Pairwise Sequence Research Articles

EEG-based Emotion Recognition Using Similarity Measure of Brain Rhythm Sequencing.

The similarity is a fundamental measure from the homology theory in bioinformatics, and the biological sequence can be classified based on it. However, such an approach has not been utilized for electroencephalography (EEG)-based emotion recognition. To this end, the sequence generated by choosing the dominant brain rhythm owning maximum instantaneous power at each 0.2 s timestamp of the EEG signal has been proposed. Then, to recognize emotional arousal and valence, the similarity measures between pairwise sequences have been performed by dynamic time warping (DTW). After evaluations, the sequence that provides the highest accuracy has been obtained. Thus, the representative channel has been found. Besides, the appropriate time segment for emotion recognition has been estimated. Those findings helpfully exclude redundant data for assessing emotion. Results from the DEAP dataset displayed that the classification accuracies between 72%-75% can be realized by applying the single-channel data with a 5 s length, which is impressive when considering fewer data sources as the primary concern. Hence, the proposed idea would open a new way that uses the similarity measures of sequences for EEG-based emotion recognition.

Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.

Molecular identification of a ‘Candidatus Phytoplasma australasia’ strainin radish showing a little leaf disease in Andhra Pradesh, India

Symptoms of little leaf, proliferation of axillary buds and pale green colour leaves were observed in radish plants grown in the farmer fields at Anantapuram, Andhra Pradesh. DNA was extracted from symptomatic and asymptomatic leaves and subjected to nested PCR assay with P1/P7 and R16F2n/R16R2 primers. The about 1,250 bp amplicon was obtained only from symptomatic radish plants and the positive control, but not from any asymptomatic plants. Pair wise sequence comparison and phylogenetic analyses of 16S rRNA gene sequences of the radish phytoplasma strain suggested that it is related to ‘Candidatus Phytoplasma australasia’. Further virtual RFLP analysis of 16S rDNA sequences allowed the classification of the radish phytoplasma strain in the 16SrII-D subgroup that results to be in great expansion in this area of India.

Molecular identification of phytoplasmas associated with little leaf disease of brinjal in Andhra Pradesh and Telangana states of India

Brinjal little leaf (BLL) is a very important phytoplasma disease in India that causes severe economic losses every year. During 2020, symptoms of little leaf and witches’ broom were observed in brinjal plants grown in the farmer fields at Kadapa, Andhra Pradesh and Mahabubnagar district, Telangana states. Four symptomatic and two symptomless plants collected from the surveyed places of both states were subjected to DNA extraction and used as template in nested PCR assays with universal phytoplasma 16S rRNA primers. Amplification of about 1.25 kb product with primers R16F2n/R2 was obtained only from symptomatic BLL plants and the positive control, but not from asymptomatic plants. Pair wise sequence comparison and phylogenetic analyses of 16S rRNA gene sequences of these phytoplasma strains confirmed that the phytoplasmas from Mahabubnagar district in Telangana were ‘Candidatus Phytoplasma trifolii’-related strains, while those from Kadapa, Andhra Pradesh, were related to Ca. P australasia’. Further virtual RFLP analysis of 16S rDNA sequences allowed the classification of these strains into 16SrVI-D and 16SrII-D subgroups, respectively.

Prevalence and molecular analysis of Sarcocystis infections in cattle in Northwest Iran and the first global report of S. gigantea in cattle

Cattle are intermediate host for several species of Sarcocystis, including S. cruzi, S. hirsuta, and S. hominis with high prevalence worldwide. The present study aimed to determine the prevalence of Sarcocystis infection, species identification, and phylogenetic analysis of the parasite in cattle in Northwest Iran. The samples of diaphragm and esophagus from 290 cattle were collected from slaughterhouses in Northwest Iran and subjected to macroscopic, microscopic, and histopathology examinations, PCR-RFLP, sequencing and phylogenetic analyses. Tissue cysts of Sarcocystis spp. were detected in 92% of cattle by digestion and microscopic tests. Based on the PCR–RFLP and specific PCR, 87.9% and 1.03% of isolates were identified as S. cruzi, and S. hominis, respectively. Macrocyst was seen in a single sample that was identified as S. gigantea. The haplotype network exhibited the extension of the various haplotypes of S. cruzi between neighboring provinces in Northwest Iran. Heterogeneity analysis of S. cruzi 18S-rRNA sequences indicated genetic diversity among S. cruzi isolates (Haplotype diversity: 0.733-0.854) consisting 16 haplotypes; however, the nucleotide differences showed low diversity (0.01481 to 0.03351). Pair wise sequence distance matrix amongst S. cruzi sequences indicated an intra-species divergence of 0%-7.8% and identity of 92.6%-100%. Sarcocystis infection is highly prevalent in cattle in Northwest Iran, with the predominance of S. cruzi, and genetic variants of this species are unequivocally distributing in Northwest provinces. First global detection of S. gigantea in cattle reflects new insights of transmission dynamic and biology of this parasite in Iran.

