scholarly journals Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6898 ◽  
Author(s):  
Xavier Pochon ◽  
Patricia Wecker ◽  
Michael Stat ◽  
Véronique Berteaux-Lecellier ◽  
Gaël Lecellier
Keyword(s):  
High Throughput Sequencing ◽  
Critical Role ◽  
Cost Savings ◽  
Giant Clam ◽  
Sequence Coverage ◽  
Index Sequence ◽  
Single Marker ◽  
Coral Reef Ecosystems ◽  
Phylogenetic Resolution ◽  
Single Amplicon

High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.

scholarly journals Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons

2019 ◽  
Author(s):  
Xavier Pochon ◽  
Patricia Wecker ◽  
Michael Stat ◽  
Veronique Berteaux-Lecellier ◽  
Gael Lecellier
Keyword(s):  
High Throughput Sequencing ◽  
Critical Role ◽  
Cost Savings ◽  
Giant Clam ◽  
Sequence Coverage ◽  
Index Sequence ◽  
Single Marker ◽  
Coral Reef Ecosystems ◽  
Phylogenetic Resolution ◽  
Single Amplicon

High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rational for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach decribed here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.

scholarly journals Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons

2019 ◽  
Author(s):  
Xavier Pochon ◽  
Patricia Wecker ◽  
Michael Stat ◽  
Veronique Berteaux-Lecellier ◽  
Gael Lecellier
Keyword(s):  
High Throughput Sequencing ◽  
Critical Role ◽  
Cost Savings ◽  
Giant Clam ◽  
Sequence Coverage ◽  
Index Sequence ◽  
Single Marker ◽  
Coral Reef Ecosystems ◽  
Phylogenetic Resolution ◽  
Single Amplicon

High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rational for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach decribed here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.

scholarly journals Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via multiplex metabarcoding

2018 ◽  
Author(s):  
Xavier Pochon ◽  
Patricia Wecker ◽  
Michael Stat ◽  
Veronique Berteaux-Lecellier ◽  
Gael Lecellier
Keyword(s):  
High Throughput Sequencing ◽  
Critical Role ◽  
Cost Savings ◽  
Giant Clam ◽  
Sequence Coverage ◽  
Single Marker ◽  
Coral Reef Ecosystems ◽  
Phylogenetic Resolution ◽  
Small Set ◽  
Tridacna Maxima

High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and developed a multiplex metabarcoding method that pools and simultaneously sequences multiple Symbiodiniaceae genes for in-depth biodiversity assessments. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three multiplexed genes investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. Multiplex metabarcoding offers significant analytical cost savings while providing exceptional phylogenetic information and sequence coverage.

Multiphase Flow Meter Health Monitoring Strategy: Maximizing the Value of Real-Time Sensors and Automation for Industrial Revolution 4.0

2021 ◽  
Author(s):  
Mohammad Al-Kadem ◽  
Mohammad Gomaa ◽  
Karam Al Yateem ◽  
Abdulmonam Al Maghlouth
Keyword(s):  
Industrial Revolution ◽  
Lower Cost ◽  
Critical Role ◽  
Cost Savings ◽  
Reservoir Quality ◽  
Hardened Cement ◽  
Gas Reservoirs ◽  
First Choice ◽  
Integrity Tests ◽  
Group 1

