, 2007     

Aspects cliniques et biologiques de l’azoospermie chez l’homme infertile en Tunisie

Objective

It is now very important to investigate azoospermia because the introduction of the intracytoplasmic sperm injection technique during the last decade has allowed many infertile men to achieve their dreams of fatherhood. The purpose of this study was to define the characteristics of infertile men with azoospermia, and to analyse the clinical and laboratory features and the causes of infertility in Tunisia. The authors also discuss various aspects that they consider to be very important in the diagnosis of male fertility.

Material and Methods

This retrospective study analysed the parameters of physical examination, laboratory tests, semen analysis, radiographic examinations, testicular biopsy, karyotype and AZF microdeletions.

Results

Based on the results of endocrinological and cytogenetic examinations, the aetiology of azoospermia was considered to be secretory in 43 cases of azoospermia. Physical examination revealed a high percentage of hypotrophic/atrophic testes (43.9%). Serum follicle stimulating hormone levels were high in 58.5% of cases. The overall incidence of chromosomal abnormalities was 31.4%. The most frequent anomaly was Klinefelter syndrome (9 cases). Seven out of 28 patients (25%) with nonobstructive azoospermia had AZF deletions. None of the patients with excretory azoospermia and severe oligospermia had an abnormal karyotype or AZF microdeletions. 48.8% of patients presented a varicocele, 13.9% had cryptorchidism and 13.0% had a history of genital tract infection.

Conclusion

In line with the literature, genetic abmormalities are the main causes of severe forms of impaired spermatogenesis in the Tunisian population.     

Localization of Usher 1 proteins to the photoreceptor calyceal processes,which are absent from mice

The mechanisms underlying retinal dystrophy in Usher syndrome type I (USH1) remain unknown because mutant mice lacking any of the USH1 proteins—myosin VIIa, harmonin, cadherin-23, protocadherin-15, sans—do not display retinal degeneration. We found here that, in macaque photoreceptor cells, all USH1 proteins colocalized at membrane interfaces (i) between the inner and outer segments in rods and (ii) between the microvillus-like calyceal processes and the outer segment basolateral region in rods and cones. This pattern, conserved in humans and frogs, was mediated by the formation of an USH1 protein network, which was associated with the calyceal processes from the early embryonic stages of outer segment growth onwards. By contrast, mouse photoreceptors lacked calyceal processes and had no USH1 proteins at the inner–outer segment interface. We suggest that USH1 proteins form an adhesion belt around the basolateral region of the photoreceptor outer segment in humans, and that defects in this structure cause the retinal degeneration in USH1 patients.     

CCSV-MPase,a Novel Procoagulant Metalloproteinase from <Emphasis Type="Italic">Cerastes cerastes</Emphasis> Venom: Purification,Biochemical Characterization and Protein Identification

A procoagulant metalloproteinase called CCSV-MPase was purified from C. cerastes venom by successive chromatographic methods starting with gel-filtration through Sephadex G-75; ion-exchange DEAE-Cellulose A-50; affinity chromatography on Benzamidine Sepharose 6B and RP-HPLC on a C8 column. CCSV-MPase has been isolated to an extent of about tenfolds and its molecular mass was evaluated at 70 kDa by SDS–PAGE. CCSV-MPase hydrolyzes casein and fibrinogene as natural substrates. Its proteolytic activity was inhibited by EDTA and 1.10-phenanthroline, a chelators of bivalent cation metals and Zn²⁺ respectively. CCSV-MPase is therefore a Zn²⁺-metalloproteinase with fibrinogenolytic but not hemorrhagic activity. It greatly decreased levels of plasmatic fibrinogen when administered to rats for 24 h. This fibrinogenase hydrolyzes the Bβ chain of human fibrinogen in vitro releasing fibrinopeptide B only. LC MS/MS analysis of tryptic fragments of CCSV-MPase demonstrated that it showed some sequence similarities with four other venom metalloproteinases. CCSV-MPase could be considered as a potential therapeutic agent as it is a non-hemorrhagic enzyme and could be useful in thrombotic diseases because of its defibrinogenation of blood.     

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses

Human pathogenic protozoa of the genus Leishmania undergo various developmental transitions during the infectious cycle that are triggered by changes in the host environment. How these parasites sense, transduce, and respond to these signals is only poorly understood. Here we used phosphoproteomic approaches to monitor signaling events in L. donovani axenic amastigotes, which may be important for intracellular parasite survival. LC-ESI-MS/MS analysis of IMAC-enriched phosphoprotein extracts identified 445 putative phosphoproteins in two independent biological experiments. Functional enrichment analysis allowed us to gain insight into parasite pathways that are regulated by protein phosphorylation and revealed significant enrichment in our data set of proteins whose biological functions are associated with protein turn-over, stress response, and signal transduction. LC-ESI-MS/MS analysis of TiO(2)-enriched phosphopeptides confirmed these results and identified 157 unique phosphopeptides covering 181 unique phosphorylation sites in 126 distinct proteins. Investigation of phosphorylation site conservation across related trypanosomatids and higher eukaryotes by multiple sequence alignment and cluster analysis revealed L. donovani-specific phosphoresidues in highly conserved proteins that share significant sequence homology to orthologs of the human host. These unique phosphorylation sites reveal important differences between host and parasite biology and post-translational protein regulation, which may be exploited for the design of novel anti-parasitic interventions.