Mrakia panshiensis sp. nov. a new member of the Cystofilobasidiales from soil in China, and description of the teleomorphic-stage of M. arctica.

In a study on the fungal diversity in Northeast China, twelve yeast isolates were obtained from soils collected in three provinces, Helongjiang, Jilin and Liaoning. Morphological assessment and phylogenetic analyses of the nuc rDNA internal transcribed spacer (ITS) region and the D1/D2 domains of the nuc 28S rDNA (nuc 28S) gene of the 12 cultures placed them in the genus Mrakia, namely Mrakia aquatica, Mrakia arctica, Mrakia frigida, Mrakia gelida and Mrakia robertii. A total of three isolates represented a hitherto undescribed species, which is described here as M. panshiensissp. nov. (MB 834813). The species M. panshiensissp. nov. shares several morphological characters with M. niccombsii, M. aquatica, M. fibulata and M. hoshinonis. These species can be distinguished based on physiological traits and pairwise rDNA sequence similarities. The study also describes for the first time the formation of teliospores by previously described M. arctica.

A panel of anti-influenza virus nucleoprotein antibodies selected from phage-displayed synthetic antibody libraries with rapid diagnostic capability to distinguish diverse influenza virus subtypes

Immunoassays based on sandwich immuno-complexes of capture and detection antibodies simultaneously binding to the target analytes have been powerful technologies in molecular analyses. Recent developments in single molecule detection technologies enable the detection limit of the sandwich immunoassays approaching femtomolar (10–15 M), driving the needs of developing sensitive and specific antibodies for ever-increasingly broad applications in detecting and quantifying biomarkers. The key components underlying the sandwich immunoassays are antibody-based affinity reagents, for which the conventional sources are mono- or poly-clonal antibodies from immunized animals. The downsides of the animal-based antibodies as affinity reagents arise from the requirement of months of development timespan and limited choices of antibody candidates due to immunodominance of humoral immune responses in animals. Hence, developing animal antibodies capable of distinguishing highly related antigens could be challenging. To overcome the limitation imposed by the animal immune systems, we developed an in vitro methodology based on phage-displayed synthetic antibody libraries for diverse antibodies as affinity reagents against closely related influenza virus nucleoprotein (NP) subtypes, aiming to differentiating avian influenza virus (H5N1) from seasonal influenza viruses (H1N1 and H3N2), for which the NPs are closely related by 90–94% in terms of pairwise amino acid sequence identity. We applied the methodology to attain, within four weeks, a panel of IgGs with distinguishable specificities against a group of representative NPs with pairwise amino acid sequence identities up to more than 90%, and the antibodies derived from the antibody libraries without further affinity refinement had comparable affinity of mouse antibodies to the NPs with the detection limit less than 1 nM of viral NP from lysed virus with sandwich ELISA. The panel of IgGs were capable of rapidly distinguishing infections due to virulent avian influenza virus from infections of seasonal flu, in responding to a probable emergency scenario where avian influenza virus would be transmissible among humans overlapping with the seasonal influenza infections. The results indicate that the in vitro antibody development methodology enables developing diagnostic antibodies that would not otherwise be available from animal-based antibody technologies.

Identification and genome characterization of a novel picornavirus from ducks in China.

A novel picornavirus, referred to as Duck/FC22/China/2017, was isolated from breeding ducks in China and genetically characterized by conducting metagenomics studies. The complete genome consists of a single-stranded, positive-sense RNA made up of 7448 nucleotides (nt) and follows the common picornavirus genome layout: 5' UTR-VP0-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3' UTR. A typical type-IV internal ribosomal entry site and a conserved 'barbell-like' structure were identified in the 5' UTR and 3' UTR, respectively. The unique 6423-nt open reading frame was predicted to encode a 2141-amino-acid (aa) polyprotein precursor. A pairwise aa sequence identity comparison and phylogenetic analysis revealed that Duck/FC22/China/2017 is closely related to duck aalivirus, duck hepatitis A virus, turkey avisivirus, and red-crowned crane picornavirus.

