GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data

SUMMARY: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate. AVAILABILITY: http://garban.tecnun.es.     

Diversity of moderately halophilic bacteria producing extracellular hydrolytic enzymes

AIMS: The aim of this study was to determine the diversity of moderately halophilic bacteria with hydrolase activities. METHODS AND RESULTS: Screening bacteria from different hypersaline environments in South Spain led to the isolation of a total of 122 moderately halophilic bacteria able to produce different hydrolases (amylases, DNases, lipases, proteases and pullulanases). These bacteria are able to grow optimally in media with 5-15% salts and in most cases up to 20-25% salts. In contrast to strains belonging to previously described species, that showed very little hydrolase activities, environmental isolates produced a great variety of hydrolases. These strains were identified as members of the genera: Salinivibrio (55 strains), Halomonas (25 strains), Chromohalobacter (two strains), Bacillus-Salibacillus (29 strains), Salinicoccus (two strains) and Marinococcus (one strain), as well as eight non-identified isolates. CONCLUSIONS: Moderately halophilic bacteria are a source of hydrolytic enzymes such as amylases, DNases, lipases, proteases and pullulanases. SIGNIFICANCE AND IMPACT OF THE STUDY: Although most culture collection strains are not able to produce hydrolases, it has been shown that environmental isolates can produce these potentially biotechnological important enzymes.     

In vitro activity of allicin against Staphylococcus epidermidis and influence of subinhibitory concentrations on biofilm formation

AIMS: The aim of this study is to determine the in vitro activity of allicin against Staphylococcus epidermidis and to evaluate the influence of allicin on biofilm formation. METHODS AND RESULTS: In vitro activity of allicin (diallyl thiosulphinate) against 38 strains of S. epidermidis was investigated. The activity of allicin was similar against S. epidermidis methicillin susceptible and methicillin resistant strains [minimum inhibitory concentration (MIC)90=8 mg l(-1)]. In general, subinhibitory concentrations (sub-MIC) of allicin diminished biofilm formation in the five strains analysed. CONCLUSION: The results confirm the antibacterial effect of allicin. Sub-MICs of allicin also diminished the biofilm formations by S. epidermidis. SIGNIFICANCE AND IMPACT OF THE STUDY: The present study shows that allicin is active in vitro against S. epidermidis and that sub-MICs of allicin may play a role in the prevention of adherence of this bacteria to medical devices.     

The Tissue Bank at the National Nuclear Research Institute in Mexico

The Instituto Nacional de Investigaciones Nucleares (ININ, The National Nuclear Research Institute) received during 1997-1998 strong support of the International Atomic Energy Agency (IAEA), to establish the first and only one tissue bank (BTR ININ tissue bank) in Mexico that uses ionising radiation as sterilising agent. In that time, the BTR staff was trained in different tissue banks in several countries. Basic equipment for tissue processing donated by the IAEA was received in 1998. In July, 1999 the Mexican Health Secretariat gave the Sanitary License No. 1062000001 to the BTR to operate as an official organ and tissue bank. In August, 2001 the ININ and the Hospital Materno Infantil (HMI-ISSEMYM) signed an agreement to collaborate in amnion processing. The hospital is responsible for donor selection, serology tests, tissue procurement and washing, since this hospital is the BTR amnion supplier. The tissues are collected by ININ weekly with complete documentation. The BTR is responsible for processing: cleaning, air drying, packaging, labelling, microbiological control and sterilisation by gamma irradiation. The sterilised tissue is kept under quarantine for 6 months to obtain the results of the donor second serology test. From March to June, 2002 the BTR has processed 347.86 units (50 cm(2) each), is say, 17,393 cm(2). In addition, the pig skin xenograft process has been implemented and a protocol for clinical applications of it is running at the Hospital Central Sur de Alta Especialidad (PEMEX). Also the ININ tissue bank present status and perspectives are described.     

Cytogenetics of the razor clam Solen marginatus (Mollusca: Bivalvia: Solenidae)

The razor clam Solen marginatus has a diploid chromosome number of 38. The karyotype consists of one metacentric/submetacentric, three submetacentric/metacentric, five submetacentric, one submetacentric/subtelocentric, one subtelocentric/submetacentric, six subtelocentric and two telocentric chromosome pairs. Staining with chromomycin A3 revealed bright positive bands subcentromerically in the long arms of one medium-sized subtelocentric pair, while DAPI staining showed uniform fluorescence in all chromosomes of the complement. Fluorescence in situ hybridization using an 18S-5.8S-28S rDNA probe locates these loci at the subcentromeric region of one subtelocentric pair and at the subtelomeric region of another subtelocentric pair.     

