Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond,and its relationships with agronomic traits

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.     

Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis

The mechanisms controlling axon guidance are of fundamental importance in understanding brain development. Growing corticospinal and somatosensory axons cross the midline in the medulla to reach their targets and thus form the basis of contralateral motor control and sensory input. The motor and sensory projections appeared uncrossed in patients with horizontal gaze palsy with progressive scoliosis (HGPPS). In patients affected with HGPPS, we identified mutations in the ROBO3 gene, which shares homology with roundabout genes important in axon guidance in developing Drosophila, zebrafish, and mouse. Like its murine homolog Rig1/Robo3, but unlike other Robo proteins, ROBO3 is required for hindbrain axon midline crossing.     

Determination of neomycin in animal tissues, using ion-pair liquid chromatography with fluorometric detection

A liquid chromatographic (LC) method is described for the determination of neomycin in animal tissues. Tissues are homogenized in 0.2M potassium phosphate buffer (pH 8.0); the homogenate is centrifuged, and the supernate is heated to precipitate the protein. The heat-deproteinated extract is acidified to pH 3.5-4 and directly analyzed by LC. The LC method consists of an ion-pairing mobile phase, a reverse phase ODS column, post-column derivatization with o-phthalaldehyde reagent, and fluorometric detection. The LC method uses paromomycin as an internal standard, and separates neomycin from streptomycin or dihydrostreptomycin because they have different retention times. The LC column separates neomycin in 25 min; the detection limit is about 3.5 ng neomycin. The overall recovery of neomycin from kidney tissues spiked at 1-30 ppm was 96% with a 9.0% coefficient of variation. The method was also applied to muscle tissue.     

Earthworm casts form stable aggregates in physically degraded soils

Topsoils affected by surface mining suffer severe physical degradation and lose most of their earthworm populations. After mining, replaced soils are planted to grassland and managed to improve soil structure. Earthworm inoculation into selected restored areas produced populations similar to those of undisturbed soils within 3 years. Soil properties in inoculated areas were compared with those of controls to evaluate the contribution of casts to bulk soil aggregation, and soil organic matter and root content responses to earthworm activity. Crumb porosity and coarse particle content were measured in water-stable macro-aggregates and earthworm casts to establish whether aggregates were formed by earthworms. Over a 5- to 6-year period, inoculation increased stable aggregation (>2 μm, >60 μm and >3 mm), even at 0- to 5-cm depth where it reduced soil organic matter content. Productivity and root content were also increased by inoculation; roots and organic matter were re-distributed to greater depth. Crumb porosity decreased with casts > aggregates (inoculated plots) > aggregates (control plots). Coarse particle content increased with casts < aggregates (inoculated plots) < aggregates (control plots). Coarse particle and porosity data were consistent with much of the newly aggregated soil being processed and formed by earthworms as casts. Whilst levels of soil organic matter were often closely associated with percentage stable aggregation, root content showed weaker associations. Aggregation percentage was most closely associated with abundance of Aporrectodea longa, although at particular depths significant correlations were also obtained for Aporrectodea caliginosa and Lumbricus terrestris. Results suggest that earthworms, rather than plant roots, initiate aggregation in severely degraded grassland soils.     

Molecular modeling of syringyl and p-hydroxyphenyl beta-O-4 dimers. Comparative study of the computed and experimental conformational properties of lignin beta-O-4 model compounds

As a new approach for the study of the ultrastructure of lignin, the conformational preferences of lignin beta-O-4 model compounds have been investigated by molecular modeling. The computed results have been compared with the experimental data (X-ray crystal structures and (3)J(H)(alpha)(H)(beta) NMR coupling constant values) reported in the literature. This comparison has led to an improved understanding of the influence of the structure, stereochemistry, and intramolecular H-bonding upon the conformational properties of the beta-O-4 dimers. A large number of low-energy conformations have been predicted for the structures. It has also appeared that the conformational features are predominantly governed by local steric interactions rather than by differences in the H-bonding interactions. The threo and erythro forms differ significantly in their conformational features, with a preferential extended overall shape for the threo form in which the bulky aromatic groups are distant from each other.     

Development and Characterization of Novel Polymorphic Microsatellite Markers for Tapinoma indicum (Hymenoptera: Formicidae)

Tapinoma indicum (Forel) (Hymenoptera: Formicidae) is a nuisance pest in Asia countries. However, studies on T. indicum are limited, especially in the field of molecular biology, to investigate the species characteristic at the molecular level. This paper aims to provide valuable genetic markers as tools with which to study the T. indicum population. In this study, a total of 143,998 microsatellite markers were developed based on the 2.61 × 10⁶ microsatellites isolated from T. indicum genomic DNA sequences. Fifty selected microsatellite markers were amplified with varying numbers of alleles ranging from 0 to 19. Seven out of fifty microsatellite markers were characterized for polymorphism with the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) analysis. All seven microsatellite markers demonstrated a high polymorphic information content (PIC) value ranging from 0.87 to 0.93, with a mean value of 0.90. There is no evidence of scoring errors caused by stutter peaks, no large allele dropout, and no linkage disequilibrium among the seven loci; although loci Ti-Tr04, Ti-Tr09, Ti-Te04, Ti-Te13, and Ti-Pe5 showed signs of null alleles and deviation from the HWE due to excessive homozygosity. In conclusion, a significant amount of microsatellite markers was developed from the data set of next-generation sequencing, and seven of microsatellite markers were validated as informative genetic markers that can be utilized to study the T. indicum population.     

Isolation and characterisation of local strains of Chlamydophila abortus (Chlamydia psittaci serotype 1) from Tunisia

Chlamydiosis is one of the major diseases that can lead to abortion in ewes. Since 1997, in 5 regions of Tunisia, Chlamydia-related abortions have been reported in 15 sheep and goat flocks. One hundred and sixty-six sera and 50 vaginal swab samples were collected from adult ewes. Chlamydial antigens were detected in 29 (58%) of the vaginal swabs using Enzyme Linked Immunosorbent Assay (ELISA) while 9 (18%) were positive by cell culture. Five strains were recovered from 4 different sheep flocks. Monoclonal antibody profiles and restriction fragment length polymorphism (RFLP) analysis of the 16S-23S rRNA spacer region showed that these isolates were C. abortus. Using amplified fragment length polymorphism (AFLP), these Tunisian strains were shown to exhibit the same pattern as strains isolated in France.     

Determination of total 14C residues of sarafloxacin in eggs of laying hens

[14C]sarafloxacin was orally administered to six laying hens for five consecutive days. Eggs were collected for 15 days after the initial drug treatment. Egg yolk and egg albumen were separated and assayed for total radioactive residues (TRR) using a combustion oxidizer and scintillation counting techniques. Radioactivity was detected in egg yolk and egg albumen on the second day of dosing and reached a maximum at 24 h after drug withdrawal. Thereafter, the sarafloxacin TRR levels in egg albumen declined rapidly and were undetectable 2 days after the last dose, whereas the levels in egg yolk declined at a much slower rate and were undetectable 7 days after drug withdrawal. In both the egg albumen and yolk, HPLC analysis indicated that the parent sarafloxacin was the major component.