scholarly journals Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef

2021 ◽  
Author(s):  
Molly A. Moynihan ◽  
Nathalie F. Goodkin ◽  
Kyle M. Morgan ◽  
Phyllis Y. Y. Kho ◽  
Adriana Lopes dos Santos ◽  
...  
Keyword(s):  
Scleractinian Coral ◽  
18S Rrna ◽  
Coral Species ◽  
Coral Tissue ◽  
Dna And Rna ◽  
Tropical Coral ◽  
Endolithic Community ◽  
N Demand ◽  
Diazotrophic Community

AbstractThe role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based 15N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont’s N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm−2 per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.

scholarly journals Role of Long Non-Coding RNA Polymorphisms in Cancer Chemotherapeutic Response

2021 ◽  
Vol 11 (6) ◽  
pp. 513
Author(s):  
Zheng Zhang ◽  
Meng Gu ◽  
Zhongze Gu ◽  
Yan-Ru Lou
Keyword(s):  
Molecular Mechanisms ◽  
Neurological Diseases ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Chemotherapeutic Response ◽  
Non Coding Rna ◽  
Response To Chemotherapy ◽  
Personalized Oncology ◽  
Long Non Coding Rna

Genetic polymorphisms are defined as the presence of two or more different alleles in the same locus, with a frequency higher than 1% in the population. Since the discovery of long non-coding RNAs (lncRNAs), which refer to a non-coding RNA with a length of more than 200 nucleotides, their biological roles have been increasingly revealed in recent years. They regulate many cellular processes, from pluripotency to cancer. Interestingly, abnormal expression or dysfunction of lncRNAs is closely related to the occurrence of human diseases, including cancer and degenerative neurological diseases. Particularly, their polymorphisms have been found to be associated with altered drug response and/or drug toxicity in cancer treatment. However, molecular mechanisms are not yet fully elucidated, which are expected to be discovered by detailed studies of RNA–protein, RNA–DNA, and RNA–lipid interactions. In conclusion, lncRNAs polymorphisms may become biomarkers for predicting the response to chemotherapy in cancer patients. Here we review and discuss how gene polymorphisms of lncRNAs affect cancer chemotherapeutic response. This knowledge may pave the way to personalized oncology treatments.

Endolithic community composition of Orbicella faveolata (Scleractinia) underneath the interface between coral tissue and turf algae

Coral Reefs ◽  
2015 ◽  
Vol 34 (2) ◽  
pp. 625-630 ◽  
Author(s):  
N. Gutiérrez-Isaza ◽  
J. Espinoza-Avalos ◽  
H. P. León-Tejera ◽  
D. González-Solís
Keyword(s):  
Community Composition ◽  
Coral Tissue ◽  
Turf Algae ◽  
Orbicella Faveolata ◽  
Endolithic Community

scholarly journals The kinase activity of human Rio1 is required for final steps of cytoplasmic maturation of 40S subunits

2012 ◽  
Vol 23 (1) ◽  
pp. 22-35 ◽  
Author(s):  
Barbara Widmann ◽  
Franziska Wandrey ◽  
Lukas Badertscher ◽  
Emanuel Wyler ◽  
Jens Pfannstiel ◽  
...  
Keyword(s):  
Rna Interference ◽  
Protein Kinases ◽  
18S Rrna ◽  
Kinase Activity ◽  
Ribosomal Biogenesis ◽  
Ribosomal Subunits ◽  
Binding Partner ◽  
Rrna Maturation ◽  
Cytoplasmic Maturation

RIO proteins form a conserved family of atypical protein kinases. Humans possess three distinct RIO kinases—hRio1, hRio2, and hRio3, of which only hRio2 has been characterized with respect to its role in ribosomal biogenesis. Here we show that both hRio1 and hRio3, like hRio2, are associated with precursors of 40S ribosomal subunits in human cells. Furthermore, we demonstrate that depletion of hRio1 by RNA interference affects the last step of 18S rRNA maturation and causes defects in the recycling of several trans-acting factors (hEnp1, hRio2, hLtv1, hDim2/PNO1, and hNob1) from pre-40S subunits in the cytoplasm. Although the effects of hRio1 and hRio2 depletion are similar, we show that the two kinases are not fully interchangeable. Moreover, rescue experiments with a kinase-dead mutant of hRio1 revealed that the kinase activity of hRio1 is essential for the recycling of the endonuclease hNob1 and its binding partner hDim2 from cytoplasmic pre-40S. Kinase-dead hRio1 is trapped on pre-40S particles containing hDim2 and hNob1 but devoid of hEnp1, hLtv1, and hRio2. These data reveal a role of hRio1 in the final stages of cytoplasmic pre-40S maturation.

Measuring Coral Skeletal Architecture Using Image Analysis v1

2021 ◽  
Author(s):  
Rowan Mclachlan ◽  
Ashruti Patel ◽  
Andrea G Grottoli
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Image Analysis ◽  
Scleractinian Coral ◽  
Coral Species ◽  
Energy Materials ◽  
Simple Method ◽  
Coral Skeletons ◽  
Skeletal Structures ◽  
Scanning Electron

