LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

Background The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.

Structural analysis and seismic stratigraphy for delineation of Neoproterozoic-Cambrian petroleum system in central and eastern part of Bikaner–Nagaur basin, India

Bikaner–Nagaur basin is located in the northwestern part of India and lies on the rising flank of Punjab platform of Middle Indus basin in Pakistan. Existence of Neoproterozoic-Cambrian petroleum system was confirmed by the exploration activities in the western periphery of the basin, whereas vast areas of central and eastern parts remain unexplored. Knowledge of petroleum system in this unexplored part of the basin is limited due to non-availability of data. Recently, 2525 line km of regional 2D seismic data acquired for the first time by Government of India under National Seismic Program (NSP) unlocks the opportunity for comprehensive understanding of subsurface geology in unexplored part of the basin. Present work aims to interpret recently acquired 2D seismic data and integrate with available surface (outcrop) data, gravity and well data (drilled in western part of basin) for unfolding the petroleum system elements, structural configurations and stratigraphic features in the hitherto central-eastern part of the basin. Two Neoproterozoic-Cambrian hydrocarbon plays: (1) Jodhpur and (2) overlying Bilara/Hanseran Evaporite Group (HEG) were envisaged. Both the plays depicted distinctive seismic characteristics, structural alignment and distribution of reservoir, source and seal. Fluvio-deltaic sandstone within Jodhpur group and shallow marine fractured dolomites within Bilara/HEG showed potential reservoir characteristics whereas organic rich laminated dolomites, stromatolites and argillaceous litho-units within Bilara/HEG group have been predicted as prospective source. The Halite layers within HEG group were considered as effective regional seals. Fault bounded anticlinal structures associated with Cambrian compression have been identified as the main entrapment for hydrocarbon accumulation. The basin witnessed long tectonostratigraphic history with two major compressional phases Structures formed by Cambrian compression are likely to be charged as the time of source maturity and peak expulsion was later, during early Mesozoic period. Overall, the study indicates new opportunities and potential accumulation of hydrocarbon in the unexplored part of the basin.

Enabling the potential of Mission-led Research in New Zealand: Conceptualisations, Structures, and Relationships in the National Science Challenges

<p>Addressing the Grand Challenges of the world requires a mode of research that can mirror their scale and complexity. Traditional investigator- and industry-led research frameworks, although useful in their own right, fail to capture the collaborative, transdisciplinary approach that can both generate the necessary knowledge and apply research outcomes on the scale needed to resolve the ‘big picture’ problems. Mission-led research provides a framework that attempts to strike that balance of knowledge generation and application; and New Zealand’s National Science Challenges (NSCs) provide a representation of missionled research that may exemplify the relationships and processes needed to enact it. This thesis aims to understand how the relationships and processes designed to facilitate mission-led research in the NSCs impacts their ability to achieve their missions. Research was undertaken through semi-structured interviews with participants from two NSCs, representing four of the key stakeholder perspectives: Management, Researchers, Industry, and Māori. These interviews sought to understand how different stakeholder groups conceptualised mission-led research itself, the processes within it, and their relationships with other stakeholder groups. The results demonstrated that stakeholders perceived mission-led research in four interdependent ways, driven by a core concept of ‘Big Picture’ problems. These problems were seen to necessitate ‘Transdisciplinarity’ in their resolution, that research would be ‘Long-term/Strategic’, and that research outcomes would have a ‘Collective Benefit’. Alignment between conceptualisations of mission-led research and how closely processes and stakeholder groups adhered to those conceptualisations was central to positive engagement and collaboration. Alignment between stakeholders was seen to occur through three modes: Conceptual, Structural, and Relational. Conceptual alignment promoted a common understanding of the mission; Structural alignment ensured research practices reflected mission-led values; and Relational alignment improved stakeholder understanding of diverse expectations and motivations amongst other worldviews. Successful NSCs used the three modes of alignment to improve transdisciplinary collaboration while maintaining diversity of worldviews and skillsets, enabling them to more effectively address their missions.</p>

Enabling the potential of Mission-led Research in New Zealand: Conceptualisations, Structures, and Relationships in the National Science Challenges

