Diversity of desert rangelands of Tunisia

Plants are important components of any rangeland. However, the importance of desert rangeland plant diversity has often been underestimated. It has been argued that desert rangelands of Tunisia in good ecological condition provide more services than those in poor ecological condition. This is because rangelands in good condition support a more diverse mixture of vegetation with many benefits, such as forage for livestock and medicinal plants. Nearly one-quarter of Tunisia, covering about 5.5 million hectares, are rangelands, of which 87% are located in the arid and desert areas (45% and 42%, respectively). Here, we provide a brief review of the floristic richness of desert rangelands of Tunisia. Approximately 135 species are specific to desert rangelands. The predominant families are Asteraceae, Poaceae, Brassicaceae, Chenopodiaceae, and Fabaceae. These represent approximately 50% of Tunisian desert flora.     

Probiotic Characteristics of <Emphasis Type="Italic">Lactobacillus curvatus</Emphasis> DN317, a Strain Isolated from Chicken Ceca

The probiotic characteristics of Lactobacillus curvatus DN317, a strain isolated from chicken ceca, were evaluated. This strain was selected for study from the isolated Lactobacillus strains because it has specific anti-microbial activity against Campylobacter jejuni ATCC 33560, Camp. jejuni NCTC 11168, Listeria monocytogenes ATCC 7644, and Bacillus subtilis ATCC 8633. Lact. curvatus DN317 showed an auto-aggregation percentage of 72% and presented the highest co-aggregation with Lact. monocytogenes ATCC 7644 (68%) compared to B. subtilis ATCC 8633 (45%), Camp. jejuni ATCC 33560 (36%), and Camp. jejuni NCTC 11168 (35%). The data revealed that Lact. curvatus DN317 could survive at 0.25% bile, maintain viability at pH 2.5 for 30 min, produce biosurfactants, and adhere to Caco-2 cells. Quantification of IL-6, IL-8, IL-10, and β-defensin 2 levels shows that Lact. curvatus DN317 induces an increase in IL-8 and β-defensin 2 secretion, while the levels of IL-6 and IL-10 do not change. Lact. curvatus DN317 showed high levels of esterase and cysteine arylamidase activities (5); moderate levels of esterase lipase, β-galactosidase, and α-galactosidase activities (4, 3); and weak levels of leucine arylamidase, valine arylamidase, and acid phosphatase activity (1). Various activities were obtained of α-chymotrypsin, β-glucuronidase, β-glucosidase, and N-acetyl-β-glucosaminidase, which have been associated with intestinal diseases. Lact. curvatus DN317 lowered the cholesterol level in MRS with and without bile. Antibiotic susceptibility tests indicated that DN317 was sensitive to ampicillin, gentamicin, kanamycin, streptomycin, tetracycline, clindamycin, erythromycin, and vancomycin but was resistant to chloramphenicol and ciprofloxacin. These results suggest that Lact. curvatus DN317 could potentially function as a probiotic.     

Coupled motions between pore and voltage-sensor domains: a model for Shaker B, a voltage-gated potassium channel

A high-resolution crystal structure of KvAP, an archeabacterial voltage-gated potassium (Kv) channel, complexed with a monoclonal Fab fragment has been recently determined. Based on this structure, a mechanism for the activation (opening) of Kv channels has been put forward. This mechanism has since been criticized, suggesting that the resolved structure is not representative of the family of voltage-gated potassium channels. Here, we propose a model of the transmembrane domain of Shaker B, a well-characterized Kv channel, built by homology modeling and docking calculations. In this model, the positively charged S4 helices are oriented perpendicular to the membrane and localized in the groove between segments S5 and S6 of adjacent subunits. The structure and the dynamics of the full atomistic model embedded in a hydrated lipid bilayer were investigated by means of two large-scale molecular dynamics simulations under transmembrane-voltage conditions known to induce, respectively, the resting state (closed) and the activation (opening) of voltage-gated channels. Upon activation, the model undergoes conformational changes that lead to an increase of the hydration of the charged S4 helices, correlated with an upward translation and a tilting of the latter, concurrently with movements of the S5 helices and the activation gate. Although small, these conformational changes ultimately result in an alteration of the ion-conduction pathway. Our findings support the transporter model devised by Bezanilla and collaborators, and further underline the crucial role played by internal hydration in the activation of the channel.     

Conservation of amino acids into multiple alignments involved in pairwise interactions in three-dimensional protein structures

We present an original strategy, that involves a bioinformatic software structure, in order to perform an exhaustive and objective statistical analysis of three-dimensional structures of proteins. We establish the relationship between multiple sequences alignments and various structural features of proteins. We show that amino acids implied in disulfide bonds, salt bridges and hydrophobic interactions have been studied. Furthermore, we point out that the more variable the sequences within a multiple alignment, the more informative the multiple alignment. The results support multiple alignments usefulness for predictions of structural features.     

