University of Agriculture in Krakow

This paper aims to discuss various aspects of the use of reference genes in qPCR technique used in the thousands of present studies. Most frequently, these are housekeeping genes and they must meet several criteria so that they can lay claim to the name. Lots of papers report that in different conditions, for different organisms and even tissues the basic assumption—the constant level of the expression is not maintained for many genes that seem to be perfect candidates. Moreover, their transcription can not be affected by experimental factors. Sounds simple and clear but a great number of designed protocols and lack of consistency among them brings confusion on how to perform experiment properly. Since during selection of the most stable normalizing gene we can not use any reference gene, different ways and algorithms for their selection were developed. Such methods, including examples of best normalizing genes in some specific cases and possible mistakes are presented based on available sources. Numerous examples of reference genes applications, which are usually in too few numbers in relevant articles not allowing to make a solid fundament for a reader, will be shown along with instructive compilations to make an evidence for presented statements and an arrangement of future qPCR experiments. To include all the pitfalls and problems associated with the normalization methods there is no way not to begin from sample preparation and its storage going through candidate gene selection, primer design and statistical analysis. This is important because numerous short reviews available cover the topic only in lesser extent at the same time giving the reader false conviction of complete topic recognition.

Wild and managed bees are well documented as effective pollinators of global crops of economic importance. However, the contributions by pollinators other than bees have been little explored despite their potential to contribute to crop production and stability in the face of environmental change. Non-bee pollinators include flies, beetles, moths, butterflies, wasps, ants, birds, and bats, among others. Here we focus on non-bee insects and synthesize 39 field studies from five continents that directly measured the crop pollination services provided by non-bees, honey bees, and other bees to compare the relative contributions of these taxa. Non-bees performed 25-50% of the total number of flower visits. Although non-bees were less effective pollinators than bees per flower visit, they made more visits; thus these two factors compensated for each other, resulting in pollination services rendered by non-bees that were similar to those provided by bees. In the subset of studies that measured fruit set, fruit set increased with non-bee insect visits independently of bee visitation rates, indicating that non-bee insects provide a unique benefit that is not provided by bees. We also show that non-bee insects are not as reliant as bees on the presence of remnant natural or seminatural habitat in the surrounding landscape. These results strongly suggest that non-bee insect pollinators play a significant role in global crop production and respond differently than bees to landscape structure, probably making their crop pollination services more robust to changes in land use. Non-bee insects provide a valuable service and provide potential insurance against bee population declines.

The paper provides a complex, critical assessment of heavy metal soil pollution using different indices. Pollution indices are widely considered a useful tool for the comprehensive evaluation of the degree of contamination. Moreover, they can have a great importance in the assessment of soil quality and the prediction of future ecosystem sustainability, especially in the case of farmlands. Eighteen indices previously described by several authors (Igeo, PI, EF, Cf, PIsum, PINemerow, PLI, PIave, PIVector, PIN, MEC, CSI, MERMQ, Cdeg, RI, mCd and ExF) as well as the newly published Biogeochemical Index (BGI) were compared. The content, as determined by other authors, of the most widely investigated heavy metals (Cd, Pb and Zn) in farmland, forest and urban soils was used as a database for the calculation of all of the presented indices, and this shows, based on statistical methods, the similarities and differences between them. The indices were initially divided into two groups: individual and complex. In order to achieve a more precise classification, our study attempted to further split indices based on their purpose and method of calculation. The strengths and weaknesses of each index were assessed; in addition, a comprehensive method for pollution index choice is presented, in order to best interpret pollution in different soils (farmland, forest and urban). This critical review also contains an evaluation of various geochemical backgrounds (GBs) used in heavy metal soil pollution assessments. The authors propose a comprehensive method in order to assess soil quality, based on the application of local and reference GB.

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.

Abstract Tree species can influence biogeochemistry through variation in the quantity and chemistry of their litter, and associated impacts on the soil heterotrophic community. However, the role that different plant traits play in these processes is not well understood, nor is it clear whether species effects on soils largely reflect a gymnosperm vs. angiosperm contrast. Using a replicated, long‐term monoculture plot experiment, we examined variation in soils among 14 gymnosperm and angiosperm tree species 30 years after plot establishment, and assessed the role of litter chemistry vis‐à‐vis such variation. Differences in litter calcium concentrations among tree species resulted in profound changes in soil acidity and fertility that were similar within and among tree groups. Tree species rich in calcium were associated with increased native earthworm abundance and diversity, as well as increased soil pH, exchangeable calcium, per cent base saturation and forest floor turnover rate.

Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.

The intestinal microbiome plays an important role in the metabolism of chemical compounds found within food. Bacterial metabolites are different from those that can be generated by human enzymes because bacterial processes occur under anaerobic conditions and are based mainly on reactions of reduction and/or hydrolysis. In most cases, bacterial metabolism reduces the activity of dietary compounds; however, sometimes a specific product of bacterial transformation exhibits enhanced properties. Studies on the metabolism of polyphenols by the intestinal microbiota are crucial for understanding the role of these compounds and their impact on our health. This review article presents possible pathways of polyphenol metabolism by intestinal bacteria and describes the diet-derived bioactive metabolites produced by gut microbiota, with a particular emphasis on polyphenols and their potential impact on human health. Because the etiology of many diseases is largely correlated with the intestinal microbiome, a balance between the host immune system and the commensal gut microbiota is crucial for maintaining health. Diet-related and age-related changes in the human intestinal microbiome and their consequences are summarized in the paper.

Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events. We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.

Waste from non-degradable plastics is becoming an increasingly serious problem. Therefore, more and more research focuses on the development of materials with biodegradable properties. Bio-polymers are excellent raw materials for the production of such materials. Bio-based biopolymer films reinforced with nanostructures have become an interesting area of research. Nanocomposite films are a group of materials that mainly consist of bio-based natural (e.g., chitosan, starch) and synthetic (e.g., poly(lactic acid)) polymers and nanofillers (clay, organic, inorganic, or carbon nanostructures), with different properties. The interaction between environmentally friendly biopolymers and nanofillers leads to the improved functionality of nanocomposite materials. Depending on the properties of nanofillers, new or improved properties of nanocomposites can be obtained such as: barrier properties, improved mechanical strength, antimicrobial, and antioxidant properties or thermal stability. This review compiles information about biopolymers used as the matrix for the films with nanofillers as the active agents. Particular emphasis has been placed on the influence of nanofillers on functional properties of biopolymer films and their possible use within the food industry and food packaging systems. The possible applications of those nanocomposite films within other industries (medicine, drug and chemical industry, tissue engineering) is also briefly summarized.

Abstract Over the last decades, the natural disturbance is increasingly putting pressure on European forests. Shifts in disturbance regimes may compromise forest functioning and the continuous provisioning of ecosystem services to society, including their climate change mitigation potential. Although forests are central to many European policies, we lack the long‐term empirical data needed for thoroughly understanding disturbance dynamics, modeling them, and developing adaptive management strategies. Here, we present a unique database of >170,000 records of ground‐based natural disturbance observations in European forests from 1950 to 2019. Reported data confirm a significant increase in forest disturbance in 34 European countries, causing on an average of 43.8 million m 3 of disturbed timber volume per year over the 70‐year study period. This value is likely a conservative estimate due to under‐reporting, especially of small‐scale disturbances. We used machine learning techniques for assessing the magnitude of unreported disturbances, which are estimated to be between 8.6 and 18.3 million m 3 /year. In the last 20 years, disturbances on average accounted for 16% of the mean annual harvest in Europe. Wind was the most important disturbance agent over the study period (46% of total damage), followed by fire (24%) and bark beetles (17%). Bark beetle disturbance doubled its share of the total damage in the last 20 years. Forest disturbances can profoundly impact ecosystem services (e.g., climate change mitigation), affect regional forest resource provisioning and consequently disrupt long‐term management planning objectives and timber markets. We conclude that adaptation to changing disturbance regimes must be placed at the core of the European forest management and policy debate. Furthermore, a coherent and homogeneous monitoring system of natural disturbances is urgently needed in Europe, to better observe and respond to the ongoing changes in forest disturbance regimes.

