GADIS: algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins

Many intrinsically disordered proteins (IDPs) participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding to the binding interface; and (iii) maintaining the native amino acid composition. Here, we report the development of a G: enetic A: lgorithm for D: esign of I: ntrinsic secondary S: tructure (GADIS) for designing sequences that satisfy the specified constraints. We describe the algorithm and present results to demonstrate the applicability of GADIS by designing sequence variants of the intrinsically disordered PUMA system that undergoes coupled folding and binding to Mcl-1. Our sequence designs span a range of intrinsic helicity profiles. The predicted variations in sequence-encoded mean helicities are tested against experimental measurements

Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists. © 2011 Hatfull et al

Heritable symbionts in a world of varying temperature

Heritable microbes represent an important component of the biology, ecology and evolution of many plants, animals and fungi, acting as both parasites and partners. In this review, we examine how heritable symbiont–host interactions may alter host thermal tolerance, and how the dynamics of these interactions may more generally be altered by thermal environment. Obligate symbionts, those required by their host, are considered to represent a thermally sensitive weak point for their host, associated with accumulation of deleterious mutations. As such, these symbionts may represent an important determinant of host thermal envelope and spatial distribution. We then examine the varied relationship between thermal environment and the frequency of facultative symbionts that provide ecologically contingent benefits or act as parasites. We note that some facultative symbionts directly alter host thermotolerance. We outline how thermal environment will alter the benefits/costs of infection more widely, and additionally modulate vertical transmission efficiency. Multiple patterns are observed, with symbionts being cold sensitive in some species and heat sensitive in others, with varying and non-coincident thresholds at which phenotype and transmission are ablated. Nevertheless, it is clear that studies aiming to predict ecological and evolutionary dynamics of symbiont–host interactions need to examine the interaction across a range of thermal environments. Finally, we discuss the importance of thermal sensitivity in predicting the success/failure of symbionts to spread into novel species following natural/engineered introduction

Estimates of live-tree carbon stores in the Pacific Northwest are sensitive to model selection

<p>Abstract</p> <p>Background</p> <p>Estimates of live-tree carbon stores are influenced by numerous uncertainties. One of them is model-selection uncertainty: one has to choose among multiple empirical equations and conversion factors that can be plausibly justified as locally applicable to calculate the carbon store from inventory measurements such as tree height and diameter at breast height (DBH). Here we quantify the model-selection uncertainty for the five most numerous tree species in six counties of northwest Oregon, USA.</p> <p>Results</p> <p>The results of our study demonstrate that model-selection error may introduce 20 to 40% uncertainty into a live-tree carbon estimate, possibly making this form of error the largest source of uncertainty in estimation of live-tree carbon stores. The effect of model selection could be even greater if models are applied beyond the height and DBH ranges for which they were developed.</p> <p>Conclusions</p> <p>Model-selection uncertainty is potentially large enough that it could limit the ability to track forest carbon with the precision and accuracy required by carbon accounting protocols. Without local validation based on detailed measurements of usually destructively sampled trees, it is very difficult to choose the best model when there are several available. Our analysis suggests that considering tree form in equation selection may better match trees to existing equations and that substantial gaps exist, in terms of both species and diameter ranges, that are ripe for new model-building effort.</p

Nutrition aspects in children receiving maintenance hemodialysis: impact on outcome

Children with end-stage renal disease (ESRD) have rates of mortality estimated to be 30-times higher than expected for age compared with those of healthy children. Physical manifestations of under-nutrition, such as body mass index (BMI) and low height standard deviation score (SDS), have been associated with increased risk of mortality. Traditional measures, such as height, weight and serum albumin concentration, may not be accurate indicators to assess the nutritional status of children receiving maintenance hemodialysis. Normalized protein catabolic rate (nPCR) has emerged as a better marker of nutritional status of such children. Meeting the special nutritional needs of these children often requires nutritional supplementation, by either the enteral or the parenteral route. Recently, in children receiving maintenance hemodialysis who are malnourished, intradialytic parenteral nutrition (IDPN) has been utilized as a means to provide additional protein and calories. This article is a state-of-the-art review of malnutrition in children receiving maintenance hemodialysis, with special focus on outcome, nPCR and IDPN

Overcoming Barriers to Skills Training in Borderline Personality Disorder: A Qualitative Interview Study

Despite evidence suggesting that skills training is an important mechanism of change in dialectical behaviour therapy, little research exploring facilitators and barriers to this process has been conducted. The study aimed to explore clients’ experiences of barriers to dialectical behaviour therapy skills training and how they felt they overcame these barriers, and to compare experiences between treatment completers and dropouts. In-depth qualitative interviews were conducted with 40 clients with borderline personality disorder who had attended a dialectical behaviour therapy programme. A thematic analysis of participants’ reported experiences found that key barriers to learning the skills were anxiety during the skills groups and difficulty understanding the material. Key barriers to using the skills were overwhelming emotions which left participants feeling unable or unwilling to use them. Key ways in which participants reported overcoming barriers to skills training were by sustaining their commitment to attending therapy and practising the skills, personalising the way they used them, and practising them so often that they became an integral part of their behavioural repertoire. Participants also highlighted a number of key ways in which they were supported with their skills training by other skills group members, the group therapists, their individual therapist, friends and family. Treatment dropouts were more likely than completers to describe anxiety during the skills groups as a barrier to learning, and were less likely to report overcoming barriers to skills training via the key processes outlined above. The findings of this qualitative study require replication, but could be used to generate hypotheses for testing in further research on barriers to skills training, how these relate to dropout, and how they can be overcome. The paper outlines several such suggestions for further research

