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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.

Nucleotide-based molecules called DNA and RNA are essential for several biological processes that affect both normal and cancerous cells. They contain the critical genetic material needed for normal cell growth and functioning. The DNA structure patterns that make up the genetic code affect cells' growth, behavior, and control. Different DNA structure patterns indicate different physiological effects in the cell. Knowledge of these patterns is necessary to identify the molecular origins of cancer and other disorders. Analyzing these patterns can help in the early detection of diseases, which is essential for the effectiveness of cancer research and therapy. The novelty of this study is to examine the patterns of dinucleotide structure in many genomic regions, including the non-coding region sequence (N-CDS), coding region sequence (CDS), and whole raw DNA sequence (W.R. sequence). It provides an in-depth discussion of dinucleotide patterns related to these diverse genetic environments and contains malignant and non-malignant DNA sequences. The Markovian modeling that predicts dinucleotide probabilities also reduces feature complexity and minimizes computational costs compared to the approaches of Kernelized Logistic Regression (KLR) and Support Vector Machine (SVM). This technique is effectively evaluated in essential case studies, as indicated by accuracy metrics and 10-fold cross-validation. The classifier and feature reduction, which are generated by Markovian probability, operate well together and can help predict cancer. Our findings successfully distinguish DNA sequences related to cancer from those diagnostics of non-cancerous diseases by analyzing the W.R. DNA sequence as well as its CDS and N-CDS regions. [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.

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 study evaluated the genetic profile of a low passaged BGM-70 adapted very virulent infectious bursal disease virus (vvIBDV) isolated in Malaysia in the year 2004 based on the VP2 hypervariable region. Embryonated chicken eggs were first used to propagate UPM190 12 times before being low passaged in BGM-70 cell line 7 times yielding UMP190BGMP7 whose VP2 nucleotide and amino acid sequences were determined and compared with reference sequences after Sanger sequencing of the low passage virus. The nucleotide and amino acid sequences of UPM190BGMP7 virus were similar with the sequences of viruses passaged in chicken embryonated eggs (CEE) but differed with higher BGM-70 passaged viruses. The E270 amino acid mutation associated with higher BGM-70 passaged viruses was absent in UPM190BGMP7. However, it has another amino acid mutation at position D279N that back-mutated on continuous BGM-70 cell propagation. [ABSTRACT FROM AUTHOR]

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]

This work presents a novel feature extraction method for identifying complex patterns in genomic sequences by employing the Hidden Markov Model (HMM). In this study, we use HMM to identify gene nucleotide patterns that are specific to malignant and non-malignant cells. Crucial genetic components DNA and RNA are involved in many biological processes that impact both healthy and malignant cells. Early patient identification is essential to successful cancer diagnosis and therapy. Varying nucleotide patterns indicate different cellular responses, which are important to understanding the molecular causes of cancer and associated disorders. We present a detailed study of nucleotide patterns in whole raw nucleotide sequences with variations in both protein sequence (CDS) and non-protein sequence (NCDS) in both malignant and non-malignant cells. Nucleotide prediction has been achieved while computational expenses are reduced by using the proposed HMM for feature extraction and selection. The classification models implemented in this work for cancer detection are Gradient-Boosted Decision Trees (GBDT), Random Forests (RF), Decision Trees (DT), and Support Vector Machines (SVM) with kernels. The suggested classification model's accuracy and 10-fold cross-validation have been validated via comprehensive case studies. The results reveal that DT and ensemble learning techniques significantly differentiate between malignant and non-malignant DNA sequences. SVM with suitable kernels improves cancer detection accuracy significantly. Combining feature reduction approaches with nucleotide pattern classifiers based on Hidden Markov models improves performance and ensures reliable cancer detection. [Display omitted] • The HMM is used for a novel feature extraction approach to find complicated patterns in genomic sequences. • Comprehensive feature extraction of nucleotide patterns in whole sequences (CDS/NCDS) for malignant and non-malignant cells. • Here DT and ensemble learning algorithms effectively distinguish malignant and non-malignant DNA sequences. • The use of SVM with appropriate kernels significantly improves accuracy in cancer diagnosis. [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]

