Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families

The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.

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Identification and Characterization of Satellite DNAs in Poa L.

10.21203/rs.3.rs-92594/v1 ◽

2020 ◽

Author(s):

Linna Wei ◽

Bo Liu ◽

Chunping Zhang ◽

Yang Yu ◽

Xiaoxia Yang ◽

...

Keyword(s):

5S Rdna ◽

Plant Genome ◽

Satellite Dnas ◽

Hybridization Intensity ◽

Large Genus ◽

Multiple Regions ◽

Rdna Fish ◽

Main Components ◽

Definition Of ◽

Relationship Of

Abstract BackgroundPoa L is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited.ResultsFour satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326bp (Poa-326) and 353bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species.ConclusionFour identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.

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Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal- X) of Monoclonal mice/human antibodies

10.1101/2021.07.09.451785 ◽

2021 ◽

Author(s):

IVAN VITO FERRARI ◽

Paolo PATRIZIO

Keyword(s):

Amino Acids ◽

Monoclonal Antibodies ◽

Sequence Alignment ◽

Heavy Chain ◽

Light Chain ◽

Light Chains ◽

Local Alignment ◽

Multiple Sequence ◽

Heavy Chains ◽

Search Tool

In this work, we have focused on the study of the Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal- X) of different monoclonal mice antibodies to understand better the multiple alignments of sequences. Our strategy was to compare the light chains of multiple monoclonal antibodies to each other, calculating their identity percentage and in which amino acid portion. (See below figure 2) Subsequently, the same survey of heavy chains was carried out with the same methodology. (See below figure 3) Finally, sequence alignment between the light chain of one antibody and the heavy chain of another antibody was studied to understand what happens if chains are exchanged between antibodies. (See below figure 4) From our results of BLAST estimation alignment, we have reported that the Light Chains (Ls) of Monoclonal Antibodies in Comparison have a sequence Homology of about 60-80% and they have a part identical in sequence zone in range 100-210 residues amino acids, except ID PDB 4ISV, which it turns out to have a 40% lower homology than the others antibodies. As far as, the heavy chains (Hs) of Monoclonal Antibodies are concerned, however they tend to have a less homology of sequences, compared to lights chains consideration, equal to 60%-70% and they have an identical part in the sequence zone between 150-210 residues amino acids; with the exception of ID PDB 3I9G-3W9D antibodies that have an equal homology at 50%. ( See supporting part) Summing up: about 70-80% identity among 2 light chains of 2 antibodies, 60-70% identity between 2 heavy chains of 2 antibodies, 30% identity between the two chains of a antibody and 30% if you compare the light chain of one antibody with the heavy chain of another antibody.

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Identification and characterization of satellite DNAs in Poa L.

Molecular Cytogenetics ◽

10.1186/s13039-020-00518-x ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Linna Wei ◽

Bo Liu ◽

Chunping Zhang ◽

Yang Yu ◽

Xiaoxia Yang ◽

...

Keyword(s):

5S Rdna ◽

Plant Genome ◽

Satellite Dnas ◽

Hybridization Intensity ◽

Large Genus ◽

Multiple Regions ◽

Rdna Fish ◽

Main Components ◽

Definition Of ◽

Relationship Of

Abstract Background Poa L. is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited. Results Four satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326 bp (Poa-326) and 353 bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species. Conclusion Four identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.

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Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Brazilian Journal of Biology ◽

10.1590/1519-6984.240725 ◽

2022 ◽

Vol 82 ◽

Author(s):

Z. Ahmad ◽

M. H. Abbasi ◽

S. R. Ahmad ◽

N. Sheikh

Keyword(s):

Molecular Classification ◽

Genetic Distances ◽

Coi Gene ◽

Local Alignment ◽

Identity Match ◽

Gene Coi ◽

Search Tool ◽

Identity Score ◽

First Time

Abstract Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

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MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720014500139 ◽

2014 ◽

Vol 12 (03) ◽

pp. 1450013 ◽

Cited By ~ 6

Author(s):

R. Dias ◽

M. G. Xavier ◽

F. D. Rossi ◽

M. V. Neves ◽

T. A. P. Lange ◽

...

Keyword(s):

High Performance ◽

Parallel Implementation ◽

Metagenomic Analysis ◽

Local Alignment ◽

Metagenomic Sequencing ◽

Multiple Sequence ◽

Genetic Sequencing ◽

Sequencing Technologies ◽

Sequence Search ◽

Search Tool

Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min.

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Isolation and HPLC Determination of the Chemical Components of Gentianella acuta (Michx.) Hulten

Current Analytical Chemistry ◽

10.2174/1573411014666180730113804 ◽

2018 ◽

Vol 15 (1) ◽

pp. 21-33

Author(s):

Ying Wei ◽

Yongqiao Liu ◽

Yifan Hele ◽

Weiwei Sun ◽

Yang Wang ◽

...

Keyword(s):

Medicinal Plant ◽

High Speed ◽

Chemical Constituents ◽

Folk Medicine ◽

Gradient Elution ◽

Chemical Components ◽

Isolation And Characterization ◽

Major Chemical ◽

Main Components ◽

First Time

Background: Gentianella acuta (Michx.) Hulten is an important type of medicinal plant found in several Chinese provinces. It has been widely used in folk medicine to treat various illnesses. However, there is not enough detailed information about the chemical constituents of this plant or methods for their content determination. Objective: The focus of this work is the isolation and characterization of the major chemical constituents of Gentianella acuta, and developing an analytical method for their determination. Methods: The components of Gentianella acuta were isolated using (1) ethanol extraction and adsorption on macroporous resin. (2) and ethyl acetate extraction and high speed countercurrent chromatography. A HPLC-DAD method was developed using a C18 column and water-acetonitrile as the mobile phase. Based on compound polarities, both isocratic and gradient elution methods were developed. Results: A total of 29 compounds were isolated from this plant, of which 17 compounds were isolated from this genus for the first time. The main components in this plant were found to be xanthones. The HPLC-DAD method was developed and validated for their determination, and found to show good sensitivity and reliability. Conclusion: The results of this work add to the limited body of work available on this important medicinal plant. The findings will be useful for further investigation and development of Gentianella acuta for its valuable medicinal properties.

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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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Assessment of recreational use of specially protected natural territories of Tatishchevsky district of Saratov region

RUDN Journal of Ecology and Life Safety ◽

10.22363/2313-2310-2019-27-2-117-127 ◽

2019 ◽

Vol 27 (2) ◽

pp. 117-127

Author(s):

Yulia M Andriyanova ◽

Irina V Sergeeva ◽

Yulia M Mokhonko ◽

Natalia N Gusakova

Keyword(s):

Natural Resources ◽

Protected Areas ◽

Saratov Region ◽

Future State ◽

Forest Phytocenoses ◽

Long Time ◽

Main Components ◽

First Time ◽

Recreational Use ◽

Specially Protected Natural Territories

The influence of recreation being a set of measures to restore health and recreation, on the main components of forest phytocenoses in specially protected natural territories of the Tatishchevsky district of the Saratov region has been studied for the first time. These phytocenoses have been intensively used for tourism for a long time. The intensity and visits activity of protected areas has been determined; the recreational capacity of territorial objects has been studied. The degree of forest landscapes has been revealed in specially protected natural territories. The findings allow predicting the future state of the natural resources of the Saratov region and can be taken into account when assessing their optimal use.

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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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