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Purpose of this work is the comparative analysis of two approaches to the synthesis of two-dimensional binary identifiers of nucleotide sequences obtained using DNA sequencing of biological objects. Methods. One of the approaches is based on modeling the polarization-dependent diffraction of a coherent readout beam on a two-dimensional phase-modulating structure (phase screen) associated with the symbolic sequence obtained as a result of DNA sequencing. Another approach uses a two-dimensional representation of the symbolic sequence using a chaos game representation (CGR). To obtain a finite-element CGR mapping, it is fragmented into a given number of cells, ensuring acceptable sensitivity of the synthesized binary identifier to structural changes in the displayed sequence. Results. The comparative analysis was carried out using fragments of symbol sequences corresponding to various strains (Wuhan, Delta, Omicron) of the SarSCoV2 virus. In the course of the analysis, the correlation coefficients between the binary identifiers corresponding to various strains were obtained and compared with each other. Conclusion. It has been established that binary identifiers synthesized using the polarization encoding technique are characterized by significantly higher sensitivity to structural changes in the analyzed sequences and smaller sizes compared to CGR binary identifiers.

Ceresium sinicum ornaticolle Pic, 1907 (Coleoptera: Cerambycidae) is one of the main pests of pomegranate and citrus trees. In this study, we described the complete mitochondrial genome of C. sinicum ornaticolle. The total length of the mitochondrial genome was 15,817 bp, and the entire content of GC was 27.8%. The genome encoded 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The phylogenetic tree showed that C. sinicum ornaticolle was clustered with Allotraeus orientalis and Zoodes fulguratus. These results will provide the genetic information for understanding the genetic evolution of C. sinicum ornaticolle and the insights to control cerambycid pests.

Ceresium sinicum ornaticolle Pic, 1907 (Coleoptera: Cerambycidae) is one of the main pests of pomegranate and citrus trees. In this study, we described the complete mitochondrial genome of C. sinicum ornaticolle. The total length of the mitochondrial genome was 15,817 bp, and the entire content of GC was 27.8%. The genome encoded 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The phylogenetic tree showed that C. sinicum ornaticolle was clustered with Allotraeus orientalis and Zoodes fulguratus. These results will provide the genetic information for understanding the genetic evolution of C. sinicum ornaticolle and the insights to control cerambycid pests. [ABSTRACT FROM AUTHOR]

Features of shell and genitalia as well as nucleotide sequences of selected mitochondrial and nuclear genes of specimens of Monacha cantiana from ten northern French and two Dutch populations were compared with the same features of British and Italian populations. They were found to be very similar to populations previously identified as belonging to the CAN-1 lineage of M. cantiana. This confirms previous suggestions that M. cantiana was introduced to western Europe (England, France and the Netherlands) in historical times. [ABSTRACT FROM AUTHOR]

Two approaches to the synthesis of 2D binary identifiers (“fingerprints”) of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).

The article presents the results of a molecular genetic study of two isolates of the Pseudorabies virus that were isolated from pigs in Ukraine. Bioinformatic analysis of the gE gene fragment of Aujeszky's disease virus (Pseudorabies virus) isolates was carried out in order to determine the phylogenetic relationships and homology of nucleotide sequences. Fragments of the Aujeszky disease virus genome corresponding to the C-terminal region of the gE gene were selected for sequencing and further analysis. As a result of the conducted studies, it was demonstrated that the nucleotide sequences of the analyzed samples differ from each other by the presence of ACG insert in the tandem repeats region. Comparison of the studied sequences with the sequences of strains/isolates of the Aujeszky's disease virus found in Europe and Asia, presented in the GenBank database, indicates that such an insert is characteristic for the Min-A and HNJZ strains (position 1487 in the gE gene) isolated in Asia. Analysis of the homology of nucleotide sequences showed that the sequence of the gE gene fragment of sample No. 1 is 100% identical to the sequences of strains 89V87 and 00V72 isolated in Belgium. The homology of the nucleotide sequence of the gE gene fragment of sample No. 3 with strains 89V87 and 00V72 was 99.13%. In order to clarify the analyzed samples belonging to a particular genogroup (genetic cluster), a phylogenetic dendrogram was constructed. This demonstrates the phylogenetic relationships between strains/isolates of the Aujeszky's disease virus. It was found that the analyzed samples belong to the genetic cluster uniting European strains/isolates, and the studied isolates are most genetically close to strains 89V87 and 00V72.

