Ssa miRNAs DB: Online repository of in silico predicted miRNAs in Salmo salar

The Atlantic salmon (Salmo salar) is a very valuable commercial salmonid species. As with other aquaculture species, intensive aquaculture of Atlantic salmon often faces disease problems especially in early life stages which can limit stable production of the species. 'Ssa miRNAs DB', a bioinformatics and manually curated database, aims at providing a comprehensive resource of microRNA in Altantic salmon, with a user friendly interface for a convenient retrieval of each entry by microRNA ID or target gene. The current version of Ssa miRNAs DB involved the prediction of 41 and 266 homologous and novel microRNAs, respectively. AVAILABILITY: The database is available for free at http://www.molgenv.com/ssa_mirnas_db_home.php.     

Human and canine echinococcosis infection in informal, unlicensed abattoirs in Lima, Peru

Echinococcus granulosus infections are a major public health problem in livestock-raising regions around the world. The life cycle of this tapeworm is sustained between dogs (definitive host, canine echinococcosis), and herbivores (intermediary host, cystic hydatid disease). Humans may also develop cystic hydatid disease. Echinococcosis is endemic in rural areas of Peru; nevertheless, its presence or the extension of the problem in urban areas is basically unknown. Migration into Lima, an 8-million habitant's metropolis, creates peripheral areas where animals brought from endemic areas are slaughtered without veterinary supervision. We identified eight informal, unlicensed abattoirs in a peripheral district of Lima and performed a cross-sectional study in to assess the prevalence of canine echinococcosis, evaluated by coproELISA followed by PCR evaluation and arecoline purge. Eight of 22 dogs (36%) were positive to coproELISA, and four (18%) were confirmed to be infected with E. granulosus tapeworms either by PCR or direct observation (purge). Later evaluation of the human population living in these abattoirs using abdominal ultrasound, chest X-rays and serology, found 3 out of 32 (9.3%) subjects with echinococcal cysts in the liver (two viable, one calcified), one of whom had also lung involvement and a strongly positive antibody response. Autochthonous transmission of E. granulosus is present in Lima. Informal, unlicensed abattoirs may be sources of infection to neighbouring people in this urban environment.     

Candidiasis invasora en una paciente sometida a retrasplante unipulmonar

BackgroundLung-graft loss is a potential problem for the majority of lung-transplant recipients. Retransplantation could be a treatment option, despite significant morbidity and mortality due to infectious complications. The epidemiology, clinical presentation and early treatment are still the basis of the overall approach to the fungal invasive infection after repeated transplant.Clinical caseThis is the case of a 29 year-old woman who underwent a left lung retransplantation due to bronchiolitis obliterans syndrome and developed Candida albicans invasive disease. She received the usual prophylaxis with nebulized liposomal amphotericin B and was also treated with anidulafungin. She received corticosteroid therapy and plasma exchange as acute lung transplant rejection was suspected with subsequent progressive deterioration and death. In the culture of blood samples yeasts were isolated, later identified as C. albicans resistant to fluconazole, caspofungin and micafungin (MCI 128 μg/ml, 8 μg/ml, 4 μg/ml, respectively) and susceptible to anidulafungin and amphotericin B (MCI 0.25 μg/ml, 0.5 μg/ml, respectively).ConclusionsThe empirical management of acute transplant rejection with corticosteroid boluses and plasma exchange can help to spread the underlying and undiagnosed fungal infection. It is considered that an increase in the regular dose of anidulafungin is necessary after plasma exchange. To date, fungal echinocandin resistance did not seem to be a major cause for concern in the treatment of patients with invasive mycoses. However, there is increasing evidence of natural and acquired resistance resulting in life-threatening infections and clinical failure.     

Clarifying the roles of kinetics and diffusion in activated sludge filamentous bulking

We hypothesized that the growth rates of filaments and floc formers in activated sludge are affected by the combination of kinetic selection (Lou and de los Reyes, Biotechnol Bioeng 92(6): 729-739, 2005b) and substrate diffusion limitation (Martins et al., Water Res 37:2555-2570, 2003). To clarify the influence of these factors in explaining filamentous bulking, a conceptual framework was developed in this study. The framework suggests the existence of three different regions corresponding to bulking, non-bulking, and intermediate regions, based on substrate concentration. In the bulking and non-bulking regions, kinetic growth differences control the competition process, and filaments or floc formers dominate, respectively. In the intermediate region, substrate diffusion limitation, determined by the floc size, plays the major role in causing bulking. To test this framework, sequencing batch reactors (SBRs) were operated with influent COD of 100, 300, 600, and 1,000 mg/L, and the sludge settleability was measured at various floc size distributions that were developed using different mixing strengths. The experimental data in the bulking and intermediate regions supported the proposed framework. A model integrating the two factors was developed to simulate the substrate concentrations at different depths and floc sizes under intermittently feeding conditions. The modeling results confirmed that substrate diffusion limitation occurs inside the flocs at a certain range of activated sludge floc sizes over the operation cycle, and provided additional support for the proposed framework.     

