The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at , and , respectively

GP and nurses' perceptions of how after hours care for people receiving palliative care at home could be improved: a mixed methods study

<p>Abstract</p> <p>Background</p> <p>Primary health care providers play a dominant role in the provision of palliative care (PC) in Australia but many gaps in after hours service remain. In some rural areas only 19% of people receiving palliative care achieve their goal of dying at home. This study, which builds on an earlier qualitative phase of the project, investigates the gaps in care from the perspective of general practitioners (GPs) and PC nurses.</p> <p>Methods</p> <p>Questionnaires, developed from the outcomes of the earlier phase, and containing both structured and open ended questions, were distributed through Divisions of General Practice (1 urban, 1 rural, 1 mixed) to GPs (n = 524) and through a special interest group to palliative care nurses (n = 122) in both rural and urban areas.</p> <p>Results</p> <p>Questionnaires were returned by 114 GPs (22%) and 52 nurses (43%). The majority of GPs were associated with a practice which provided some after hours services but PC was not a strong focus for most. This was reflected in low levels of PC training, limited awareness of the existence of after hours triage services in their area, and of the availability of Enhanced Primary Care (EPC) Medicare items for care planning for palliative patients. However, more than half of both nurses and GPs were aware of accessible PC resources.</p> <p>Factors such as poor communication and limited availability of after hours services were identified the as most likely to impact negatively on service provision. Strategies considered most likely to improve after hours services were individual patient protocols, palliative care trained respite carers and regular multidisciplinary meetings that included the GP.</p> <p>Conclusion</p> <p>While some of the identified gaps can only be met by long term funding and policy change, educational tools for use in training programs in PC for health professionals, which focus on the utilisation of EPC Medicare items in palliative care planning, the development of advance care plans and good communication between members of multidisciplinary teams, which include the GP, may enhance after hours service provision for patients receiving palliative care at home. The role of locums in after PC is an area for further research</p

Good physicians from the perspective of their patients

BACKGROUND: It is not currently known what is the patient's viewpoint of a "good" physician. We set out to define patient's priorities regarding different physician's attributes in 3 domains important in medical care. METHODS: Patients hospitalized or attending clinics at a large teaching hospital selected the 4 attributes that they considered most important out of 21 listed arbitrarily in a questionnaire. The questionnaire included 7 items each in the domains of patient autonomy, professional expertise and humanism. RESULTS: Participating patients (n = 445, mean age 57.5 ± 16 years) selected professional expertise (50%), physician's patience and attentiveness (38% and 30%, respectively), and informing the patient, representing the patient's interests, being truthful and respecting patient's preferences (25–36% each) as the most essential attributes. Patient's selections were not significantly influenced by different demographic or clinical background. Selections of attributes in the domain of patient's autonomy were significantly more frequent and this was the preferred domain for 31% and as important as another domain for 16% – significantly more than the domain of professional expertise (P = 0.008), and much more than the domain of humanism and support (P < 0.0005). CONCLUSIONS: Patients studied want their physicians to be highly professional and expert clinicians and show humaneness and support, but their first priority is for the physician to respect their autonomy

Mechanics of extended masses in general relativity

The "external" or "bulk" motion of extended bodies is studied in general relativity. Compact material objects of essentially arbitrary shape, spin, internal composition, and velocity are allowed as long as there is no direct (non-gravitational) contact with other sources of stress-energy. Physically reasonable linear and angular momenta are proposed for such bodies and exact equations describing their evolution are derived. Changes in the momenta depend on a certain "effective metric" that is closely related to a non-perturbative generalization of the Detweiler-Whiting R-field originally introduced in the self-force literature. If the effective metric inside a self-gravitating body can be adequately approximated by an appropriate power series, the instantaneous gravitational force and torque exerted on it is shown to be identical to the force and torque exerted on an appropriate test body moving in the effective metric. This result holds to all multipole orders. The only instantaneous effect of a body's self-field is to finitely renormalize the "bare" multipole moments of its stress-energy tensor. The MiSaTaQuWa expression for the gravitational self-force is recovered as a simple application. A gravitational self-torque is obtained as well. Lastly, it is shown that the effective metric in which objects appear to move is approximately a solution to the vacuum Einstein equation if the physical metric is an approximate solution to Einstein's equation linearized about a vacuum background.Comment: 39 pages, 2 figures; fixed equation satisfied by the Green function used to construct the effective metri

