Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

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The Influence of Memory-Aware Computation on Distributed BLAST

Current Bioinformatics ◽

10.2174/1574893613666180601080811 ◽

2019 ◽

Vol 14 (2) ◽

pp. 157-163

Author(s):

Majid Hajibaba ◽

Mohsen Sharifi ◽

Saeid Gorgin

Keyword(s):

Search Time ◽

Genomic Research ◽

Local Alignment ◽

Negative Effects ◽

Sequencing Technologies ◽

Percent Improvement ◽

Fast Processing ◽

Search Tool ◽

Memory Awareness ◽

Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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Sense codon reassignment enables viral resistance and encoded polymer synthesis

Science ◽

10.1126/science.abg3029 ◽

2021 ◽

Vol 372 (6546) ◽

pp. 1057-1062

Author(s):

Wesley E. Robertson ◽

Louise F. H. Funke ◽

Daniel de la Torre ◽

Julius Fredens ◽

Thomas S. Elliott ◽

...

Keyword(s):

Stop Codon ◽

Synonymous Codon ◽

Viral Resistance ◽

Release Factor ◽

Codon Reassignment ◽

Efficient Synthesis ◽

Noncanonical Amino Acids ◽

Laboratory Evolution ◽

Transfer Rnas ◽

Sense Codon

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)—making their cognate codons unreadable—might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.

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Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

Scientific Reports ◽

10.1038/s41598-021-81063-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dimitri Boeckaerts ◽

Michiel Stock ◽

Bjorn Criel ◽

Hans Gerstmans ◽

Bernard De Baets ◽

...

Keyword(s):

Machine Learning ◽

Predictive Model ◽

Receptor Binding ◽

Bacterial Infections ◽

Sequence Data ◽

Sequence Similarity ◽

Area Under The Curve ◽

Local Alignment ◽

Search Tool ◽

Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

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Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

Malaria Journal ◽

10.1186/s12936-020-03467-3 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Ommer Mohammed Dafalla ◽

Mohammed Alzahrani ◽

Ahmed Sahli ◽

Mohammed Abdulla Al Helal ◽

Mohammad Mohammad Alhazmi ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Saudi Arabia ◽

Parasite Clearance ◽

Sub Saharan Africa ◽

Local Alignment ◽

Nucleotide Polymorphisms ◽

Gene Encoding ◽

Synonymous Mutations ◽

Search Tool ◽

Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

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Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202132201038 ◽

2021 ◽

Vol 322 ◽

pp. 01038

Author(s):

Tuah N. M. Wulandari

Keyword(s):

Phylogenetic Tree ◽

Coi Gene ◽

Local Alignment ◽

Mtdna Sequences ◽

Mitochondrial Coi ◽

Search Tool ◽

Very High ◽

I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

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A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient

European Journal of Medical and Health Sciences ◽

10.24018/ejmed.2021.3.2.744 ◽

2021 ◽

Vol 3 (2) ◽

pp. 19-21

Author(s):

Marjia Khatun ◽

Laila Anjuman Banu

Keyword(s):

Transcription Factor ◽

Pediatric Patient ◽

Congenital Hypothyroidism ◽

Sanger Sequencing ◽

Demographic Data ◽

Local Alignment ◽

Cycle Sequencing ◽

Thyroid Transcription Factor ◽

Search Tool ◽

Information Database

A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardian of the pediatric patient, socio-demographic data was collected. Isolation of DNA, quantitation and qualitation of DNA was ensured, polymerase chain reaction (PCR) was performed, the amplicons that was obtained from PCR; validated visually by gel electrophoresis methods; cycle sequencing was performed by Sanger sequencing. The chromatogram data that was obtained from Sanger sequencing was analyzed and compared with the National Center for Biotechnology Information database by Basic Local Alignment Search Tool search. Sanger sequencing revealed substitution (c.1051G>T) in the Sequence Tagged Site of the exon2 of Thyroid transcription factor 2 gene and this is new variants and not reported in National Center for Biotechnology Information database.

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Dietary Effect of Kelp (Saccharina japonica) on Gonad Quantity and Quality in Sea Urchins (Mesocentrotus nudus) Collected from a Barren Before the Fishing Season

Journal of Shellfish Research ◽

10.2983/035.037.0318 ◽

2018 ◽

Vol 37 (3) ◽

pp. 659-669 ◽

Cited By ~ 9

Author(s):

Satomi Takagi ◽

Yuko Murata ◽

Eri Inomata ◽

Hikaru Endo ◽

Masakazu N. Aoki ◽

...

