scholarly journals Astaxanthin-Producing Microalgae Identification Using 18S rRNA : Isolates from Bangkalan Mangrove Waters and Sowan Tuban Northern Waters, East Java, Indonesia

2021 ◽  
Vol 6 (3) ◽  
pp. 64882
Author(s):  
Dini Ermavitalini ◽  
Siska Yulia Rukhmana ◽  
Thalita Meidina ◽  
Leonardo Pascalis Dimas Cahyo Baskoro ◽  
Triono Bagus Saputro ◽  
...  
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Spectrophotometric Analysis ◽  
Control Treatment ◽  
Natural Food ◽  
Gene Marker ◽  
Rrna Gene ◽  
Stress Regime ◽  
Food Ingredients ◽  
Chlorella Sp

Microalgae are a group of micro-sized photosynthetic organisms that range from prokaryotic cyanobacteria to eukaryotic algae. Microalgae are widely used as a source  of natural food, cosmetic ingredients, food ingredients, and a source of pigments. This study aims to identify species of four microalgae isolates named B1, B2, B3, and S2 from Bangkalan Mangrove Waters and Sowan Tuban Northern Waters, and to determine their astaxanthin pigment concentration under 1 M NaCl. Species identification was carried out through a molecular approach by utilization of an 18S rRNA gene marker. A quantitative test of astaxanthin concentration was carried out by spectrophotometric analysis. Molecular identification results show that isolates B1 and B3 are closely related to Chlorella sp., while isolates B2 and S2  are closely related to Picochlorum maculatum. Moreover, under salinity stress condition of 1 M NaCl shown a significant decrement of astaxanthin production compared to the control treatment. At 1 M NaCl, the astaxanthin content of isolate B1 was 4x10-5 mgL-1, isolate B2 was 2x10-5 mgL-1, isolate B3 was 1x10-5 mgL-1, and isolate S2 was 6x10-6 mgL-1. All in all, isolate S2 has the highest astaxanthin among the other isolates at normal conditions, while under salt stress regime, isolate B1 shown to be the best source for astaxanthin. 

scholarly journals Biochemical parameters and 18S rRNA gene sequence analysis amongst green microalgal strains from selected aquatic sites of Eastern India

2020 ◽  
Vol 82 (6) ◽  
pp. 1205-1216
Author(s):  
Rashi Vishwakarma ◽  
Dolly Wattal Dhar ◽  
Mrutyunjay Jena ◽  
Madhulika Shukla
Keyword(s):  
18S Rrna ◽  
Reference Strain ◽  
Biochemical Characterization ◽  
Compositional Analysis ◽  
Dry Weight ◽  
18S Rrna Gene ◽  
Soluble Proteins ◽  
Rrna Gene ◽  
Chlorella Sp ◽  
Gene Sequence Analysis

Abstract In the present study, 24 green microalgae strains were isolated from selected aquatic sites of India. These were microscopically identified as Chlamydomonas sp., Scenedesmus sp., Chlorella sp., Dictyosphaerium sp. and Dunaliella sp. Nannochloropsis sp. (MCC 25), was used as a reference strain. Results showed that Dictyosphaerium sp. (MCC 10 and MCC 12) showed relatively higher nutritive content. The total soluble proteins in the reference strain was 21.4%, whereas it showed carbohydrate content of 17.2% and the lipids were 3.4% on a dry weight basis. Best performing strains were identified by biochemical characterization. Five genera were selected for molecular identification since they were the most representative based upon their area of isolation and their optimum content of total soluble proteins, carbohydrates and lipids. 18S rRNA sequencing authenticated their identification as Scenedesmus sp., Dictyosphaerium sp. and Chlorella sp. The sequences of these have been submitted in NCBI database with accession numbers as KT808247–KT808251. The correlation matrix showed positive correlation between carbohydrates and lipids, while negative correlation was seen between proteins and carbohydrates and between proteins and lipids. This study emphasizes the need for complete compositional analysis of the biomass for the possible applicability in the area of value addition.

