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Abstract

The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques. Successful state inference of RNA sequences can be used to generate auxiliary information for data-directed RNA secondary structure prediction. Typical tools for state inference, such as hidden Markov models, exhibit poor performance in RNA state inference, owing in part to their inability to recognize nonlocal dependencies. Bidirectional long short-term memory (LSTM) neural networks have emerged as a powerful tool that can model global nonlinear sequence dependencies and have achieved state-of-the-art performances on many different classification problems.

This paper presents a practical approach to RNA secondary structure inference centered around a deep learning method for state inference. State predictions from a deep bidirectional LSTM are used to generate synthetic SHAPE data that can be incorporated into RNA secondary structure prediction via the Nearest Neighbor Thermodynamic Model (NNTM). This method produces predicted secondary structures for a diverse test set of 16S ribosomal RNA that are, on average, 25 percentage points more accurate than undirected MFE structures. Accuracy is highly dependent on the success of our state inference method, and investigating the global features of our state predictions reveals that accuracy of both our state inference and structure inference methods are highly dependent on the similarity of pairing patterns of the sequence to the training dataset. Availability of a large training dataset is critical to the success of this approach. Code available at https://github.com/dwillmott/rna-state-inf.

Abstract

Recently, persistent homology has had tremendous success in biomolecular data analysis. It works by examining the topological relationship or connectivity of a group of atoms in a molecule at a variety of scales, then rendering a family of topological representations of the molecule. However, persistent homology is rarely employed for the analysis of atomic properties, such as biomolecular flexibility analysis or B-factor prediction. This work introduces atom-specific persistent homology to provide a local atomic level representation of a molecule via a global topological tool. This is achieved through the construction of a pair of conjugated sets of atoms and corresponding conjugated simplicial complexes, as well as conjugated topological spaces. The difference between the topological invariants of the pair of conjugated sets is measured by Bottleneck and Wasserstein metrics and leads to an atom-specific topological representation of individual atomic properties in a molecule. Atom-specific topological features are integrated with various machine learning algorithms, including gradient boosting trees and convolutional neural network for protein thermal fluctuation analysis and B-factor prediction. Extensive numerical results indicate the proposed method provides a powerful topological tool for analyzing and predicting localized information in complex macromolecules.

Abstract

In forests, edaphic microbial communities are involved in litter decomposition and soil forming processes, with major contribution to humification, especially bacteria and fungi being responsible for the main ecosystem services fulfilled by the soil. Research has been carried out aiming to characterize the structure and diversity of microbial communities in the Rendzic Leptosols (WRB) under natural deciduous forest from Visterna, Babadag Plateau and to assess their contribution to ecosystem services provided by soil. The paper presents the results of quantitative estimations and taxonomic composition of soil and litter communities of heterotrophic bacteria and fungi, identification of cellulolytic species, as well as the microbial biomass and global physiological activities expressed as soil respiration potential. More than a half of bacterial species were common in litter and soil (SI=57.14%) and were represented by dominant species of fluorescent or non-fluorescent pseudomonads and Bacillus subtilis but no similarity was found between the two fungal communities. Fungal populations included cosmopolitan species, such as antagonists and strong cellulolytic representatives of genera Penicillium, Trichoderma, Mortierella, Chaetomium, Epicoccum, Aspergillus. Microbial density and microbial biomass presented the highest values in the litter (684 mg C x kg-1 d.s.) and in surface horizon Am1 of soil profile than in the bottom layers. The highest diversity was found in Am1 horizon (0-5 cm) H’=1.983 bits and ε=0.869 for cellulolytic community. Soil respiration reflected the intense physiological activity of microbiome, with high values associated to numerous effectives of bacteria and fungi especially in surface horizon. Microorganisms identified contribute to formation of soil by recycling of nutrients, cellulose decomposition, the synthesis of stable organic matter (humic acids), aggregation of soil particles, biological control of pathogens by antagonistic activity. They improve plant uptake of water and nutrients by forming symbioses (ectomycorrhizae), thus modelling the structure of vegetation.

Abstract

Stressful saline concentrations in soils affect photosynthesis by damaging pigments, photosystems, components of electron transport system, and enzymes involved in the process. Plants respond through very complex stress adaptation mechanisms including proteome modulation, alterations in pigment content, cell osmotic adjustment and control of ion and water homeostasis mechanisms, which stabilize cytosolic glutathione redox potential, etc. The level of plant sensitivity depends on salt toxicity levels, growth stage, physiological and genetic factors. With aim the investigation of the salinity tolerant cultivars, and for the elucidation of mechanisms underlying this complex biological process, here we analyze the impact of four NaCl concentrations (0-50-100-200mM) in growth parameters (root, shoot and leaves length), pigment content (chla, chlb, carotenoids), and GSH content, during seedling of five bread wheat (Triticum aestivum L.) cultivars in modified Hoagland solutions. Based on biometric parameters, pigment synthesis and GSH content cultivar Nogal is salt-sensitive (growth and pigments reduced); cultivar Viktoria is medium-tolerant (growth partially impaired, pigments constant), cultivar Toborzo and cultivar Suba are medium-tolerant (growth partially impaired, pigments increased), cultivar Dajti salt-tolerant (growth partially impaired/ leaves developed, pigments increased). Quantity of GSH in response to different levels of salinity is cultivar specific, and time of exposure to salinity is in negative correlation to GSH content for all investigated cultivars.