Abstract Aim Primary forests have high conservation value but are rare in Europe due to historic land use. Yet many primary forest patches remain unmapped, and it is unclear to what extent they are effectively protected. Our aim was to (1) compile the most comprehensive European‐scale map of currently known primary forests, (2) analyse the spatial determinants characterizing their location and (3) locate areas where so far unmapped primary forests likely occur. Location Europe. Methods We aggregated data from a literature review, online questionnaires and 32 datasets of primary forests. We used boosted regression trees to explore which biophysical, socio‐economic and forest‐related variables explain the current distribution of primary forests. Finally, we predicted and mapped the relative likelihood of primary forest occurrence at a 1‐km resolution across Europe. Results Data on primary forests were frequently incomplete or inconsistent among countries. Known primary forests covered 1.4 Mha in 32 countries (0.7% of Europe’s forest area). Most of these forests were protected (89%), but only 46% of them strictly. Primary forests mostly occurred in mountain and boreal areas and were unevenly distributed across countries, biogeographical regions and forest types. Unmapped primary forests likely occur in the least accessible and populated areas, where forests cover a greater share of land, but wood demand historically has been low. Main conclusions Despite their outstanding conservation value, primary forests are rare and their current distribution is the result of centuries of land use and forest management. The conservation outlook for primary forests is uncertain as many are not strictly protected and most are small and fragmented, making them prone to extinction debt and human disturbance. Predicting where unmapped primary forests likely occur could guide conservation efforts, especially in Eastern Europe where large areas of primary forest still exist but are being lost at an alarming pace.

Some environmental contaminants interact with hormones and may exert adverse consequences as a result of their actions as endocrine disrupting chemicals (EDCs). Exposure in people is typically a result of contamination of the food chain, inhalation of contaminated house dust or occupational exposure. EDCs include pesticides and herbicides (such as dichlorodiphenyl trichloroethane or its metabolites), methoxychlor, biocides, heat stabilisers and chemical catalysts (such as tributyltin), plastic contaminants (e.g. bisphenol A), pharmaceuticals (i.e. diethylstilbestrol; 17α-ethinylestradiol) or dietary components (such as phytoestrogens). The goal of this review is to address the sources, effects and actions of EDCs, with an emphasis on topics discussed at the International Congress on Steroids and the Nervous System. EDCs may alter reproductively-relevant or nonreproductive, sexually-dimorphic behaviours. In addition, EDCs may have significant effects on neurodevelopmental processes, influencing the morphology of sexually-dimorphic cerebral circuits. Exposure to EDCs is more dangerous if it occurs during specific 'critical periods' of life, such as intrauterine, perinatal, juvenile or puberty periods, when organisms are more sensitive to hormonal disruption, compared to other periods. However, exposure to EDCs in adulthood can also alter physiology. Several EDCs are xenoestrogens, which can alter serum lipid concentrations or metabolism enzymes that are necessary for converting cholesterol to steroid hormones. This can ultimately alter the production of oestradiol and/or other steroids. Finally, many EDCs may have actions via (or independent of) classic actions at cognate steroid receptors. EDCs may have effects through numerous other substrates, such as the aryl hydrocarbon receptor, the peroxisome proliferator-activated receptor and the retinoid X receptor, signal transduction pathways, calcium influx and/or neurotransmitter receptors. Thus, EDCs, from varied sources, may have organisational effects during development and/or activational effects in adulthood that influence sexually-dimorphic, reproductively-relevant processes or other functions, by mimicking, antagonising or altering steroidal actions.

Abstract Aim The EUNIS Habitat Classification is a widely used reference framework for European habitat types (habitats), but it lacks formal definitions of individual habitats that would enable their unequivocal identification. Our goal was to develop a tool for assigning vegetation‐plot records to the habitats of the EUNIS system, use it to classify a European vegetation‐plot database, and compile statistically‐derived characteristic species combinations and distribution maps for these habitats. Location Europe. Methods We developed the classification expert system EUNIS‐ESy, which contains definitions of individual EUNIS habitats based on their species composition and geographic location. Each habitat was formally defined as a formula in a computer language combining algebraic and set‐theoretic concepts with formal logical operators. We applied this expert system to classify 1,261,373 vegetation plots from the European Vegetation Archive (EVA) and other databases. Then we determined diagnostic, constant and dominant species for each habitat by calculating species‐to‐habitat fidelity and constancy (occurrence frequency) in the classified data set. Finally, we mapped the plot locations for each habitat. Results Formal definitions were developed for 199 habitats at Level 3 of the EUNIS hierarchy, including 25 coastal, 18 wetland, 55 grassland, 43 shrubland, 46 forest and 12 man‐made habitats. The expert system classified 1,125,121 vegetation plots to these habitat groups and 73,188 to other habitats, while 63,064 plots remained unclassified or were classified to more than one habitat. Data on each habitat were summarized in factsheets containing habitat description, distribution map, corresponding syntaxa and characteristic species combination. Conclusions EUNIS habitats were characterized for the first time in terms of their species composition and distribution, based on a classification of a European database of vegetation plots using the newly developed electronic expert system EUNIS‐ESy. The data provided and the expert system have considerable potential for future use in European nature conservation planning, monitoring and assessment.