Background and Objectives: The method of identification of symbolic sequences associated with the genetic structure of biological objects using the principles of small-angle polarimetry is considered. This method of analyzing and visualizing symbolic sequences obtained by sequencing DNA fragments can be defined as small-angle polarimetry of phase-modulating structures associated with genetic information. Materials and Methods: The analyzed symbolic sequence is represented by a two-dimensional phase-modulating matrix, each element of which corresponds to one of the four basic nucleotides (adenine, cytosine, thymine, guanine), and the depth of modulation of the phase of the reading coherent linearly polarized beam is determined by the content of this nucleotide in the corresponding triplet in the nucleotide sequence. As a result of the diffraction of a reading coherent beam with a polarization plane oriented at an angle of 45° to the sides of the phase-modulating matrix, a spatial distribution of local polarization states of the reading field diffracted on the matrix is formed in the paraxial region of the far diffraction zone. Discrimination of local polarization states in accordance with the proposed algorithm makes it possible to synthesize a binary spatial distribution, which is a unique identifier of the analyzed symbol sequence. Results: Modeling of the processes of phase coding and subsequent analysis of local polarization states in the near-axial region using sequencing results for the strains “Wuhan”, “Delta” and “Omicron” of the SARS-CoV-2 virus has shown a high sensitivity of the method to local changes in the structure of nucleotide sequences. Conclusion: The results of the simulation allow us to conclude that binary distributions of local polarization states of light fields diffracted on DNA-associated phase-modulating structures recorded in the axial region are characterized by high sensitivity to local mutational changes in the structure of nucleotide sequences. The results obtained can be used as a basis for creating effective hybrid methods for analyzing genetic information using the principles of polarization coding and small-angle polarimetry.

Results of computational analysis and visualization of differences in gene structures using polarization coding are presented. A two-dimensional phase screen, where each element of which corresponds to a specific basic nucleotide (adenine, cytosine, guanine, or thymine), displays the analyzed nucleotide sequence. Readout of the screen with a coherent beam characterized by a given polarization state forms a diffracted light field with a local polarization structure that is unique for the analyzed nucleotide sequence. This unique structure is described by spatial distributions of local values of the Stokes vector components. Analysis of these distributions allows the comparison of nucleotide sequences for different strains of pathogenic microorganisms and frequency analysis of the sequences. The possibilities of this polarization-based technique are illustrated by the model data obtained from a comparative analysis of the spike protein gene sequences for three different model variants (Wuhan, Delta, and Omicron) of the SARS-CoV-2 virus. Various modifications of polarization encoding and analysis of gene structures and a possibility for instrumental implementation of the proposed method are discussed.

Abstract As of June 2022, the GISAID database contains more than 11 million SARS-CoV-2 genomes, including several thousand nucleotide sequences for the most common variants such as delta or omicron. These SARS-CoV-2 strains have been collected from patients around the world since the beginning of the pandemic. We start by assessing the similarity of all pairs of nucleotide sequences using the Jaccard index and principal component analysis. As shown previously in the literature, an unsupervised cluster analysis applied to the SARS-CoV-2 genomes results in clusters of sequences according to certain characteristics such as their strain or their clade. Importantly, we observe that nucleotide sequences of common variants are often outliers in clusters of sequences stemming from variants identified earlier on during the pandemic. Motivated by this finding, we are interested in applying outlier detection to nucleotide sequences. We demonstrate that nucleotide sequences of common variants (such as alpha, delta, or omicron) can be identified solely based on a statistical outlier criterion. We argue that outlier detection might be a useful surveillance tool to identify emerging variants in real time as the pandemic progresses.

The article presents the results of a molecular genetic study of two isolates of the Pseudorabies virusthat were isolated from pigs in Ukraine. Bioinformatic analysis of the gE gene fragment of Aujeszky's disease virus (Pseudorabies virus) isolates was carried out in order to determine the phylogenetic relationships and homology of nucleotide sequences. Fragments of the Aujeszky disease virus genome corresponding to the C-terminal region of the gE gene were selected for sequencing and further analysis. As a result of the conducted studies, it was demonstrated that the nucleotide sequences of the analyzed samples differ from each other by the presence of ACG insert in the tandem repeats region. Comparison of the studied sequences with the sequences of strains/isolates of the Aujeszky's disease virusfound in Europe and Asia, presented in the GenBank database, indicates that such an insert is characteristic for the Min-A and HNJZ strains (position 1487 in the gE gene) isolated in Asia. Analysis of the homology of nucleotide sequences showed that the sequence of the gE gene fragment of sample No. 1 is 100% identical to the sequences of strains 89V87 and 00V72 isolated in Belgium. The homology of the nucleotide sequence of the gE gene fragment of sample No. 3 with strains 89V87 and 00V72 was 99.13%. In order to clarify the analyzed samples belonging to a particular genogroup (genetic cluster), a phylogenetic dendrogram was constructed. This demonstrates the phylogenetic relationships between strains/isolates of the Aujeszky's disease virus. It was found that the analyzed samples belong to the genetic cluster uniting European strains/isolates, and the studied isolates are most genetically close to strains 89V87 and 00V72 [ABSTRACT FROM AUTHOR]

Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae) is the trunk borer of orange trees. In this study, we sequenced and annotated the whole mitochondrial genome of P. closteroides. The results showed that the length of the complete mitochondrial genome is 15,854 bp with an overall GC content of 32.11%. The genome encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The relevant phylogenetic tree distinctly showed that P. closteroides is clustered with Dorysthenes paradoxus and Dorysthenes granulosus. This study provides a piece of valuable genomic information for the population genetics, evolution, and classification of P. closteroides.

