scholarly journals Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology

2018 ◽  
Vol 27 (24) ◽  
pp. 5279-5293 ◽  
Author(s):  
Nathan A. M. Chrismas ◽  
Christopher J. Williamson ◽  
Marian L. Yallop ◽  
Alexandre M. Anesio ◽  
Patricia Sánchez‐Baracaldo
Keyword(s):  
Comparative Genomics ◽  
Community Analysis ◽  
The Antarctic

scholarly journals Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota

2015 ◽  
Vol 197 (14) ◽  
pp. 2383-2391 ◽  
Author(s):  
Semen A. Leyn ◽  
Irina A. Rodionova ◽  
Xiaoqing Li ◽  
Dmitry A. Rodionov
Keyword(s):  
Carbon Dioxide ◽  
Transcriptional Regulation ◽  
Comparative Genomics ◽  
Dna Binding ◽  
Transcriptional Control ◽  
Binding Assays ◽  
Promoter Regions ◽  
Content Type ◽  
Genome Context

ABSTRACTAutotrophic microorganisms are able to utilize carbon dioxide as their only carbon source, or, alternatively, many of them can grow heterotrophically on organics. Different variants of autotrophic pathways have been identified in various lineages of the phylumCrenarchaeota. Aerobic members of the orderSulfolobalesutilize the hydroxypropionate-hydroxybutyrate cycle (HHC) to fix inorganic carbon, whereas anaerobicThermoprotealesuse the dicarboxylate-hydroxybutyrate cycle (DHC). Knowledge of transcriptional regulation of autotrophic pathways inArchaeais limited. We applied a comparative genomics approach to predict novel autotrophic regulons in theCrenarchaeota. We report identification of two novel DNA motifs associated with the autotrophic pathway genes in theSulfolobales(HHC box) andThermoproteales(DHC box). Based on genome context evidence, the HHC box regulon was attributed to a novel transcription factor from the TrmB family named HhcR. Orthologs of HhcR are present in allSulfolobalesgenomes but were not found in other lineages. A predicted HHC box regulatory motif was confirmed byin vitrobinding assays with the recombinant HhcR protein fromMetallosphaera yellowstonensis. For the DHC box regulon, we assigned a different potential regulator, named DhcR, which is restricted to the orderThermoproteales. DhcR inThermoproteus neutrophilus(Tneu_0751) was previously identified as a DNA-binding protein with high affinity for the promoter regions of two autotrophic operons. The global HhcR and DhcR regulons reconstructed by comparative genomics were reconciled with available omics data inMetallosphaeraandThermoproteusspp. The identified regulons constitute two novel mechanisms for transcriptional control of autotrophic pathways in theCrenarchaeota.IMPORTANCELittle is known about transcriptional regulation of carbon dioxide fixation pathways inArchaea. We previously applied the comparative genomics approach for reconstruction of DtxR family regulons in diverse lineages ofArchaea. Here, we utilize similar computational approaches to identify novel regulatory motifs for genes that are autotrophically induced in microorganisms from two lineages ofCrenarchaeotaand to reconstruct the respective regulons. The predicted novel regulons in archaeal genomes control the majority of autotrophic pathway genes and also other carbon and energy metabolism genes. The HhcR regulon was experimentally validated by DNA-binding assays inMetallosphaeraspp. Novel regulons described for the first time in this work provide a basis for understanding the mechanisms of transcriptional regulation of autotrophic pathways inArchaea.

scholarly journals Fungal Community Analysis and Biodeterioration of Waterlogged Wooden Lacquerware from the Nanhai No. 1 Shipwreck

2020 ◽  
Vol 10 (11) ◽  
pp. 3797
Author(s):  
Yin Jia ◽  
Liuyu Yin ◽  
Fengyu Zhang ◽  
Mei Wang ◽  
Mingliang Sun ◽  
...  
Keyword(s):  
Fusarium Solani ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Community Analysis ◽  
Fungal Species ◽  
Potato Dextrose Agar ◽  
Fungal Communities ◽  
Cellulolytic Enzymes ◽  
Biocidal Products

To avoid the lacquerware of the Nanhai No. 1 shipwreck from being corroded by microorganisms and to improve the knowledge on microbial ecology of the wood lacquers, we conducted a series of tests on the two water samples storing the lacquerware and colonies on the surface of the lacquerware. The high-throughput sequencing detected dominant fungal communities. After that, the fungal strains were isolated and then identified by amplification of ITS- 18S rRNA. Then the activity of ligninolytic and cellulolytic enzymes was detected on potato dextrose agar (PDA) plates with 0.04% (v/v) guaiacol and carboxymethyl cellulose (CMC) agar plates. Finally, we tested the biocide susceptibility of these fungi. Penicillium chrysogenum (NK-NH3) and Fusarium solani (NK- NH1) were the dominant fungi in the sample collected in April 2016 and June 2017. What is more, both showed activity of ligninolytic and cellulolytic enzymes. Four biocidal products (Preventol® D7, P91, BIT 20N, and Euxyl® K100) inhibited the growth of the fungal species in vitro effectively. In further research, the microbial community and environmental parameters in the museum should be monitored to assess the changes in the community and to detect potential microbial outbreaks.

scholarly journals New Discorhabdin Alkaloids from the Antarctic Deep-Sea Sponge Latrunculia biformis