Understanding recurrent neural network for texts using English-Korean corpora

Deep Learning is the most important key to the development of Artificial Intelligence (AI). There are several distinguishable architectures of neural networks such as MLP, CNN, and RNN. Among them, we try to understand one of the main architectures called Recurrent Neural Network (RNN) that differs from other networks in handling sequential data, including time series and texts. As one of the main tasks recently in Natural Language Processing (NLP), we consider Neural Machine Translation (NMT) using RNNs. We also summarize fundamental structures of the recurrent networks, and some topics of representing natural words to reasonable numeric vectors. We organize topics to understand estimation procedures from representing input source sequences to predict target translated sequences. In addition, we apply multiple translation models with Gated Recurrent Unites (GRUs) in Keras on English-Korean sentences that contain about 26,000 pairwise sequences in total from two different corpora, colloquialism and news. We verified some crucial factors that influence the quality of training. We found that loss decreases with more recurrent dimensions and using bidirectional RNN in the encoder when dealing with short sequences. We also computed BLEU scores which are the main measures of the translation performance, and compared them with the score from Google Translate using the same test sentences. We sum up some difficulties when training a proper translation model as well as dealing with Korean language. The use of Keras in Python for overall tasks from processing raw texts to evaluating the translation model also allows us to include some useful functions and vocabulary libraries as well.

Mussaenda erythrophylla: A new host of ‘Candidatus Phytoplasma asteris’ in India

Leaf yellowing symptoms were observed in Mussaenda erythrophylla at Digiyana Park, Jammu during June 2016. Leaf yellowing and flat stem symptoms were also observed on nearby planted Catharanthus roseus and Celosia argentea, respectively. Amplicons of ~ 1.25 kb were consistently amplified in nested PCR assays with DNA extracted from all the symptomatic Mussaenda erythrophylla, Catharanthus roseus and Celosia argentea samples using primer pairs P1/P7 followed by R16F2n/R2. However, no amplifications were achieved with any of the asymptomatic plant samples. Pair wise sequence comparison of the ~ 1.25 kb products of 16S rDNA sequence of M. erythrophylla leaf yellowing, C. roseus leaf yellowing and C. argentea flat stem phytoplasma isolates revealed 99.8% sequence identity with ‘Candidatus Phytoplasma asteris’ related strains. Phylogeny and virtual RFLP analysis of 16S rDNA sequences confirmed the affiliation of ‘Ca. P. asteris’ subgroup I-B with all the three symptomatic plant samples. This is the first report of association of ‘Ca. P. asteris’ subgroup I-B with M. erythrophylla worldwide.

Mitochondrial DNA (hypervariable region I) diversity in Basrah population – Iraq

In attempt to investigate the origin of Basrah, we examined the mitochondrial DNA(mt-DNA) variations by hypervariable segment 1(HVS1) Sequencing and determination of specific site haplogroups. In Basrah, no significant differences diversity among Iraqis' HVS1 compared with other countries. The values were within the range of gene diversity across the Middle East and exhibited the unimodal pattern of differences in the pairwise sequence. Given the small genetic differences between people living in this area, phylogenetic analysis showed a large variability of the communities of Basrah; they didn't cluster on the phylogenetic tree.

An Implementation of Three-level Multi-objective ABC Algorithm for RNA Multiple Structural Alignment

Background: Structural alignment of ribose nucleic acid (RNA) is one of the most challenging multi-objective real world problems from the field of bioinformatics. Objective: RNA molecules are less stable; hence they require inclusion of most stable secondary structure during their alignment. Therefore, the structural alignment requires the consideration of similarity score and structure score, as two objectives. Trade-off between these two objectives exists since obtaining optimum similarity score at concurrent optimum structure score is not possible. This paper presents artificial bee colony algorithm based three level multi-objective approach for performing structural alignment of RNA sequences, namely MO-3LABC. Methods: Algorithm firstly builds the secondary structure of all sequences at minimum free energy (MFE). Then sequence alignment is performed in level one at average percent sequence identity (APSI) score based gap length, optimized by ABC algorithm. Level two now builds the secondary structure of these aligned sequences based on base-pair probability and co-variation. Now the scores of level one and level two move towards level three for multi-objective optimization at Pareto optimality criteria with few additional strategies. Results: The results of MO-3LABC are compared with an already established efficient strategy MO-TLPSO; multi-objective two level strategy based on particle swarm optimization. The outputs are compared for pairwise and multiple sequence alignment datasets at prediction accuracy and solution quality criteria. Conclusion: MO-3LABC is found significantly better than MO-TLPSO at all the four evaluation criteria for both the datasets.

