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The Effect of Glacier Recession on Benthic and Pelagic Communities: Case Study in Herve Cove, Antarctica
Get PDFChanges in macrobenthic and pelagic communities in the postglacial, partially isolated, lagoon Herve Cove in Admiralty Bay, King George Island, were investigated 15 years after the first comprehensive studies had been conducted in this region. The bottom area of the cove has enlarged from approximately 12 ha to 19 ha after the retreat of the Dera Icefall. Based on a photographic survey of the benthos and taxonomic composition of zooplankton, ecological succession and the colonization of new species have been observed. Several new species occur such as gastropods,
seastars, sea urchins and isopods, and their presence in different parts of the cove, as well as breeding aggregations suggests that they reproduce there. The influence of glacial streams is notable in bottom assemblages. We propose that Herve Cove is a good research area for studies on ecological succession in newly opened areas. The colonization of this lagoon has been recognized to be in its developing stage, and research should be continued
Actinobacteria Structure in Autogenic, Hydrogenic and Lithogenic Cultivated and Non-Cultivated Soils: A Culture-Independent Approach
Get PDFThe aim of the study was to determine the Actinobacteria structure in cultivated (C) versus non-cultivated (NC) soils divided into three groups (autogenic, hydrogenic, lithogenic) with consideration its formation process in order to assess the Actinobacteria sensitivity to agricultural soil use and soil genesis and to identify factors affecting their abundance. Sixteen C soil samples and sixteen NC samples serving as controls were taken for the study. Next generation sequencing (NGS) of the 16S rRNA metagenomic amplicons (Ion Torrent™ technology) and Denaturing Gradient Gel Electrophoresis (DGGE) were applied for precise determination of biodiversity. Generally, greater abundance of Actinobacteria in the NC soils relative to the C soils was found. Moreover, it was indicated that the actinobacterial diversity depended on both the soil genesis and the land use; however, this effect directly depended on the particular family and genera. Two factors: redox potential (Eh) and total carbon (TC) seemed to had a significant effect on the diversity of Actinobacteria. More precisely, Actinobacteria from the NC soils displayed a greater affinity for each other and were clearly influenced by Eh, whilst those from the C soils were mostly influenced by T
Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.
Get PDFEcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, we report that NEco and full-length EcoKMcrA specificities are consistent. NEco affinity to DNA increases more from hemi- to full-methylation than from non- to hemi-methylation, indicating cooperative binding of the methyl groups. We determined the crystal structures of NEco in complex with fully modified DNA containing three variants of the Y5mCGR EcoKMcrA target sequence: C5mCGG, T5mCGA and T5hmCGA. The structures explain the specificity for the two central base pairs and one of the flanking pairs. As predicted based on earlier biochemical experiments, NEco does not flip any DNA bases. The proximal and distal methyl groups are accommodated in separate pockets. Changes to either pocket reduce DNA binding by NEco and restriction by EcoKMcrA, confirming the relevance of the crystallographically observed binding mode in solution
Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.
Get PDFRestriction endonucleases (REs) of the CCGG-family recognize a set of 4-8 bp target sequences that share a common CCGG or CCNGG core and possess PD…D/ExK nuclease fold. REs that interact with 5 bp sequence 5'-CCNGG flip the central N nucleotides and 'compress' the bound DNA to stack the inner base pairs to mimic the CCGG sequence. PfoI belongs to the CCGG-family and cleaves the 7 bp sequence 5'-T|CCNGGA ("|" designates cleavage position). We present here crystal structures of PfoI in free and DNA-bound forms that show unique active site arrangement and mechanism of sequence recognition. Structures and mutagenesis indicate that PfoI features a permuted E…ExD…K active site that differs from the consensus motif characteristic to other family members. Although PfoI also flips the central N nucleotides of the target sequence it does not 'compress' the bound DNA. Instead, PfoI induces a drastic change in DNA backbone conformation that shortens the distance between scissile phosphates to match that in the unperturbed CCGG sequence. Our data demonstrate the diversity and versatility of structural mechanisms employed by restriction enzymes for recognition of related DNA sequences
Genistein modulates gene activity in psoriatic patients
Get PDFDespite the impressive advancements in the treatment
of psoriasis over the past two decades, there is still a
need for further improvement. As previously shown in
the literature, genistein (5,7-dihydroxy-3-(4-hydroxyphenyl)
chromen-4-one), naturally occurring plant compound
displays multidirectional action, also in relation to alleviating
psoriasis symptoms. In this work we focused our
attention on genistein impact on expression of genes
when treating moderate-to-severe psoriasis patients.