As of June 2022, the GISAID database contains more than 11 million SARS-CoV-2 genomes, including several thousand nucleotide sequences for the most common variants such as delta or omicron. These SARS-CoV-2 strains have been collected from patients around the world since the beginning of the pandemic. We start by assessing the similarity of all pairs of nucleotide sequences using the Jaccard index and principal component analysis. As shown previously in the literature, an unsupervised cluster analysis applied to the SARS-CoV-2 genomes results in clusters of sequences according to certain characteristics such as their strain or their clade. Importantly, we observe that nucleotide sequences of common variants are often outliers in clusters of sequences stemming from variants identified earlier on during the pandemic. Motivated by this finding, we are interested in applying outlier detection to nucleotide sequences. We demonstrate that nucleotide sequences of common variants (such as alpha, delta, or omicron) can be identified solely based on a statistical outlier criterion. We argue that outlier detection might be a useful surveillance tool to identify emerging variants in real time as the pandemic progresses. [ABSTRACT FROM AUTHOR]

In trending research arena, image encryption is taken as one of the important security aspect and has drawn the attention of many researchers around the globe. There are many literatures available where different methods are proposed for improving the encryption standards for a secured image. In the recent times, the chaotic techniques are made used for the improvement in encryption standards of the image. These are also applied many domains such as in design of cryptosystems and also in encryption of image. The chaotic techniques based encryptions are novel encryption techniques. Random chaos based sequences are made used for the process of encryption and has also proven fast. One of the major setback in using this technique is the less accuracy. A video compressive encryption method is proposed to accomplish compression as well as encryption based technique that incorporate compressive sensing (CS), pixel level scrambling, bit level scrambling and Nucleotide Sequences operations. The proposed method employs fractional order hyperchaotic chen system for generation of measurement matrix. The matrix measurements are done through the hyper chaotic with intelligent scrambling in pixel level thus strengthens the efficiency of the encryption process. The CS measurement is scrambled to its pixel level to resist plain text attack, bit level scrambling reduces the correlation between the adjacent measurements and the operations of the nucleotide sequence are performed on the scrambled bits, enhancing the encryption. The reconstruction technique includes two stages, the first stage of which utilizes intra-frame similarity and offers strong preliminary retrieval for each frame, and the stage two iteratively improves the efficiency of reconstruction by integrating interframe multi hypothesis (MH) estimation and weighted residual sparsity modeling. By using a mathematical approach based on the MH predictions, the weights of the residual coefficients are modified in each iteration and Split Bregman iteration algorithm is devise to resolve weighted l1 regularization. The experimental result are compared between proposed and existing approaches like HC-DNA, C-DNA, CDCP and CHC. Experimental findings show that the proposed algorithm provides good compression of video coupled with an efficient encryption method that is resistant to multiple attacks. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the mutational analysis of human-derived SARS-CoV-2 have been published, but insight into the mink-derived SARS-CoV-2 genome of mutations is still required. Here, we performed a mutation analysis of the mink-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink-derived SARS-CoV-2 genome sequences on GISAID (214 genome sequences from the Netherlands and 133 genome sequences from Denmark). We found a striking resemblance between human-derived and mink-derived SARS-CoV-2. Our study showed that mutation patterns in the SARS-CoV-2 genome samples from the Netherlands and Denmark were different. Out of the 201 mutations we found, only 13 mutations were shared by the Netherlands' and Denmark's mink-derived samples. We found that six mutations were prevalent in the mink-derived SARS-CoV-2 genomes, and these six mutations are also known to be prevalent in human-derived SARS-CoV-2 variants. Our study reveals that the G27948T mutation in SARS-CoV-2 leads to truncation of ORF8, which was also reported in human-derived SARS-CoV-2, thus indicating that the virus can replicate without the full-length ORF8. These resemblances between mink-derived and human-derived SARS-CoV-2 enable the virus to cross the species barrier and suggest mink a potential reservoir for the virus. [ABSTRACT FROM AUTHOR]

