Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada

2021 ◽  
Author(s):  
Yvain Desplat ◽  
Jacob F Warner ◽  
Jose V Lopez
Keyword(s):  
Marine Sponge ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Model Organism ◽  
Sequence Length ◽  
Microbial Abundance ◽  
Average Sequence Length ◽  
The Common ◽  
Transcriptome Sequences ◽  
Average Sequence

Abstract Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only two sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species Cinachyrella alloclada. After Illumina high throughput sequencing, the data assembled using Trinity v2.5 confirmed a highly symbiotic organism, with the complexity of high microbial abundance (HMA) sponges. This dataset is enriched in poly-A selected eukaryotic, rather than microbial transcripts. Overall, 39,813 transcripts with verified sponge sequence homology coded for 8,496 unique proteins. The average sequence length was found to be 946 bp with an N50 sequence length of 1290 bp. Overall, the sponge assembly resulted in a GC content of 51.04%, which is within the range of GC bases in a eukaryotic transcriptome. BUSCO scored completeness analysis revealed a completeness of 60.3% and 60.1% based on the Eukaryota and Metazoa databases, respectively. Overall, this study points to an overarching goal of developing the Cinachyrella alloclada sponge as a useful new experimental model organism.

scholarly journals Synthesis, Characterization, and Aqueous Properties of an Amphiphilic Terpolymer with a Novel Nonionic Surfmer

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Qin Yu ◽  
Xiaolin Wu ◽  
Yanqiu Li ◽  
Tenglong Gao ◽  
Siliang Liu ◽  
...  
Keyword(s):  
Surface Activity ◽  
Oil Recovery ◽  
Mixed Micelles ◽  
Polymer Surface ◽  
Active Agent ◽  
Hydrophobic Association ◽  
Sequence Length ◽  
Sodium Acrylate ◽  
Average Sequence Length ◽  
Average Sequence

A series of surfactive amphiphilic polymer PAADs were prepared from the copolymerization of sodium acrylate, dodecyl polyoxyethylene acrylate (DPA, a surfmer), and acrylamide under the action of a mixed initiating agent consisting of ammonium persulfate-sodium bisulfite/2,2′-azobis[2-(2-imidazolin-2-yl) propane] dihydrochloride. The aggregative behaviors of PAADs were explored by 13C nuclear magnetic resonance, a viscometer, and a surface tension instrument. It was found that the apparent viscosity and surface activity of PAADs were significantly improved by the increase of average sequence length of hydrophobic micro blocks, strong intermolecular hydrophobic association, or the formation of mixed micelles between hydrophobic micro blocks and micromolecular surface-active agent. The introduction of long-chain alkyls on molecular chains prolonged the average sequence length of hydrophobic micro blocks in molecular chains and enhanced the hydrophobic association between molecular chains and the tight arrangement of molecular chains on water surfaces, thereby increasing the surface activity. Moreover, the anionic monomer sodium acrylate on molecular chains, via electrostatic repulsion, promoted the conversion from intrachain association to intermolecular association and thereby facilitated the formation of dense interfacial films, enhancing the surface activity of water solutions. Then, the anion surfmer sodium dodecylbenzenesulfonate interacted with the hydrophobic micro blocks on the molecular chains to form mixed micelles, which accelerated the interchain association and enhanced the polymer surface activity. The novel polymeric micelle with higher viscosifying ability and surface activity was expected to be a promising oil drive agent for tertiary oil recovery.

Relationship between Sequence Length and Thermal Properties of Poly(ethylene Terephthalate-Co-4, 4’-Bibenzoate) (PETBB)

2012 ◽  
Vol 476-478 ◽  
pp. 2243-2247
Author(s):  
Jian Ming Jiang ◽  
Jun Ming Dai ◽  
Sheng Lin Yang ◽  
Guang Li
Keyword(s):  
Chemical Composition ◽  
Melting Temperature ◽  
Ethylene Terephthalate ◽  
Feed Ratio ◽  
Sequence Length ◽  
Poly Ethylene Terephthalate ◽  
Average Sequence Length ◽  
Average Sequence ◽  
Poly Ethylene ◽  
High Level

Poly(ethylene terephthalate-co-4,4’-bibenzoate)s (PETBBs) with 0-25mol% bibenzoate unit were prepared from terephthalic acid (PTA), 4,4'- bibenzoic acid (BBA) and ethylene glycol (EG). The chemical composition and number-average sequence length of the resultant PETBBs were investigated by 13C-NMR. It was improved that the chemical composition of PETBBs is identical with the feed ratio, and the number-average sequence length of PET segment (LPET) becomes reduced with increasing BBA unit. The molecular weights of PETBBs reaches the high level for practical use. DSC analysis explains that the glass transition temperature (Tg) increases almost linearly and the crystallization becomes difficulty with increasing content of BBA unit. X-ray diffraction also illustrates that both crystallinity and crystal size reduced as more BBA unit is incorporated. Moreover, the relationship between the number-average sequence length and the melting temperature was investigated. The linear correlation between the number-average sequence length (LPET) and the melting temperature was observed.

