Environmental relationships of aquatic vegetation in the fresh water ecosystem of the Nile Delta,Egypt

In generalized four sectors, 350 stands (water channels) in 50 selected and geo‐referenced sites with eighteen environmental factors were surveyed. The total number of recorded species varied from a sector to another: 21 in the northern, nineteen in the middle, seventeen in the western and sixteen in the eastern. New populations of Cyperus papyrus were explored. Vallisneria spiralis, Elodea canadensis and Najas armata were among seven extinct species that were not recorded few decades ago. The floristic composition alteration may be because of the addition of organic matter of plant and animal origin and the discharge of industrial and sewage effluents. Classification and ordination analyses (DCA) resulted in the segregation of seventeen vegetation groups (communities), three of them were repeatedly recorded; namely Phragmites australis‐Eichhornia crassipes, Phragmites australis‐Myriophyllum spicatum and Potamogeton pectinatus‐Myriophyllum spicatum. Phragmites australis‐Cyperus papyrus group was a new community spreading in the eastern sector of the Delta. Electric conductivity, Fe, Hg and chemical oxygen demand (COD) showed high significant variation (P < 0.001) among the vegetation groups. Other significant variables were Cl, Ca, NO₃, pH and SO₄ (P < 0.047). Redundancy analysis (RDA) was chosen as the appropriate ordination method to perform direct gradient analysis. Trace elements Cu, Fe, Hg and Pb participated in the floristic and chemical composition of each sector.     

Prediction and analysis of protein palmitoylation sites

Palmitoylation is a universal and important lipid modification, involving a series of basic cellular processes, such as membrane trafficking, protein stability and protein aggregation. With the avalanche of new protein sequences generated in the post genomic era, it is highly desirable to develop computational methods for rapidly and effectively identifying the potential palmitoylation sites of uncharacterized proteins so as to timely provide useful information for revealing the mechanism of protein palmitoylation. By using the Incremental Feature Selection approach based on amino acid factors, conservation, disorder feature, and specific features of palmitoylation site, a new predictor named IFS-Palm was developed in this regard. The overall success rate thus achieved by jackknife test on a newly constructed benchmark dataset was 90.65%. It was shown via an in-depth analysis that palmitoylation was intimately correlated with the feature of the upstream residue directly adjacent to cysteine site as well as the conservation of amino acid cysteine. Meanwhile, the protein disorder region might also play an import role in the post-translational modification. These findings may provide useful insights for revealing the mechanisms of palmitoylation.     

Causes and consequences of biological diversity in soil

There is a vast diversity of organisms that live in the soil, and the activities of the total soil biota, together with the diverse forms and functions of plant roots, have critical roles in soil functioning. In this paper I discuss the likely determinants of soil diversity and also comment on recent studies that have explored whether or not there is a relationship between soil organism diversity and ecosystem function. There is little evidence to suggest that soil diversity is regulated in a predicable fashion by competition or disturbance; rather it is attributed to the nature of the soil environment, in that soil offers an extremely heterogeneous habitat, both spatially and temporally, proving unrivalled potential for niche partitioning, or resource or habitat specialisation, thereby enabling co-existence of species. Most evidence that is available suggests that there is no predictable relationship between diversity and function in soils, and that ecosystem properties are governed more by individual traits of dominant species, and by the extraordinary complexity of biotic interactions that occur between components of soil food webs. There is evidence of redundancy in soil communities with respect to soil functions, but the scale of effect of changes in soil diversity on process rates depends on which species are removed from the community and the degree to which remaining species can compensate. As in aboveground communities, therefore, it would appear that species traits and changes in species composition, and alterations in the nature of the many important species interactions that occur in soil, are likely to be the main biotic control of ecosystem function. In view of this, consideration of these important biotic interactions and their sensitivity to environmental change must be a key priority for future research.     

Evaluation of the rrn operon copy number in Bifidobacterium using real-time PCR

AIMS: A real-time PCR-based method was developed to evaluate the Bifidobacterium rRNA operon copy number. As a result of their repetitive nature, rRNA operons are very suitable targets for chromosomal integration of heterologous genes. METHODS AND RESULTS: The rrn operon multiplicity per chromosome was determined by real-time PCR quantification of the 16S rRNA amplicons obtained from genomic DNA. The values obtained in several bifidobacterial strains of human origin ranged from 1 to 5. The reliability of the method developed was confirmed by Southern hybridization technique. CONCLUSIONS: In the Bifidobacterium genus the rrn operon copies showed variability at species and strain level. The identification of Bifidobacterium strains with high rRNA multiplicity allowed the selection of potential hosts for chromosomal integration. SIGNIFICANCE AND IMPACT OF THE STUDY: The methodology here proposed represents a rapid, reliable and sensitive new tool for the quantification of rrn operon copy number in bacteria.     

Ehd4 is required to attain normal prepubertal testis size but dispensable for fertility in male mice

The four highly homologous members of the C‐terminal EH domain‐containing (EHD) protein family (EHD1‐4) regulate endocytic recycling. To delineate the role of EHD4 in normal physiology and development, mice with a conditional knockout of the Ehd4 gene were generated. PCR of genomic DNA and Western blotting of organ lysates from Ehd4^−/− mice confirmed EHD4 deletion. Ehd4^−/− mice were viable and born at expected Mendelian ratios; however, males showed a 50% reduction in testis weight, obvious from postnatal day 31. An early (Day 10) increase in germ cell proliferation and apoptosis and a later increase in apoptosis (Day 31) were seen in the Ehd4^−/− testis. Other defects included a progressive reduction in seminiferous tubule diameter, dysregulation of seminiferous epithelium, and head abnormalities in elongated spermatids. As a consequence, lower sperm counts and reduced fertility were observed in Ehd4^−/− males. Interestingly, EHD protein expression was seen to be temporally regulated in the testis and EHD4 levels peaked between days 10 and 15. In the adult testis, EHD4 was highly expressed in primary spermatocytes and EHD4 deletion altered the levels of other EHD proteins in an age‐dependent manner. We conclude that high levels of EHD1 in the adult Ehd4^−/− testis functionally compensate for lack of EHD4 and prevents the development of severe fertility defects. Our results suggest a role for EHD4 in the proper development of postmitotic and postmeiotic germ cells and implicate EHD protein‐mediated endocytic recycling as an important process in germ cell development and testis function. genesis 48:328–342, 2010. © 2010 Wiley‐Liss, Inc.