FLCN,a novel autophagy component,interacts with GABARAP and is regulated by ULK1 phosphorylation

Birt-Hogg-Dubé (BHD) syndrome is a rare autosomal dominant condition caused by mutations in the FLCN gene and characterized by benign hair follicle tumors, pneumothorax, and renal cancer. Folliculin (FLCN), the protein product of the FLCN gene, is a poorly characterized tumor suppressor protein, currently linked to multiple cellular pathways. Autophagy maintains cellular homeostasis by removing damaged organelles and macromolecules. Although the autophagy kinase ULK1 drives autophagy, the underlying mechanisms are still being unraveled and few ULK1 substrates have been identified to date. Here, we identify that loss of FLCN moderately impairs basal autophagic flux, while re-expression of FLCN rescues autophagy. We reveal that the FLCN complex is regulated by ULK1 and elucidate 3 novel phosphorylation sites (Ser406, Ser537, and Ser542) within FLCN, which are induced by ULK1 overexpression. In addition, our findings demonstrate that FLCN interacts with a second integral component of the autophagy machinery, GABA(A) receptor-associated protein (GABARAP). The FLCN-GABARAP association is modulated by the presence of either folliculin-interacting protein (FNIP)-1 or FNIP2 and further regulated by ULK1. As observed by elevation of GABARAP, sequestome 1 (SQSTM1) and microtubule-associated protein 1 light chain 3 (MAP1LC3B) in chromophobe and clear cell tumors from a BHD patient, we found that autophagy is impaired in BHD-associated renal tumors. Consequently, this work reveals a novel facet of autophagy regulation by ULK1 and substantially contributes to our understanding of FLCN function by linking it directly to autophagy through GABARAP and ULK1.     

Optimization and clinical validation of a pathogen detection microarray

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.     

The effect of low temperatures on fatty acid composition of crops with different cold resistance

The study was focused on fatty acid (FA) composition of lipids from the seedlings and roots of crops having different cold resistance and grown at 27°C or 4°C. Biosynthesis of FA in the lipids of seedlings and roots of cold-susceptible maize (Zea mays L.) at both growth temperatures was controlled by chloroplast ω6 desaturase and microsomal ω6 desaturase, respectively. The content of linoleic acid was 56.2% and 43.3% in the coleoptiles of maize seedlings grown at 4 and 27°C, respectively, and in the roots it was 52.2% and 38.5%, respectively. The content of α-linolenoic acid in the coleoptiles was 6.7–6.8% at both temperatures, while in the root lipids it was higher at low temperature (3.15% at 27°C vs. 4.7% at 4°C). FA biosynthesis in the seedling coleoptiles of wheat (Triticum aestivum L.) and Siberian wild rye (Elymus sibiricus L.) grown at low temperature was controlled by the chloroplast ω3 desaturase. A minor increase in the content of α-linolenoic acid was observed at low temperature: 29.7% to 30.2% in wheat and 22.8% to 25.8% in wild rye. In the root tissues of these species, the biosynthesis of α-linolenoic acid was controlled by the microsomal ω3 desaturase. The content of α-linolenoic acid was higher at low temperature: in wheat it was 6.1% at 27°C and 17.1%, and 4°C, while in Siberian wild rye, 7.1% and 12.0% at 4 and 27°C, respectively.     

Diatoms of modern bottom sediments in Siberian arctic

The investigation of the species composition and ecology of diatoms of modern bottom sediments in water bodies of arctic polygonal tundra in three subregions of North Yakutiya has been carried out. As a result, 161 taxons of diatoms were determined; the determinant role of the depth, conductivity, pH of the water, and geographic latitude in their distribution was confirmed, and two complexes of species with respect to the leading abiotic factors were distinguished. The diatoms of the first complex prefer shallow water bodies of high latitudes with neutral and slightly alkaline water and relatively high conductivity. The second complex is confined to the water bodies of lower latitudes with small conductivity, as well as neutral and slightly acidic water.     