This review presents the comprehensive knowledge about the bidirectional relationship between polyphenols and the gut microbiome. The first part is related to polyphenols' impacts on various microorganisms, especially bacteria, and their influence on intestinal pathogens. The research data on the mechanisms of polyphenol action were collected together and organized. The impact of various polyphenols groups on intestinal bacteria both on the whole "microbiota" and on particular species, including probiotics, are presented. Moreover, the impact of polyphenols present in food (bound to the matrix) was compared with the purified polyphenols (such as in dietary supplements) as well as polyphenols in the form of derivatives (such as glycosides) with those in the form of aglycones. The second part of the paper discusses in detail the mechanisms (pathways) and the role of bacterial biotransformation of the most important groups of polyphenols, including the production of bioactive metabolites with a significant impact on the human organism (both positive and negative).

Summary A new species of the hyphomycete genus Chalara is described. It has been frequently isolated from stems and branches and sometimes also from roots of wilting and dying Fraxinus excelsior in Poland. It differs from previously described species of Chalara by its small, short cylindrical phialoconidia extruded in chains or in slimy droplets, morphological features of the phialophores and by colony characteristics. It is non‐tolerant to cycloheximide.

Mixing of complementary tree species may increase stand productivity, mitigate the effects of drought and other risks, and pave the way to forest production systems which may be more resource-use efficient and stable in the face of climate change. However, systematic empirical studies on mixing effects are still missing for many commercially important and widespread species combinations. Here we studied the growth of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) in mixed versus pure stands on 32 triplets located along a productivity gradient through Europe, reaching from Sweden to Bulgaria and from Spain to the Ukraine. Stand inventory and taking increment cores on the mainly 60–80 year-old trees and 0.02–1.55 ha sized, fully stocked plots provided insight how species mixing modifies the structure, dynamics and productivity compared with neighbouring pure stands. In mixture standing volume (+12 %), stand density (+20 %), basal area growth (+12 %), and stand volume growth (+8 %) were higher than the weighted mean of the neighbouring pure stands. Scots pine and European beech contributed rather equally to the overyielding and overdensity. In mixed stands mean diameter (+20 %) and height (+6 %) of Scots pine was ahead, while both diameter and height growth of European beech were behind (−8 %). The overyielding and overdensity were independent of the site index, the stand growth and yield, and climatic variables despite the wide variation in precipitation (520–1175 mm year−1), mean annual temperature (6–10.5 °C), and the drought index by de Martonne (28–61 mm °C−1) on the sites. Therefore, this species combination is potentially useful for increasing productivity across a wide range of site and climatic conditions. Given the significant overyielding of stand basal area growth but the absence of any relationship with site index and climatic variables, we hypothesize that the overyielding and overdensity results from several different types of interactions (light-, water-, and nutrient-related) that are all important in different circumstances. We discuss the relevance of the results for ecological theory and for the ongoing silvicultural transition from pure to mixed stands and their adaptation to climate change.

Despite advances in antimicrobial and anti-inflammatory therapies, inflammation and its consequences still remain a significant problem in medicine. Acute inflammatory responses are responsible for directly life-threating conditions such as septic shock; on the other hand, chronic inflammation can cause degeneration of body tissues leading to severe impairment of their function. Neuroinflammation is defined as an inflammatory response in the central nervous system involving microglia, astrocytes, and cytokines including chemokines. It is considered an important cause of neurodegerative diseases, such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Lipopolysaccharide (LPS) is a strong immunogenic particle present in the outer membrane of Gram-negative bacteria. It is a major triggering factor for the inflammatory cascade in response to a Gram-negative bacteria infection. The use of LPS as a strong pro-inflammatory agent is a well-known model of inflammation applied in both in vivo and in vitro studies. This review offers a summary of the pathogenesis associated with LPS exposure, especially in the field of neuroinflammation. Moreover, we analyzed different in vivo LPS models utilized in the area of neuroscience. This paper presents recent knowledge and is focused on new insights in the LPS experimental model.