Alternative splicing enables a gene translating into different isoforms and into the corresponding proteoforms, which actually accomplish various biological functions of a living body. Isoform-isoform interactions (IIIs) provide a higher resolution interactome to explore the cellular processes and disease mechanisms than the canonically studied protein-protein interactions (PPIs), which are often recorded at the coarse gene level. The knowledge of IIIs is critical to map pathways, understand protein complexity and functional diversity, but the known IIIs are very scanty. In this paper, we propose a deep learning based method called DeepIII to systematically predict genome-wide IIIs by integrating diverse data sources, including RNA-seq datasets of different human tissues, exon array data, domain-domain interactions (DDIs) of proteins, nucleotide sequences and amino acid sequences. Particularly, DeepIII fuses these data to learn the representation of isoform pairs with a four-layer deep neural networks, and then performs binary classification on the learnt representation to achieve the prediction of IIIs. Experimental results show that DeepIII achieves a superior prediction performance to the state-of-the-art solutions and the III network constructed by DeepIII gives more accurate isoform function prediction. Case studies further confirm that DeepIII can differentiate the individual interaction partners of different isoforms spliced from the same gene. The code and datasets of DeepIII are available at http://mlda.swu.edu.cn/codes.php?name=DeepIII. [ABSTRACT FROM AUTHOR]

Branch canker disease caused by the fungus Macrophoma theicola is a major stem disease that reduces the yield of south Indian tea plantations. Hence the present study aimed to assess the efficacy of the biocontrol agent Trichoderma spp against various isolates of Macrophoma spp. For this matter, different tea-growing regions of south India were surveyed for the isolation and characterization of Macrophoma spp. Then, fungal biocontrol strains (Trichoderma viride, Trichoderma atroviride, Trichoderma harzianum , and Gliocladium virens) were procured from microbial type culture collection Centre (MTCC) to screen their antagonistic potential on different isolates Macrophoma spp. The spores of Macrophoma spp were examined through a light microscope and identified by their peculiar morphological features such as non-septum pycnidiospores present in the sac and oval shape spore with stalk and confirmed using 18S rRNA gene sequence. The results revealed that the biocontrol G. virens followed by T. harzianum showed a higher inhibitory effect on different isolates of Macrophoma spp in the dual plate and culture filtrate studies. In the well diffusion method, the fungal biocontrol agents were found to be exhibit non-significant differences on different isolates of branch canker pathogen. The hyphal interactions studies showed that the pathogenic hyphal wall shrunk and penetrated by the interaction of G. virens. [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]

Classification of Homo sapiens gene behavior employing computational biology is a recent research trend. But monitoring gene activity profile and genetic behavior from the alphabetic DNA sequence using a non-invasive method is a tremendous challenge in functional genomics. The present paper addresses such issue and attempts to differentiate Homo sapiens genes using linear discriminant analysis (LDA) method. Annotated protein coding sequences of Homo sapiens genes, collected from NCBI, are taken as test samples. Minimum entropy-based mapping (MEM) technique assists to extract highest information from the numerical DNA sequences. The proposed LDA technique has successfully classified Homo sapiens genes based on the following features: composition of hydrophilic amino acids, dominance of arginine amino acid, and magnitude and size of individual amino acids. The proposed algorithm is successfully tested on 84 Homo sapiens healthy and cancer genes of the prostate and breast cells. Classification performance of the proposed LDA technique is judged by sensitivity (89.12%), specificity (91.9%), accuracy (90.87%), F1 score (92.03%), Matthews' correlation coefficients (81.04%), and miss rate (9.12%), and it outperforms other four existing classifiers. The results are cross-validated through Rayleigh PDF and mutual information technique. Fisher test, 2-sample T-test, and relative entropy test are considered to verify the efficacy of the present classifier. [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]

