MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry.

Oligonucleotide therapeutics have emerged as an important class of drugs offering targeted therapeutic strategies that complement traditional modalities, such as monoclonal antibodies and small molecules. Their unique ability to precisely modulate gene expression makes them vital for addressing previously undruggable targets. A critical aspect of developing these therapies is characterizing their molecular composition accurately. This includes determining the monoisotopic mass of oligonucleotides, which is essential for identifying impurities, degradants, and modifications that can affect the drug efficacy and safety. Mass spectrometry (MS) plays a pivotal role in this process, yet the accurate interpretation of complex mass spectra remains challenging, especially for large molecules, where the monoisotopic peak is often undetectable. To address this issue, we have adapted the MIND algorithm, originally developed for top-down proteomics, for use with oligonucleotide data. This adaptation allows for the prediction of monoisotopic mass from the more readily detectable, most-abundant peak mass, enhancing the ability to annotate complex spectra of oligonucleotides. Our comprehensive validation of this modified algorithm on both in silico and real-world oligonucleotide data sets has demonstrated its effectiveness and reliability. To facilitate wider adoption of this advanced analytical technique, we have encapsulated the enhanced MIND algorithm in a user-friendly Shiny application. This online platform simplifies the process of annotating complex oligonucleotide spectra, making advanced mass spectrometry analysis accessible to researchers and drug developers. The application is available at https://valkenborg-lab.shinyapps.io/mind4oligos/.

The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity.

Organic debris accumulated in bird nests creates a unique environment for organisms, including microbes. Built from various plant materials that are typically enriched by animal residues, bird nest favours the development of various fungal groups. The aim of this study was to investigate the chemical properties of the material deposited in the white stork Ciconia ciconia nests and the link between extracellular enzyme activity and the diversity and composition of culturable fungi. Our findings revealed low C/P and N/P ratio values in the nest materials, which indicate a high P availability. Nest material C/N/P ratio ranged from 67/8/1 to 438/33/1. Enzymatic activity strongly correlated with the content of carbon, nitrogen, and pH of the material deposited in the nests. A total of 2726 fungal isolates were obtained from the nests, from which 82 taxa were identified based on morphology and DNA sequence data. The study indicates that white stork nests are microhabitat characterised by diverse chemical and biochemical properties. We found relationship between the fungal richness and diversity and the C/P and N/P ratios of materials from the nests. Our study showed that culturable fungi occurred frequently in materials with high levels of C, N, and P, as well as high concentrations of base alkaline elements (Ca, Mg, and K).

Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts.

1H NMR spectroscopy is a powerful tool for analyzing mixtures including determining the concentrations of individual components. When signals from multiple compounds overlap, this task requires computational solutions. They are typically based on peak-picking and the comparison of obtained peak lists with libraries of individual components. This can fail if peaks are not sufficiently resolved or when peak positions differ between the library and the mixture. In this paper, we present Magnetstein, a quantification algorithm rooted in the optimal transport theory that makes it robust to unexpected frequency shifts and overlapping signals. Thanks to this, Magnetstein can quantitatively analyze difficult spectra with the estimation trueness an order of magnitude higher than that of commercial tools. Furthermore, the method is easier to use than other approaches, having only two parameters with default values applicable to a broad range of experiments and requiring little to no preprocessing of the spectra.

Profile of tree-related microhabitats in the primeval Bialowieza Forest: A benchmark for temperate woodlands.

