Identification and characterization of a freshwater Pyrococcus sp. strain PK 5017 and identification of pfu-like IS elements in Thermococcus sibiricus MM 739

12 pages, 7 figures, 1 table, 32 references.A strictly anaerobic, hyperthermophilic Pyrococcus sp. strain PK 5017 (PK 5017) was isolated from a freshwater hot spring in Thailand. Cells of strain PK 5017 are irregular cocci occurring singly and in pairs with a diameter range of 0.7-1.2 µm. Temperature, pH and NaCl concentration ranges for growth are 75-105 oC (opt. temp. = 95-100 oC), pH 5-7.8 (opt. pH = 7.2) and 2.5-IS-pfu-Ts1> and >IS-pfu-Ts2> are identified in the complete genome sequence of Thermococcus sibiricus MM 739. Pyrococcus sp. strain PK 5017 = Pyrococcus sp. strain Pikanate 5017 = JCM17043 = ATCC BAA-2246.This work was supported by the Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (RGI 2553-06) and Silpakorn University Research and Development Institute (SURDI 54/01/18 and SURDI 55/01/05). JMG and MCP acknowledge support from a CSIC movility program, PA1001993 and PA1002058, and the Andalusian Government Bio288 which included FEDER funds.Peer Reviewe

Fervidobacterium thailandense sp. nov., an extremely thermophilic bacterium isolated from a hot spring

4 páginas.-- 2 figuras.-- 19 referencias.-- Two supplementary tables and four supplementary figures are available with the online Supplementary Material.Strain FC2004T, a strictly anaerobic, extremely thermophilic heterotroph, was isolated from a hot spring in Thailand. Typical cells of strain FC2004T were rod shaped (0.5–0.6×1.1–2.5 µm) with an outer membrane swelling out over an end. Filaments (10–30 µm long) and membrane-bound spheroids containing two or more cells inside (3–8 µm in diameter) were observed. The temperature range for growth was 60–88°C (optimum 78–80°C), pH range was 6.5–8.5 (optimum pH 7.5) and NaCl concentration range was 0 to <5 g l−1 (optimum 0.5 g l−1). S0 stimulated growth yield. S2O3 2– and NO3 − did not influence growth. Glucose, maltose, sucrose, fructose, cellobiose, CM-cellulose and starch were utilized for growth. The membrane was composed mainly of the saturated fatty acids C16:0 and C18:0. The DNA G+C content was 45.8 mol%. The 16S rRNA gene sequence of strain FC2004T revealed highest similarity to species of the genus Fervidobacterium : F. pennivorans DSM 9078T (97–96 %), F. islandicum AW-1 (96 %), F. changbaicum CBS-1T (96 %), F. islandicum H21T (95 %), F. nodosum Rt17-B1T (95 %), F. riparium 1445tT (95 %) and F. gondwanense AB39T (93 %). Phylogenetic analysis of 16S rRNA gene sequences and average nucleotide identity analysis suggested that strain FC2004T represented a novel species within the genus Fervidobacterium , for which the name Fervidobacterium thailandense sp. nov. is proposed. The type strain is FC2004T (=JCM 18757T=ATCC BAA-2483T).Peer reviewe

Differentiation of a hyperthermophilic archaeon Pyrococcus sp. Strain Pikanate 5017, by arbitrarily primed PCR

Pyrococcus and Thermococcus are hyperthermophilic archaea in the order Thermococcales. Both genera are strictly anaerobes, gaining energy by fermentation of peptide and several carbohydrates at optimal temperature above 70 ° C. A Pyrococcus sp. strain Pikanate 5017 (PK 5017) was recently isolated from a hot spring in Northern Thailand. The strain PK 5017 is a valuable source of numerous genes encoding thermostable enzymes. Growth kinetics determined at various temperatures (75-105 ° C) indicates that strain PK5017 is a fast growing archaeon. An arbitrarily primed PCR (AP-PCR) technique was successfully applied to differentiate the genome sequences of six members of Thermococcales. Two single primers, ARB-1f (5’ ATGAG GACT GAAA CCATT 3’) and ARB-2f (5’ GTAAA ACGA CGGC CAGT 3’), are effective in producing polymorphisms of the PCR products at 3-10 ng of DNAs. The unique AP-PCR fingerprints distinguish the strain PK5017 from P. furiosus, P. horikoshii, P. abyssi, T. litoralis, and T. celer. The results indicate a clear distinction of genome sequences among Pyrococcus and Thermococcus genera.This work was supported by a grant from the Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (Grant number RGI 2553-06). JMG and MCP acknowledge the support from a CSIC movility program, PA1001993 and PA1002058, and the Andalusian Government Bio288Peer Reviewe