Domestic sheep are raised for meat, milk and wool production and are found all around the world in many types of environments. Sheep have been shown to be genetically diverse but this genetic diversity has not been fully described, there are still many sheep populations which have not yet been studied. The purpose of this study were to investigate the polymorphism in the calpain gene (CAPNS1) in Iraqi awassi sheep by using PCR-SSCP method. A 192-bp fragment of exons 5 and 6 including intron region of the CAPNS1 gene was amplified and subjected to PCR-SSCP method to screen for polymorphisms. The observed variants had exhibited different distributions in the analyzed samples in terms of the targeted 192 bp amplicons. Were detected five CAPNS1 genetic patterns according to SSCP technology: A, B, C, D and E with percentage (%) of 14.92, 26.87, 9.70, 36.57, and 11.94, respectively. Results of sequence analysis revealed five nucleotide substitutions at nt 44, nt 64, nt 94, nt 103 in a part of intron 5, and nt 154 in a part of exon 6 (SNP position). The substitutions at exon 6 nt154 T > C, this SNP is a silent mutation {GGT (Glycine) > GGC (Glycine)}, which creates no substitution effect for amino acid sequence of CAPNS1 protein. Were found Three alleles named C, G and T. Also showing insertion of 'A' nucleotide at nt (72-73) in a part of intron 5. This genetic variation is in non-coding DNA, therefore it is difficult to conclude how this polymorphism may affect the CAPNS1 gene activity. It should be mentioned that it may affect mRNA splicing, or may be linked to polymorphism elsewhere in the coding sequence, which may have an impact on expression of this gene. The genotype and allele frequencies for CAPNS1 loci are presented showed that recurrence of genotype patterns CC, GG, TC, TG, and TT were 40.00, 2.39, 12.24, 37.61, and 7.76 respectively, and allele frequencies C, G and T were 0.46, 0.21, and 0.33 respectively ,Furthermore observed, expected and average heterozygosity were 0.4985, 0.6360 and 0.3583 respectively. From the above results, genotype CC, and the allele C was the highest frequency and genotype GG and the allele G was the less frequency. Also the study results showed that the breed is unbalanced because the calculated c2 values are greater than the tabular in all positions of the studied CAPNS1 gene. The imbalance, according to Hardy Weinberg rule, may be due to the possibility of out breeding. It may be the result of non-random mating for several years in awassi sheep populations. The results confirmed that the PCR-SSCP is an appropriate tool for determining genetic variability in CAPNS1 locus. Since this gene could be considered as a candidate gene of growth and meat quality traits in sheep and may affect lamb quality parameters. Further study may be conducted to ascertain the association of these genotypes with the growth and carcass/meat quality traits. [ABSTRACT FROM AUTHOR]

With the recent advances in molecular biology techniques, a great interest focused towards the improving livestock production in general and meat production in specific. In the present study is to identify the genetic polymorphism of callipyge gene (CLPG) related to meat production in Iraqi awassi sheep breed. PCR amplification of callipyge gene yielded an amplified product of 426 bp in Iraqi awassi sheep breed by PCR-SSCP method study of callipyge gene revealed presence of wild type allele A with only one genotype (AA) and absence of the mutant allele G, which is responsible for callipyge phenotype and enhanced mutton quality. The results revealed that there is absence of polymorphism at this locus and callipyge mutation is not found in all the studied Iraqi awassi sheep breed. It may be concluded that CLPG locus is a monomorphic for population sheep kept in Iraq. It was detected the genotype AA with frequency 1.00. [ABSTRACT FROM AUTHOR]

Sheep have been shown to be genetically diverse but this genetic diversity has not been fully described, there are still many sheep populations which have not yet been studied. The purpose of this study were to investigate the polymorphism in the calpain gene (CAPNS1) in Iraqi awassi sheep by using PCR-SSCP method, and their relationship to growth traits. A 192-bp fragment of exons 5 and 6 including intron region of the CAPNS1 gene was amplified and subjected to PCR-SSCP method to screen for polymorphisms. The observed variants had exhibited different distributions in the analyzed samples in terms of the targeted 192 bp amplicons. Were detected five CAPNS1 genetic patterns according to SSCP technology A, B, C, D, and E. Results of sequence analysis revealed five nucleotide substitutions at nt 44, nt 64, nt 94, nt 103 in a part of intron 5, and nt 154 in a part of exon 6 (SNP position). The substitutions at exon 6 nt154 T > C, this SNP is a silent mutation {GGT (Glycine) > GGC (Glycine)}, which creates no substitution effect for amino acid sequence of CAPNS1 protein. Were found Three alleles named C, G and T. Also showing insertion of 'A' nucleotide at nt (72-73) in a part of intron 5. This genetic variation is in noncoding DNA, therefore it is difficult to conclude how this polymorphism may affect the CAPNS1 gene activity. The lambs used in the present study were weaned at three months of age. The average weight gain for weaning weight, six, nine, and twelve months were also recorded the overall average gain 21.62 ± 0.61, 31.32 ± 0.59, 37.51 ± 0.76, 41.42 ± 0.68, and 19.80 ± 0.40 kg, respectively. The results obtained in this study showed the importance of genotypes as sources of variation, where there was significant (P <0.05) effect of genotype in different economic growth traits used in the analysis. Also the study results showed that the breed is unbalanced because the calculated x2 values are greater than the tabular in all positions of the studied CAPNS1 gene, The imbalance, according to Hardy Weinberg rule, may be due to the possibility of out breeding. It may be the result of non-random mating for several years in awassi sheep populations. The results confirmed that the PCRSSCP is an appropriate tool for determining genetic variability in CAPNS1 locus. Since this gene could be considered as a candidate gene of growth and meat quality traits in sheep and may affect lamb quality parameters., further study may be conducted to ascertain the association of these genotypes with the growth and carcass/meat quality traits. [ABSTRACT FROM AUTHOR]