Tree-related Microhabitats (TreMs) are a key structural element having a significant impact on the biodiversity and functioning of forest ecosystems. Although forests enjoying long-term protection host richer and more abundant TreMs compared to managed stands, the quantity and quality of such microstructures in primeval temperate forests are unknown. This study investigates for the first time the assemblage of TreMs in the Bialowieza Forest (BF), which is regarded as the last surviving fragment of pristine lowland forests in the temperate zone of Europe. Relatively undisturbed by human activity since the last glacial period, the BF ecosystem has remained remarkably intact, which may have given rise to its unique TreM assemblage. Here, we show that a primeval forest is characterized by an exceptionally high richness and density of TreMs compared to previously studied natural forests, and that the richness, density and diversity of TreMs are spatially heterogeneous at the micro-scale but homogeneous at the macro-scale. This indicates that adjacent small fragments of habitat (0.05 ha) may have different TreM profiles, but large patches of forest (several ha) host similar assemblages of TreMs. Our profile of TreMs depends on the basal area and density of living trees, the basal area of dead standing trees and the dominance of specific TreM-hosting tree species in a stand. Our study suggests that both the ecological continuity and complexity of a forest supporting many different tree species and the diversity of TreM-forming biota that typically occurs in primeval temperate forests are factors that appear to contribute to the observed profile of TreMs. The results of our study set a benchmark for the quantity and quality of TreMs in broadleaved temperate forests and indicate that the long-term spontaneous natural processes occurring in primeval forests lead to the emergence of ultra-rich, complex assemblages of TreMs.

Trapalyzer: a computer program for quantitative analyses in fluorescent live-imaging studies of neutrophil extracellular trap formation.

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require large, manually-prepared training data sets, are difficult to use for users without background in computer science, or have limited capabilities. To overcome these problems, we developed Trapalyzer, a computer program for automatic quantification of NETs. Trapalyzer analyzes fluorescent microscopy images of samples double-stained with a cell-permeable and a cell-impermeable dye, such as the popular combination of Hoechst 33342 and SYTOX™ Green. The program is designed with emphasis on software ergonomy and accompanied with step-by-step tutorials to make its use easy and intuitive. The installation and configuration of the software takes less than half an hour for an untrained user. In addition to NETs, Trapalyzer detects, classifies and counts neutrophils at different stages of NET formation, allowing for gaining a greater insight into this process. It is the first tool that makes this possible without large training data sets. At the same time, it attains a precision of classification on par with state-of-the-art machine learning algorithms. As an example application, we show how to use Trapalyzer to study NET release in a neutrophil-bacteria co-culture. Here, after configuration, Trapalyzer processed 121 images and detected and classified 16 000 ROIs in approximately three minutes on a personal computer. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer.

Eurasian beaver - A semi-aquatic ecosystem engineer rearranges the assemblage of terrestrial mammals in winter.

There is increasing awareness of the ecosystem engineering services provided by recovering populations of Eurasian beaver. By modifying aquatic environments, this species has a significant, positive influence on biodiversity. Beaver activity affects not only aquatic ecosystems but also terrestrial habitats and organisms. Our study compares and evaluates the species richness and activity of terrestrial mammals in winter at beaver ponds (N = 65) and randomly-selected reference sites along nearby watercourses unmodified by beavers (N = 65) in Poland (central Europe). Mammal assemblages were investigated near pond/watercourse edges, and also at some distance from them. The species richness of mammal and numbers of their tracks were respectively 25% and 33% greater on the beaver than on the reference sites. The higher species richness on beaver sites extended to areas 40-60 m distant from ponds, devoid any signs of beaver activity. Twenty-three mammal species were recorded on beaver sites (mean species richness 3.8 ± 1.6 SD), and 20 on reference ones (3.0 ± 1.5 SD). The numbers of tracks of grey wolf, least weasel and European polecat were higher on beaver than reference sites. Mammal species richness and activity were related to the existence of beaver ponds, but were also correlated with the numbers of snags and coverage of grass, bramble and coniferous saplings in neighbouring terrestrial habitats. Large and small carnivores occurred more frequently and were more active on beaver sites. The frequencies of occurrence of mesocarnivores, mesoherbivores and small herbivores were correlated with habitat characteristics, regardless of whether beavers were present or not. Our results highlight the fact that both pond creation and the habitat changes resulting from the presence of beavers rearrange the occurrence and activity of the terrestrial mammal assemblage.

