Augmented training of hidden Markov models to recognize remote homologs via simulated evolution

Motivation: While profile hidden Markov models (HMMs) are successful and powerful methods to recognize homologous proteins, they can break down when homology becomes too distant due to lack of sufficient training data. We show that we can improve the performance of HMMs in this domain by using a simple simulated model of evolution to create an augmented training set

Neutrino Target-of-Opportunity Sky Coverage and Scheduler for EUSO-SPB2

Very-high-energy neutrinos can be observed by detecting air shower signals. Detection of transient target of opportunity (ToO) neutrino sources is part of a broader multimessenger program. The Extreme Universe Space Observatory on a Super Pressure Balloon 2 (EUSO-SPB2) Mission, launched on May 12, 2023, was equipped with an optical Cherenkov Telescope (CT) designed to detect up-going air showers sourced by Earth-skimming neutrinos that interact near the Earth's limb. Presented here is an overview of the sky coverage and ToO scheduler software for EUSO-SPB2. By using the balloon trajectory coordinates and setting constraints on the positions of the Sun and Moon to ensure dark skies, we can determine if and when a source direction is slightly below the Earth's limb. From a source catalog, CT scheduling and pointing is performed to optimize the search for high-energy neutrinos coming from astrophysical sources. Some sample results for EUSO-SPB2 are shown.Comment: 10 pages, 6 figures, ICRC2023 Conference Proceeding

Hybrid material based on hyaluronan hydrogels and poly(l-lactide-co-1,3-trimethylene carbonate) scaffolds toward a cell-instructive microenvironment with long-term in vivo degradability

Degradable polyester-based scaffolds are ideal for tissue engineering applications where long-term structural integrity and mechanical support are a requisite. However, their hydrophobic and unfunctionalized surfaces restrain their tissue-mimetic quality. Instead, hyaluronan (HA) hydrogels are able to act as cell-instructive materials with the ability to recapitulate native tissue, although HA is rapidly metabolized in vivo. Taking advantage of these distinctly diverse material properties, a degradable and concurrent hybrid hydrogel material was developed that combines the short-term tissue-relevant properties of bio-orthogonal crosslinked HA with the long-term structural and mechanical support of poly(l-lactide-co-trimethylene carbonate) (PLATMC) scaffolds. This method rendered the formulation of transparent, minimally swelling hydrogel compartments with a desirable cell-instructive “local” elastic modulus within the scaffold matrix without impeding key material properties of PLATMC. Long-term degradability over 180 days in vivo was realized by the integral PLATMC scaffold architecture obtained through either extrusion-based 3D printing or salt-particulate leaching. Intrinsic diffusion capacity within the hydrogel elicited unaffected degradation kinetics of PLATMC in vivo, despite its autocatalytic bulk degradation characteristics displayed when 3D-printed. The effect of the processing method on the material properties of PLATMC markedly extends to its in vivo degradation characteristics, and essential uniform degradation behavior can be advanced using salt-particulate leaching. Regardless of the scaffold fabrication method, the polymer exhibited a soft and flexible nature throughout the degradation period, governed by the rubbery state of the polymer. Our results demonstrate that the physicochemical properties of the hybrid hydrogel scaffold endow it with the potential to act as a cell instructive microenvironment while not affecting key material properties of PLATMC postprocessing. Importantly, the HA hydrogel does not adversely impact the degradation behavior of PLATMC, a vital aspect in the fabrication of tissue engineering constructs. The results presented herein open new avenues for the adoption of concurrent and well-defined tissue-relevant materials exhibiting the potential to recreate microenvironments for cell encapsulation and drug delivery in vivo while providing essential structural integrity and long-term degradability.publishedVersio

Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution

Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related, has been profile hidden Markov models. However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in β-sheets. We thus explore methods for incorporating pairwise dependencies into these models

A perspective of solutions for membrane instabilities in olefin/paraffin separations: a review