Genome sequence of the broad-host-range Pseudomonas phage Phi-S1

The broad-host-range lytic Pseudomonas phage Φ-S1 possess a 40,192 bp double-stranded DNA (dsDNA) genome of 47 open reading frames (ORFs) and belongs to the family Podoviridae, subfamily Autographivirinae, genus T7likevirus.S.S. acknowledges the financial support from the Portuguese Foundation for Science and Technology (FCT) (grant SFRH/BPD/48803/2008) and the FCT project PTDC/EBB-BIO/114760/2009

The glycan-binding protein galectin-1 controls survival of epithelial cells along the crypt-villus axis of small intestine

Abstract: Intestinal epithelial cells serve as mechanical barriers and active components of the mucosal immune system. These cells migrate from the crypt to the tip of the villus, where different stimuli can differentially affect their survival. Here we investigated, using in vitro and in vivo strategies, the role of galectin-1 (Gal-1), an evolutionarily conserved glycan-binding protein, in modulating the survival of human and mouse enterocytes. Both Gal-1 and its specific glyco-receptors were broadly expressed in small bowel enterocytes. Exogenous Gal-1 reduced the viability of enterocytes through apoptotic mechanisms involving activation of both caspase and mitochondrial pathways. Consistent with these findings, apoptotic cells were mainly detected at the tip of the villi, following administration of Gal-1. Moreover, Gal-1-deficient (Lgals-1-) mice showed longer villi compared with their wild-type counterparts in vivo. In an experimental model of starvation, fasted wild-type mice displayed reduced villi and lower intestinal weight compared with Lgals-1- mutant mice, an effect reflected by changes in the frequency of enterocyte apoptosis. Of note, human small bowel enterocytes were also prone to this pro-apoptotic effect. Thus, Gal-1 is broadly expressed in mucosal tissue and influences the viability of human and mouse enterocytes, an effect which might influence the migration of these cells from the crypt, the integrity of the villus and the epithelial barrier function.Facultad de Ciencias Exacta

Germinal Center B Cells Regulate Their Capability to Present Antigen by Modulation of HLA-DO

Peptide acquisition by MHC class II molecules is catalyzed by HLA-DM (DM). In B cells, HLA-DO (DO) inhibits or modifies the peptide exchange activity of DM. We show here that DO protein levels are modulated during B cell differentiation. Remarkably, germinal center (GC) B cells, which have low levels of DO relative to naive and memory B cells, are shown to have enhanced antigen presentation capabilities. DM protein levels also were somewhat reduced in GC B cells; however, the ratio of DM to DO in GC B cells was substantially increased, resulting in more free DM in GC B cells. We conclude that modulation of DM and DO in distinct stages of B cell differentiation represents a mechanism by which B cells regulate their capacity to function as antigen-presenting cells. Efficient antigen presentation in GC B cells would promote GC B cell–T cell interactions that are essential for B cells to survive positive selection in the GC

Human plasmacytoid dendritic cells elicited different responses after infection with pathogenic and nonpathogenic Junin virus strains

The arenavirus Junin virus (JUNV) is the etiologic agent of Argentine hemorrhagic fever. We characterized the JUNV infection of human peripheral blood-derived plasmacytoid dendritic cells (hpDC), demonstrating that hpDC are susceptible to infection with the C#1 strain (attenuated) and even more susceptible to infection with the P (virulent) JUNV strain. However, hpDC elicited different responses in terms of viability, activation, maturation, and cytokine expression after infection with both JUNV strains.Instituto de Biotecnologia y Biologia Molecula