In vitro antimicrobial effect of metallic nanoparticles on phytopathogenic strains of crop plants

In this research, the in vitro antimicrobial effect of zinc oxide (ZnO), copper oxide (CuO) and iron oxide (Fe₂O₃) nanoparticles (NPs)—with average sizes of 20, 46 and 30 nm, respectively—on the root rot disease caused by the fungus Fusarium oxysporum and on blight disease caused by the fungus Alternaria solani were studied. Also, bacterial diseases caused by Clavibacter michiganensis and Pseudomonas syringae that infects a wide range of plant species were assessed. Different concentrations of NPs (0, 100, 250, 500, 700 and 1,000 mg/L) were prepared on PDA agar or King's B medium in a complete randomized design with four replicates. According to the results, ZnO NPs exhibited an outstanding inhibitory effect against fungi and bacteria strains. The above results were associated with the smaller particle size. Fungi strains showed a differential sensitivity depending on the kind of NPs used. A. solani showed the highest sensitivity to ZnO NPs at 1,000 mg/L (99%), followed by CuO NPs at the same dose (95%). Fe₂O₃ NPs at all evaluated doses had no inhibitory effects on the mycelia growth of this strain, although F. oxysporum revealed greater effectiveness of the CuO NPs (96%) compared with ZnO NPs since it only inhibited 91% of the mycelial growth. The antibacterial activity was studied through optical density. C. michiganensis was found to be more sensitive to ZnO NPs because a lesser dose (700 mg/L) was required to reduce the bacterial growth (90%); in comparison, P. syringae required a dose of 1,000 mg/L to inhibit its growth (67%). CuO NPs displayed the smallest growth inhibition against the bacteria strains analysed. The antimicrobial effect of the metallic NPs that were assayed increased with higher doses.     

Phytoplankton dynamics in a deep, tropical, hyposaline lake

The annual variation of the phytoplankton assemblage of deep (64.6 m), hyposaline (8.5 g l^–1) Lake Alchichica, central Mexico (19 ° N, 97° W), was analyzed in relation to thermal regime, and nutrients concentrations. Lake Alchichica is warm monomictic with a 3-month circulation period during the dry, cold season. During the stratified period in the warm, wet season, the hypolimnion became anoxic. N–NH₃ ranged between non detectable (n.d.) and 0.98 mg l^–1, N–NO₂ between n.d. and 0.007 mg l^–1, N–NO₃ from 0.1 to 1.0 mg l^–1 and P–PO₄ from n.d. to 0.54 mg l^–1. Highest nutrient concentrations were found in the circulation period. Chlorophyll a varied from <1 to 19.8 g l^–1 but most values were <5 g l^–1. The euphotic zone (>1% PAR) usually comprised the top 15–20 m. Nineteen algae species were identified, most of them are typical inhabitants of salt lakes. Diatoms showed the highest species number (10) but the small chlorophyte Monoraphidium minutum, the single-cell cyanobacteria, Synechocystis aquatilis, and the colonial chlorophyte, Oocystis parva, were the numerical dominant species over the annual cycle. Chlorophytes, small cyanobacteria and diatoms dominated in the circulation period producing a bloom comparable to the spring bloom in temperate lakes. At the end of the circulation and at the beginning of stratification periods, the presence of a bloom of the nitrogen-fixing cyanobacteria, N. spumigena, indicated nitrogen-deficit conditions. The well-stratified season was characterized by low epilimnetic nutrients levels and the dominance of small single-cell cyanobacteria and colonial chlorophytes. Phytoplankton dynamics in tropical Lake Alchichica is similar to the pattern observed in some deep, hyposaline, North American temperate lakes.     