Light olefins are mainly produced by naphtha steam cracking, which is among the more energy intensive processes in the petrochemical industry. To save energy, some alternatives have been proposed to partially replace or combine with cryogenic distillation the conventional technology to separate olefins and paraffins. Within this aim, facilitated transport membranes, mainly with Ag+cations as selective carriers, have received great attention owing to the high selectivity and permeance provided. However, to be used industrially, the undesirable instability associated with the Ag+ cation should be considered. Poisonous agents and polymer membrane materials are sources of Ag+ deactivation. In recent years, great achievements on the separation performance have been reported, but the current challenge is to maintain the selectivity in long-term separation processes. This work presents a critical analysis of the potential causes of Ag+ deactivation and points out some alternatives that have been proposed to overcome the hurdle. This review highlights and critically analyses some perspectives of the ongoing development and application of facilitated transport membranes.The authors thank the Brazilian Federal Agency for Support and Evaluation of Graduate Education − CAPES (PDSE Grant 88881.134232/2016-01) and the Spanish Ministry of Economy, Industry and Competitiveness (CTQ2015-66078-R and CTQ2016-75158-R projects, Spain-FEDER 2014-2020) for financial support

The effectiveness of position- and composition-specific gap costs for protein similarity searches

The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments. We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance.Comment: 17 pages, 4 figures, 2 table

Improving model construction of profile HMMs for remote homology detection through structural alignment

<p>Abstract</p> <p>Background</p> <p>Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the <it>Twilight Zone</it>, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.</p> <p>Results</p> <p>We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test.</p> <p>Conclusion</p> <p>We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.</p

RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils

RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins. Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a representative dataset of membrane proteins (‘Pfam-domains’). The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters (‘channels’) or other membrane proteins (‘membrane-coils’). The output provides information on the secondary structure and topology of the protein and specifically on the contact type of each residue and its conservation. This information can be downloaded as a graphical file for illustration, a text file for analysis and statistics and a PyMOL file for modeling purposes. The server can be freely accessed at: URL: http://proteinformatics.de/rhyth

Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex

Olfactory receptors (Ors) convert chemical signals—the binding of odors and pheromones—to electrical signals through the depolarization of olfactory sensory neurons. Vertebrates Ors are G-protein-coupled receptors, stimulated by odors to produce intracellular second messengers that gate ion channels. Insect Ors are a heteromultimeric complex of unknown stoichiometry of two seven transmembrane domain proteins with no sequence similarity to and the opposite membrane topology of G-protein-coupled receptors. The functional insect Or comprises an odor- or pheromone-specific Or subunit and the Orco co-receptor, which is highly conserved in all insect species. The insect Or-Orco complex has been proposed to function as a novel type of ligand-gated nonselective cation channel possibly modulated by G-proteins. However, the Or-Orco proteins lack homology to any known family of ion channel and lack known functional domains. Therefore, the mechanisms by which odors activate the Or-Orco complex and how ions permeate this complex remain unknown. To begin to address the relationship between Or-Orco structure and function, we performed site-directed mutagenesis of all 83 conserved Glu, Asp, or Tyr residues in the silkmoth BmOr-1-Orco pheromone receptor complex and measured functional properties of mutant channels expressed in Xenopus oocytes. 13 of 83 mutations in BmOr-1 and BmOrco altered the reversal potential and rectification index of the BmOr-1-Orco complex. Three of the 13 amino acids (D299 and E356 in BmOr-1 and Y464 in BmOrco) altered both current-voltage relationships and K+ selectivity. We introduced the homologous Orco Y464 residue into Drosophila Orco in vivo, and observed variable effects on spontaneous and evoked action potentials in olfactory neurons that depended on the particular Or-Orco complex examined. Our results provide evidence that a subset of conserved Glu, Asp and Tyr residues in both subunits are essential for channel activity of the heteromeric insect Or-Orco complex