Tree microhabitats in natural temperate riparian forests: An ultra-rich biological complex in a globally vanishing habitat.

Tree-related microhabitats (TreMs) are among the most important structural components of a forest, and have a significant impact on biodiversity and influence ecosystem functioning. Although forests that depend on natural lowland water regimes are severely endangered worldwide, and floodplain forests are considered to be the most complex and biologically rich habitats in the temperate zone, the TreMs in them have yet to be identified. This study investigates the assemblage of TreMs in natural Willow-Poplar riparian forests and analyses the environmental factors that influence their qualitative and quantitative compositions. A total of 90 sample plots (0.05 ha each) were selected at random in old-growth riparian forests that occur along a large unregulated river, the Vistula (Poland). A total of 62 TreM types were identified with a mean number of 16.0 ± 4.6 SD TreM types per plot and a mean density of 829.4 ± 360.1 SD TreM-bearing trees ha-1. The number of TreMs found on an individual tree depends on its diameter, the number of trunks, its living status (living vs. dead tree) and the species it belongs to. The richness, density and diversity of TreMs found on a plot depends on the density of living trees, the basal area of living or dead trees, the number of tree species, and the percentage of Willows Salix sp. or of multi-trunk trees. Our study records for the first time the assemblage of TreMs in natural Willow-Poplar riparian forests and provides a reference for floodplain habitats. The results indicate that multi-species forests influenced by natural waterflow-related disturbances are hot-spots of TreM richness and abundance, and highlight the urgent need for the protection or restoration of these vanishing habitats.

Harvest time affects antioxidant capacity, total polyphenol and flavonoid content of Polish St John's wort's (Hypericum perforatum L.) flowers.

The polyphenol content and antioxidant capacity of hyperforin and hypericin-standardized H. perforatum L. extracts may vary due to the harvest time. In this work, ethanol and ethanol-water extracts of air-dried and lyophilized flowers of H. perforatum L., collected throughout a vegetation season in central Poland, were studied. Air-dried flowers extracts had higher polyphenol (371 mg GAE/g) and flavonoid (160 mg CAE/g) content, DPPH radical scavenging (1672 mg DPPH/g), ORAC (5214 µmol TE/g) and FRAP (2.54 mmol Fe2+/g) than lyophilized flowers extracts (238 mg GAE/g, 107 mg CAE/g, 1287 mg DPPH/g, 3313 µmol TE/g and 0.31 mmol Fe2+/g, respectively). Principal component analysis showed that the collection date influenced the flavonoid and polyphenol contents and FRAP of ethanol extracts, and DPPH and ORAC values of ethanol-water extracts. The ethanol extracts with the highest polyphenol and flavonoid content protected human erythrocytes against bisphenol A-induced damage. Both high field and benchtop NMR spectra of selected extracts, revealed differences in composition caused by extraction solvent and raw material collection date. Moreover, we have shown that benchtop NMR can be used to detect the compositional variation of extracts if the assignment of signals is done previously.

Biological and physicochemical properties of the nests of White Stork Ciconia ciconia reveal soil entirely formed, modified and maintained by birds.

The physiological and behavioural activities of animals have far-reaching impacts on the characteristics and functioning of soil. This includes vertebrates, which are capable of modifying the physicochemical and biochemical properties of soil. To date, however, no species is known to be responsible for the entire process of soil formation, modification and maintenance. Large-bodied birds build nests which they then use for several years or even decades. During nest construction or renovation, birds gather and transport to the nesting site organic and mineral matter that includes tree branches of various sizes, twigs, turf, straw and hay. Over time, during subsequent breeding events, adult birds supply further loads of organic matter to the nest, such as food remains, excrement, pellets, feathers, egg shells and other materials. Taking the White Stork Ciconia ciconia as an example, we have shown that the materials deposited in the nests of large-bodied birds gradually produce ornithogenic soils over the years, with distinguishable layers having different physicochemical characteristics and biochemical activities. The tested nesting substrate met the criteria for ornithogenic material; the layers had appropriate thickness and phosphorus pentoxide (P2O5) content. Results of the study indicates that the material contained in White Stork nests have the characteristics of Histosols. Moreover, such nests harbour assemblages of fungi and arthropods that contain species typical of soil mycobiota and fauna, respectively. This study is the first to describe a soil that is formed, modified and maintained entirely by vertebrates and is physically isolated from the ground. Our results highlight the fact that the nests of large birds are unique structures in ecosystems and provide a habitat for a rich and diverse assemblage of organisms.