Poster Sessions AP01: Gene Expression and Regulation. Regulation of gene expression during the development of cortico‐thalamic connection in rat

The formation of Cortico‐Thalamic projections requires the precise spatial and temporal expression of proteins that are involved in the different stages of synaptogenesis. We reasoned that the underlying molecular mechanism of this process is the differential expression of genes that code for stage specific proteins. Our research objective was to identify the differential expressed mRNAs during the main stages of synapses formation, which starts at embryonic day 12 (E12) and finishes on the first postnatal days in the rat. We approach this problem using Differential Display technique on three distinct ages of rat cerebral cortex that were: E13, E18 and postnatal day 0 (P0). We found 80 differential bands using 54 random primers and 18 of them were cloned and sequenced. The sequence analysis showed among others, a cDNA fragment highly homologous with the human A Kinase Anchoring Protein 450/350 also called CG‐NAP. We found that this cDNA fragment homologous to AKAP was up regulated at E15 when cortical cells are undergoing active axogenesis. The expression pattern of this cDNA was confirmed by Real Time PCR. Our findings suggest a possible function for AKAP 450 in the regulation of the state of phosphorylation of centrosomal components during the initial stages of synapses formation during the establishment of Cortico‐Thalamic connection.     

Anti-inflammatory constituents of Mortonia greggii Gray

A new phytochemical study of Mortonia greggii (Celastraceae) afforded four friedelan derivatives (1-4), three lupanes (5-7), retusine (8), two esterified polyhydroxyagarofurans (9-10), mortonin C (11) and photomortonin C (12). The anti-inflammatory activity on carrageenan and 12-O-tetradecanoylphorbol-13-acetate induced models of inflammation, as well as the ability to inhibit the nitric oxide (NO) produced by lipopolysaccharide-stimulated mouse peritoneal macrophages were evaluated for the main metabolites. Our results showed that the friedelan dehydrocanophyllic acid methyl ester (1) exhibits an anti-inflammatory effect which could be related to an inhibition of prostaglandin and NO production. The activity of lupeol (5), 29-hydroxylupeol (6) and 29-hydroxylupenone (7) might be involved with the prostanoid synthesis. The presence of the hydroxy groups in 6 appears to be important for activity. The edema inhibition capacity of retusine (8) could be related to a reduction of the prostaglandin production. The agarofuran derivative 10 is an NO inhibitor whose activity is probably not involved in the synthesis of prostaglandins.     

YAdumper: extracting and translating large information volumes from relational databases to structured flat files

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.     

SQUARE--determining reliable regions in sequence alignments

The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.     

SPOC: A widely distributed domain associated with cancer,apoptosis and transcription

Background  

The Split ends (Spen) family are large proteins characterised by N-terminal RNA recognition motifs (RRMs) and a conserved SPOC (Spen paralog and ortholog C-terminal) domain. The aim of this study is to characterize the family at the sequence level.     

Predicting reliable regions in protein alignments from sequence profiles

For applications such as comparative modelling one major issue is the reliability of sequence alignments. Reliable regions in alignments can be predicted using sub-optimal alignments of the same pair of sequences. Here we show that reliable regions in alignments can also be predicted from multiple sequence profile information alone.Alignments were created for a set of remotely related pairs of proteins using five different test methods. Structural alignments were used to assess the quality of the alignments and the aligned positions were scored using information from the observed frequencies of amino acid residues in sequence profiles pre-generated for each template structure. High-scoring regions of these profile-derived alignment scores were a good predictor of reliably aligned regions.These profile-derived alignment scores are easy to obtain and are applicable to any alignment method. They can be used to detect those regions of alignments that are reliably aligned and to help predict the quality of an alignment. For those residues within secondary structure elements, the regions predicted as reliably aligned agreed with the structural alignments for between 92% and 97.4% of the residues. In loop regions just under 92% of the residues predicted to be reliable agreed with the structural alignments. The percentage of residues predicted as reliable ranged from 32.1% for helix residues to 52.8% for strand residues.This information could also be used to help predict conserved binding sites from sequence alignments. Residues in the template that were identified as binding sites, that aligned to an identical amino acid residue and where the sequence alignment agreed with the structural alignment were in highly conserved, high scoring regions over 80% of the time. This suggests that many binding sites that are present in both target and template sequences are in sequence-conserved regions and that there is the possibility of translating reliability to binding site prediction.