Yi-Hau Chen,1 Hsiuying Wang2 1Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan; 2Institute of Statistics, National Chiao Tung University, Hsinchu, TaiwanCorrespondence: Hsiuying WangInstitute of Statistics, National Chiao Tung University, 1001 University Road, Hsinchu 30010, TaiwanTel +886-3-5712121 ext 56813Email wang@stat.nctu.edu.twBackground: The number of COVID-19 infections worldwide has reached 10 million. COVID‑19 caused by SARS-CoV-2 is more contagious than SARS-CoV-1. There is a dispute about the origin of COVID-19. Study results showed that all SARS-CoV-2 sequences around the world share a common ancestor towards the end of 2019.Methods: Virus sequences from COVID-19 samples at the early time should be less diversifiable than those from samples at the later time because there might be more mutations when the virus evolutes over time. The diversity of virus nucleotide sequences can be measured by the nucleotide substitution distance. To explore the diversity of SARS-CoV-2, we use different nucleotide substitution models to calculate the distances of SARS-CoV-2 samples from 3 different areas, China, Europe, and the USA. Then, we use these distances to infer the origin of COVID-19.Results: It is known that COVID-19 originated in Wuhan China and then spread to Europe and the USA. By using different substitution models, the distances of SARS-CoV-2 samples from these areas are significantly different. By ANOVA testing, the p-value is less than 2.2e-16. The analyzed results in most substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. This outcome coincides with the virus transmission time order that SARS-CoV-2 starts in China, then outbreaks in Europe and finally in the USA.Conclusion: The magnitude of nucleotide substitution distance of SARS-CoV-2 is closely related to the transmission time order of SARS-CoV-2. This outcome reveals that the nucleotide substitution distance of SARS-CoV-2 may be used to infer the origin of COVID-19.Keywords: coronavirus, diversity, nucleotide sequences, nucleotide substitution model, SARS-CoV-2

This paper adopted in silico and bioinformatics scientific approaches in revealing the nature of the COVID-19 coronavirus strain in Nigeria. These was revealed in terms of the physical, chemical and biological nature, as well as the isoelectric point, evolutionary relationship, mutation rate and pathway, molecular weight amongst other attributes which project the coronaviruses mutant strains causing the current global pandemic as very deadly and a threat to humanity. The paper revealed the genetic and thermal stability status of the Nigerian (COVID-19) isolate using instability index, aliphatic index, guanine – cytosine content, hydropathicity, nucleotide diversity, amino acids side chains and half-life of the isolate on in vitro human reticulocyte cells as criteria. The paper also revealed the variations in protein structures, phylogeny, bad angles, bad bonds, C-Beta deviations, Ramachandran outliers and Molprobity scores of the virus pathogen in Nigeria and that of Wuhan China, the global epicenter of the pandemic and deduced strong relationship between the strains confirming their common ancestry and nature. The paper revealed that efforts geared towards the development of suitable therapy and vaccines for the COVID-19 globally has not yet been successful due to the variable attenuation coefficients and the fast rate of the S gene mutations of the coronaviruses mutant strains. Hence, the nature of COVID-19 revealed in this study, is necessary for the identification, design and development of effective treatment.

Yellow mosaic symptoms were identified from cucumber production systems in Gianyar and were similar to symptoms of PRSV infection. Further research was conducted to determine diseases incidence and molecular characteristic of PRSV. Ninety leaf samples were collected from Gianyar by purposive sampling and disease incidence calculations were based on symptoms in the field. Detection and identification were done using a RT-PCR with specific primers of CP PRSV-P, CP PRSV-W and DNA sequencing. Disease incidences in the fields ranged between 5.81–66.87%. Specific DNA band 470 bp was successfully amplified from several cucumber leaf samples collected from Ubud, Payangan, Tegallalang, Sukawati, Gianyar, and Blahbatuh; but no DNA were amplified from all samples when using CP PRSV-W specific primer. Nucleotide and amino acid analysis showed nucleotides homology to isolates from Ubud, Payangan, Tegallalang, Sukawati, Gianyar, and Blahbatuh, i.e. 98.9–99.5% and 99.1–100%, respectively. Results indicated that genetic variation of PRSV-P from Gianyar was low. Furthermore, the nucleotides homology of PRSV-P isolates from Ubud, Payangan, Tegallalang, Sukawati, Gianyar, and Blahbatuh were with PRSV-P isolates which infected cucumbers from Nganjuk (LC311783) and Brebes (LC311784), while from native papaya collected in Bali Bali (LC223115) were 97.2–98.4% and 98.6–100%, respectively. Phylogenetic analysis confirmed that PRSV-P isolates from Indonesia were in the same cluster with Thailand isolates. The results showed that sources of PRSV-P inoculums spreading into new areas.

Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae) is the trunk borer of orange trees. In this study, we sequenced and annotated the whole mitochondrial genome of P. closteroides. The results showed that the length of the complete mitochondrial genome is 15,854 bp with an overall GC content of 32.11%. The genome encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The relevant phylogenetic tree distinctly showed that P. closteroides is clustered with Dorysthenes paradoxus and Dorysthenes granulosus. This study provides a piece of valuable genomic information for the population genetics, evolution, and classification of P. closteroides. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the mutational analysis of human-derived SARS-CoV-2 have been published, but insight into the mink-derived SARS-CoV-2 genome of mutations is still required. Here, we performed a mutation analysis of the mink-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink-derived SARS-CoV-2 genome sequences on GISAID (214 genome sequences from the Netherlands and 133 genome sequences from Denmark). We found a striking resemblance between human-derived and mink-derived SARS-CoV-2. Our study showed that mutation patterns in the SARS-CoV-2 genome samples from the Netherlands and Denmark were different. Out of the 201 mutations we found, only 13 mutations were shared by the Netherlands’ and Denmark’s mink-derived samples. We found that six mutations were prevalent in the mink-derived SARS-CoV-2 genomes, and these six mutations are also known to be prevalent in human-derived SARS-CoV-2 variants. Our study reveals that the G27948T mutation in SARS-CoV-2 leads to truncation of ORF8, which was also reported in human-derived SARS-CoV-2, thus indicating that the virus can replicate without the full-length ORF8. These resemblances between mink-derived and human-derived SARS-CoV-2 enable the virus to cross the species barrier and suggest mink a potential reservoir for the virus.