Different immune response of mice immunized with conjugates containing multiple copies of either consensus or mixotope versions of the V3 loop peptide from human immunodeficiency virus type 1

The critical role that antibody responses to the V3 loop epitope play in human immunodeficiency virus type 1 (HIV-1) neutralization has caused this peptide to be used in many HIV-1 vaccine candidates. To enhance cross-reactivity toward several V3 sequences, a database of 50 peptides of the V3 region from HIV-1 subtype A was used to design both a consensus peptide and a combinatorial peptide (mixotope) library representative of these sequences. The two immunogens (consensus and mixotope) were incorporated into multiple antigen peptide (MAP) constructions, conjugated to a recombinant surface antigen from hepatitis B virus (HbsAg) carrier protein, and inoculated to mice in combination with a C4 (CD4-binding) peptide MAP construction, also conjugated to HBsAg. The respective responses and cross-reactivity to several V3 loop sequences of both types of immunogens were compared. Mice inoculated with the V3 consensus-MAP-HBsAg + C4-MAP-HBsAg mixture elicited higher antibody responses than those given the V3 mixotope-MAP-HBsAg + C4-MAP-HBsAg mixture. In addition, pooled serum from the first group of immunogens analyzed at dilution 1:100 had higher cross-reactivity against V3 peptides on cellulose membranes than those from mice given the combinatorial immunogen. Fine epitope mapping of both consensus and C4 peptide by the spot synthesis technique showed that sera of the first group strongly recognized both sequences in their entirety, whereas mice immunized with the mixotope library recognized only the N-terminal region of V3. These results seem to suggest that the V3 consensus peptide is superior to the combinatorial strategy in inducing potent and cross-reactive responses to HIV.     

The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization

Many copies of mammalian mitochondrial DNA contain a short triple-stranded region, or displacement loop (D-loop), in the major noncoding region. In the 35 years since their discovery, no function has been assigned to mitochondrial D-loops. We purified mitochondrial nucleoprotein complexes from rat liver and identified a previously uncharacterized protein, ATAD3p. Localization studies suggested that human ATAD3 is a component of many, but not all, mitochondrial nucleoids. Gene silencing of ATAD3 by RNA interference altered the structure of mitochondrial nucleoids and led to the dissociation of mitochondrial DNA fragments held together by protein, specifically, ones containing the D-loop region. In vitro, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-loop, with a marked preference over partially relaxed molecules with a D-loop or supercoiled DNA circles. These results suggest that mitochondrial D-loops serve to recruit ATAD3p for the purpose of forming or segregating mitochondrial nucleoids.     

Correlation between signal input and output in PctA and PctB amino acid chemoreceptor of Pseudomonas aeruginosa

The PctA and PctB chemoreceptors of Pseudomonas aeruginosa mediate chemotaxis toward amino acids. A general feature of signal transduction processes is that a signal input is converted into an output. We have generated chimeras combining the Tar signaling domain with either the PctA or PctB ligand binding domain (LBD). Escherichia coli harboring either PctA‐Tar or PctB‐Tar mediated chemotaxis toward amino acids. The responses of both chimeras were determined using fluorescence resonance energy transfer, and the derived EC₅₀ values are a measure of output. PctA‐Tar and PctB‐Tar responded to 19 and 11 L‐amino acids respectively. The EC₅₀ values of PctA‐Tar responses differed by more than three orders of magnitude, whereas PctB‐Tar responded preferentially to L‐Gln. The comparison of amino acid binding constants and the corresponding EC₅₀ values for both receptors revealed statistically significant correlations between inputs and outputs. PctA and PctB possess a double PDC (PhoQ‐DcuS‐CitA) LBD – a family of binding domain found in various other amino acid chemoreceptors. Similarly, various chemoreceptors share the preferential response to certain amino acids (e.g. L‐Cys, L‐Ser and L‐Thr) that we observed for PctA. Defining the specific inputs and outputs of these chemoreceptors is an important step toward better understanding of their physiological role.     

Rising synchrony controls western North American ecosystems

Along the western margin of North America, the winter expression of the North Pacific High (NPH) strongly influences interannual variability in coastal upwelling, storm track position, precipitation, and river discharge. Coherence among these factors induces covariance among physical and biological processes across adjacent marine and terrestrial ecosystems. Here, we show that over the past century the degree and spatial extent of this covariance (synchrony) has substantially increased, and is coincident with rising variance in the winter NPH. Furthermore, centuries‐long blue oak (Quercus douglasii) growth chronologies sensitive to the winter NPH provide robust evidence that modern levels of synchrony are among the highest observed in the context of the last 250 years. These trends may ultimately be linked to changing impacts of the El Niño Southern Oscillation on midlatitude ecosystems of North America. Such a rise in synchrony may destabilize ecosystems, expose populations to higher risks of extinction, and is thus a concern given the broad biological relevance of winter climate to biological systems.