Abstract

This study aimed to investigate the effects of possible zinc (Zn) and molybdenum (Mo) contaminations on the critically endangered European Bluestar (Amsonia orientalis). The effects of Zn and Mo were tested in a dose-dependent manner on in vitro cultures. Zn at 0.1 mM in the medium inhibited root development whereas Mo showed the same effect only at ≥2.5 mM concentration. Gradual inhibition of shoot development was observed after treatment with both metals. Protein contents were also negatively affected by increasing metal concentrations, while proline levels increased gradually. Successive increases in metal concentrations resulted in higher hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentrations. The activity of the antioxidant enzymes, peroxidase (POD) and catalase (CAT), were found to be enhanced in response to increasing metal concentrations. Superoxide dismutase (SOD) activity decreased after Zn treatment but increased after Mo treatment. A marked increase in POD and CAT in response to metal stress suggests that these enzymes might have a significant cooperative role in regulating H2O2 production, although CAT, in response to drought and salt stress, has been reported to only play a supplementary role in A. orientalis. These results indicated that A. orientalis is susceptible to long-term Zn stress but can tolerate up to 2.5 mM Mo in the long-term. Deficiency of Mo is more common than high toxic concentrations in the environment. Therefore Zn contamination should be considered as one of the major threats for A. orientalis in its native habitat.

Abstract

Yarrow essential oil is used in complementary and alternative therapy for several diseases. Biological effects of essential oils span various cells and microorganisms. The aim of this study was to investigate the effects of different concentrations of the essential oil obtained from the yarrow plant (Achillea millefolium) on HeLa (CCL-2) cells. The components of the essential oil were studied by means of GC-MS analysis. Out of 10 determined compounds in the essential oil; 1,8-Cineole, Camphor, Beta-eudesmol and Camphene were found to be higher than others; and their biological effects were depicted with Ingeniuty Pathway Analysis (IPA) analysis. Moreover, cell cycle and proliferation tests were conducted on HeLa cells where yarrow plant’s essential oil was used. When extracted yarrow oil applied on HeLA Cells, apoptotic effects had been determined, furthermore proliferation of these cells decreased. In addition, activation of cell cycle control points was observed . Essential oil components could arrest the development of HeLa cells due to induction of cellular damage control mechanisms. In conclusion, we propose that the essential oil had a more repressive effect on HeLa cells, decreases their proliferation and prevented the increase in the number of cells.

Abstract

The potential use of asparaginases has gained tremendous significance in the treatment of acute lymphoblastic leukemia (ALL). Earlier studies suggest L-asparaginases (L-ASP) extracted from Escherichia coli and Erwinia aroideae regulates L-asparagine (L-Asn) from the circulating blood. Prolonged exposure to these enzymes may lead to hypersensitivity reactions. So, it is important to find novel asparaginases with anti-cancer properties. The three-dimensional structure of L-ASP I from Vibrio campbellii was determined by homology modeling using EasyModeller v.4.0. The structure was validated with quality indexing tools and was deposited in Protein Model DataBase. Molecular docking was performed between L-ASP I and ligand substrate L-Asn to study enzyme-substrate interactions. Qualitative and quantitative analysis of L-ASP I enzyme was found to be reliable and stable with a significant protein quality factor (LG score: 7.129). The enzyme is a dimer, belongs to α/β class of proteins. The active sites comprises of N-glycosylation site and a catalytic triad (T14-S117-D92). The binding energy of the docked complex was calculated to be -7.45 kcal/mol. The amino acid T14 identified as a primary nucleophile essential for catalytic reaction. The enzyme L-ASP I of V. campbellii provides a detailed view of structure and functional aspects with ligand substrate L-Asn. This in silico investigation has explicitly demonstrated for the first time that cytosolic L-ASP Type I of V. campbellii to have a catalytic triad which was attributed only to periplasmic L-ASP Type II. Thus, L-ASP I can serve as anti-leukemic agent in the treatment, management and control of ALL.

Abstract

C-terminal amidation is a common feature of wild type membrane disrupting antimicrobial peptides (AMPs). Empirical evidence suggests that this modification increases antimicrobial efficacy. However, the actual role of C-terminal amidation in the molecular mechanism of action of AMPs is not fully understood. Amidation alters two key properties simultaneously: the net charge and helicity of the peptide, both of which are implicated in the mechanism of action. However, the differences between the physicochemical properties of the carboxyl and amide moieties have been disregarded in former studies. In this study we assessed whether the difference in activity is only caused by changes in the helicity and overall charge of a peptide, i.e. whether the chemistry of the terminus is otherwise irrelevant. To do so, the membrane disrupting activity of a modified aurein 1.2 peptide was studied in which a secondary amide was formed with a terminal methyl group, instead of the primary amide as in the wild type peptide. Results of quartz crystal microbalance, dye leakage and circular dichroism experiments show that the activity of the modified peptide is substantially reduced compared to the wild type peptide, in particular that the modified peptide exhibited a much-reduced ability to bind to the membrane. Thus, the primary amide at the C-terminus is required to bind to the membrane, and a secondary amide cannot serve the same purpose. We hypothesize that this difference is related to the hydration state of the terminus. The lack of membrane binding ability of the modified peptide identifies the primary amide moiety at the C terminus as a specific membrane binding motif.

Thermodynamics of Cycling Between Coupled Reactions
Science and Technology