Astaxanthin is produced by Xanthophyllomyces dendrorhous as its principle carotenoid but the production in the wild type strain is relatively low. A stable astaxanthinhyperproducing strain, M34, was obtained in our previous work from N-methyl-N'-nitro-Nnitrosoguanidin mutagenesis. In this study the wild type and M34 strains were compared in terms of growth and carotenoid production. The expression levels and nucleotide sequences of carotenogenic genes idi, crtE, crtYB, crtI, crtR and crtS of both strains were studied by realtime polymerase chain reaction and polymerase chain reaction respectively. Gene expression results indicated that both crtE and crtS genes showed significantly higher expressions relative to the wild type throughout the production cycle, the highest being 1.3-fold and 3.8-fold respectively. The six carotenogenic genes exhibited a total of 38 nucleotide changes after mutation, including a missense mutation in idi gene (glutamic acid→alanine) and crtI gene (histidine→glutamine), and two missense mutations in crtE (lysine→arginine; serine→aspartic acid) and crtR genes (serine→valine; glutamine→proline). [ABSTRACT FROM AUTHOR]

Ceresium sinicum ornaticolle Pic, 1907 (Coleoptera: Cerambycidae) is one of the main pests of pomegranate and citrus trees. In this study, we described the complete mitochondrial genome of C. sinicum ornaticolle . The total length of the mitochondrial genome was 15,817 bp, and the entire content of GC was 27.8%. The genome encoded 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The phylogenetic tree showed that C. sinicum ornaticolle was clustered with Allotraeus orientalis and Zoodes fulguratus . These results will provide the genetic information for understanding the genetic evolution of C. sinicum ornaticolle and the insights to control cerambycid pests., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

We isolated 17 viral strains capable of causing cytopathic effects in mammalian cells and death in neonatal mice from sand flies in China. Phylogenetic analysis showed that these strains belonged to the genus Phlebovirus. These findings highlight the need to control this potentially emerging virus to help safeguard public health. [ABSTRACT FROM AUTHOR]

Objective: To study genetic variation in buffalo follicle stimulating hormone beta-subunit (FSHB) gene and its association with fertility.Methods: In this experimental study, blood samples were collected by standard methods using EDTA anticoagulant and transrectal ultrasound examination was conducted on fertile (n=74) and infertile buffaloes with a history of anestrum (n=30) or repeat breeding (n=12). The genomic DNA was extracted for PCR followed by single strand conformation polymorphism analysis. DNA sequencing was performed for the determination of single nucleotide polymorphism of FSHB gene.Results: The study results showed that there was genetic polymorphism with two different single strand conformation polymorphism patterns, AA and AB. The former pattern was associated with fertility in Egyptian buffaloes. Pair wise alignment of the two patterns sequences revealed that FSHB pattern II (AB) has C nucleotide insertion as SNP at the site of 208 bp of sequenced fragment.Conclusions: FSHB is polymorphic in the Egyptian buffaloes, suggesting its practicability as a candidate marker for female fertility.

Predicting the location of the translation initiation sites (TIS) is an important problem of molecular biology. In this field, the computational cost for balancing non-TIS sequences is substantial and demands high-performance computing. In this article, we present an optimized version of the K-modes algorithm to cluster TIS sequences and a comparison with the standard K-means clustering. The adapted algorithm uses simple instructions and fewer computational resources to deliver a significant speedup without compromising the sequence clustering results. We also implemented two optimized parallel versions of the algorithm, one for graphics processing units (GPUs) and the other one for general-purpose multicore processors. In our experiments, the GPU K-modes's performance was up to 203 times faster than the respective sequential version for processing Arabidopsis thaliana sequence. [ABSTRACT FROM AUTHOR]

The nucleotide sequences of two strains of CMV isolated from cucumber and ageratum in the Primorsk region and one strain from pepper isolated in the North Korea have been studied. The phylogenetic linkages among isolated strains and strains of CMV from Genbank were revealed. The intragroup position of the isolated strains of CMV widespread in the Far East was specified.