Keyword(s):

Sea Urchins ◽

Saccharina Japonica ◽

Fishing Season ◽

Mesocentrotus Nudus

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Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

Genes ◽

10.3390/genes9110546 ◽

2018 ◽

Vol 9 (11) ◽

pp. 546 ◽

Cited By ~ 9

Author(s):

David Schwark ◽

Margaret Schmitt ◽

John Fisk

Keyword(s):

Stop Codon ◽

Release Factor ◽

Codon Reassignment ◽

Methanocaldococcus Jannaschii ◽

E Coli ◽

Amber Stop Codon ◽

Orthogonal Pair ◽

Amber Codon ◽

Quantitative Contribution ◽

Stop Codon Reassignment

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.

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Impacts of water temperature on the physiology and behaviours of the sea urchins Heliocidaris crassispina and Mesocentrotus nudus that reflect their range extension and disappearance in the Oga Peninsula, northern Honshu, Japan

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2020-0327 ◽

2020 ◽

Author(s):

Wenping Feng ◽

Nobuyasu Nakabayashi ◽

Eri Inomata ◽

Masakazu N. Aoki ◽

Yukio Agatsuma

Keyword(s):

Low Temperature ◽

Native Species ◽

Feeding Rate ◽

Sea Urchins ◽

Temperature Limit ◽

Feeding Rates ◽

Righting Response ◽

Mesocentrotus Nudus ◽

Temperature Rate ◽

High Or Low Temperature

Ocean warming has facilitated the extension of Heliocidaris crassispina to Oga Peninsula, Japan, where the native species Mesocentrotus nudus has disappeared. To verify the temperature impacts on the physiology and behaviour of the two species, we reared small sea urchins at the increasing/decreasing temperature rate of 2.5°C week-1. The righting response, lantern reflex, gonad and gut carbon (C) and nitrogen (N) contents, and feeding rate were investigated. The high and low temperature limits of H. crassispina were 33.3°C and 3.9°C, respectively, which were higher than those of M. nudus. The optimal temperature ranges for behaviour and feeding in H. crassispina were 10.3–31.0°C and 10.3–33.4°C, respectively, which were higher than those in M. nudus. Feeding rates decreased significantly in both species when the temperature approached the high or low temperature limit, but the gut C and N contents of were not greatly affected. At 26–31°C, the feeding rate significantly decreased in M. nudus but not in H. crassispina, which may explain the replacement of M. nudus by H. crassispina in the Oga Peninsula.

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CaPSY1 gene plays likely the key role in carotenoid metabolism of pepper (Capsicum annuum) at ripening

Functional Plant Biology ◽

10.1071/fp19287 ◽

2021 ◽

Vol 48 (2) ◽

pp. 141

Author(s):

Xiaochun Wei ◽

Chunyang Meng ◽

Yuxiang Yuan ◽

Ujjal Kumar Nath ◽

Yanyan Zhao ◽

...

Keyword(s):

Developmental Stages ◽

Carotenoid Biosynthesis ◽

Local Alignment ◽

Fruit Colour ◽

Virus Induced Gene Silencing ◽

Carotenoid Metabolism ◽

Pepper Fruit ◽

Search Tool ◽

Pepper Genome ◽

Aba Content

Phytoene synthase (PSY) is the first committed enzyme in carotenoid biosynthesis, which plays important role in ripen fruit colour. However, the roles of CaPSY genes are not explained detail in ripen pepper fruit colour. In this study, three CaPSY genes (CaPSY1, CaPSY2 and CaPSY3) were identified through basic local alignment search tool (BLAST) in pepper genome. Among them, CaPSY1 was predicted as putative candidate based on relative expression values using five developmental stages of fruit in Zunla-1 cultivar and also in ripen fruits of five contrasting pepper lines. The CaPSY1 was characterised functionally through virus-induced gene silencing (VIGS) in ripen fruits and overexpression in Arabidopsis thaliana (L.) Heynh. Silencing of CaPSY1 gene altered colour with increased lutein and decreased zeaxanthin content in pepper fruits. The transgenic Arabidopsis line CaPSY1 gene showed higher expression of PSY1 gene compared with WT and dwarf phenotype due to reduction of GA3 (gibberellic acid) and higher abscisic acid (ABA) content. Our results confirmed that CaPSY1 gene involved in carotenoid metabolism in ripen pepper fruit and provide clue to develop bright red coloured pepper lines through breeding.

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