Anna Davydova

Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks

Northern high-latitude rivers are major conduits of carbon from land to coastal seas and the Arctic Ocean. Arctic warming is promoting terrestrial permafrost thaw and shifting hydrologic flowpaths, leading to fluvial mobilization of ancient carbon stores. Here we describe 14C and 13C characteristics of dissolved organic carbon from fluvial networks across the Kolyma River Basin (Siberia), and isotopic changes during bioincubation experiments. Microbial communities utilized ancient carbon (11,300 to >50,000 14C years) in permafrost thaw waters and millennial-aged carbon (up to 10,000 14C years) across headwater streams. Microbial demand was supported by progressively younger (14C-enriched) carbon downstream through the network, with predominantly modern carbon pools subsidizing microorganisms in large rivers and main-stem waters. Permafrost acts as a significant and preferentially degradable source of bioavailable carbon in Arctic freshwaters, which is likely to increase as permafrost thaw intensifies causing positive climate feedbacks in response to on-going climate change.

Dissolved organic carbon loss from Yedoma permafrost amplified by ice wedge thaw

Pleistocene Yedoma permafrost contains nearly a third of all organic matter (OM) stored in circum-arctic permafrost and is characterized by the presence of massive ice wedges. Due to its rapid formation by sediment accumulation and subsequent frozen storage, Yedoma OM is relatively well preserved and highly biologically available (biolabile) upon thaw. A better understanding of the processes regulating Yedoma degradation is important to improve estimates of the response and magnitude of permafrost carbon feedbacks to climate warming. In this study, we examine the composition of ice wedges and the influence of ice wedge thaw on the biolability of Yedoma OM. Incubation assays were used to assess OM biolability, fluorescence spectroscopy to characterize the OM composition, and potential enzyme activity rates to examine the controls and regulation of OM degradation. We show that increasing amounts of ice wedge melt water in Yedoma-leached incubations enhanced the loss of dissolved OM over time. This may be attributed to the presence of low-molecular weight compounds and low initial phenolic content in the OM of ice wedges, providing a readily available substrate that promotes the degradation of Yedoma OC. The physical vulnerability of ice wedges upon thaw (causing irreversible collapse), combined with the composition of ice wedge-engrained OM (co-metabolizing old OM), underlines the particularly strong potential of Yedoma to generate a positive feedback to climate warming relative to other forms of non-ice wedge permafrost.

Insulators form gene loops by interacting with promoters in Drosophila

Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.

Aptamers against pathogenic microorganisms

Abstract An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.

Eleuthesides and their analogs: IX. Synthesis of C3–C8 eleutheside block from levoglucosenone

A chiral building block containing C3–C8 eleutheside carbon chain fragment has been synthesized starting from the 1,2-addition product of methylmagnesium iodide with levoglucosenone.

Key Aspects of Nucleic Acid Library Design for in Vitro Selection

Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.