Physico-chemical characteristics and total quality of date palm varieties grown in the southern of Tunisia

The date palm, Phoenix dactylifera, is a palm extensively cultivated for its edible fruit. The chemical composition and the water content of ten Tunisian date varieties were determined. For all analysis, the Deglet Nour variety was taken as reference. Compositional analysis showed that the littoral varieties were very rich in reducing sugars (26 to 51%) than Deglet Nour which was rich in sucrose (54%). The relative results of the moisture content showed that the littoral varieties were classified as soft dates. The vitamin C analysis showed that the littoral varieties were very rich in this compound (24 to 46 mg/100 g) than Deglet Nour (1.12 mg/100 g). The mineral analysis showed that the littoral dates were relatively rich in potassium (283 to 733 mg/100 g) and presented a weak content in sodium (0.06 to 0.09 mg/100 g).     

Sensitive PCR analysis of animal tissue samples for fragments of endogenous and transgenic plant DNA

An optimized DNA extraction protocol for animal tissues coupled with sensitive PCR methods was used to determine whether trace levels of feed-derived DNA fragments, plant and/or transgenic, are detectable in animal tissue samples including dairy milk and samples of muscle (meat) from chickens, swine, and beef steers. Assays were developed to detect DNA fragments of both the high copy number chloroplast-encoded maize rubisco gene (rbcL) and single copy nuclear-encoded transgenic elements (p35S and a MON 810-specific gene fragment). The specificities of the two rbcL PCR assays and two transgenic DNA PCR assays were established by testing against a range of conventional plant species and genetically modified maize crops. The sensitivities of the two rbcL PCR assays (resulting in 173 and 500 bp amplicons) were similar, detecting as little as 0.08 and 0.02 genomic equivalents, respectively. The sensitivities of the p35S and MON 810 PCR assays were approximately 5 and 10 genomic equivalents for 123 bp and 149 bp amplicons, respectively, which were considerably less than the sensitivity of the rbcL assays in terms of plant cell equivalents, but approximately similar when the higher numbers of copies of the chloroplast genome per cell are taken into account. The 173 bp rbcL assay detected the target plant chloroplast DNA fragment in 5%, 15%, and 53% of the muscle samples from beef steers, broiler chickens, and swine, respectively, and in 86% of the milk samples from dairy cows. Reanalysis of new aliquots of 31 of the pork samples that were positive in the 173 bp rbcL PCR showed that 58% of these samples were reproducibly positive in this same PCR assay. The 500 bp rbcL assay detected DNA fragments in 43% of the swine muscle samples and 79% of the milk samples. By comparison, no statistically significant detections of transgenic DNA fragments by the p35S PCR assay occurred with any of these animal tissue samples.     

Real-time RT-PCR quantification of pregnancy-associated plasma protein-A mRNA abundance in bovine granulosa and theca cells: effects of hormones in vitro

Ovarian follicular growth and dominance are controlled by a series of hormonal and intraovarian events including a decrease in intrafollicular IGF-binding proteins −2, −4 and −5 levels. Proteolytic enzymes such as pregnancy-associated plasma protein-A (PAPP-A) degrade IGFBPs and increase bioavailability of IGF-I and -II during follicular development. The objective of this study was to determine the effect of IGF-I, IGF-II, insulin (INS), LH, FSH, estradiol (E2), leptin or cortisol on ovarian PAPP-A mRNA levels. Granulosa (GC) from small (SM) (1–5 mm) and large (LG) (8–22 mm) follicles as well as theca cells (TC) from LG follicles were collected from bovine ovaries and cultured for 48 h in medium containing 10% FCS and then treated with various hormones in serum-free medium for an additional 24 h. Cells were treated with various concentrations (3–500 ng/ml) and combinations of IGF-I, IGF-II, FSH, LH, E2, INS, leptin and (or) cortisol for 24 h (Experiments 1–10). PAPP-A mRNA levels were measured using quantitative real-time RT-PCR. In SM-GC and LG-GC, none of the treatments significantly affected (P > 0.10) PAPP-A mRNA abundance. In LG-TC, IGF-I, LH or cortisol did not affect (P > 0.10) PAPP-A mRNA levels, whereas INS with or without LH decreased (P < 0.05) PAPP-A mRNA. E2 alone decreased PAPP-A mRNA levels in LG-TC, and E2 amplified the insulin-induced inhibition of PAPP-A mRNA abundance in LG-TC. We conclude that control of PAPP-A mRNA abundance in granulosa and theca cells differs, and that E2 may be part of an intraovarian negative feedback system which may reduce the bioavailable IGFs in the theca layer during growth and selection of follicles.     

Genomics and the irreducible nature of eukaryote cells

Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins.     

Evolving social capital and networks in the post‐disaster rebuilding process: The case of Typhoon Yolanda

Typhoon Yolanda brought major devastation to the local communities and infrastructure and also reshaped social structures and networks in the Philippines. During the immediate recovery process, bridging, bonding and linking social capital have had differential impacts and outcomes on how communities cope with the aftermath of the disaster. This article investigates the interplay between the various types of social capital and their contributions to immediate coping strategies of Typhoon Yolanda communities. This article also evaluates the complexity of defining social capital in a disaster context. In particular, it unpacks the blurring of the bridging and linking social capital at the immediate stage of rehabilitation in a post‐disaster context and its impacts on the social fabric of the communities. We deduce from this case study the social capital strategies necessary for a speedy recovery process both economically and socially for disaster‐affected communities.     

Culture-independent molecular techniques for soil microbial ecology

The advent of nucleic acid-based molecular methods, in particular the polymerase chain reaction (PCR), has revolutionised the study of soil microbial ecology, previously constrained by an inability to culture the majority of cells detected by direct microscopic observation. Extraction of DNA and RNA directly from cells in soil circumvents the requirement to grow microorganisms in laboratory culture, avoiding problems associated with the differential growth rates of the estimated 1% that can be grown routinely. However, not all cells that contain DNA are capable of growth, and in some conditions such as air-dried soil, DNA can be extracted from non-viable microorganisms after 140 years of storage. To investigate the active microbial community, RNA can also be isolated directly from soil. Analysis of ribosomal RNA (rRNA) indicates the dominant active population in any particular set of conditions and the large, constantly increasing electronic database of gene sequences for the small subunit of rRNA (16S for prokaryotes, 18S for eukaryotes) provides identification of many soil bacteria, archaea and fungi with varying degrees of certainty to the genus, species or sub-species level. More precise information on which functional genes are active can be obtained from messenger RNA (mRNA). Newer methods including high-throughput (massively parallel) sequencing and microarrays offer further advances. We describe a range of molecular techniques used to investigate soil microbial communities, discuss how they relate to other methods for investigating bacterial and fungal activity, and explore their drawbacks and limitations.