Marine Drugs ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. 439 ◽  
Author(s):  
Li ◽  
Peifer ◽  
Janussen ◽  
Tasdemir
Keyword(s):  
Anticancer Activity ◽  
Deep Sea ◽  
Topoisomerase I ◽  
Active Sites ◽  
Binding Potential ◽  
Chemical Structures ◽  
Ic50 Values ◽  
Ft Ir ◽  
The Antarctic

The sponge genus Latrunculia is a prolific source of discorhabdin type pyrroloiminoquinone alkaloids. In the continuation of our research interest into this genus, we studied the Antarctic deep-sea sponge Latrunculia biformis that showed potent in vitro anticancer activity. A targeted isolation process guided by bioactivity and molecular networking-based metabolomics yielded three known discorhabdins, (−)-discorhabdin L (1), (+)-discorhabdin A (2), (+)-discorhabdin Q (3), and three new discorhabdin analogs (−)-2-bromo-discorhabdin D (4), (−)-1-acetyl-discorhabdin L (5), and (+)-1-octacosatrienoyl-discorhabdin L (6) from the MeOH-soluble portion of the organic extract. The chemical structures of 1–6 were elucidated by extensive NMR, HR-ESIMS, FT-IR, [α]D, and ECD (Electronic Circular Dichroism) spectroscopy analyses. Compounds 1, 5, and 6 showed promising anticancer activity with IC50 values of 0.94, 2.71, and 34.0 µM, respectively. Compounds 1–6 and the enantiomer of 1 ((+)-discorhabdin L, 1e) were docked to the active sites of two anticancer targets, topoisomerase I-II and indoleamine 2,3-dioxygenase (IDO1), to reveal, for the first time, the binding potential of discorhabdins to these proteins. Compounds 5 and 6 are the first discorhabdin analogs with an ester function at C-1 and 6 is the first discorhabdin bearing a long-chain fatty acid at this position. This study confirms Latrunculia sponges to be excellent sources of chemically diverse discorhabdin alkaloids.

Phagocytosis in vitro and in vivo in the Antarctic sea urchin Sterechinus neumayeri at 0°C

Polar Biology ◽  
2002 ◽  
Vol 25 (12) ◽  
pp. 891-897 ◽  
Author(s):  
João Borges ◽  
Laércio Porto-Neto ◽  
Maria Mangiaterra ◽  
Bernard Jensch-Junior ◽  
José da Silva
Keyword(s):  
Sea Urchin ◽  
Sterechinus Neumayeri ◽  
The Antarctic

scholarly journals Ramalin, a Novel Phenyl Hydrazide from the Lichen Ramalina Terebrata; Isolation, Total Synthesis and Biological Activities

2016 ◽  
Vol 30 (2) ◽  
pp. 35-42
Author(s):  
Durga Prasad Pandey ◽  
Hari Datta Bhattarai
Keyword(s):  
Total Synthesis ◽  
Antioxidant Activities ◽  
Biological Activities ◽  
Cost Effective ◽  
Scale Production ◽  
In Vivo Test ◽  
The Antarctic ◽  
Industrial Scale Production

Ramalin, a new L-glutamic acid derivative of phenylhydrazide (Y-glutamyl-N'-(2-hydroxyphenyl) hydrazide, 1) was isolated from the Antarctic lichen, Ramalina terebrata after a series of bioactivity guided fractionation of crude aqueous methanolic extract. Ramalin showed stronger antioxidant activities than commercially available standards, ascorbic acid, trolox, BHA, kojic acid in both, in vitro and in vivo test systems. In addition, ramalin showed no/less toxicity effects against two human cell lines; fibroblast (CCD-986SK) cells and keratinocyte (HaCaT). Thus, realign merits for cosmetic application and industrial scale production were needed. We developed a cost effective total synthesis of ramalin with 71.5% yield and described here.

Use of in vitro OmniPlex libraries for high-throughput comparative genomics and molecular haplotyping

2002 ◽  
Author(s):  
Emmanuel Kamberov ◽  
Irina Sleptsova ◽  
Stephen Suchyta ◽  
Eric D. Bruening ◽  
William Ziehler ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
High Throughput

scholarly journals Comparative Genomics Suggests Primary Homothallism of Pneumocystis Species

mBio ◽  
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
João M. G. C. F. Almeida ◽  
Ousmane H. Cissé ◽  
Álvaro Fonseca ◽  
Marco Pagni ◽  
Philippe M. Hauser
Keyword(s):  
Comparative Genomics ◽  
Sexual Reproduction ◽  
Mating Type ◽  
Fungal Pathogens ◽  
Pneumocystis Carinii ◽  
Severe Pneumonia ◽  
Genomic Region ◽  
Pneumocystis Jirovecii ◽  
Content Type

ABSTRACT   Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans. IMPORTANCE   Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.

scholarly journals Microbial Community Composition Affects Soil Fungistasis

2003 ◽  
Vol 69 (2) ◽  
pp. 835-844 ◽  
Author(s):  
Wietse de Boer ◽  
Patrick Verheggen ◽  
Paulien J. A. Klein Gunnewiek ◽  
George A. Kowalchuk ◽  
Johannes A. van Veen
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Fusarium Culmorum ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Carbon Limitation ◽  
Soil Fungistasis

ABSTRACT Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

The in vitro investigation of four radioactive corticosteroids in the antarctic seal (Leptonychotes weddellii)

1974 ◽  
Vol 22 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Miguel Borruel ◽  
Patricia Borruel ◽  
Maria Cristina Damasco ◽  
Carlos P. Lantos
Keyword(s):  
Leptonychotes Weddellii ◽  
In Vitro Investigation ◽  
The Antarctic
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