Climate drove the fire cycle and humans influenced fire occurrence in the East European boreal forest

Understanding long-term forest fire histories of boreal landscapes is instrumental for parameterizing climate-fire interactions and the role of humans affecting natural fire regimes. The eastern sections of the European boreal zone currently lack a network of annually resolved and centuries-long forest fire histories. To fill in this knowledge gap, we dendrochronologically reconstructed the 600-year fire history of a middle boreal pine-dominated landscape of the southern part of the Republic of Komi, Russia. We combined the reconstruction of fire cycle (FC) and fire occurrence with the data on the village establishment and climate proxies and discussed the relative contribution of climate versus human land use in shaping historic fire regimes. Over the 1340-1610 ce period, the territory had a FC of 66 years (with the 90% confidence envelope of 56.8 and 78.6 years). Fire activity increased during the 1620-1730 ce period, with the FC reaching 32 years (31.0-34.7 years). Between 1740-1950, the FC increased to 47 years (41.9-52.0). The most recent period, 1960-2010, marks FC's historic maximum, with the mean of 153 years (102.5-270.3). Establishment of the villages, often as small harbors on the Pechora River, was associated with a non-significant increase in fire occurrence in the sites nearest the villages (p = 0.07-0.20). We, however, observed a temporal association between village establishment and fire occurrence at the scale of the whole studied landscape. There was no positive association between the former and the FC. In fact, we documented a decline in the area burned, following the wave of village establishment during the second half of the 1600s and the first half of the 1700s. The lack of association between the dynamics of FC and the dates of village establishments, and the significant association between large fire years and the early and latewood pine chronologies, used as historic drought proxy, indirectly suggests that the climate was the primary control of the landscape-level FCs in the studied forests. Pine-dominated forests of the Komi Republic may hold a unique position as the ecosystem with the shortest history of human-related shifts in fire cycles across the European boreal region

Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases

Chronic kidney disease (CKD) is a worldwide public health problem that is associated with substantial morbidity and mortality. To search for sequence variants that associate with CKD, we conducted a genome-wide association study (GWAS) that included a total of 3,203 Icelandic cases and 38,782 controls. We observed an association between CKD and a variant with 80% population frequency, rs4293393-T, positioned next to the UMOD gene (GeneID: 7369) on chromosome 16p12 (OR = 1.25, P = 4.1×10−10). This gene encodes uromodulin (Tamm-Horsfall protein), the most abundant protein in mammalian urine. The variant also associates significantly with serum creatinine concentration (SCr) in Icelandic subjects (N = 24,635, P = 1.3×10−23) but not in a smaller set of healthy Dutch controls (N = 1,819, P = 0.39). Our findings validate the association between the UMOD variant and both CKD and SCr recently discovered in a large GWAS. In the Icelandic dataset, we demonstrate that the effect on SCr increases substantially with both age (P = 3.0×10−17) and number of comorbid diseases (P = 0.008). The association with CKD is also stronger in the older age groups. These results suggest that the UMOD variant may influence the adaptation of the kidney to age-related risk factors of kidney disease such as hypertension and diabetes. The variant also associates with serum urea (P = 1.0×10−6), uric acid (P = 0.0064), and suggestively with gout. In contrast to CKD, the UMOD variant confers protection against kidney stones when studied in 3,617 Icelandic and Dutch kidney stone cases and 43,201 controls (OR = 0.88, P = 5.7×10−5)

Rapid KRAS, EGFR, BRAF and PIK3CA Mutation Analysis of Fine Needle Aspirates from Non-Small-Cell Lung Cancer Using Allele-Specific qPCR

Endobronchial Ultrasound Guided Transbronchial Needle Aspiration (EBUS-TBNA) and Trans-esophageal Ultrasound Scanning with Fine Needle Aspiration (EUS-FNA) are important, novel techniques for the diagnosis and staging of non-small cell lung cancer (NSCLC) that have been incorporated into lung cancer staging guidelines. To guide and optimize treatment decisions, especially for NSCLC patients in stage III and IV, EGFR and KRAS mutation status is often required. The concordance rate of the mutation analysis between these cytological aspirates and histological samples obtained by surgical staging is unknown. Therefore, we studied the extent to which allele-specific quantitative real-time PCR with hydrolysis probes could be reliably performed on EBUS and EUS fine needle aspirates by comparing the results with histological material from the same patient. We analyzed a series of 43 NSCLC patients for whom cytological and histological material was available. We demonstrated that these standard molecular techniques can be accurately applied on fine needle cytological aspirates from NSCLC patients. Importantly, we show that all mutations detected in the histological material of primary tumor were also identified in the cytological samples. We conclude that molecular profiling can be reliably performed on fine needle cytology aspirates from NSCLC patients

Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays

A user's guide to the Encyclopedia of DNA elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Dimensional, age and spatial structure of middle taiga post­fire pine stands on automorphic soils (on the example of Komi Republic)