Global relationships between tree-cavity excavators and forest bird richness.

Global monitoring of biodiversity and ecosystem change can be aided by the effective use of indicators. Tree-cavity excavators, the majority of which are woodpeckers (Picidae), are known to be useful indicators of the health or naturalness of forest ecosystems and the diversity of forest birds. They are indicators of the latter due to shared associations with particular forest elements and because of their role in facilitating the occurrence of other species through the provision of nesting cavities. Here, we investigated whether these positive correlations between excavators and other forest birds are also found at broad geographical scales. We used global distribution maps to extract richness estimates of tree-cavity nesting and forest-associated birds, which we grouped by zoogeographic regions. We then created generalized least-squares models to assess the relationships between these groups of birds. We show that richness of tree-cavity excavating birds correlates positively with that of secondary cavity nesters and other forest birds (generalists and specialists) at global scales, but with variation across zoogeographic regions. As many excavators are relatively easy to detect, play keystone roles at local scales and are effective management targets, we propose that excavators are useful for biodiversity monitoring across multiple spatial scales and geographical regions, especially in the tropics.

Masserstein: Linear regression of mass spectra by optimal transport.

RATIONALE: The linear regression of mass spectra is a computational problem defined as fitting a linear combination of reference spectra to an experimental one. It is typically used to estimate the relative quantities of selected ions. In this work, we study this problem in an abstract setting to develop new approaches applicable to a diverse range of experiments. METHODS: To overcome the sensitivity of the ordinary least-squares regression to measurement inaccuracies, we base our methods on a non-conventional spectral dissimilarity measure, known as the Wasserstein or the Earth Mover's distance. This distance is based on the notion of the cost of transporting signal between mass spectra, which renders it naturally robust to measurement inaccuracies in the mass domain. RESULTS: Using a data set of 200 mass spectra, we show that our approach is capable of estimating ion proportions accurately without extensive preprocessing of spectra required by other methods. The conclusions are further substantiated using data sets simulated in a way that mimics most of the measurement inaccuracies occurring in real experiments. CONCLUSIONS: We have developed a linear regression algorithm based on the notion of the cost of transporting signal between spectra. Our implementation is available in a Python 3 package called masserstein, which is freely available at https://github.com/mciach/masserstein.

Human-induced environmental changes influence habitat use by an ungulate over the long term.

Habitat use and preferences may be subject to spatial and temporal changes. However, long-term studies of species-habitat relationships are the exception. In the present research, long-term trends in habitat use by an alpine ungulate, the Tatra chamois Rupicapra rupicapra tatrica, were analyzed. We examined how environmental changes attributable to climate change, removal of sheep, and habituation to hikers, which took place over the last half-century have changed the spatial distribution of animals. Data on the localities of groups sighted between 1957 and 2013 during autumnal population surveys were used to evaluate habitat associations: these were correlated with year, group size, population size, and climatic conditions. The results indicate that the Tatra chamois is tending, over the long term, to lower its altitude of occurrence, reduce its average distance to hiking trails, and stay less often on slopes with a southerly aspect. These trends are independent of group size, population size, and the weather conditions prevailing during observations, though not for altitude, where increases in air temperature are related to finding chamois at higher elevations. The proportion of alpine meadows and slope in the places used by chamois is correlated with population size, while the proportion of areas with trees and/or shrubs is correlated with group size and air temperature, though long-term changes were not evident for these variables. To the best of our knowledge, this work is the first to document long-term trends in habitat use by ungulates. It shows that a species' ecology is influenced by human-induced changes: abandonment of pasturage, high-mountain tourism, and climate changes, which constitute the most probable reasons for this aspect of behavioral evolution in the Tatra chamois.