Copolymerzation of L,L-lactide with ε-caprolactone by using novel zinc L-proline organometallic catalyst

e-Polymers ◽  
2010 ◽  
Vol 10 (1) ◽  
Author(s):  
Asutosh K. Pandey
Keyword(s):  
Nmr Spectroscopy ◽  
Block Copolymer ◽  
Ring Opening ◽  
Random Copolymer ◽  
Ring Opening Polymerization ◽  
Sequence Length ◽  
Spectroscopy Analysis ◽  
Average Sequence Length ◽  
Sequential Addition ◽  
Average Sequence

AbstractCopolyesters based on L,L-lactide (LA) and ε-caprolactone (CL) with different LA: ε-CL ratios were synthesized by ring opening polymerization using zinc (L-proline) as a catalyst. Ring opening polymerization results in random P(L, L-lactide-ε-caprolactone) copolymers of molecular weights between 9,800 to 30,000 and block copolymer up to 51,800 Da. 1H NMR spectroscopy analysis was used for calculation of monomer incorporation in the copolymer. FT-IR spectra were used to differentiate between random and block copolymer using carbonyl region splitting. 13C quantitative NMR spectroscopy analysis coupled with information from TGA and DSC allowed determination of the polymer structure. Copolymers (CP-1, CP-2 and CP-3) prepared by ROP are random copolymer (h>1), while CP-4 prepared by ROP (sequential addition of έ-caprolactone and L, L-lactide) has a multi block character (h<1). The LA number-average sequence length (LLA) decreased from 14 to 5 for LA-CL 80:20 to 50:50 copolymers prepared by ROP. The copolymer (CP-4) prepared by sequential addition showed the number-average sequence length (LLA) to be 83.0.

Poly(ethylene glycol-co-1,4-cyclohexanedimethanol terephthalate) random copolymers: effect of copolymer composition and microstructure on the thermal properties and crystallization behavior

RSC Advances ◽  
2015 ◽  
Vol 5 (74) ◽  
pp. 60570-60580 ◽  
Author(s):  
Tingting Chen ◽  
Guodong Jiang ◽  
Guoyu Li ◽  
Zhipeng Wu ◽  
Jun Zhang
Keyword(s):  
Glass Transition ◽  
Thermal Properties ◽  
Crystallization Behavior ◽  
Random Copolymers ◽  
Sequence Length ◽  
Copolymer Composition ◽  
Poly Ethylene Glycol ◽  
Average Sequence Length ◽  
Average Sequence ◽  
Poly Ethylene

The glass transition temperature of the statistically random PETG copolymers increased linearly with the increasing CT content. An increase in the average sequence length resulted in a higher melting temperature.

scholarly journals In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols

2021 ◽  
Vol 7 (2) ◽  
pp. 99
Author(s):  
Hamza Mbareche ◽  
Marc Veillette ◽  
Guillaume J. Bilodeau
Keyword(s):  
In Silico ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Sequence Length ◽  
Universal Method ◽  
Continuous Work ◽  
Its1 And Its2

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

scholarly journals First Complete Genome Sequence of Brucella abortus 2308 isolated from an abortion storm in a dairy farm in India

2021 ◽  
Author(s):  
Amit Kumar ◽  
Malyaj R Prajapati ◽  
Surendra Upadhyay ◽  
Anamika Bhordia ◽  
Vinod Kumar Singh ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Brucella Abortus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Messenger Rna ◽  
Gc Content ◽  
Dairy Farm ◽  
Rrna Genes ◽  
Sequence Length

Abstract The present report communicates the first complete genome sequence of Brucella abortus 2308 strain isolated from a an abortion storm in a dairy farm located at Kanpur, Uttar Pradesh in India. It caused the last trimester abortions of 32 animals out of 100 cows in a dairy over a period of 60 days. The bacteria were isolated in pure culture from the placenta of aborted cows. The genome sequence length of isolated bacteria is 3,285,606 bp with a 57.25 % GC content, an N50 value of 296,426, L50 value of 4 containing 3,119 coding DNA sequences (CDSs), 49 tRNAs, 1 transfer messenger RNA (mRNA), and 3 rRNA genes. It is the first report of Brucella abortus 2308 isolation and complete genome sequence from Indian subcontinent.

scholarly journals Characterization of the genome of the mealybug Planococcus lilacinus, a model organism for studying whole-chromosome imprinting and inactivation

2002 ◽  
Vol 79 (2) ◽  
pp. 111-118 ◽  
Author(s):  
K. NAGA MOHAN ◽  
PARAMITA RAY ◽  
H. SHARAT CHANDRA
Keyword(s):  
Drosophila Melanogaster ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Model Organism ◽  
Fruit Fly ◽  
Single Copy ◽  
Coding Sequences ◽  
Repeat Sequences ◽  
Chromosome Imprinting

The co-occurrence of three chromosome-wide phenomena – imprinting, facultative heterochromatization and diffuse centromere – in the mealybug Planococcus lilacinus makes investigation of the genomics of this species an attractive prospect. In order to estimate the complexity of the genome of this species, 300 random stretches of its DNA, constituting ∼0·1% of the genome, were sequenced. Coding sequences appear to constitute ∼53·5%, repeat sequences ∼44·5% and non-coding single-copy sequences ∼2% of the genome. The proportion of repetitive sequences in the mealybug is higher than that in the fruit fly Drosophila melanogaster (∼30%). The mealybug genome (∼220 Mb) is about 1·3 times the size of the fly genome (∼165 Mb) and its GC content (∼35%) less than that of the fly genome (∼40%). The relative abundance of various dinucleotides, as analysed by the method of Gentles and Karlin, shows that the dinucleotide signatures of the two species are moderately similar and that in the mealybug there is neither over-representation nor under-representation of any dinucleotide.

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