Maintenance of photosynthesis and the antioxidant defence systems have key roles for survival of Halopeplis perfoliata (Amaranthaceae) in a saline environment

• Coastal salt marsh plants employ various combinations of morphological and physiological adaptations to survive under saline conditions. Little information is available on salinity tolerance mechanisms of Halopeplis perfoliata, a C3 stem succulent halophyte.
• We investigated the growth, photosynthesis and antioxidant defence mechanisms of H. perfoliata under saline conditions (0, 150, 300 and 600 mM NaCl) in an open greenhouse.
• Optimal shoot succulence, projected shoot area and relative growth rate were obtained in the low (150 mm NaCl) salinity treatment, while growth was inhibited at the highest salinity (600 mm NaCl). The CO₂ compensation point and carbon isotope composition of biomass confirmed C₃ photosynthesis. Increases in salinity did not affect the photosynthetic pigment content or maximum quantum efficiency of PSII of H. perfoliata. Assimilation of CO₂ (A) also remained unaffected by salinity. A modest effect on some gas exchange and photochemistry parameters was observed at 600 mm NaCl. With increasing salinity, there was a continual increase in respiration, suggesting utilisation of energy to cope with saline conditions. Under 300 and 600 mm NaCl, there was an increase in H₂O₂ and MDA with a concomitant rise in AsA, GR content and CAT activity.
• Hence, H. perfoliata appears to be an obligate halophyte that can grow up to seawater salinities by modulating photosynthetic gas exchange, photochemistry and the antioxidant defence systems.

     

Functional and bioenergetic modulations in the infarct border zone following autologous mesenchymal stem cell transplantation

Preclinical and clinical studies have demonstrated that stem cell transplantation can improve the left ventricular (LV) contractile performance, yet the underlying mechanisms remain unknown. We examined whether mesenchymal stem cell (MSC) transplantation-induced beneficial effects are secondary to paracrine-associated improvements in LV contractile performance, wall stress, and myocardial bioenergetics in hearts with postinfarction LV remodeling. Myocardial contractile function and bioenergetics were compared 4 wk after acute myocardial infarction in normal pigs (n = 6), untreated pigs with myocardial infarction (MI group; n = 6), and pigs receiving autologous MSC transplantation (MI + MSC group; n = 5). A distal occlusion of the left anterior descending coronary artery instigated significant myocardial hypertrophy. Ejection fraction decreased from 55.3 +/- 3.1% (normal) to 30.4 +/- 2.3% (MI group; P < 0.01) and to 45.4 +/- 3.1% (MI + MSC group; P < 0.01 vs. MI). Hearts in the MI group developed severe contractile dyskinesis in the infarct zone and border zone (BZ). MSC transplantation significantly improved contractile performance from dyskinesis to active contraction (P < 0.01 vs. MI). BZ systolic wall stress was severely increased in MI hearts but significantly improved after MSC transplantation (P < 0.01 vs. MI). The BZ demonstrated profound bioenergetic abnormalities in MI pigs; this was significantly improved after MSC transplantation (P < 0.01 vs. MI). Patchy spared myocytes were found in the infarct zone of hearts receiving MSC transplantation but not in control hearts. These data demonstrate that MSC transplantation into the BZ causes significant improvements in myocardial contractile performance and reduction in wall stress, which ultimately results in significant bioenergetic improvements. Low cell engraftment indicates that MSCs did not provide a structural contribution to the damaged heart and that the observed beneficial effects likely resulted from paracrine repair mechanisms.     

Airborne dust,bacteria, actinomycetes and fungi at a flourmill

A study was carried out on suspended dust, bacterial and fungal aerosols in a four-storey flourmill building located in Giza, Egypt. Airborne microorganisms were quantitatively isolated using liquid impinger and gravimetric samplers during the period from March 2004 to February 2005. Suspended dust varied from 1.96 to 16.3 mg m⁻³ and 0.69 to 1.8 mg m⁻³ in the indoor and outdoor environments, respectively. Suspended dust was significantly greater (P < 0.05) at bran package, double roller, purifiers and flour storage units in comparison to the outdoor reference site. The dust levels exceed the occupational exposure limit (OEL) of 0.5 mg m⁻³ for flour dust. Airborne microbial counts were found at median values, between sampling locations, ranged from 0 to >10⁴ CFU m⁻³. Gram-negative bacteria were found in small numbers (0–10² CFU m⁻³). The highest concentration of actinomycetes (>10³ CFU m⁻³) was detected in the storage unit. Airborne fungal counts were found at the median values, between sampling locations, varied from 10³ to 10⁴ CFU m⁻³. The counts of airborne bacteria and fungi were significantly greater (P < 0.05) at the purifiers and double roller mill units in comparison to the outdoor reference site using the liquid impinger sampler. Microbial levels associated with bulk deposited dust averaged between 10⁵ and 10⁶ CFU g⁻¹. Alcaligenes (5.4%) Pseudomonas (3.87%) and Enterobacter (3.1%) were the predominant Gram-negative species while Bacillus (29.4%) and Micrococci (13.9%) were the major components of Gram-positive bacteria. Aspergillus and Penicillium were the predominant fungal types indoor whereas Cladosporium (35.2%) and Aspergillus species (22.2%) were the predominant fungal types outdoor. A number of allergenic and toxigenic bioaerosols were found in the flourmill workplace.     

Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae,harboring biphenyl- and phenolic acid-metabolizing genes,isolated from a long-term ecological research field

Antonie van Leeuwenhoek - A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501T, harboring xenobiotic- and...     