Identification of phytoplasma in six fruit crops in India

Symptoms of decline, leaf yellowing and reddening, little leaf and malformation were observed in apricot, guava, lychee, mango, pomegranate and grapevine in fruit orchards belonging to three states of India namely Delhi, Maharashtra and Jammu & Kashmir during 2016–2017. Phytoplasmas belonging to three different groups were detected in all the symptomatic fruit tree samples in polymerase chain reaction with phytoplasma specific primer pairs amplifying 16S rRNA and secA genes. Pair wise sequence comparison and phylogenetic analysis confirmed the presence of phytoplasmas. A ‘Candidatus Phytoplasma asteris’ - related strain was detected in apricot showing decline symptoms in Siot (Jammu & Kashmir). ‘Ca. P. australasia’ - related strain was identified in guava, lychee, mango and pomegranate in Rajbag, Sunjwan (Jammu & Kashmir), Pusa (Delhi) and Baramati (Maharashtra), respectively, exhibiting little leaf, leaf yellows and malformation symptoms. Furthermore, a rice yellow dwarf group (16SrXI-B) - related strain was detected in pomegranate and grapevine that showed leaf yellowing and reddening at Pusa (Delhi) and Baramati (Maharashtra), respectively. Subgroup analysis using virtual RFLP of 16S rDNA sequences allowed enclosing these phytoplasma strains into 16SrI-B, 16SrII-D and 16SrXI-B subgroups. In the study, identification of phytoplasma subgroups, 16SrI-B in apricot, 16SrII-D in guava, lychee, mango and pomegranate (Pusa) and 16SrXI-B in pomegranate (Baramati) and grapevine, are the first records globally.

Characterization and genetic diversity of phytoplasmas associated with elephant foot yam (Amorphophallus paeoniifolius) in India.

During the growing season of 2015 and 2016, leaf yellowing, stunting, and declining symptoms were observed on elephant foot yam in three states of India.The 1.3kb 16S rDNA fragments were amplified from genomic DNA extracted from all the symptomatic elephant foot yam samples in nested PCR assays using primer pairs, P1/P7 followed by 3F/3R. Pair wise sequence comparison, virtual RFLP and phylogenetic analysis of 16S rRNA gene sequences confirmed association of 'Candidatus Phytoplasma trifolii' (16SrVI-D) and 'Candidatus Phytoplasma oryzae' (16SrXI-B) related strains in Uttar Pradesh, Uttarakhand and Tripura states, respectively. To our knowledge, this is the first report of association of 'Ca. P. trifolii' and 'Ca. P. oryzae' related strains in elephant foot yam in world. In the present study, we also reported Datura stramonium showing witches' broom as a natural weed host for 'Ca. P. trifolii' phytoplasma in Gorakhpur and Kushinagar districts of Uttar Pradesh state, India.

High scoring segment selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs

Whole genome alignment programs use string matching with hash tables to identify high scoring fragments between a query and target sequence around which a full alignment is then built. A recent study comparing alignment programs showed that while evolutionary similar genomes were easy to align, divergent genomes still posed a challenge to existing methods. To fill this gap we explore the use of the maximum scoring subsequence to identify high scoring fragments. We split the query genome into several fragments and align them to the target with a previously published parallel algorithm for short read alignment. We then pass such high scoring fragments on to the LASTZ program to obtain a more complete alignment. On simulated data we obtain an average of at least 20% higher accuracy than the alignment given by LASTZ at the expense of few hours of additional runtime. Our source code is freely available at http://web.njit.edu/usman/MSGA

A new strain of ‘Candidatus phytoplasma asteris’ associated with bottlegourd phyllody disease in South India

Bottle gourd is an important cucurbitaceous vegetable crop and plants showing phyllody symptoms were observed in Bangaluru rural area of Karnataka state, India. To verify the presence of phytoplasmas total genomic DNA was extracted from symptomatic plants using a CTAB-based method and subjected to PCR assay using 16S rRNA gene specific primer pair P1/P7 followed by R16F2n/R2 nested primer pairs. The amplicons of about 1.2 kb were observed in all the symptomatic samples in nested PCR assays. The comparison of 16S rRNA gene sequence through pair wise sequence analysis and phylogeny analysis confirmed that the detected phytoplasma was closely related to those enclosed in the aster yellows group. The virtual RFLP analysis of the 16Sr DNA sequence showed restriction profiles very close to those of the 16SrI-S subgroup strain except for the MseI restriction profile, which suggested that this could be a new strain in the 16SrI group.