This paper demonstrates the special advantages of FT-Raman spectroscopy for in situ studies of several carotenoids that occur ubiquitously in the plant kingdom. Spectra obtained from various tissues of a range of plant species indicate that the wavenumber location of C=C stretching vibrations is mainly influenced both by the length as well as by the terminal substituents of the polyene chain of carotenoids and by their interaction with other plant constituents. The obtained results show also the usefulness of Raman spectroscopy in the investigation of cis-trans isomerization of carotenoids during processing. Additionally, 2-D Raman mappings present a unique possibility to evaluate the individual distribution of carotenoids in the intact plant tissue; in this context different 7-, 8-, and 9-double bond conjugated carotenoids can be analyzed independently in the same sample. Furthermore, the use of Raman spectroscopy for in situ detection of unstable substances such as epoxycarotenoids is discussed.

1. There are conflicting reports concerning the adaptive features of tree populations originating from cold, high‐altitude environments. We hypothesize that such trees will possess adaptive features that will be demonstrated in a common environment, such as elevated rates of net CO 2 exchange, elevated needle nitrogen concentration and high proportional biomass allocation to roots. To test this hypothesis we measured tree and seed properties of 54 populations of Norway spruce [ Picea abies (L.) Karst.] located along eight altitudinal transects (from c. 600 to 1500m) in southern Poland. We also measured growth, biomass partitioning, net photosynthetic capacity ( A max ), needle dark respiration (RS) and carbohydrate, nitrogen (N) and chlorophyll concentration of seedlings originating from these populations grown for 2 to 7 years in a common garden at 150m elevation. Measured in situ along the elevational transects, there were linear declines in seed mass, average d.b.h. and height growth increment of seed trees with increased altitude or lower mean annual temperature. 2. In the common garden, the Norway spruce populations from colder, high‐altitude habitats had higher N concentration in needles than those from low altitudes. Both A max and needle RS increased with altitude of seed origin and were significantly related to needle N concentration. High‐altitude populations also had higher concentrations of chlorophyll and carotene than those from low elevations. Despite higher photosynthetic rates in high‐altitude populations, seedling height and dry mass in the common garden declined with altitude of seed origin. Proportional dry mass partitioning to roots nearly doubled with increasing altitude of origin, while the length of the shoot‐growth period was reduced. The high respiration rates, high allocation to roots and reduced shoot‐growth period are probably responsible for the low growth rate potential of high‐altitude populations, more than offsetting their higher photosynthetic rates. 3. The results of this study showed that Norway spruce populations from cold mountain environments are characterized by several potentially adaptive features. Because these were similar to conifer population responses along a latitudinal gradient of origin, they are probably driven by climate. These climate‐driven differences were common to all transects: for a given altitude or mean annual temperature, plant traits were independent of mountain range of origin. However, populations originating from cold high‐elevation sites often differed per unit change in altitude or mean annual temperature more than did low elevation populations. The scaling of nitrogen, CO 2 exchange and biomass and allocation patterns may be useful in modelling Norway spruce response on montane forest ecosystems under changing environments.

Turcz. (Baill.) is a plant species whose fruits have been well known in Far Eastern medicine for a long time. However, schisandra seems to be a plant still underestimated in contemporary therapy still in the countries of East Asia. The article presents latest available information on the chemical composition of this plant species. Special attention is given to dibenzo cyclooctadiene lignans. In addition, recent studies of the biological activity of dibenzocyclooctadiene lignans and schisandra fruit extracts are recapitulated. The paper gives a short resume of their beneficial effects in biological systems in vitro, in animals, and in humans, thus underlining their medicinal potential. The cosmetic properties are depicted, too. The analytical methods used for assaying schisandra lignans in the scientific studies and also in industry are also presented. Moreover, special attention is given to the information on the latest biotechnological studies of this plant species. The intention of this review is to contribute to a better understanding of the huge potential of the pharmacological relevance of