Deciphering genetic diversity analysis of saffron (Crocus sativus L.) using RAPD and ISSR markers

The existence of genetic diversity in Crocus sativus has globally remained a mystery till date. The study investigated PCR based DNA amplification profile of saffron using ISSR and RAPD based primers. A total of 38 amplicons were generated by ISSR primers in the range from 7 to 12 with an average of 9.50 bands per primer. 20 bands were found to be polymorphic and 18 were monomorphic with an average percentage of polymorphism as 52.48%. RAPD based amplification revealed a total 161 amplicons, 107 as polymorphic and 54 as monomorphic with an average percentage of polymorphism as 66.44%. Cumulative results of RAPD and ISSR demonstrated that Nei-Li’s similarity index ranged between 0.70 and 0.97. The results of AMOVA has revealed 9% of variance among populations and 91% of variance within populations, Φ PT was found as 0.089, which indicates existence of genetic differences though limited. In conclusion, the results indicate that saffron accessions are minimally genetically differentiated, which could be capitalized in future breeding programmes to ameliorate this precious crop.     

Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past

Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non‐ or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment‐based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi‐gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).     

Cloning and characterization of Na+/H+ antiporter (LfNHX1) gene from a halophyte grass Leptochloa fusca for drought and salt tolerance

Abiotic stresses such as salinity and drought have adverse effects on plants. In the present study, a Na⁺/H⁺ antiporter gene homologue (LfNHX1) has been cloned from a local halophyte grass (Leptochloa fusca). The LfNHX1 cDNA contains an open reading frame of 1,623 bp that encodes a polypeptide chain of 540 amino acid residues. LfNHX1 protein sequence showed high similarity with NHX1 homologs reported from other halophyte plants. Amino acid and nucleotide sequence similarity, protein topology modeling and the presence of conserved functional domains in the LfNHX1 protein sequence classified it as a vacuolar NHX1 homolog. The overexpression of LfNHX1 gene under CaMV35S promoter conferred salt and drought tolerance in tobacco plants. Under drought stress, transgenic plants showed higher relative water contents, photosynthetic rate, stomatal conductance and membrane stability index as compared to wild type plants. More negative value of leaf osmotic potential was also observed in transgenic plants when compared with wild type control plants. Transgenic plants showed better germination and root growth at 2 mg L^?1 Basta herbicide and three levels (100, 200 and 250 mM) of sodium chloride. These results showed that LfNHX1 is a potential candidate gene for enhancing drought and salt tolerance in crops.     

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background  

There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Insight into the diversity and evolution of the cryptomonad nucleomorph genome

The cryptomonads are an enigmatic group of marine and freshwater unicellular algae that acquired their plastids through the engulfment and retention of a eukaryotic ("secondary") endosymbiont. Together with the chlorarachniophyte algae, the cryptomonads are unusual in that they have retained the nucleus of their endosymbiont in a miniaturized form called a nucleomorph. The nucleomorph genome of the cryptomonad Guillardia theta has been completely sequenced and with only three chromosomes and a total size of 551 kb, is a model of nuclear genome compaction. Using this genome as a reference, we have investigated the structure and content of nucleomorph genomes in a wide range of cryptomonad algae. In this study, we have sequenced nine new cryptomonad nucleomorph 18S ribosomal DNA (rDNA) genes and four heat shock protein 90 (hsp90) gene fragments, and using pulsed-field gel electrophoresis and Southern hybridizations, have obtained nucleomorph genome size estimates for nine different species. We also used long-range polymerase chain reaction to obtain nucleomorph genomic fragments from Hanusia phi CCMP325 and Proteomonas sulcata CCMP704 that are syntenic with the subtelomeric region of nucleomorph chromosome I in G. theta. Our results indicate that (1) the presence of three chromosomes is a common feature of the nucleomorph genomes of these organisms, (2) nucleomorph genome size varies dramatically in the cryptomonads examined, (3) unidentified cryptomonad species CCMP1178 has the largest nucleomorph genome identified to date at approximately 845 kb, (4) nucleomorph genome size reductions appear to have occurred multiple times independently during cryptomonad evolution, (5) the relative positions of the 18S rDNA, ubc4, and hsp90 genes are conserved in three different cryptomonad genera, and (6) interchromosomal recombination appears to be rapidly changing the size and sequence of a repetitive subtelomeric region of the nucleomorph genome between the 18S rDNA and ubc4 loci. These results provide a glimpse into the genetic diversity of nucleomorph genomes in cryptomonads and set the stage for more comprehensive sequence-based studies in closely and distantly related taxa.     

Anatomical adaptations to salinity in cogon grass [Imperata cylindrica (L.) Raeuschel] from the Salt Range, Pakistan

To examine anatomical adaptations in a potential forage grass, Imperata cylindrica (L.) Raeuschel, a population was collected from the natural salt-affected soils of the Salt Range, Pakistan. Using a hydroponic system, the degree of salt tolerance in terms of structural modifications in the Salt Range ecotype was compared with that in an ecotype collected from a normal non-saline habitat of the Faisalabad region. The Salt Range ecotype was superior to the Faisalabad ecotype in biomass production under saline conditions. High salt tolerance of the Salt Range ecotype was associated with increased succulence in root and leaf (mainly midrib), formation of aerenchyma in leaf sheath, increased vascular bundle area, metaxylem area and phloem area, highly developed bulliform cells on leaves and increased sclerification in root and leaf. Furthermore, both stomatal density and stomatal area were considerably reduced under high salinities in the Salt Range ecotype.