Biomedical subjects

J M Arrieta

Publications and source records attributed to J M Arrieta.

6 recordsLinked to original sources

PubMed2001

Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes.

T-RFLP clone characterization (screening) was optimized for a fast and basepair-accurate characterization of clones from marine Archaea collected from the Eastern Mediterranean Sea. Because of the high sensitivity of T-RFLP fingerprinting, a protocol was developed where 10 initial PCR cycles gave detectable terminal fragments from clones. Additionally, forward and reverse primers for PCR were individually labeled and detected simultaneously to assess the suitability of the forward and reverse fragments for T-RFLP screening. Based on independent restriction digests with the tetrameric restriction enzymes HhaI, RsaI and HaeIII to characterize the 49 archaeal clones in our library, the clones were grouped into 13 T-RFLP operational taxonomic units (OTUs). Reverse fragments generally gave less heterogeneous fragments in size. The accuracy of T-RFLP screening was evaluated by sequencing representative clones. Closely related clones ( approximately 97% similarity) could only be resolved with multiple restriction digests where forward and reverse fragments were included in the analysis. All fragments from the clone library were detected in the T-RFLP fingerprint from the complex archaeal community. We found representatives of marine group I, II and III Archaea. Thus, the recently discovered low abundant marine group III Archaea could be clearly differentiated from the other clones in our library and comprised a considerable fraction of the clone library ( approximately 12%). Therefore, our T-RFLP screening approach proved successful in characterizing novel archaeal sequences from the marine environment.

Archaea↗

PubMed2001

Magnetic properties of diruthenium(II,III) carboxylate compounds with large zero-field splitting and strong antiferromagnetic coupling.

The magnetic properties of mixed-valent compounds of general formula Ru2Cl(mu-O2CR)4 [R = CH2-CH3 (1), C(Me)=CHEt) (2)] have been studied in the 2-300 K temperature range. This magnetic study also includes a revision of the magnetic properties of the complex Ru2Cl(mu-O2CCMePh2)4 (3). Compounds 1-3 show a linear structure and a strong antiferromagnetic coupling between the diruthenium units through the chlorine atoms according to previous studies. Two fitting models to explain the magnetic properties of these complexes that incorporate a large zero-field splitting together with a strong antiferromagnetic coupling are described. These models consider that each diruthenium unit (S = 3/2) is magnetically coupled to the nearest diruthenium unit and ignores the longer distance magnetic coupling. The fitting models were found to be successful in fitting the magnetic data of the linear diruthenium(II,III) complexes. The zero-field splitting, D, and the antiferromagnetic coupling, zJ, vary from 37.8 to 48.0 cm-1 and from -7.43 to -13.30 cm-1, respectively, for complexes. The D values are similar to those calculated for the nonlinear diruthenium(II,III) compounds and confirm the validity of the proposed fitting models.

Journal Article↗

PubMed2001

Assessing the diversity of marine bacterial beta-glucosidases by capillary electrophoresis zymography.

We propose a new method for the fast separation and detection of beta-glucosidases in environmental samples. With this approach, beta-glucosidases extracted from bacteria are evidenced by substrate-incorporated capillary electrophoresis (CE zymography) and their kinetic parameters can be determined by repeated injections using different substrate concentrations. Preliminary results obtained with natural bacterial communities from the coastal North Sea suggest that the diversity of beta-glucosidases in the marine environment might be much higher than previously observed.

Electrophoresis, Capillary↗

PubMed2000

Interspecific variability in sensitivity to UV radiation and subsequent recovery in selected isolates of marine bacteria.

The interspecific variability in the sensitivity of marine bacterial isolates to UV-B (295- to 320-nm) radiation and their ability to recover from previous UV-B stress were examined. Isolates originating from different microenvironments of the northern Adriatic Sea were transferred to aged seawater and exposed to artificial UV-B radiation for 4 h and subsequently to different radiation regimens excluding UV-B to determine the recovery from UV-B stress. Bacterial activity was assessed by thymidine and leucine incorporation measurements prior to and immediately after the exposure to UV-B and after the subsequent exposure to the different radiation regimens. Large interspecific differences among the 11 bacterial isolates were found in the sensitivity to UV-B, ranging from 21 to 92% inhibition of leucine incorporation compared to the bacterial activity measured in dark controls and from 14 to 84% for thymidine incorporation. Interspecific differences in the recovery from the UV stress were also large. An inverse relation was detectable between the ability to recover under dark conditions and the recovery under photosynthetic active radiation (400 to 700 nm). The observed large interspecific differences in the sensitivity to UV-B radiation and even more so in the subsequent recovery from UV-B stress are not related to the prevailing radiation conditions of the microhabitats from which the bacterial isolates originate. Based on our investigations on the 11 marine isolates, we conclude that there are large interspecific differences in the sensitivity to UV-B radiation and even larger differences in the mechanisms of recovery from previous UV stress. This might lead to UV-mediated shifts in the bacterioplankton community composition in marine surface waters.

Bacteria↗

PubMed1999

Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis.

The potential of terminal-restriction fragment length polymorphism (T-RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1, 632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.

Animals↗

PubMed1999

Interaction between specific hydrological and microbial activity leading to extensive mucilage formation in the northern Adriatic Sea.

The massive formation of marine snow and the senescent stage of it, the mucilage, is a phenomenon largely restricted to the Adriatic Sea. In this contribution the major environmental factors potentially leading to the formation of this mucilage are discussed. It is proposed that the specific hydrological conditions in combination with severe phosphorus depletion lead to excessive formation of colloidal organic matter by phytoplankton. This colloidal organic matter coagulates to marine snow due to the low-turbulence regimes prevailing in the water column. Subsequently, this marine snow is colonized by bacteria which, in turn, produce and release copious amounts of capsular polymers into the matrix of marine snow. It is speculated that a significant fraction of the later stages of marine snow (mucilage) consists of bacterial-derived organic matter which has been shown to be semi-labile to refractory for further bacterial utilization. The marine snow matrix acts as efficient adsorption site and allows the bacteria to utilize scavenged molecules from the ambient water. Thus it is proposed that the matrix ages without significant biotic degradation.

Colloids↗