Business process modelling to improve incident management process

Business process management (BPM) is an approach focused on the continuous improvement of business processes, providing for this a collection of best practices. These best practices enable the redesign of business processes to meet the desired performance. IT service management (ITSM) defines the management of IT operations as a service. There are several ITSM frameworks available, consisting in best practices that propose standardizing these pro- cesses for the respective operations. By adopting these frameworks, organisations can align IT with their business objectives. Therefore, the objective of this research is to understand how BPM can be used to improve of ITSM processes. An exploratory case study in a multinational company based in Lisbon, Portugal, is conducted for the improvement of the time performance of an inci- dent management process. Data were gained through documentation, archival records, interviews and focus groups with a team involved in IT support service. So far, the as-is process was elicited, and respective incongruences clarified. During the next months the authors intend to identify the main problems and simulate the appropriate BPM heuristics to understand the impact in the busi- ness organisation.info:eu-repo/semantics/acceptedVersio

The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

<p>Abstract</p> <p>Background</p> <p>Oomycetes are a large group of economically and ecologically important species. Its most notorious member is <it>Phytophthora infestans</it>, the cause of the devastating potato late blight disease. The life cycle of <it>P. infestans </it>involves hyphae which differentiate into spores used for dispersal and host infection. Protein phosphorylation likely plays crucial roles in these stages, and to help understand this we present here a genome-wide analysis of the protein kinases of <it>P. infestans </it>and several relatives. The study also provides new insight into kinase evolution since oomycetes are taxonomically distant from organisms with well-characterized kinomes.</p> <p>Results</p> <p>Bioinformatic searches of the genomes of <it>P. infestans</it>, <it>P. ramorum</it>, and <it>P. sojae </it>reveal they have similar kinomes, which for <it>P. infestans </it>contains 354 eukaryotic protein kinases (ePKs) and 18 atypical kinases (aPKs), equaling 2% of total genes. After refining gene models, most were classifiable into families seen in other eukaryotes. Some ePK families are nevertheless unusual, especially the tyrosine kinase-like (TKL) group which includes large oomycete-specific subfamilies. Also identified were two tyrosine kinases, which are rare in non-metazoans. Several ePKs bear accessory domains not identified previously on kinases, such as cyclin-dependent kinases with integral cyclin domains. Most ePKs lack accessory domains, implying that many are regulated transcriptionally. This was confirmed by mRNA expression-profiling studies that showed that two-thirds vary significantly between hyphae, sporangia, and zoospores. Comparisons to neighboring taxa (apicomplexans, ciliates, diatoms) revealed both clade-specific and conserved features, and multiple connections to plant kinases were observed. The kinome of <it>Hyaloperonospora arabidopsidis</it>, an oomycete with a simpler life cycle than <it>P. infestans</it>, was found to be one-third smaller. Some differences may be attributable to gene clustering, which facilitates subfamily expansion (or loss) through unequal crossing-over.</p> <p>Conclusion</p> <p>The large sizes of the <it>Phytophthora </it>kinomes imply that phosphorylation plays major roles in their life cycles. Their kinomes also include many novel ePKs, some specific to oomycetes or shared with neighboring groups. Little experimentation to date has addressed the biological functions of oomycete kinases, but this should be stimulated by the structural, evolutionary, and expression data presented here. This may lead to targets for disease control.</p

Accounting for density reduction and structural loss in standing dead trees: Implications for forest biomass and carbon stock estimates in the United States

<p>Abstract</p> <p>Background</p> <p>Standing dead trees are one component of forest ecosystem dead wood carbon (C) pools, whose national stock is estimated by the U.S. as required by the United Nations Framework Convention on Climate Change. Historically, standing dead tree C has been estimated as a function of live tree growing stock volume in the U.S.'s National Greenhouse Gas Inventory. Initiated in 1998, the USDA Forest Service's Forest Inventory and Analysis program (responsible for compiling the Nation's forest C estimates) began consistent nationwide sampling of standing dead trees, which may now supplant previous purely model-based approaches to standing dead biomass and C stock estimation. A substantial hurdle to estimating standing dead tree biomass and C attributes is that traditional estimation procedures are based on merchantability paradigms that may not reflect density reductions or structural loss due to decomposition common in standing dead trees. The goal of this study was to incorporate standing dead tree adjustments into the current estimation procedures and assess how biomass and C stocks change at multiple spatial scales.</p> <p>Results</p> <p>Accounting for decay and structural loss in standing dead trees significantly decreased tree- and plot-level C stock estimates (and subsequent C stocks) by decay class and tree component. At a regional scale, incorporating adjustment factors decreased standing dead quaking aspen biomass estimates by almost 50 percent in the Lake States and Douglas-fir estimates by more than 36 percent in the Pacific Northwest.</p> <p>Conclusions</p> <p>Substantial overestimates of standing dead tree biomass and C stocks occur when one does not account for density reductions or structural loss. Forest inventory estimation procedures that are descended from merchantability standards may need to be revised toward a more holistic approach to determining standing dead tree biomass and C attributes (i.e., attributes of tree biomass outside of sawlog portions). Incorporating density reductions and structural loss adjustments reduces uncertainty associated with standing dead tree biomass and C while improving consistency with field methods and documentation.</p