We have investigated a mutation frequency within the human genome for the set of known single nucleotide polymorphisms (SNPs) from the “1000 genomes” project. We have developed and applied novel statistical computational methods to analyze genetic text based on its complexity. A complexity profiling in a sliding window is applied to the sites containing single nucleotide polymorphisms within the human genome. A local decrease in text complexity level in SNP-containing sites has been shown. Analysis of the complexity profiles for SNPcontaining sites shows that flanking monomer repeats define a lower context complexity of sites containing SNPs within the human genome. An effect of local decrease in text complexity in SNP-containing sites is confirmed by analysis of polymorphisms in the rat and mouse genomes. We have found context differences between coding and regulatory sequences. These differences reflect a complexity of SNP-containing loci. The changes in point mutation frequency were shown previously for microsatellite containing sequences. Using enhanced mathematical tools and larger data sets this work shows enrichment of polytracks and simple sequence repeats in local genome surroundings of SNP containing sites. We have found high-frequency oligonucleotides within genomic regions containing SNPs. Such oligonucleotides are related to nucleotide polytracks. The presence of poly-A tracks might be associated with an increased probability of double helix DNA breaks around mutable loci and following fixation of nucleotide changes. The complexity estimates were computed using a previously developed program tool. This tool allows for both (i) complexity estimation of phased samples, and (ii) rapid and effective identification of the frequency spectrum of oligonucleotides with fixed lengths, and a comparison of oligonucleotide frequencies in different samples

One way to study the variability of biologic objects is their geometrization: the objects are presented by points in a multidimensional space in such a way that the distances between the points would be best consistent with the dissimilarities between objects. If the dissimilarities between the objects are Euclidean distances, this task (up to translation, rotation and reflection) is solved by metric scaling. We consider the metric properties of some well-known evolutionary distances of nucleotide sequences. It is shown that the Jukes-Cantor and Kimura distances are not metrics. We introduce a new Kimura distance analog, the PQdistance. It is shown that the p and PQ distances are the squares of Euclidean metrics named Ep-distance and EPQ-distance, respectively. The applicability of the EPQ distance is illustrated by the example of a cytochrome b sequence set of 12 rodent species from West Siberia and Altai, taken from the GenBank, and compared with the results of the use of the LogDet-distance.

Two approaches to the synthesis of 2D binary identifiers ("fingerprints") of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).

The landscape for patenting products and processes tied to the natural world has changed dramatically in recent times as a result of a series of decisions of the US Supreme Court, particularly Mayo Collaborative Services v Prometheus Laboratories 566 U.S. 66 (2012) and Association for Molecular Pathology v Myriad Genetics, Inc. 569 U.S. 576 (2013) (Myriad). This article critically analyses these decisions and the multitude of lower court decisions that have followed them. This analysis provides support for the growing concern in the United States that it will be increasingly difficult to use the patent system to encourage the development of therapies and research intermediates useful in developing new therapeutic interventions. One option being posited in the industry to deal with this problem is to lobby Congress to reform the threshold patent eligibility standard in US patent law. It is argued in this paper that a more nuanced approach is preferable. Using the experience in Australia as a case study, this paper argues that such an approach is feasible. Australia has been chosen for analysis because the threshold patent eligibility standard is similar in both countries, much more so that with the European Union, and because the highest court in Australia has ruled on essentially the same patent as in Myriad, in D'Arcy v Myriad Genetics, Inc [2015] HCA 35. In addition to the nuanced approach to eligibility currently exercised by the Australian courts and patent office, Australia also has a number of post-grant options for addressing the dynamics of patent monopolies. These include experimental use, compulsory licensing, and government use. It is concluded that, while it would be impractical to attempt to replicate the Australian environment in the United States, there is no reason why some lessons can't be learned from the Australian experience with patenting nature. [ABSTRACT FROM AUTHOR]

The pilot program complex for analysis of symbol sequences in genomics, ICGenomics, has been designed for storage, mining, and analysis of sequences related to theoretical and applied genomics. ICGenomics enables wet-lab biologists to perform high-quality processing of data in the fields of genomics, biomedicine, and biotechnology. ICGenomics implements both conventional and modern methods for processing, analyzing, and visualizing sequence data. They include novel methods of the processing of initial high-throughput sequencing data. Examples are: ChIP-seq analysis; functional annotation of gene regulatory regions in nucleotide and amino acid sequences; prediction of nucleosome positioning; and structural and functional annotation of proteins, including their allergenicity and evolution features. Application of ICGenomics to the analysis of genomic sequences of the parasite Opisthorchis felineus and to ChIP-seq data on the mouse and human is considered. The system is available at http://www-bionet.sscc.ru/icgenomics.

To assess, if the SARS-CoV-2 mutate in a similar pattern globally or has a specific pattern in any given population. We report, the insertion of TTT at 11085, which adds an extra amino acid, F to the NSP6 at amino acid position 38. The highest occurrence of TTT insertion at 11,085 position was found in UK derived samples (65.97%). The second and third highest occurrence of the mutation were found in Australia (8.3%) and USA (4.16%) derived samples, respectively. Another important discovery of this study is the C27945T mutation, which translates into the termination of ORF-8 after 17 amino acids, reveals that the SARS-CoV-2 can replicate without the intact ORF-8 protein. We found that the 97% of C27945T mutation of global occurrence, occurred in Europe and the USA derived samples. Two of the reported mutations (11085TTT insertion and C27945T nonsense), which seemed to reduce Type I interferon response are linked to specific geographical locations of the host and implicate region-specific mutations in the virus. The findings of this study signify that SARS-CoV-2 has the potential to adapt differently to different populations. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease (FMD) outbreaks recently affected 2 countries (Japan and South Korea) in eastern Asia that were free of FMD without vaccination. Analysis of viral protein 1 nucleotide sequences indicated that FMD serotype A and O viruses that caused these outbreaks originated in mainland Southeast Asia to which these viruses are endemic.