scholarly journals Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claire Y. T. Wang ◽  
Emma L. Ballard ◽  
Zuleima Pava ◽  
Louise Marquart ◽  
Jane Gaydon ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Plasmodium Falciparum ◽  
18S Rrna ◽  
Drug Efficacy ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Qpcr Assay ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Blood Samples

Abstract Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

scholarly journals Molecular Characterization of Ciliate Diversity in Stream Biofilms

2008 ◽  
Vol 74 (6) ◽  
pp. 1740-1747 ◽  
Author(s):  
Andrew Dopheide ◽  
Gavin Lear ◽  
Rebecca Stott ◽  
Gillian Lewis
Keyword(s):  
18S Rrna ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Sequence Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Specific Pcr ◽  
Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

scholarly journals Crassicauda boopis in a fin whale (Balaenoptera physalus) ship-struck in the eastern North Atlantic Ocean

2017 ◽  
Vol 3 ◽  
Author(s):  
LAETITIA LEMPEREUR ◽  
MORGAN DELOBELLE ◽  
MARJAN DOOM ◽  
JAN HAELTERS ◽  
ETIENNE LEVY ◽  
...  
Keyword(s):  
North Atlantic ◽  
18S Rrna ◽  
North Atlantic Ocean ◽  
18S Rrna Gene ◽  
The Body ◽  
Rrna Gene ◽  
Balaenoptera Physalus ◽  
Fin Whale ◽  
Eastern North Atlantic ◽  
The Right

SUMMARY On 9 November 2015, a juvenile male fin whale of 11·60 m length was observed on the bulb of a merchant vessel in the Channel Terneuzen – Ghent (The Netherlands – Belgium). A severe parasitosis was present in the right heart ventricle and caudal caval vein. Parasites were identified as Crassicauda boopis based on macroscopic and microscopic observations. The sequence of the 18S rRNA gene obtained from the parasite samples was 100% similar to the sequence of the 18S rRNA gene from Crassicauda magna available on GenBank. While adults of C. boopis and C. magna are morphologically distinct and found at different locations in the body, the molecular analysis of the 18S rRNA gene seems insufficient for reliable species identification. Although numerous C. boopis were found, the cause of death was identified as due to the collision with the ship, as suggested by the presence of a large haematoma, and the absence of evidence of renal failure. The young age of this whale and the absence of severe chronic reaction may suggest that the infestation was not yet at an advanced chronic stage.

Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 377-387 ◽  
Author(s):  
Jiří Neustupa ◽  
Yvonne Němcová ◽  
Jana Veselá ◽  
Jana Steinová ◽  
Pavel Škaloud
Keyword(s):  
18S Rrna ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Algal Species ◽  
18S Rrna Gene ◽  
Tree Bark ◽  
Rrna Gene ◽  
Green Microalgae ◽  
Green Algal

The diversity of green microalgae in subaerial habitats remains largely unexplored and a number of new genus- and species-level lineages have been discovered recently. The traditional green algal genus, Chlorella, which accommodated coccoid unicellular green algal species with globular to oval cells, reproducing entirely by autospores, has been found to be polyphyletic. In this study, we provide a detailed characterization of two strains of microalgae isolated from tree bark in the Mediterranean. These algae share the general Chlorella-like morphology and their 18S rRNA and rbcL gene sequences place them in the Trebouxiophyceae. Strain CAUP H8401 forms an independent trebouxiophycean lineage, together with three previously published 18S rRNA gene environmental sequences of undescribed microalgae, which were retrieved from profoundly different habitats. In contrast, strain CAUP H7902 is related to Kalinella bambusicola in the Watanabea clade of the Trebouxiophyceae on the basis of its 18S rRNA gene sequence. This relationship is also supported by the rbcL gene sequence, acquired from the type strain of K. bambusicola. The investigated strains are described as representatives of a novel species in a new genus, Leptochlorella corticola gen. et sp. nov., and a novel species, Kalinella apyrenoidosa sp. nov., according to the International Code of Nomenclature for Algae, Fungi and Plants.

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