Abstract The Cement Packer approach has been successfully implemented to pursue and monetize minor gas reservoirs of poorer quality. Due to its critical role in power supply to meet the nation's needs, license to operate gas fields oftentimes come with contractual obligations to deliver a certain threshold of gas capacity. The cement packer method is a cheaper alternative to workovers that enables operators to build gas capacity by monetizing minor gas reservoirs at lower cost. Group 1 reservoirs are the shallowest hydrocarbon bearing sand with poorer reservoir quality and relatively thin reservoirs. The behind-casing-opportunities in Minor Group-1 reservoirs previously required a relatively costly pull-tubing rig workover to monetize the reservoir. Opportunities in two wells were optimized from pull –tubing rig workovers to a non-rig program by implementing Cement Packer applications. The tubing was punched to create tubing-casing communication and cement was subsequently pumped through the tubing and into the casing. The hardened cement then acted as a barrier to satisfy operating guidelines. The reservoir was then additionally perforated, flow tested and successfully monetized at a lower cost. Tubing and casing integrity tests prior to well entry demonstrated good tubing and casing integrity. This is critical to ensure that cement will only flow into the casing where the tubing was punched. Once the cement hardened, pressure test from the tubing and from the casing indicated that the cement has effectively isolated both tubulars. Subsequent Cement Bond Log and Ultrasonic Imaging Tool showed fair to good cement above the target perforation depth. These data supported the fact that the cement packer was solid and the reservoir was ready for additional perforation. Taking into account the reservoir quality, it was decided to perforate the reservoir twice with the biggest gun available to ensure the lowest skin possible. Post perforation, there was a sharp increase in the tubing pressure indicating pressure influx from the reservoir. Despite that, casing pressure remained low, confirming no communication and thus the success of the cement packer.The well was later able to unload naturally due to its high reservoir pressure, confirming the producibility of the reservoirs and unlocking similar opportunities in other wells. Additionally, the cement packer approach delivered tremendous cost savings between $6 – 8 mil per well. Besides confirming the reservoirs' producibility,the success also unlocked additional shallow gas behind casing opportunities in the area.This method will now be the first-choice option to monetize any hydrocarbon resources in reservoirs located above the top packer.

scholarly journals Characterizing the bacterial community in bioflocs, culture water and intestines of GIFT tilapia (Oreochromis niloticus) reared in a biofloc technology (BFT) system

2020 ◽  
Author(s):  
Yang Zhang ◽  
Baoxin Cao ◽  
Godwin Abakari ◽  
Hongxin Tan ◽  
Guozhi Luo
Keyword(s):  
Oreochromis Niloticus ◽  
Intestinal Tract ◽  
High Throughput Sequencing ◽  
Breeding Period ◽  
Sequence Coverage ◽  
Dominant Group ◽  
Farmed Fish ◽  
Gift Tilapia ◽  
Biofloc Technology ◽  
Dominant Bacteria

Abstract GIFT Oreochromis niloticus was cultured in a bio-floc technology (BFT) system to identify the floral structure of the biofloc water and in the intestine of the fish. High-throughput sequencing technology was used to detect the microbes in the culture water, in the intestines and gills of farmed fish. The effective sequence coverage rate of each sample exceeded 99% and the sequencing results were true and reliable. The results show that according to Chao1 and Simpson indices, the microbial richness and diversity of flocs increase with the increase of culture time. Flocs initially favoured the thick-walled bacterium ( Firmicutes ) as the dominant fungi with abundance of 86%, whiles the rest were all less than 10% in abundance. At the end of the experiment the abundance of Chlorofiexi was 43% , Proteobacteria 26%, and Bacteroidetes 12%. During the early stages, Bacillus was the most dominant group of about 86% abundance. However, this declined towards the end of the breeding period and the abundance was recorded to reduce to about 3%. The highest abundance was associated with the bacterial described as unclassified species called N orank-f-caldilineaceae representing 40% and the abundance of Flavobacterium found to be 2%. The dominant bacteria in the intestinal tract of fish were Proteobacteria (35%), Bacillus (16%) and Cetobacterium (13%). The main heterotrophic assimilation functions in the BFT system were bacillus and chlorocampylobacter . However, flavobacterium was found in the BFT system indicating the presence of on-going denitrification

scholarly journals Digital Strategy Decision Support Systems: Agrifood Supply Chain Management in SMEs