Dynamics of morphophysiological charateristics in female water voles (Arvicola amphibius L.) during pregnancy

Pregnancy and lactation need increased energy consumption and are accompanied by morphological and physiological changes of various maternal organs and systems. In water voles, connection of female interior characteristics has been poorly studied. Under standard vivarium conditions, we evaluated morphophysiological parameters of non-reproducing females and of females at the early (1–7 days), intermediate (8–14 days), and late (15–21 days) stages of pregnancy. There were established effect of the reproductive state on mass of abdominal and brown adipose tissue, liver, adrenals, spleen and an increment of body mass (without uterus with embryos). In pregnant females, as compared with the non-pregnant ones, the blood thyroxine level was significantly lower (16.2 ± 0.8 and 21.7 ± 1.4 pmol/l) and the blood testosterone level was higher (1.29 ± 0.19 and 0.83 ± 0.09 nmol/l). The blood glucose content fell in the end of pregnancy. Dynamics of morphophysiological parameters at the period of pregnancy reflects the compensatory body reactions providing preservation of embryos and preparation to lactation of offspring.     

Metal cofactors play a dual role in Mycobacterium tuberculosis inorganic pyrophosphatase

Inorganic pyrophosphatase from Mycobacterium tuberculosis (Mt-PPase) is one of the possible targets for the rational design of anti-tuberculosis agents. In this paper, functional properties of this enzyme are characterized in the presence of the most effective activators--Mg2+ and Mn2+. Dissociation constants of Mt-PPase complexed with Mg2+ or Mn2+ are essentially similar to those of Escherichia coli PPase. Stability of a hexameric form of Mt-PPase has been characterized as a function of pH both for the metal-free enzyme and for Mg2+- or Mn2+-enzyme. Hexameric metal-free Mt-PPase has been shown to dissociate, forming monomers at pH below 4 or trimers at pH from 8 to 10. Mg2+ or Mn2+ shift the hexamer-trimer equilibrium found for the apo-Mt-PPase at pH 8-10 toward the hexameric form by stabilizing intertrimeric contacts. The pK(a) values have been determined for groups that control the observed hexamer-monomer (pK(a) 5.4), hexamer-trimer (pK(a) 7.5), and trimer-monomer (pK(a) 9.8) transitions. Our results demonstrate that due to the non-conservative amino acid residues His21 and His86 in the active site of Mt-PPase, substrate specificity of this enzyme, in contrast to other typical PPases, does not depend on the nature of the metal cofactor.     

DNA complexes with polycations used for delivery of DNA into cells

The formation and physicochemical properties of high-molecular thymus and plasmid DNA complexes with synthetic polymers based on (dimethyl-amino)ethyl methacrylate (DMAEM), (diethyl-amino)ethyl methacrylate (DEAEM), and polyvinyl amine (PVA) were investigated in solutions of different ionic strength by low-gradient viscometry, electrophoresis, circular dichroism, spectrophotometry, and dynamic light scattering. The toxicity of complexes in T98G cells was studied. It was shown that, when the ratio of polycations to DNA charged groups concentration (N+/P) reaches values > 1, DNA condensation occurs. It is accompanied by increasing optical density of solutions. Changes in DNA size after condensation were estimated. Phase diagrams of systems DNA/polycation in the presence of NaCl were obtained. It was shown by MTT-analysis that DNA complexes with polycations in the range of concentrations used have low toxicity.     

Reconstruction of palaeoecological and palaeoclimatic conditions of the Holocene in the south of the Taimyr according to an analysis of lake sediments

A sediment core from Khatanga-12 Lake (Taimyr Peninsula, Krasnoyarsk krai) has been studied. The 131.5-cm-long core covers ca. 7100 years of sedimentation. Chironomid analysis, a qualitative reconstruction of the paleoenvironment in the region, and a quantitative reconstruction of variations of the mean July air temperature and in the water depth of the lake have been performed using Northern Russia chironomid-inferred mean July temperature models (Nazarova et al., 2008, 2011, 2015). Khatanga-12 Lake was formed during the Middle Holocene warming as a result of thermokarst processes. The development of the lake ecosystem at different stages of its development was influenced by climatic and cryolithogenic factors. The Middle Holocene warming, which occurred around 7100–6250 cal. years BP, activated thermokarst processes and resulted in the formation of the lake basin. Later, between 6250 and 4500 cal. years BP, a period of cooling took place, as is proved by chironomid analysis. The bottom sediments of the lake during this period were formed by erosion processes on the lake shores. The reconstructed conditions were close to the modern after 2500 cal. years BP.