The distribution of woody plants in terms of diameter and height was studied in virgin indigenous monodominant pine communities with the last fire of 5–130 years. High lability of morphometric characters of trees and undergrowth are shown. The types of age and vertical structure of stands are revealed. Both stepwise­different­aged and conditionally different­aged stands are formed under the influence of the pyrogenic factor. Pine stands have «regular top», «regular bottom» and «symmetrical» vertical structure. The horizontal structure of stands and undergrowth was interpreted based on the analysis of point processes using the pair correlation function. Trees are distributed on area randomly. We observed weak aggregation of young trees in stands on distances of 2–6 m. Both undergrowth and self­sowing are characterized by group distribution at small distances of up to 1–2 m. The direction of the displacement of the projections of the tree crowns centers relative to the bases of their trunks is ambiguous. The shift of the crown space towards the maximum solar radiation was detected in thinned stand with high age and big size of trees. In other types of pine forests no one­sided orientation of tree crown development was revealed. The position of the tree crowns centers on the plot shows the same spatial distribution as the base of the trunks. In phytocenoses with the presence of a young generation of trees, the effect of «convergence» of crowns is manifested due to the inclination of their thin and elongated trunks under snow pressure. It leads to a denser structure of the distribution of projections of crown centers in comparison with the position of the bases of the trunks of young trees on the plots

Biological productivity of the naturally developing and disturbed by windfall lichen pine forest (Komi Republic)

The evidence characterizing the changes in the structural organization and productivity of the post-windfall middle-taiga lichen pine forest growing in the Northern Ural region are presented. It is shown that the stand after the windfall changes from a relatively uneven age with demutative phases of the dynamics of the age structure type to a conditionally uneven age. Pine undergrowth in both the background and disturbed areas is characterized as «healthy». It has been established that with an increase in the height of undergrowth, the number of individuals of the oppressed categories decreases. It was revealed that in naturally developing lichen pine forests of the same age, the morphometric indicators of trees (diameter, height), the reserves of organic matter of phytocenoses are higher than in post-windfall pine stand. A comparative analysis is made of the accumulation of the deposition of plant organic matter of naturally developing and post-windfall pine forests. Ten years after the windfall in the lichen pine forest, 91.8 t ha–1 of phytomass is concentrated, which is 1.4 times less than in the background pine forest. Ten years after the windfall, the bulk of organic matter is concentrated in large tree residues, whereas in naturally growing cenosis in growing trees, the annual production of phytomass of disturbed pine trees is 1.9 times less than in the background, makes up 1019 kg ha–1. The accumulation of phytomass production in the post-windfall lichen pine forest is equivalent to the role of woody plants and plants of ground cover, whereas in the background pine forest the main role is played by woody plants. It was revealed that after windfall there was a decrease in the participation of lichens and an increase in the participation of shrubs and mosses in the formation of ground cover. Annually, the decomposition constants of large wood residues in the windfall were 0.02 year–1

Spatial interrelations in the placement of woody plants in the middle taiga virgin spruce forests of the upper reaches of the Pechora river

Investigation was carried out in virgin spruce forests in the upper reaches of the Pechora river in middle taiga condition. It was show that spruce forests of different types are characterized by common features of the structure of stands and undergrowth. There was a large variability of trees in volume of stem and undergrowth height. Investigated stands formed a cyclical-multi-age type of age structure. The calculated data obtained using spatial statistics and analyses of point processes were presented. It was found that in spruce forests is expressed regardless of forest types, the group distribution of young individuals of woody plants, which passes into random distribution at more late stages of generation. The spatial relationships between woody plants tested using the cross-correlation function gij(r) show that the undergrowth is attracted to each other at distances of up to 1 meter. There were no spatial interrelation between the undergrowth and the trees. Trees demonstrated independent from each other placement in the area. The density of trees in the area and their phytosocial status are determining the intensity of competitive relations between woody plants in the indigenous spruce communities of the upper reaches of the Pechora River

Tree plant organic matter stocks in spruce green moss Piceetum hylocomiosum and pine lichen Pinetum cladinosum forest communities after windfall

Accumulation of organic matter in spruce green moss Piceetum hylocomiosum and pine lichen Pinetum cladinosum forest communities after windfall was investigated. Phytomass of Piceetum hylocomiosum stand is 51.8 t • ha-1, and Pinetum cladinosum stand is 7.5 t • ha-1. Phytomass in the disturbed stands is 3.5 times less than in undisturbed spruce forest and 15 times less than in undisturbed pine forest. The undergrowth accumulates 2.8 t • ha-1 in spruce forest, and 0.9 t • ha-1 in pine forest after windfall. Number of trees, volume of wood, stock of organic matter was determined in coarse woody debris subject to decay class. Most of the dead trees (77–97 %) belong to the second decay class. Reduced competition for light and mineral nutrients influences the intensity of organic matter accumulation by tree plants. We detected that increasing radial growth of spruce and fir began before windfall. This demonstrates the stand drying. However, maximal rate of annual ring increment (2.03–2.17 mm for spruce and 3.98–4.07 mm for fir) was observed in 2009–2010 years. After windfall radial growth of undergrowth increased 2 times in Piceetum hylocomiosum and 7.7 times in Pinetum cladinosum. Height increment of spruce and fir understorey increased 2.2–2.6 times in spruce forest. As compared with undisturbed ecosystems height increment of pine understorey is 1.2–2.0 times higher on windbreak in Pinetum cladinosum

ORGANIZATIONAL AND TECHNOLOGICAL SYSTEM OF ENERGY SUPPLY AND ENERGY CONSUMPTION (OTS "ENERGY")

The features of the organizational and technological systems of energy supply and energy use in manufacturing are investigated. The conceptual framework for OTS "Energy" is defined. The structure of the organizational and technological problems of the control system is defined