In an idealised vision of science the scientific literature is error-free. Errors reported during peer review are supposed to be corrected prior to publication, as further research establishes new knowledge based on the body of literature. It happens, however, that errors pass through peer review, and a minority of cases errata and retractions follow. Automated screening software can be applied to detect errors in manuscripts and publications. The contribution of this paper is twofold. First, we designed the erroneous reagent checking (ERC) benchmark to assess the accuracy of fact-checkers screening biomedical publications for dubious mentions of nucleotide sequence reagents. It comes with a test collection comprised of 1679 nucleotide sequence reagents that were curated by biomedical experts. Second, we benchmarked our own screening software called Seek&Blastn with three input formats to assess the extent of performance loss when operating on various publication formats. Our findings stress the superiority of markup formats (a 79% detection rate on XML and HTML) over the prominent PDF format (a 69% detection rate at most) regarding an error flagging task. This is the first published baseline on error detection involving reagents reported in biomedical scientific publications. The ERC benchmark is designed to facilitate the development and validation of software bricks to enhance the reliability of the peer review process. [ABSTRACT FROM AUTHOR]

Sheep have been shown to be genetically diverse but this genetic diversity has not been fully described, there are still many sheep populations which have not yet been studied. The purpose of this study were to investigate the polymorphism in the calpain gene (CAPNS1) in Iraqi awassi sheep by using PCR-SSCP method, and their relationship to growth traits. A 192-bp fragment of exons 5 and 6 including intron region of the CAPNS1 gene was amplified and subjected to PCR-SSCP method to screen for polymorphisms. The observed variants had exhibited different distributions in the analyzed samples in terms of the targeted 192 bp amplicons. Were detected five CAPNS1 genetic patterns according to SSCP technology A, B, C, D, and E. Results of sequence analysis revealed five nucleotide substitutions at nt 44, nt 64, nt 94, nt 103 in a part of intron 5, and nt 154 in a part of exon 6 (SNP position). The substitutions at exon 6 nt154 T > C, this SNP is a silent mutation {GGT (Glycine) > GGC (Glycine)}, which creates no substitution effect for amino acid sequence of CAPNS1 protein. Were found Three alleles named C, G and T. Also showing insertion of 'A' nucleotide at nt (72-73) in a part of intron 5. This genetic variation is in non-coding DNA, therefore it is difficult to conclude how this polymorphism may affect the CAPNS1 gene activity. The lambs used in the present study were weaned at three months of age. The average weight gain for weaning weight, six, nine, and twelve months were also recorded the overall average gain 21.62 ± 0.61, 31.32 ± 0.59, 37.51 ± 0.76, 41.42 ± 0.68, and 19.80 ± 0.40 kg, respectively. The results obtained in this study showed the importance of genotypes as sources of variation, where there was significant (P <0.05) effect of genotype in different economic growth traits used in the analysis. Also the study results showed that the breed is unbalanced because the calculated x2 values are greater than the tabular in all positions of the studied CAPNS1 gene, The imbalance, according to Hardy Weinberg rule, may be due to the possibility of out breeding. It may be the result of non-random mating for several years in awassi sheep populations. The results confirmed that the PCR-SSCP is an appropriate tool for determining genetic variability in CAPNS1 locus. Since this gene could be considered as a candidate gene of growth and meat quality traits in sheep and may affect lamb quality parameters., further study may be conducted to ascertain the association of these genotypes with the growth and carcass/ meat quality traits. [ABSTRACT FROM AUTHOR]

DNA data storage has gained more attention last decades. DNA molecules can be used for encoding of non-biological information and as promising carriers due to greater data capacity, higher duration of the storage, and better technical failures stability. Here we propose a new method for encoding of notes and music in DNA. The encoding technique takes into account the duration and tonality of each note, enabling to encode all seven octaves by assigning a nucleotide sequence to each key. A certain set of short sequences is suggested to define the duration of note sound. The proposed method allows to encode more complicated melodies compared to the approach based on Huffman algorithm. [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.