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

MOTIVATION: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them. In this article, we show that secondary structure prediction is a valuable way to validate protein families at low identity rate. RESULTS: We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment. AVAILABILITY: This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)     

Optimal strategy for structured model of fishing problem

In this work we study a structured fishing model, basically displaying the two stages of the ages of a fish population, which are in our case juvenile, and adults. We associate to this model the maximization of the total discounted net revenues derived by the exploitation of the stock. The exploitation strategy of the optimal control problem is then developed and presented.     

Expression of a ferredoxin-dependent glutamate synthase gene in mesophyll and vascular cells and functions of the enzyme in ammonium assimilation in Nicotiana tabacum (L.)

GLU1 encodes the major ferredoxin-dependent glutamate synthase (Fd-GOGAT, EC 1.4.7.1) in Arabidopsis thaliana (ecotype Columbia). With the aim of providing clues on the role of Fd-GOGAT, we analyzed the expression of Fd-GOGAT in tobacco (Nicotiana tabacum L. cv. Xanthi). The 5′ flanking element of GLU1 directed the expression of the uidA reporter gene in the palisade and spongy parenchyma of mesophyll, in the phloem cells of vascular tissue and in the roots of tobacco. White light, red light or sucrose induced GUS expression in the dark-grown seedlings in a pattern similar to the GLU1 mRNA accumulation in Arabidopsis. The levels of GLU2 mRNA encoding the second Fd-GOGAT and NADH-glutamate synthase (NADH-GOGAT, EC 1.4.1.14) were not affected by light. Both in the light and in darkness, ¹⁵NH₄⁺ was incorporated into [5−¹⁵N]glutamine and [2−¹⁵N]glutamate by glutamine synthetase (GS, EC 6.3.1.2) and Fd-GOGAT in leaf disks of transgenic tobacco expressing antisense Fd-GOGAT mRNA and in wild-type tobacco. In the light, low level of Fd-glutamate synthase limited the [2−¹⁵N]glutamate synthesis in transgenic leaf disks. The efficient dark labeling of [2−¹⁵N]glutamate in the antisense transgenic tobacco leaves indicates that the remaining Fd-GOGAT (15–20% of the wild-type activity) was not the main limiting factor in the dark ammonium assimilation. The antisense tobacco under high CO₂ contained glutamine, glutamate, asparagine and aspartate as the bulk of the nitrogen carriers in leaves (62.5%), roots (69.9%) and phloem exudates (53.2%). The levels of glutamate, asparagine and aspartate in the transgenic phloem exudates were similar to the wild-type levels while the glutamine level increased. The proportion of these amino acids remained unchanged in the roots of the transgenic plants. Expression of GLU1 in mesophyll cells implies that Fd-GOGAT assimilates photorespiratory and primary ammonium. GLU1 expression in vascular cells indicates that Fd-GOGAT provides amino acids for nitrogen translocation. The nucleotide sequence data of the GLU1 gene reported in the present study is available from GenBank with the following accession number: AY189525     

Genetically engineered resistance to potato virus X in four commercial potato cultivars

The genes for the capsid protein (CP) and the 8K movement protein of PVX were introduced into potato (Solanum tuberosum L.) and expressed under the control of CaMV 35S promoter using a binary vector andAgrobacterium tumefaciens. Four commercial potato cultivars (Russet Burbank, Shepody, Desirée and Bintje) have been efficiently transformed. Eleven independent transgenic clones, with CP expression levels higher than 0.05% of the soluble leaf proteins, were analyzed for resistance to inoculation with PVX (5 and 50µg/ml). The resistance of the transgenic plants to PVX was observed with the lower titer of virus inoculation (5 µg/ml) but not with higher titer (50 µg/ml). A significant reduction in the accumulation of virus in the inoculated transgenic potato plants has been observed under greenhouse and field conditions. Furthermore, the CP gene is very stable and is transferred to new plants originated from stem cuttings or from tubers. The transgenic plants appeared to be phenotypically identical to the nontransformed controls.Abbreviations BAP benzyl-aminopurine - BCIP 5-bromo-4-chloro-3-indolylphosphate p-Toluidine salt - CaMV cauliflower mosaic virus - CP capsid protein - GA₃ gibberellic acid - Kbp kilobase pair - NAA naphthalene acetic acid - NBT nitroblue tetrazolium chloride - NOS nopaline synthase - NPT II neomycin phosphotransferase II - PMSF phenyl methyl sulfonyl fluoride - PVX potato virus X - PVY potato virus Y     

Metabolomic study of the response to cold shock in a strain of <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> isolated from cloud water

Introduction

Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level.

Objectives

The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock.

Methods

Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA).

Results

Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function.

Conclusions

This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.