Sensors ◽  
2021 ◽  
Vol 22 (1) ◽  
pp. 274
Author(s):  
Maria Kamariotou ◽  
Fotis Kitsios ◽  
Chrysanthi Charatsari ◽  
Evagelos D. Lioutas ◽  
Michael A. Talias
Keyword(s):  
Supply Chain ◽  
Decision Support ◽  
Information Systems ◽  
Supply Chains ◽  
Customer Value ◽  
Critical Role ◽  
Cost Savings ◽  
Strategic Decision ◽  
Digital Tools ◽  
It Executives

The specific attributes of agrifood supply chains, along with their importance for the economy and society, have led to an increased interest in the parameters that enhance their effectiveness. Recently, numerous digital tools aimed at improving supply chain effectiveness have been developed. The majority of existing research focuses on optimizing individual processes rather than the overall growth of a food supply chain. This study aims to identify the stages of the information systems planning (ISP) process that affect the success of developing a strategic decision support system (DSS) for improving the decision-making process in the agrifood supply chains. Data were collected from 66 IT executives from Greek small and medium-sized enterprises (SMEs) in the agrifood sector and analyzed using regression analysis. The results revealed that situation analysis is the only stage of ISP that predicts ISP success. These findings can assist managers in appreciating the critical role of ISP for improving the performance of agrifood supply chain operations. Implementing the most appropriate information systems (IS) and digital tools results in increased competitive advantage, cost savings, and increased customer value.

scholarly journals Transcriptome response to elevated atmospheric CO2concentration in the Formosan subterranean termite,Coptotermes formosanusShiraki (Isoptera: Rhinotermitidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2527 ◽  
Author(s):  
Wenjing Wu ◽  
Zhiqiang Li ◽  
Shijun Zhang ◽  
Yunling Ke ◽  
Yahui Hou
Keyword(s):  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Critical Role ◽  
Coptotermes Formosanus ◽  
Chemical Stimulus ◽  
Transcriptomic Response ◽  
Sequencing Platform ◽  
Genetic Information Processing ◽  
Gut Symbionts ◽  
Odorant Binding

BackgroundCarbon dioxide (CO2) is a pervasive chemical stimulus that plays a critical role in insect life, eliciting behavioral and physiological responses across different species. High CO2concentration is a major feature of termite nests, which may be used as a cue for locating their nests. Termites also survive under an elevated CO2concentration. However, the mechanism by which elevated CO2concentration influences gene expression in termites is poorly understood.MethodsTo gain a better understanding of the molecular basis involved in the adaptation to CO2concentration, a transcriptome ofCoptotermes formosanusShiraki was constructed to assemble the reference genes, followed by comparative transcriptomic analyses across different CO2concentration (0.04%, 0.4%, 4% and 40%) treatments.Results(1) Based on a high throughput sequencing platform, we obtained approximately 20 GB of clean data and revealed 189,421 unigenes, with a mean length and an N50 length of 629 bp and 974 bp, respectively. (2) The transcriptomic response ofC. formosanusto elevated CO2levels presented discontinuous changes. Comparative analysis of the transcriptomes revealed 2,936 genes regulated among 0.04%, 0.4%, 4% and 40% CO2concentration treatments, 909 genes derived from termites and 2,027 from gut symbionts. Genes derived from termites appears selectively activated under 4% CO2level. In 40% CO2level, most of the down-regulated genes were derived from symbionts. (3) Through similarity searches to data from other species, a number of protein sequences putatively involved in chemosensory reception were identified and characterized inC. formosanus, including odorant receptors, gustatory receptors, ionotropic receptors, odorant binding proteins, and chemosensory proteins.DiscussionWe found that most genes associated with carbohydrate metabolism, energy metabolism, and genetic information processing were regulated under different CO2concentrations. Results suggested that termites adapt to ∼4% CO2level and their gut symbionts may be killed under high CO2level. We anticipate that our findings provide insights into the transcriptome dynamics of CO2responses in termites and form the basis to gain a better understanding of regulatory networks.

scholarly journals Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

2021 ◽  
Author(s):  
Alex M. Mawla ◽  
Talitha van der Meulen ◽  
Mark O. Huising
Keyword(s):  
Beta Cells ◽  
Islet Cell ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Critical Role ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Alpha Beta ◽  
Cellular Identity ◽  
Delta Cells