From February through May of 1999, 13 cases of Influenza A virus (FLUAV), type H1N1 were reported at a Department of Defense influenza surveillance sentinel site in Lima, Peru. Genetic and antigenic analysis by hemagglutination inhibition and direct nucleotide sequencing of the HA1 region of the hemagglutinin gene were performed on two isolates, A/Peru/1641/99 and A/Peru/1798/99. Both isolates were distinct from the Bayern/7/95-like viruses circulating in the Americas and closely related to a Beijing/262/95-like variant, A/New Caledonia/20/99. With the exception of travel-related cases, the detection of these isolates represents the first appearance of New Caledonia/20/99-like viruses in the Americas. Since the characterization of these Peru isolates, a number of New Caledonia/20/99-like viruses have been reported worldwide. For the 2000/01 and 2001/02 influenza seasons, the World Health Organization (WHO) has recommended the inclusion of A/New Caledonia/20/99 as the H1N1 vaccine component for both the southern and northern hemispheres.

Results of computational analysis and visualization of differences in gene structures using polarization coding are presented. A two-dimensional phase screen, where each element of which corresponds to a specific basic nucleotide (adenine, cytosine, guanine, or thymine), displays the analyzed nucleotide sequence. Readout of the screen with a coherent beam characterized by a given polarization state forms a diffracted light field with a local polarization structure that is unique for the analyzed nucleotide sequence. This unique structure is described by spatial distributions of local values of the Stokes vector components. Analysis of these distributions allows the comparison of nucleotide sequences for different strains of pathogenic microorganisms and frequency analysis of the sequences. The possibilities of this polarization-based technique are illustrated by the model data obtained from a comparative analysis of the spike protein gene sequences for three different model variants (Wuhan, Delta, and Omicron) of the SARS-CoV-2 virus. Various modifications of polarization encoding and analysis of gene structures and a possibility for instrumental implementation of the proposed method are discussed.

Specific primers play an important role in polymerase chain reaction (PCR) experiments, and therefore it is essential to find specific primers of outstanding quality. Unfortunately, many PCR constraints must be simultaneously inspected which makes specific primer selection difficult and time‐consuming. This paper introduces a novel computational intelligence‐based method, Teaching‐Learning‐Based Optimisation, to select the specific and feasible primers. The specified PCR product lengths of 150–300 bp and 500–800 bp with three melting temperature formulae of Wallace's formula, Bolton and McCarthy's formula and SantaLucia's formula were performed. The authors calculate optimal frequency to estimate the quality of primer selection based on a total of 500 runs for 50 random nucleotide sequences of 'Homo species' retrieved from the National Center for Biotechnology Information. The method was then fairly compared with the genetic algorithm (GA) and memetic algorithm (MA) for primer selection in the literature. The results show that the method easily found suitable primers corresponding with the setting primer constraints and had preferable performance than the GA and the MA. Furthermore, the method was also compared with the common method Primer3 according to their method type, primers presentation, parameters setting, speed and memory usage. In conclusion, it is an interesting primer selection method and a valuable tool for automatic high‐throughput analysis. In the future, the usage of the primers in the wet lab needs to be validated carefully to increase the reliability of the method. [ABSTRACT FROM AUTHOR]

Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae) is the trunk borer of orange trees. In this study, we sequenced and annotated the whole mitochondrial genome of P. closteroides . The results showed that the length of the complete mitochondrial genome is 15,854 bp with an overall GC content of 32.11%. The genome encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The relevant phylogenetic tree distinctly showed that P. closteroides is clustered with Dorysthenes paradoxus and Dorysthenes granulosus . This study provides a piece of valuable genomic information for the population genetics, evolution, and classification of P. closteroides ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The aim of the present study is to compare the biological and molecular properties of Ukrainian soybean mosaic virus (SMV) isolates with those of known strains or isolates from other countries, and to trace their possible origin. The methods of mechanical inoculation, reverse transcription polymerase chain reaction, DNA sequencing and phylogenetic analysis have been used. Results. Five SMV isolates have been collected and biologically purified from breeding plots in Vinnitsa region of Ukraine. It has been found that all these isolates show the same reaction patterns when infecting 11 differential soybean cultivars. Phylogenetic analysis of sequences of the coat protein coding region and P1 coding region revealed strong genetic relationships between representative Ukrainian (UA1Gr) and SMV-VA2 isolates which together were sorted in one clade with G2 strain. The investigation of sequence identity showed that different genomic regions of SMV were under different evolutionary constraints. Conclusions. SMV, isolated in Ukraine for the first time, belongs to the G2 strain group that is widespread in North America. The SMV isolates obtained in this work may be employed in the Ukrainian national breeding programs to create soybean with durable virus resistance. [ABSTRACT FROM AUTHOR]