Engaging domestic users on demand response for heating cost reduction with a recommendation tool: Case study in Belgrade

The European Union has established a legislative framework that aims to enable consumers and businesses to take information-based decisions to save energy and money. Additionally, the increase of Distributed Energy Resources (both on generation and consumption) requires additional efforts to maintain the reliability and stability of the electric grid and the need of flexibility from residential buildings. The present study introduces a domestic decision support tool for reducing heating costs. This app provides detailed recommendations to end-users based on the day-ahead hourly weather forecast, electric and district heating tariffs predictions, heating demand, and heating systems dynamic performance. The tool was tested in 6 dwellings of a neighborhood of Belgrade during the last months of 2021 heating season (March–May). Energetic results suggest that 40% of participants followed the given recommendations and changed their heating pattern. Additionally, survey results show that end-users found the lack of information and knowledge as the main barrier to actively participate in the energy market, also preferring to have automatic control in their heating system. Authors conclude that recommendation tools are key elements in user-engagement, but they should be supported by additional information and training.Research leading to these results has been supported by HOLISDER project, Spain. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 768614

Global study of is6110 in a successful mycobacterium tuberculosis strain: Clues for deciphering its behavior and for its rapid detection

The Mycobacterium tuberculosis insertion sequence IS6110, besides being a very useful tool in molecular epidemiology, seems to have an impact on the biology of bacilli. In the present work, we mapped the 12 points of insertion of IS6110 in the genome of a successful strain named M. tuberculosis Zaragoza (which has been referred to as the MTZ strain). This strain, belonging to principal genetic group 3, caused a large unsuspected tuberculosis outbreak involving 85 patients in Zaragoza, Spain, in 2001 to 2004. The mapping of the points of insertion of IS6110 in the genome of the Zaragoza strain offers clues for a better understanding of the adaptability and virulence of M. tuberculosis. Surprisingly, the presence of one copy of IS6110 was found in Rv2286c, as was recently described for a successful Beijing sublineage. As a result of this analysis, a rapid method for detecting this particular M. tuberculosis strain has been designed

Naturally-acquired humoral immune responses against the N- and C-termini of the Plasmodium vivax MSP1 protein in endemic regions of Brazil and Papua New Guinea using a multiplex assay

<p>Abstract</p> <p>Background</p> <p>Progress towards the development of a malaria vaccine against <it>Plasmodium vivax</it>, the most widely distributed human malaria parasite, will require a better understanding of the immune responses that confer clinical protection to patients in regions where malaria is endemic.</p> <p>Methods</p> <p>Glutathione <it>S</it>-transferase (GST) and GST-fusion proteins representing the N- terminus of the merozoite surface protein 1 of <it>P. vivax</it>, PvMSP1-N, and the C-terminus, PvMSP1-C, were covalently coupled to BioPlex carboxylated beads. Recombinant proteins and coupled beads were used, respectively, in ELISA and Bioplex assays using immune sera of <it>P. vivax </it>patients from Brazil and PNG to determine IgG and subclass responses. Concordances between the two methods in the seropositivity responses were evaluated using the Kappa statistic and the Spearman's rank correlation.</p> <p>Results</p> <p>The results using this methodology were compared with the classical microtitre enzyme-linked immnosorbent assay (ELISA), showing that the assay was sensitive, reproducible and had good concordance with ELISA; yet, further research into different statistical analyses seems desirable before claiming conclusive results exclusively based on multiplex assays. As expected, results demonstrated that PvMSP1 was immunogenic in natural infections of patients from different endemic regions of Brazil and Papua New Guinea (PNG), and that age correlated only with antibodies against the C-terminus part of the molecule. Furthermore, the IgG subclass profiles were different in these endemic regions having IgG3 predominantly recognizing PvMSP1 in Brazil and IgG1 predominantly recognizing PvMSP1 in PNG.</p> <p>Conclusions</p> <p>This study validates the use of the multiplex assay to measure naturally-acquired IgG antibodies against the merozoite surface protein 1 of <it>P. vivax</it>.</p