Modeling temporal and spatial colony-site dynamics in a long-lived seabird

We studied the determinants of colony site dynamics in Audouin's gull, Larus audouinii, breeding in a small archipelago of the western Mediterranean. Data on island occupation were available for a series of 25 years, since first colonization of the archipelago in 1973. Group behavior was studied in relation to the components of dispersal: permanence or abandonment (extinction) on an island previously occupied and permanence or occupation (colonization) of another island. Generalized Linear Mixed Models (GLMMs) were used to identify the relative contribution of each explanatory variable to the probability of colony abandonment. Gulls showed a low probability (3%) of abandoning one of the islands (Grossa I.), especially when the colony was increasing in numbers from time t_i-1 to t_i. However, the probability of abandoning Grossa increased up to 31% when the colony was declining. The probability of island abandonment was very high for all other islands (range 66–99%) when the colony was declining, but much lower (range 36–82%) when it was increasing. Hence, we suggest that island abandonment by Audouin's gull is at least a two-step process. The first step (dispersal of a portion of the colony) probably takes place at random, as an evolutionary load typical of a species evolved in unstable habitats. The second step, a further loss of breeding pairs, seems to feedback on the first loss of members of the colony (public information), likely perceived as a loss of colony quality. Colonization of islands by gulls abandoning Grossa I. was marginally and negatively affected by the density of breeding yellow-legged gulls, a predatory species. Results apply to conservation ecology since they highlight the need to protect not only occupied patches but also those empty at present.     

Effects of haloperidol on rat behavior and density of dopaminergic D2-like receptors

The present work shows the effects of a typical neuroleptic drug (haloperidol, HAL) on rat behavior (catalepsy and locomotor activity) and dopaminergic D2-like receptor densities in the hippocampus and striatum. Male Wistar rats (2-3 months old) were treated daily for 30 days with HAL (0.2 or 1mg/kg, intraperitoneally (i.p.)). At the end of treatment and 1h or 1, 3, 7 and 15 days after drug withdrawal, animals were subjected to behavioral tests and sacrificed afterwards for binding assays. The results showed that behavioral effects with both doses were significant only 1h and 1 day after withdrawal, and similar to controls at the third day. An up-regulation of D2 receptors was observed in the striatum (28% increase) but not in the hippocampus after 24h HAL (1mg/kg) withdrawal. However, an up-regulation was seen in both areas (1mg/kg) 3 days after drug withdrawal (58 and 42% increases in the hippocampus and striatum, respectively), and continued after 7 days of withdrawal only in the striatum (43 and 49% for the doses of 0.2 and 1mg/kg, respectively), suggesting the influence of dose, age, and time of drug withdrawal on these parameters. The up-regulation disappeared after 15 days of haloperidol withdrawal. Increases (72 and 140%) in constant dissociation values (K(d)) values were also observed 7 days after withdrawal. Results show differences on a time-basis between behavioral alterations and dopaminergic D2 receptors up-regulation.     

GASP phenotype: presence in enterobacteria and independence of sigmaS in its acquisition

The appearance of growth advantage in stationary phase or GASP was originally detected in Escherichia coli. The presence of this phenotype in other enterobacteria such as Enterobacter cloacae, Salmonella typhimurium, Providencia stuartii and Shigella dysenteriae is described in this work. E. cloacae GASP strains presented lower levels of RpoS than the parental strain, although no mutation in the gene or its promoter was detected. This work offers evidence of GASP rpoS-independent pathways as GASP was also acquired in knock-out rpoS E. cloacae and E. coli strains.     

Cloning and expression of the coding regions of the heat shock proteins HSP10 and HSP16 from Piscirickettsia salmonis

The genes encoding the heat shock proteins HSP10 and HSP16 of the salmon pathogen Piscirickettsia salmonis have been isolated and sequenced. The HSP10 coding sequence is located in an open reading frame of 291 base pairs encoding 96 aminoacids. The HSP16 coding region was isolated as a 471 base pair fragment encoding a protein of 156 aminoacids. The deduced aminoacid sequences of both proteins show a significant homology to the respective protein from other prokaryotic organisms. Both proteins were expressed in E. coli as fusion proteins with thioredoxin and purified by chromatography on Nicolumn. A rabbit serum against P. salmonis total proteins reacts with the recombinant HSP10 and HSP16 proteins. Similar reactivity was determined by ELISA using serum from salmon infected with P. salmonis. The possibility of formulating a vaccine containing these two proteins is discussed.     

Modification of phospholipids fatty acid composition in reuber H35 hepatoma cells: effect on HMG-CoA reductase activity

There is controversy about the effect of saturated and polyunsaturated fats on 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase, the main regulatory enzyme of cholesterogenic pathway. Results from dietary studies are difficult to interpret because diets normally contain a mixture of fatty acids. Therefore, we have used Reuber H35 hepatoma cells whose phospholipids were enriched in different individual fatty acids and have studied their effects on the cellular reductase activity. Lauric, myristic, eicosapentaenoic (EPA), and docosahexaenoic (DHA) acids were supplemented to the culture medium coupled to bovine serum albumin. The four fatty acids were incorporated into phospholipids from cells grown in media containing whole serum or lipoprotein-poor serum (LPPS). Reductase activity of cells cultivated in a medium with LPPS was three to four times higher than those cultivated in medium with whole serum. Saturated fatty acids increased reductase activity of cells grown in medium with whole serum, whereas n-3 polyunsaturated fatty acids (PUFA) decreased it. However, both saturated and polyunsaturated fatty acids increased reductase activity when serum lipoproteins were removed. In conclusion, this is one of the first reports demonstrating that saturated and n-3 PUFA only show differential effects on HMG-CoA reductase activity in the presence of lipoproteins.