Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins

<p>Abstract</p> <p>Background</p> <p>Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs) or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships.</p> <p>Results</p> <p>A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein's primary sequence into a group of functionally non-disruptive amino acids and a second group of functionally deleterious amino acids.</p> <p>Conclusions</p> <p>With this approach, not only conserved amino acid positions in a protein family can be labeled as functionally relevant, but also non-conserved amino acid positions can be identified to have a physicochemically meaningful functional effect. These results become a discriminative tool in the selection and elaboration of rational mutagenesis strategies for the protein. They can also be used to predict if a given nsSNP, identified, for instance, in a genomic-scale analysis, can have a functional implication for a particular protein and which nsSNPs are most likely to be functionally silent for a protein. This analytical tool could be used to rapidly and automatically discard any irrelevant nsSNP and guide the research focus toward functionally significant mutations. Based on preliminary results and applications, this technique shows promising performance as a valuable bioinformatics tool to aid in the development of new protein variants and in the understanding of function-structure relationships in proteins.</p

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413–415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response

Visuomotor Cerebellum in Human and Nonhuman Primates

In this paper, we will review the anatomical components of the visuomotor cerebellum in human and, where possible, in non-human primates and discuss their function in relation to those of extracerebellar visuomotor regions with which they are connected. The floccular lobe, the dorsal paraflocculus, the oculomotor vermis, the uvula–nodulus, and the ansiform lobule are more or less independent components of the visuomotor cerebellum that are involved in different corticocerebellar and/or brain stem olivocerebellar loops. The floccular lobe and the oculomotor vermis share different mossy fiber inputs from the brain stem; the dorsal paraflocculus and the ansiform lobule receive corticopontine mossy fibers from postrolandic visual areas and the frontal eye fields, respectively. Of the visuomotor functions of the cerebellum, the vestibulo-ocular reflex is controlled by the floccular lobe; saccadic eye movements are controlled by the oculomotor vermis and ansiform lobule, while control of smooth pursuit involves all these cerebellar visuomotor regions. Functional imaging studies in humans further emphasize cerebellar involvement in visual reflexive eye movements and are discussed

Improving care for people with heart failure in Uganda: serial in-depth interviews with patients' and their health care professionals

Abstract Background The short prognosis of patients with advanced heart failure (HF) and the associated multidimensional distress as illustrated in literature from high income countries necessitates the integration of palliative care into the care of advanced HF patients to address these needs and improve their quality of life. These needs, which are subjective, have not been described from the patients’ and health care professionals’(HPs) view point in the Ugandan setting, a low income country with a different socio-cultural context. This study aimed at bridging this gap in knowledge by eliciting patients’ and HPs’ views of HF patients’ needs over the course of their illness to enable generalists, cardiologists and palliative care clinicians to develop guidelines to provide patient-centred realistic care in Uganda. Methods Serial qualitative in-depth interviews were conducted with HF patients who were purposively sampled and recruited in Mulago National Referral Hospital (MNRH) until thematic saturation. In-depth interviews were conducted at three time points with intervals of 3 month between interviews over the course of their illness in the hospital and their home context. One-off interviews were conducted with HPs that manage HF in MNRH. We used a grounded theory approach in data analysis. The Uganda National Council of science and technology approved the research. Results Forty-eight interviews were conducted with 21 patients and their carers and eight interviews with their HPs. Multidimensional needs including physical, psychological, social, spiritual and information needs were identified. These highlighted the underpinning need to have normal functioning, control, to cope and adapt to a changed life and to find meaning. Spiritual needs were less recognised by HPs than the other multidimensional needs. Information needs were commonly unmet. Patients and HPs suggested improvements in care that were congruent with the recommendations in chronic disease care and the six pillars of the WHO health systems strengthening approach. Conclusion Management of HF in Uganda requires an approach that targets multidimensional needs, embraces multidisciplinary care and strengthens health systems which are all important tenets of palliative care

Los datos moleculares confirman las afinidades de los granitos endémicos del suroeste de Australia con Alphitonia (Rhamnaceae)

Sobre la base de los datos de la secuencia de ADN, se confirma que las afinidades del género Granitites (Rhamnaceae) recientemente descrito del sudoeste de Australia están con Alphitonia, como sugirió Rye (1996), en lugar de miembros de Pomaderreae, como pensaron autores anteriores. . Los hallazgos de este estudio proporcionan una confirmación molecular de que algunos componentes de la flora del suroeste de Australia pueden ser reliquias de antiguos linajes de la selva tropicalOn the basis of DNA sequence data, the affinities of the recently described genus Granitites (Rhamnaceae) from south-western Australia are confirmed to be with Alphitonia, as suggested by Rye (1996), rather than members of Pomaderreae, as thought by earlier authors. The findings of this study provide molecular confirmation that some components of the south-west Australian flora may be relicts of old rainforest lineages