The objective of the present study was to detect the chosen nucleotide DNA or RNA sequences of the pathogens in ticks of domestic and wild animals of Kerala, South India based on molecular techniques. Among 602 ticks collected, 413 were from bovines (cattle and buffalo), 26 from goats, 101 from dogs and 62 from wild animals. Amblyomma integrum, Am. gervaisi, Dermacentor auratus, Haemaphysalis bispinosa, Ha. intermedia, Ha. shimoga, Ha. spinigera, Rhipicephalus annulatus, Rh. microplus, Rh. haemaphysaloides and Rh. sanguineus s.l. were identified from various domestic and wild animals of Kerala. The cDNA synthesized from the RNA isolated from fully or partially engorged adult female/nymphal ticks was used as template for the specific polymerase chain reactions (PCR). Out of 602 ticks examined, nucleotide sequences of pathogens were detected in 28 ticks (4.65%). The nucleotide sequences of tick-borne pathogens like Theileria orientalis, Babesia vogeli, Hepatozoon canis, Anaplasma marginale, An. bovis, Rickettsia sp. closely related to Ri. raoultii, Ri. massiliae, Ri. africae and Ri. slovaca were detected. The identification of the previously unreported nucleotide sequences of rickettsial pathogens from India is of particular interest due to their zoonotic significance. The phylogenetic analysis of the major piroplasm surface protein (MPSP) gene of T. orientalis amplified from Rh. annulatus ticks revealed that they were genetically close to type 7, which belong to the highly pathogenic Ikeda group. [ABSTRACT FROM AUTHOR]

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 study was conducted on 50 ewes Awassi(3-6 years of age) to determine the genotypes in the 2nd exon of the GDF-9 gene and its relation to reproductive performance. The nucleotide sequences technique used to determine the DNA. Results showed two mutations in the studied area, G4 (G721A and G750A), The G4 mutation has led to a change in the genetic code of the desired amino acid (Glu241Lys)while the G750A was the variant Arg250Arg. The differences in the distribution of genotypes and the initial frequency of mutations were significant (P <0.01), 70%, 30% and 92%, 8% for GG and GA for mutations G4 and G750A, respectively. The initial recurrence of both wild allele G and mutant A for mutations was 0.85, 0.15 and 0.96, 0.04, respectively. The interaction between the studied mutations was studied to reach a precise elective recommendation GGGG-bearing ewes were highest in fertility rate (1.61) (AGAG) were the lowest in fertility rate (1.22) single births per abdomen. [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]

A new insight into the mechanisms underlying implementation of genomic information in the individual development of eukaryotes through interactions of transposons with epigenetic factors dynamically changing during each cell division is described. These mechanisms of stepwise implementation of individual genetic information with characteristic stage- and tissue-specific features in the activities of certain mobile genetic element families are evolutionarily fixed at the species level. In addition, the individual differences caused by their “unscheduled” transpositions can significantly change the regulatory network of the genome altering the phenotype. These changes in individual development can bring about new traits leading to either a disease or better fitness and represent an important component of the variation for natural selection in evolution. A large part of the eukaryotic transposons is altered by mutations and used for formation of the regulatory gene network, changes in the protein-coding genes, and emergence of new nonprotein-coding genes. When inserted into new loci, mobile genetic elements form the basis for microRNA and the domain structures of long noncoding RNA, responding to various types of stress; this is reflected in the specific features of individual development and contributes to variation. The epigenetic factors, including noncoding RNA, DNA methylation, and histone modifications, are tightly associated with mobile genetic elements. The specific features in transposon location in individuals that have emerged owing to spontaneous mutations or those caused by stress impacts can considerably change the interactions in gene networks. This influences the likelihood of survival under changing environmental conditions and reflects a distinct interrelation between the mechanisms of individual development and evolution. There is a parallelism between the mechanisms underlying the rearrangements of genomes caused by transposons in evolution and in individual development. In particular, the responsiveness of transposons to external and internal (microenvironment) factors forms the background for evolutionary construction of transposon-mediated tissue-specific activation patterns of certain transposons during each cell division, which leads to maturation of a reproductive organism. This mechanism is based on tight stage- and tissuespecific interrelation between transposons, epigenetic factors, and protein-coding genes. [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.

The type specimens of Cottus sibiricus and C. dzungaricus as well as individuals from the Olkha River (Yenisei River basin) are studied. The diagnostic features of C. sibiricus are established. Comparative morphological and molecular analysis of divergence between C. sibiricus and C. dzungaricus demonstrates that the differences lie within the limits of one polymorphous species. The rank of Dzungarian sculpin is lowered to the subspecies, C. sibiricus dzungaricus. [ABSTRACT FROM AUTHOR]