Nucleotide Sequence Of RNA Research Articles

Associations between clinical data, vaccination status, antibody responses, and post-COVID-19 symptoms in Thais infected with SARS-CoV-2 Delta and Omicron variants: a 1-year follow-up study

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), led to a global pandemic from 2020. In Thailand, five waves of outbreaks were recorded, with the fourth and fifth waves driven by the Delta and Omicron variants, resulting in over 20,000 new confirmed cases daily at their peaks.MethodsThis cross-sectional study investigated the associations between clinical symptoms, vaccination status, antibody responses, and post-COVID-19 sequelae in COVID-19 patients. Plasma samples and clinical data were collected from participants admitted to hospitals in Thailand between July 2021 and August 2022, with follow-ups conducted for one year. The study included 110 participants infected with either the Delta (n = 46) or Omicron (n = 64) variants. Virus genotypes were confirmed by RT-PCR of nasal swab RNA and partial nucleotide sequencing of the S gene. IgG and IgA antibody levels against the receptor-binding domain (RBD) of SARS-CoV-2 Delta and Omicron variants were measured in plasma samples using ELISA.ResultsPneumonia was found to be associated with Delta variant infections, while sore throat, congestion or runny nose, and headache were linked to Omicron infections. Vaccination with fewer than two doses and diabetes mellitus were significantly associated with higher disease severity. Specific IgG and IgA antibodies against the RBD of the Delta variant generally rose by day 14 and were maintained for up to two months, whereas the pattern of antibody response to the Omicron variant was less clear. Antibody risings were found to be positively associated with pneumonia, certain underlying conditions (obesity, hypertension, dyslipidemia, and diabetes mellitus), and age ≥ 60 years. Delta variant infections were associated with forgetfulness, hair loss, and headache during the 1-year post-infection period. Females were more likely to experience hair loss, forgetfulness, and joint pain, while older age was associated with joint pain.ConclusionsThis study enhances our understanding of SARS-CoV-2 infections in Thais, particularly concerning the Delta and Omicron variants. The findings can inform public health planning and response strategies for future outbreaks of SARS-CoV-2 or other emerging viral diseases.

Genetic variability of Myxobolus nagaraensis (Bivalvulida: Myxobolidae) infecting freshwater gobies Rhinogobius Gill 1859 (Gobiiformes: Oxudercidae) from rivers in Japan

Myxobolus nagaraensis is a myxozoan parasite first reported in freshwater gobies (Rhinogobius spp.) from the Nagara River, Gifu Prefecture, Japan. Myxospores of M. nagaraensis form plasmodia in the visceral cavities of gobies, commonly presenting as distended abdomens. Although Rhinogobius is a common fish genus in Japan, details of M. nagaraensis, including genetic information, remain unknown. We compared the nucleotide sequences of the ribosomal RNA gene (rDNA) of M. nagaraensis from three different host species (R. fluviatilis, R. nagoyae, and R. similis) caught in three different rivers in Japan (Sakai, Sagami, and Kaname). The ITS region (ITS-1, 5.8S rDNA, and ITS-2) and large subunit (LSU) rDNA exhibited 49 and 55 variable sites, respectively. The highest nucleotide diversity was observed in the ITS region (0.00962), whereas that of the LSU rDNA was 0.00187. Differences in host species, rather than rivers, were a significant factor for genetic variation in both the ITS region (62.58%; P < 0.001) and LSU rDNA (55.22%; P < 0.01). Significant genetic variation was observed in M. nagaraensis from R. similis compared to R. fluviatilis (P < 0.001) or R. nagoyae (P < 0.001) from the same river. Such details are valuable for understanding parasite dispersal and its ecological impact on Rhinogobius hosts.

Information Gradient among Nucleotide Sequences of Essential RNAs from an Evolutionary Perspective.