Mild stress conditions during laboratory culture promote the proliferation of mutations that negatively affect Sigma B activity in Listeria monocytogenes

In Listeria monocytogenes, the full details of how stress signals are integrated into the σB regulatory pathway are not yet available. To help shed light on this question, we investigated a collection of transposon mutants that were predicted to have compromised activity of the alternative sigma factor B (σB). These mutants were tested for acid tolerance, a trait that is known to be under σB regulation, and they were found to display increased acid sensitivity, similar to a mutant lacking σB (ΔsigB). The transposon insertions were confirmed by whole-genome sequencing, but in each case, the strains were also found to carry a frameshift mutation in the sigB operon. The changes were predicted to result in premature stop codons, with negative consequences for σB activation, independently of the transposon location. Reduced σB activation in these mutants was confirmed. Growth measurements under conditions similar to those used during the construction of the transposon library revealed that the frameshifted sigB operon alleles conferred a growth advantage at higher temperatures, during late exponential phase. Mixed-culture experiments at 42°C demonstrated that the loss of σB activity allowed mutants to take over a population of parental bacteria. Together, our results suggest that mutations affecting σB activity can arise during laboratory culture because of the growth advantage conferred by these mutations under mild stress conditions. The data highlight the significant cost of stress protection in this foodborne pathogen and emphasize the need for whole-genome sequence analysis of newly constructed strains to confirm the expected genotype.This project has received funding from the European Union’s Horizon 2020 research-and-innovation program under Marie Skłodowska-Curie grant agreement no. 721456. Jialun Wu was funded by the Department of Agriculture, Food and the Marine (17/F/244)

Holocene resource exploitation along the Nile:diet and subsistence strategies of Mesolithic and Neolithic societies at Khor Shambat 1, Sudan

The subsistence practices of Holocene communities living in the Nile Valley of Central Sudan are comparatively little known. Recent excavations at Khor Shambat, Sudan, have yielded well-defined Mesolithic and Neolithic stratigraphy. Here, for the first time, archaeozoological, palaeobotanical, phytolith and dental calculus studies are combined with lipid residue analysis of around 100 pottery fragments and comparative analysis of faunal remains and organic residues. This holistic approach provides valuable information on changes in adaptation strategies, from Mesolithic hunter-gatherers to Neolithic herders exploiting domesticates. A unique picture is revealed of the natural environment and human subsistence, demonstrating the potential wider value of combining multiple methods

Promoter regions of Plasmodium vivax are poorly or not recognized by Plasmodium falciparum

BACKGROUND: Heterologous promoter analysis in Plasmodium has revealed the existence of conserved cis regulatory elements as promoters from different species can drive expression of reporter genes in heterologous transfection assays. Here, the functional characterization of different Plasmodium vivax promoters in Plasmodium falciparum using luciferase as the reporter gene is presented. METHODS: Luciferase reporter plasmids harboring the upstream regions of the msp1, dhfr, and vir3 genes as well as the full-length intergenic regions of the vir23/24 and ef-1α genes of P. vivax were constructed and transiently transfected in P. falciparum. RESULTS: Only the constructs with the full-length intergenic regions of the vir23/24 and ef-1α genes were recognized by the P. falciparum transcription machinery albeit to values approximately two orders of magnitude lower than those reported by luc plasmids harbouring promoter regions from P. falciparum and Plasmodium berghei. A bioinformatics approach allowed the identification of a motif (GCATAT) in the ef-1α intergenic region that is conserved in five Plasmodium species but is degenerate (GCANAN) in P. vivax. Mutations of this motif in the P. berghei ef-1α promoter region decreased reporter expression indicating it is active in gene expression in Plasmodium. CONCLUSION: Together, this data indicates that promoter regions of P. vivax are poorly or not recognized by the P. falciparum transcription machinery suggesting the existence of P. vivax-specific transcription regulatory elements