Identification of phytoplasmas in 16SrI-D subgroup in mango with malformation and witches’ broom disease in Punjab, India

Symptoms of mango malformation and witches’ broom were observed in mango orchards at Ludhiana, Punjab, India during 2020. Phytoplasmas were detected in the symptomatic mango samples by polymerase chain reaction with specific primer pairs amplifying 16S rRNA and secA genes. Pair wise sequence comparison and phylogenetic analysis of 16S rRNA and secA gene sequences of mango phytoplasma strains indicate their relatedness with phytoplasmas in the aster yellows group. In silico RFLP analyses using the iPhy Classifier of the 16S rDNA sequence of the mango phytoplasma allowed its classification into the 16SrI-D subgroup. This is first report of this phytoplasma in mango plants showing a malformation and witches’ broom disease.

First report of 16Sr II‐C subgroup phytoplasma association with Acacia mangium in Tripura, India

AbstractLeaf yellowing symptoms were observed on Acacia mangium in the Sipahijala district of Tripura, India, during June 2017. Symptomatic and asymptomatic leaf samples (three of each) were collected from roadside trees of A. mangium for DNA extraction using the CTAB method. Amplicons of ~1.25 kb and ~480 bp were detected in all the symptomatic samples using the phytoplasma‐specific universal 16S rRNA and secA gene primers. Pair wise sequence analysis of 16S rRNA gene sequences, virtual RFLP and phylogenetic analysis revealed that the phytoplasma strain associated with A. mangium belonged to phytoplasma subgroup 16SrII‐C. This is the first report of an association between the 16SrII‐C subgroup and A. mangium leaf yellowing.

A common root for coevolution and substitution rate variability in protein sequence evolution

We introduce a simple model that describes the average occurrence of point variations in a generic protein sequence. This model is based on the idea that mutations are more likely to be fixed at sites in contact with others that have mutated in the recent past. Therefore, we extend the usual assumptions made in protein coevolution by introducing a time dumping on the effect of a substitution on its surrounding and makes correlated substitutions happen in avalanches localized in space and time. The model correctly predicts the average correlation of substitutions as a function of their distance along the sequence. At the same time, it predicts an among-site distribution of the number of substitutions per site highly compatible with a negative binomial, consistently with experimental data. The promising outcomes achieved with this model encourage the application of the same ideas in the field of pairwise and multiple sequence alignment.

Genome sequence and phylogenetic analysis of a novel comovirus from tabasco pepper (Capsicum frutescens).

A virus isolate from tabasco pepper (Capsicum frutescens) has been reported as a strain of the comovirus Andean potato mottle virus (APMoV). Using the replicative intermediate viral dsRNA, the pepper virus strain was sequenced by Illumina MiSeq. The viral genome was de novo assembled resulting in two RNAs with lengths of 6028 and 3646 nt. Nucleotide sequence analysis indicated that they corresponded to the RNA-1 and RNA-2 of a novel comovirus which we tentatively named pepper mild mosaic virus (PepMMV). Predictions of the open reading frame (ORF) of RNA-1 resulted in a single ORF of 5871 nt with five cistrons typical of comoviruses, cofactor proteinase, helicase, viral protein genome-linked, 3C-like proteinase (Pro), and RNA-dependent RNA polymerase (RdRP). Similarly, sequence analysis of RNA-2 resulted in a single ORF of 3009 nt with two cistrons typical of comoviruses: movement protein and coat protein (large coat protein and small coat proteins). In pairwise amino acid sequence alignments using the Pro-Pol protein, PepMMV shared the closest identities with broad bean true mosaic virus and cowpea mosaic virus, 56% and 53.9% respectively. In contrast, in alignments of the amino acid sequence of the coat protein (small and large coat proteins) PepMMV shared the closest identities to APMoV and red clover mottle virus, 54% and 40.9% respectively. A phylogenetic tree constructed using the conserved domains for the Pro-Pol from all members of the family Secoviridae confirmed the comovirus nature of the virus. Phylogenetic and sequence analyses supports proposing PepMMV as a new species of the genus Comovirus.