Coral morphology is influenced by genetics, the environment, or the interaction of both, and thus is highly variable. This protocol outlines a non-destructive and relatively simple method for measuring Scleractinian coral sub-corallite skeletal structures (such as the septa length, theca thickness, and corallite diameter, etc.) using digital images produced as a result of digital microscopy or from scanning electron microscopy. This method uses X and Y coordinates of points placed onto photomicrographs to automatically calculate the length and/or diameter of a variety of sub-corallite skeletal structures in the Scleractinian coral Porites lobata. However, this protocol can be easily adapted for other coral species - the only difference may be the specific skeletal structures that are measured (for example, not all coral species have a pronounced columella or pali, or even circular corallites). This protocol is adapted from the methods described in Forsman et al. (2015) & Tisthammer et al. (2018). There are 4 steps to this protocol: 1) Removal of Organic Tissue from Coral Skeletons 2) Imaging of Coral Skeletons 3) Photomicrograph Image Analysis 4) Calculation of Corallite Microstructure Size This protocol was written by Dr. Rowan McLachlan and was reviewed by Ashruti Patel and Dr. Andréa Grottoli. Acknowledgments Leica DMS 1000 and Scanning Electron Microscopy photomicrographs used in this protocol were acquired at the Subsurface Energy Materials Characterization and Analysis Laboratory (SEMCAL), School of Earth Sciences at The Ohio State University, Ohio, USA. I would like to thank Dr. Julie Sheets, Dr. Sue Welch, and Dr. David Cole for training me on the use of these instruments.

The role of p53 in regulating genomic stability when DNA and RNA synthesis are inhibited

1995 ◽  
Vol 20 (10) ◽  
pp. 431-434 ◽  
Author(s):  
Olga B. Chernova ◽  
Michail V. Chernov ◽  
Munna L. Agarwal ◽  
William R. Taylor ◽  
George R. Stark
Keyword(s):  
Rna Synthesis ◽  
Genomic Stability ◽  
Dna And Rna ◽  
Dna And Rna Synthesis

scholarly journals Coralivoría del gasterópodo Jenneria pustulata (Ovulidae: Pediculariinae) en dos arrecifes coralinos del PNN isla Gorgona

2018 ◽  
Vol 47 (2) ◽  
Author(s):  
Mauro Giovanni Zucconi ◽  
Levy D. Obonaga ◽  
Edgardo Londoño-Cruz
Keyword(s):  
Coral Reefs ◽  
Coral Species ◽  
Size Structure ◽  
Coral Tissue ◽  
Laboratory Conditions ◽  
Set Up ◽  
Biological Dynamics ◽  
Colombian Pacific

Coral reefs are very important and highly biodiverse ecosystems that are exposed to various stressors, including biological ones, such as parasitism and corallivory – the direct consumption of coral tissue by a predator. Knowledge on the effects of corallivory on the coral reefs in the Colombian Pacific is poor. Therefore a study was set up to quantify the abundance of and the corallivory rate by the snail Jenneria pustulata in La Azufrada and Playa Blanca coral reefs (Gorgona Island, Colombia). Snails were manually sampled from the underside of Pocillopora sp. colonies and measured in situ to determine their size structure for each reef. To measure possible damage caused by corallivory, several snails were kept under controlled laboratory conditions for 24 h. Snail sizes and corallivory varied significantly between reefs (P=0.0001; P«0.001). Snails from Playa Blanca were larger than snails from La Azufrada, while corallivory was higher in La Azufrada than in Playa Blanca. Although corallivory rates by J. pustulata are smaller than rates reported for other predators in different coral species, it is recommended to continue this kind of investigations in order to increase the knowledge on biological dynamics of this species and to understand how they affect the reefs at Gorgona Island.

scholarly journals Ocean acidification increases photosynthate translocation in a coral–dinoflagellates symbiosis

2013 ◽  
Vol 10 (1) ◽  
pp. 83-109 ◽  
Author(s):  
P. Tremblay ◽  
M. Fine ◽  
J. F. Maguer ◽  
R. Grover ◽  
C. Ferrier-Pagès
Keyword(s):  
Coral Species ◽  
Total Carbon ◽  
Coral Host ◽  
Climate Change Scenarios ◽  
Symbiotic Association ◽  
Stylophora Pistillata ◽  
Gross Photosynthesis ◽  
Total Percentage ◽  
Carbon Translocation ◽  
Tropical Coral

Abstract. This study has examined the effect of an increased seawater pCO2 on the rates of photosynthesis and carbon translocation in the scleractinian coral species Stylophora pistillata using a new model based on 13C-labelling of the photosynthetic products. Symbiont photosynthesis contributes for a large part of the carbon acquisition in tropical coral species and is therefore an important process that may determine their survival under climate change scenarios. Nubbins of S. pistillata were maintained for six months under two pHs (8.1 and 7.2). Rates of photosynthesis and respiration of the symbiotic association and of isolated symbionts were assessed at each pH. The fate of 13C-photosynthates was then followed in the symbionts and the coral host for 48 h. Nubbins maintained at pH 7.2 presented a lower areal symbiont concentration, lower areal rates of gross photosynthesis, and lower carbon incorporation rates compared to nubbins maintained at pH 8.1, therefore suggesting that the total carbon acquisition was lower in this first set of nubbins. However, the total percentage of carbon translocated to the host, as well as the amount of carbon translocated per symbiont cell was significantly higher under pH 7.2 than under pH 8.1 (70% at pH 7.2 versus 60% at pH 8.1), so that the total amount of photosynthetic carbon received by the coral host was equivalent under both pHs (5.5 to 6.1 μg C cm−2 h−1). Although the carbon budget of the host was unchanged, symbionts acquired less carbon for their own needs (0.6 against 1.8 μg C cm−2 h−1), explaining the overall decrease in symbiont concentration at low pH. In the long-term, this decrease might have important consequences for the survival of corals under an acidification stress.

scholarly journals Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

2020 ◽  
Author(s):  
Qiulong Yan ◽  
Yu Wang ◽  
Xiuli Chen ◽  
Hao Jin ◽  
Guangyang Wang ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Chinese Adults ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Bacterial Microbiome ◽  
Chinese Cohort ◽  
Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

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