Nocturnal noise and habitat homogeneity limit species richness of owls in an urban environment.

Habitat loss and fragmentation are listed among the most significant effects of urbanization, which is regarded as an important threat to wildlife. Owls are the top predators in most terrestrial habitats, and their presence is a reliable indicator of ecosystem quality and complexity. However, influence of urbanization on owl communities, anthropogenic noise in particular, has not been investigated so far. The aim of this study was to identify the role of noise and landcover heterogeneity in the species richness of owl assemblage in the urban ecosystem. Owls were surveyed in the city of Kraków (southern Poland) on 65 randomly selected sample plots (1 km2). The area of main landcover types, landcover diversity index, mean size of landcover patch, and nocturnal noise level were defined within the sample plots and correlated with owl species richness. Five owl species were recorded in the study area with forests as the dominant landcover type for Tawny and Ural owls, grasslands for Long-eared and Barn owls, and gardens for Little owls. In total, 52% of sample plots were occupied by at least one species (1-3 species per plot). The number of owl species was positively correlated with landcover diversity index and negatively correlated with nocturnal noise emission. This study demonstrates that species richness of owls in urban areas may be shaped by landcover heterogeneity and limited by noise intensity. This indicates that noise changes top predator assemblage, which in consequence may disturb predator-prey interactions within human-transformed habitats.

Noise shapes the distribution pattern of an acoustic predator.

Noise, an obvious effect of urbanization, has a negative impact on animal vocalizations and the hunting efficiency of acoustic predators. However, the influence of noise pollution on the spatial distribution of populations remains understudied. The aim was to assess the factors shaping the distribution pattern of an acoustic predator (long-eared owl Asio otus) in an urban-farmland matrix. We hypothesized that the probability of an acoustic predator occurring decreases with growing nocturnal noise emission. This owl survey was conducted in Kraków (S Poland) on 79 randomly selected sample plots (1 km × 1 km). Six habitat variables (area of parks, woodlands, grassland, arable land, habitat diversity index, and noise pollution) were identified and correlated with the probability of the species' occurrence. Proximity to pedestrian routes and roads, habitat fragmentation, and noise intensity was also defined at nest sites and random sites. Long-eared owls occurred on 37% of the sample plots. Occupied plots had a greater area of grassland and arable land as well as a lower level of noise pollution than the unoccupied ones. A multivariate model revealed that area of grassland and nocturnal noise emission was significantly correlated with the probability of long-eared owls occurring and that the high probability of occurrence recorded on plots with large areas of grassland was reduced by noise pollution. The noise intensity recorded at nest sites was also significantly lower than at random sites. This study suggests that apart from habitat factors, the distribution of acoustic predators in an urban matrix is driven by noise pollution. This highlights the importance of proper landscape management, that is, maintaining large grassland areas and preventing noise from increasing within them.

Impact of climate on the population dynamics of an alpine ungulate: a long-term study of the Tatra chamois Rupicapra rupicapra tatrica.