<p>Addressing the Grand Challenges of the world requires a mode of research that can mirror their scale and complexity. Traditional investigator- and industry-led research frameworks, although useful in their own right, fail to capture the collaborative, transdisciplinary approach that can both generate the necessary knowledge and apply research outcomes on the scale needed to resolve the ‘big picture’ problems. Mission-led research provides a framework that attempts to strike that balance of knowledge generation and application; and New Zealand’s National Science Challenges (NSCs) provide a representation of missionled research that may exemplify the relationships and processes needed to enact it. This thesis aims to understand how the relationships and processes designed to facilitate mission-led research in the NSCs impacts their ability to achieve their missions. Research was undertaken through semi-structured interviews with participants from two NSCs, representing four of the key stakeholder perspectives: Management, Researchers, Industry, and Māori. These interviews sought to understand how different stakeholder groups conceptualised mission-led research itself, the processes within it, and their relationships with other stakeholder groups. The results demonstrated that stakeholders perceived mission-led research in four interdependent ways, driven by a core concept of ‘Big Picture’ problems. These problems were seen to necessitate ‘Transdisciplinarity’ in their resolution, that research would be ‘Long-term/Strategic’, and that research outcomes would have a ‘Collective Benefit’. Alignment between conceptualisations of mission-led research and how closely processes and stakeholder groups adhered to those conceptualisations was central to positive engagement and collaboration. Alignment between stakeholders was seen to occur through three modes: Conceptual, Structural, and Relational. Conceptual alignment promoted a common understanding of the mission; Structural alignment ensured research practices reflected mission-led values; and Relational alignment improved stakeholder understanding of diverse expectations and motivations amongst other worldviews. Successful NSCs used the three modes of alignment to improve transdisciplinary collaboration while maintaining diversity of worldviews and skillsets, enabling them to more effectively address their missions.</p>

Effect of perceived product innovativeness on consumers' product attribute preferences: The mediating role of self-efficacy

On the basis of the structural alignment model, we conducted two experiments to examine the effect of consumers' perceived product innovativeness on their product attribute preferences, and to test the mediating role of self-efficacy. Data were obtained from 263 participants, and the results showed that consumers paid more attention to alignable (vs. nonalignable) attributes when purchasing new products with low (vs. high) perceived innovativeness. Our results enrich previous findings on product innovativeness and the structural alignment model, and provide practical suggestions for enterprises to develop effective marketing strategies for new products.

EXPRESS: GMO Labeling Policy and Consumer Choice

Most scientists claim that genetically modified organisms (GMOs) in foods are safe for human consumption and offer societal benefits such as better nutritional content. In contrast, many consumers remain skeptical about their safety. Against this backdrop of diverging views, the authors investigate the impact of different GMO labeling policy regimes on products consumers choose. Guided by the literature on negativity bias, structural alignment theory, and message presentation, and based on findings from four experiments, authors show that consumer demand for GM foods depends on the labeling regime policymakers adopt. Both absence-focused (“non-GMO”) and presence-focused (“contains GMO”) labeling regimes reduce the market share of GM foods, with the reduction being greater in the latter case. GMO labels reduce the importance consumers place on price and enhance their willingness-to-pay for non-GM products. Results indicate that specific label design choices policymakers implement (in the form of color and style) also affect consumer responses to GM labeling. Consumer attitudes toward GMOs moderate this effect – consumers with neutral attitudes toward GMOs are influenced most significantly by the label design.

VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes

Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macromolecular structures such as proteins. Here we show VTR, a new method for the detection of analogous contacts in protein pairs. The VTR web tool performs structural alignment between proteins and detects interactions that occur in similar regions. To evaluate our tool, we proposed three case studies: we 1) compared vertebrate myoglobin and truncated invertebrate hemoglobin; 2) analyzed interactions between the spike protein RBD of SARS-CoV-2 and the cell receptor ACE2; and 3) compared a glucose-tolerant and a non-tolerant β-glucosidase enzyme used for biofuel production. The case studies demonstrate the potential of VTR for the understanding of functional similarities between distantly sequence-related proteins, as well as the exploration of important drug targets and rational design of enzymes for industrial applications. We envision VTR as a promising tool for understanding differences and similarities between homologous proteins with similar 3D structures but different sequences. VTR is available at http://bioinfo.dcc.ufmg.br/vtr.

Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea

Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.