This paper describes the principal molecular markers used to identify B. bovis and B. bigemina reported in the scientific literature. A systematic review was designed based on the application of the PICO methodologic modified strategy to define the nucleotide sequences detected in different geographical locations and their diagnostic utility. An advanced search was made in data bases ScienceDirect, SpringerLink and PubMed. Using the terms "Babesia bovis" and "DNA" and "Babesia bigemina" and "DNA". A total of 68 original articles were selected after the information was filtered. Both included and excluded articles were registered in tables, where its position of their status, within the study, was represented. The 68 articles were evaluated using a previously defined criteria of inclusion or exclusion. A total of 21 articles met the inclusion criteria and were included in this study. It was described the usefulness of molecular markers referenced in the scientific literature from 1995 to 2010: small-subunit ribosomal rna, cytochrome b gene, msa-1 and msa-2c gene, bv gene, elongation factor-1 alpha (ef-1α), beta-tubulin gene, sbp 1-2-3, and rap genes, its diagnostic application and its use in different geographical locations. Molecular markers used for detection of bovine babesia vary by geographic region, degree of genetic conservation and results of previous studies that conclude their diagnostic utility. [ABSTRACT FROM AUTHOR]

Maximum-likelihood models of codon and amino acid substitution were used to analyze the lung-specific surfactant protein C (SP-C) from terrestrial, semi-aquatic, and diving mammals to identify lineages and amino acid sites under positive selection. Site models used the nonsynonymous/synonymous rate ratio (ω) as an indicator of selection pressure. Mechanistic models used physicochemical distances between amino acid substitutions to specify nonsynonymous substitution rates. Site models strongly identified positive selection at different sites in the polar N-terminal extramembrane domain of SP-C in the three diving lineages: site 2 in the cetaceans (whales and dolphins), sites 7, 9, and 10 in the pinnipeds (seals and sea lions), and sites 2, 9, and 10 in the sirenians (dugongs and manatees). The only semi-aquatic contrast to indicate positive selection at site 10 was that including the polar bear, which had the largest body mass of the semi-aquatic species. Analysis of the biophysical properties that were influential in determining the amino acid substitutions showed that isoelectric point, chemical composition of the side chain, polarity, and hydrophobicity were the crucial determinants. Amino acid substitutions at these sites may lead to stronger binding of the N-terminal domain to the surfactant phospholipid film and to increased adsorption of the protein to the air-liquid interface. Both properties are advantageous for the repeated collapse and reinflation of the lung upon diving and resurfacing and may reflect adaptations to the high hydrostatic pressures experienced during diving. [ABSTRACT FROM AUTHOR]

Abstract: In this study, a set of 80 completely sequenced procaryotic genomes has been analysed by an alignment-free method, namely the expectancy-rectified frequency of bigrams or 2-tuples, representing the 16 combinations of A, T, G, C. It demonstrates that all genomes exhibit periodic oscillations of their nucleotide sequence, with a period close to 11 phosphodiester bonds, and resembling in shape an exponentially dampened sinusoid at the distance from 5 to 49 bonds. Interestingly, the amplitude of nucleotide oscillation (but not the period) can differ drastically from one species to another. I show that these differences are due neither to the (G + C) content, nor to the size of the genome. They are not directly related to phylogeny, since specific genomes from Archaea and Bacteria can display large as well as small amplitudes. I have compared also a set of genes coding for proteins rich in alpha helical structures (as determined by X-ray diffraction) with a set of genes coding for proteins devoid of alpha helices. The first set has periodic oscillations of large amplitude, with an 11-bond period, while the second has none. Furthermore, I analysed a large number of sets of homologous genes from several different species. They exhibit very different amplitudes of oscillations. Altogether, the data with their statistical analyses strongly suggest that the nucleotide oscillations are due to the ‘genomic style of proteins’, which means that homologous proteins, having the same biochemical function in different organisms, may have different secondary structures or may use different ways to be constructed. I realize that this idea is a heterodox one, but I believe that it can shed a new light both on phylogenies and on constraints between proteins and their coding sequences. To cite this article: P.P. Slonimski, C. R. Biologies 330 (2007). [Copyright &y& Elsevier]

Techniques such as detrended fluctuation analysis (DFA) and its extensions have been widely used to determine the nature of scaling in nucleotide sequences. In this brief communication we show that tandem repeats which are ubiquitous in nucleotide sequences can prevent reliable estimation of possible long-range correlations. Therefore, it is important to investigate the presence of tandem repeats prior to scaling exponent estimation. [ABSTRACT FROM AUTHOR]