Global warming is considered as a phenomenon having a negative effect on animals living in cold climate. However, herbivorous species inhabiting cold zones may potentially benefit from increase of temperature as this influence duration of vegetation period and increase food resources. In this study, we analyze the impact of climate factors on the long-term dynamics of an isolated and unhunted population of the Tatra chamois Rupicapra rupicapra tatrica. The population growth rate, based on autumnal chamois counting carried out from 1957 to 2016, were correlated with a set of climatic variables. We tested the hypothesis that high temperatures in summer could have a positive impact on the population, since they influence vegetation growth, which ensure food resources. On the other hand, heavy falls of snow and long-lasting and deep snow cover could adversely affect the population by reducing population survival during the winter. The results of this study indicate that climatic variables best explaining the autoregressed population growth rate (from the autumn of year t-1 to the autumn of year t) were the mean summer temperature of year t-1: the population increase was greater following a warmer summer in year t-1 and, in lower extent, the total precipitation during winter: the population decrease was greater following a winter with heavy snowfall. Duration and thickness of snow cover have no negative effect on population growth rate. The results indicate that the population dynamic of the Tatra chamois is determined in the long term by weather conditions, mainly by temperature, when kids are birthing and growing. The results of this work highlight that climatic changes may be responsible for the population dynamic of high-mountain species. Climate warming may lead to increase in duration of vegetation period in cold climatic zones, what may in turn have positive effect on herbivorous species, which relay upon food resources limited by low temperatures within vegetation period.

Locus-aware decomposition of gene trees with respect to polytomous species trees.

BACKGROUND: Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values. RESULTS: We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification. CONCLUSIONS: Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https://github.com/mciach/LocusTreeInference.

Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry.

Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information for sequence and structure analyses. In this study, we propose a formal mathematical model of the ETD fragmentation process in the form of a system of stochastic differential equations describing its joint dynamics. Parameters of the model correspond to the rates of occurring reactions. Their estimates for various experimental settings give insight into the dynamics of the ETD process. We estimate the model parameters from the relative quantities of fragmentation products in a given mass spectrum by solving a nonlinear optimization problem. The cost function penalizes for the differences between the analytically derived average number of reaction products and their experimental counterparts. The presented method proves highly robust to noise in silico. Moreover, the model can explain a considerable amount of experimental results for a wide range of instrumentation settings. The implementation of the presented workflow, code-named ETDetective, is freely available under the two-clause BSD license.

From Agricultural Benefits to Aviation Safety: Realizing the Potential of Continent-Wide Radar Networks.

Migratory animals provide a multitude of services and disservices-with benefits or costs in the order of billions of dollars annually. Monitoring, quantifying, and forecasting migrations across continents could assist diverse stakeholders in utilizing migrant services, reducing disservices, or mitigating human-wildlife conflicts. Radars are powerful tools for such monitoring as they can assess directional intensities, such as migration traffic rates, and biomass transported. Currently, however, most radar applications are local or small scale and therefore substantially limited in their ability to address large-scale phenomena. As weather radars are organized into continent-wide networks and also detect "biological targets," they could routinely monitor aerial migrations over the relevant spatial scales and over the timescales required for detecting responses to environmental perturbations. To tap these unexploited resources, a concerted effort is needed among diverse fields of expertise and among stakeholders to recognize the value of the existing infrastructure and data beyond weather forecasting.

Urbanization affects neophilia and risk-taking at bird-feeders.

Urban environments cover vast areas with a high density of humans and their dogs and cats causing problems for exploitation of new resources by wild animals. Such resources facilitate colonization by individuals with a high level of neophilia predicting that urban animals should show more neophilia than rural conspecifics. We provided bird-feeders across urban environments in 14 Polish cities and matched nearby rural habitats, testing whether the presence of a novel item (a brightly coloured green object made out of gum with a tuft of hair) differentially delayed arrival at feeders in rural compared to urban habitats. The presence of a novel object reduced the number of great tits Parus major, but also the total number of all species of birds although differentially so in urban compared to rural areas. That was the case independent of the potentially confounding effects of temperature, population density of birds, and the abundance of cats, dogs and pedestrians. The number of great tits and the total number of birds attending feeders increased in urban compared to rural areas independent of local population density of birds. This implies that urban birds have high levels of neophilia allowing them to readily exploit unpredictable resources in urban environments.