Testing the effects of this isoflavone on transcript levels
in both skin specimens and peripheral blood cells of four
psoriatic subjects, we found that this compound modulated
activities of genes coding for anti-psoriatic members
and anti-inflammatory mediators of inflammation.
It impairs the activity of certain genes which are overexpressed
in psoriasis, while stimulating the expression of
other transcripts that are repressed in dermatosis
Long-Chain Polyisoprenoids Are Synthesized by AtCPT1 in Arabidopsis thaliana
Get PDFArabidopsis roots accumulate a complex mixture of dolichols composed of three families, (i.e., short-, medium- and long-chain dolichols), but until now none of the cis-prenyltransferases (CPTs) predicted in the Arabidopsis genome has been considered responsible for their synthesis. In this report, using homo- and heterologous (yeast and tobacco) models, we have characterized the AtCPT1 gene (At2g23410) which encodes a CPT responsible for the formation of long-chain dolichols, Dol-18 to -23, with Dol-21 dominating, in Arabidopsis. The content of these dolichols was significantly reduced in AtCPT1 T-DNA insertion mutant lines and highly increased in AtCPT1-overexpressing plants. Similar to the majority of eukaryotic CPTs, AtCPT1 is localized to the endoplasmic reticulum (ER). Functional complementation tests using yeast rer2Δ or srt1Δ mutants devoid of medium- or long-chain dolichols, respectively, confirmed that this enzyme synthesizes long-chain dolichols, although the dolichol chains thus formed are somewhat shorter than those synthesized in planta. Moreover, AtCPT1 acts as a homomeric CPT and does not need LEW1 for its activity. AtCPT1 is the first plant CPT producing long-chain polyisoprenoids that does not form a complex with the NgBR/NUS1 homologue
Building Machine-Learning Scoring Functions for Structure-Based Prediction of Intermolecular Binding Affinity
No full textA structural model of the immune checkpoint CD160-HVEM complex derived from HDX-mass spectrometry and molecular modeling
Get PDFCD160 is a T cell coinhibitory molecule that interacts with the herpes virus entry mediator (HVEM) on antigen-presenting cells to provide an inhibitory signal to T cells. To date, the structure of CD160 and its complex with HVEM are unknown. Here, we have identified the fragments of CD160 interacting with HVEM using ELISA tests, hydrogen/deuterium studies, affinity chromatography and mass spectrometry (MS). By combining hydrogen/deuterium exchange and mass spectrometry (HDX-MS) we obtained key information about the tertiary structure of CD160, predicting the 3D structure of the CD160-HVEM complex. Our results provide insights into the molecular architecture of this complex, serving as a useful basis for designing inhibitors for future immunotherapies
Butyric acid, a gut bacteria metabolite, lowers arterial blood pressure via colon-vagus nerve signaling and GPR41/43 receptors
Get PDFSearching for Metabolic Pathways of Anaerobic Digestion: A Useful List of the Key Enzymes
Get PDFThe general scheme of anaerobic digestion is well known. It is a complex process promoted by the interaction of many groups of microorganisms and has four major steps: hydrolysis, acidogenesis, acetogenesis, and methanogenesis. The aim of the study was to prepare a systematized list of the selected enzymes responsible for the key pathways of anaerobic digestion based on the Kyoto Encyclopedia of Genes and Genomes database resource. The list contains (i) key groups of hydrolases involved in the process of degradation of organic matter; (ii) the enzymes catalyzing reactions
leading to pyruvate formation; (iii) the enzymes of metabolic pathways of further pyruvate transformations; (iv) the enzymes of glycerol transformations; (v)the enzymes involved in transformation of gaseous or nongaseous products of acidic fermentations resulting from nonsyntrophic nutritional interactions between microbes; (vi) the enzymes of amino acid fermentations; (vii) the enzymes involved in acetogenesis; and (viii) the enzymes of the recognized pathways of methanogenesis. Searching for the presence and activity of the enzymes as well as linking structure and function of microbial communities allows to develop a fundamental understanding of the processes, leading to methane production. In this contribution, the present study is believed to be a piece to the enzymatic road map
of anaerobic digestion research