We hypothesize that the first ancestral "protocell" molecular structures, i.e., the first RNAs and peptides that gradually transformed into real cells once the Earth had cooled sufficiently for organic molecules to appear, have left traces in the RNAs and the genes in present cells. We propose a circular RNA that could have been one of these ancestral structures whose vestigial pentameric subsequences would mark the evolution from this key moment when the protocells began to join with living organisms. In particular, we propose that, in present RNAs (ribosomal or messenger), which play an important role in the metabolism of current cells, we look for traces of the proposed primitive structure in the form of pentamers (or longer fragments) that belong to their nucleotide sequence. The result obtained can be summarized in the existence of a gradient of occurrence of such pentamers, with a high frequency for the most vital functions (protein synthesis, nucleic synthesis, cell respiration, etc.). This gradient is also visible between organisms, from the oldest (Archaea) to the most recent (Eukaryotes) in the evolution of species.

Switching from combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate to tenofovir alafenamide fumarate monotherapy in patients with chronic hepatitisB based on nucleotide sequences of hepatitisB virus pregenome RNA.

Patients with chronic hepatitisB virus (HBV) infection experiencing viral breakthrough (BTH) or partial response (PR) during lamivudine (LAM) or entecavir hydrate (ETV) administration often took ETV plus tenofovir alafenamide fumarate (TAF) due to the emergence of a drug-resistance mutation. However, in patients lacking drug-resistance mutation against TAF, sufficient antiviral effects may be achievable with TAF monotherapy. We assessed the drug-resistance profile through nucleotide sequences of HBV pregenome RNA, and subsequently changed to TAF monotherapy from ETV plus TAF. This prospective study included 25 patients with serum HBV-DNA below 20IU/mL under ETV plus TAF administration. Pregenome RNA nucleotide sequences of HBV in the sera were analyzed using direct sequencing and deep sequencing. ETV was discontinued in patients without rtA194T and rtS106C+rtH126Y +rtD134E +rtL269I quadruple mutations in direct sequencing. LAM-PR, LAM-BTH, ETV-PR, and ETV-BTH were observed in 1, 16, 7, and 1 patient(s), respectively. Pregenome RNA nucleotide sequences were analyzable in 20 patients. Among the 12 patients classified as LAM-BTH, six patients showed rtL180M+rtM204V/I in direct sequencing, and one patient showed minor clones containing rtL180M+rtM204V+A194T in deep sequencing at a frequency of 0.3%. In the six patients classified as ETV-PR, one patient harbored rtM204I. No clones showing rtS106C+rtH126Y+rtD134E+rtL269I quadruple mutation were detected in deep sequencing. Subsequently, ETV was discontinued, and serum HBV-DNA remained undetectable up to 48weeks in all patients. Patients receiving ETV plus TAF due to partial response or BTH during initial LAM or ETV administration were able to safely transition to TAF monotherapy based on nucleotide sequences of HBV pregenome RNA in the sera.

Multi-locus sequence analysis of ‘Candidatus Mycoplasma haematomacacae’ in free-ranging macaques from Thailand suggestive of a closer relationship to hemotropic mycoplasmas in capuchins and potential origin from bats