AbstractHigh throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. Chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we identify and visualize both novel and previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin.

scholarly journals Systems Biology and Experimental Model Systems of Cancer

2020 ◽  
Vol 10 (4) ◽  
pp. 180
Author(s):  
Gizem Damla Yalcin ◽  
Nurseda Danisik ◽  
Rana Can Baygin ◽  
Ahmet Acar
Keyword(s):  
Systems Biology ◽  
Experimental Model ◽  
High Throughput Sequencing ◽  
Critical Role ◽  
Genetic Alterations ◽  
Model Systems ◽  
Treatment Modalities ◽  
Omics Data ◽  
Cancer Systems Biology ◽  
Experimental Model Systems

Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling networks through the disruption of normal cellular homeostasis is seen both in cancer cells and also in the neighboring tumor microenvironment. Cancer systems biology approaches have enabled the efficient integration of experimental data with computational algorithms and the implementation of actionable targeted therapies, as the exceptions, for the treatment of cancer. Comprehensive multi-omics data obtained through the sequencing of tumor samples and experimental model systems will be important in implementing novel cancer systems biology approaches and increasing their efficacy for tailoring novel personalized treatment modalities in cancer. In this review, we discuss emerging cancer systems biology approaches based on multi-omics data derived from bulk and single-cell genomics studies in addition to existing experimental model systems that play a critical role in understanding (epi)genetic heterogeneity and therapy resistance in cancer.

Abstract MP15: Single And Joint Associations Of Genetic Variants In The Serum/glucocorticoid Regulated Kinase (sgk) Genes With Blood Pressure Responses To Sodium Intake: The Gensalt Study

Circulation ◽  
2014 ◽  
Vol 129 (suppl_1) ◽  
Author(s):  
Changwei Li ◽  
Xueli Yang ◽  
Jiang He ◽  
James E Hixson ◽  
Dongfeng Gu ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Multiple Testing ◽  
Sodium Intake ◽  
Critical Role ◽  
Salt Sensitivity ◽  
P Value ◽  
Association Analyses ◽  
High Sodium ◽  
Single Marker ◽  
Blood Pressure Responses

Background: Serum and glucocorticoid regulated kinase (SGK) plays a critical role in the regulation of renal sodium transport. We examined the association between SGK genes and salt sensitivity of blood pressure (BP) using single-marker and gene-based association analyses. Methods: A 7-day low-sodium (51.3 mmol sodium/day) followed by a 7-day high-sodium intervention (307.8 mmol sodium/day) was conducted among 1,906 Chinese participants. BP measurements were obtained at baseline and each intervention using a random-zero sphygmomanometer. Additive associations between each SNP and salt-sensitivity phenotypes were assessed using a mixed linear regression model to account for family dependencies. Gene-based analyses were conducted using the truncated p-value method. The Bonferroni-method was used to adjust for multiple testing in all analyses. Results: In single-marker association analyses, SGK1 marker rs2758151 was significantly associated with diastolic BP (DBP) response to high-sodium intervention (P=0.0010). DBP responses (95% confidence interval) to high-sodium intervention for genotypes C/C, C/T, and T/T were 2.04 (1.57 to 2.52), 1.79 (1.42 to 2.16), and 0.85 (0.30 to 1.41) mmHg, respectively. Similar non-significant trends were observed for SBP and MAP responses (P=0.15 and 0.0026, respectively). In addition, gene-based analyses demonstrated significant associations between SGK1 and SBP, DBP and MAP responses to high sodium intervention (P=0.0002, 0.0076, and 0.00001, respectively). Neither SGK2 nor SGK3 were associated with the salt-sensitivity phenotypes in single-maker and gene-based analyses. Conclusions: The current study identified single-marker and gene-based association of the SGK1 gene and BP salt-sensitivity in the Han Chinese population. Further studies are warranted to identify causal SGK1 gene variants.

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