Although ‘Candidatus Mycoplasma haematomacacae’ (formerly known as ‘Candidatus Mycoplasma haemomacaque’) has been reported on extensively in macaques from Thailand, the USA, Japan, and Brazil, its genetic characterization has primarily been restricted to the 16S rRNA sequences with no exploration on multi-locus sequence analysis. The primary goal of this study was to characterize ‘Ca. M. haematomacacae’ among Thai macaques based on multiple genetic markers. Between April 2018 and November 2021, blood samples were taken from 580 free-ranging macaques (560 Macaca fascicularis and 20 Macaca nemestrina) in 15 locations encompassing 10 provinces throughout Thailand. Using the conventional PCR assay targeting the 16S ribosomal RNA (16S rRNA) gene, 338 out of 580 macaques (58.27 %) tested hemoplasma-positive. Of these, 40 positive samples were further subjected to DNA sequencing, and all were identified as ‘Ca. M. haematomacacae’. Subsequently, the partial nucleotide sequences of 23S ribosomal RNA (23S rRNA) and RNase P RNA (rnpB) genes of this particular hemoplasma species were amplified through nested PCR assay. The analysis of multi-locus genetic markers revealed that the 23S rRNA and rnpB sequences exhibited higher levels of genetic diversity than the 16S rRNA sequences. Furthermore, the 16S rRNA analyses demonstrated that ‘Ca. M. haematomacacae’ infecting Old World monkeys (Macaca spp.) was most closely related to hemotropic Mycoplasma spp. in black-capped capuchins (Sapajus apella) and Marcgrave's capuchins (Sapajus flavius) from Brazil, as well as establishing a common ancestor clade with hemotropic Mycoplasma spp. from the Neotropical bats in Belize and Peru and an Old World bat in Spain. The 23S rRNA analyses likewise evidenced that ‘Ca. M. haematomacacae’ formed a sister clade with hemotropic Mycoplasma spp. in Neotropical bats from Belize and Panama. Thus, the present findings, based on multi-locus sequence analysis, suggest a potential origin of ‘Ca. M. haematomacacae’ from Neotropical and Old World bats. To the best of the authors’ knowledge, this study provided the largest dataset so far of multi-locus genetic sequences of ‘Ca. M. haematomacacae’ isolated from Thai macaques and enhanced the accuracy of phylogenetic analyses, providing insights into their origins among hemotropic Mycoplasma spp. discovered worldwide.

Natural occurrence of cucumber mosaic virus infecting Adenium obesum plants in Brazil

AbstractIn 2022, virus‐like symptoms were observed in Adenium obesum plants in Brazil. High‐throughput sequencing analysis found three contig sequences of cucumber mosaic virus (CMV) genome segments, which were of 3352, 3006 and 2221 nucleotides, and shared 98.59%, 95.02% and 98.05% nucleotide identities with the nucleotide sequences of CMV RNAs 1, 2 and 3, respectively. Phylogenetic analysis of the coat protein gene indicated that the CMV isolate belongs to the subgroup IB. Symptoms of mottle like those observed in the field samples were reproduced on mechanically inoculated plants of A. obesum, and RT‐PCR confirmed the CMV infection. CMV was transmitted by Aphis gossypii to A. obesum plants. This is the first report of CMV infecting A. obesum plants in Brazil.

The role of microRNAs in preeclampsia

AIM: The aim of this study was to review current sources of scientific literature covering the role of miRNAs in preeclampsia.&#x0D; BASIC PROVISIONS: MicroRNAs are a class of short RNA nucleotide sequences that are not involved in protein synthesis, but are capable of controlling complex processes such as cell growth, differentiation, stress response, and tissue remodeling, which under certain conditions play a key role in a variety of pathological processes, including preeclampsia. MicroRNAs regulate up to 60% of the human genome. There are three types of placental miRNAs: placenta-specific, placenta-associated and circulating ones. Three miRNA gene clusters, namely chromosome 19 cluster (C19MC), chromosome 14 cluster (C14MC), and miR-371 ~ 373 cluster, encode most placenta-specific miRNAs. C19MC encodes 58 mature miRNAs and is expressed in trophoblast cells in early pregnancy and then, in placental differentiated cells. C14MC encodes 63 mature microRNAs, which are also expressed in trophoblasts. The miR-371~373 cluster only encodes six mature microRNAs expressed in placental differentiated cells and embryonic stem cells. The functions of placenta-specific miRNAs are being actively studied now. It has been established that the action of these microRNAs is associated with proliferation, apoptosis, migration, angiogenesis of trophoblast cells and placentation in early pregnancy. Recently, special attention has been paid to identifying microRNAs as possible predictors of preeclampsia in early pregnancy.&#x0D; CONCLUSIONS: Literature data indicate that miRNAs are associated with the pathogenesis of preeclampsia. It has been proven that more than a hundred types of miRNAs are expressed in placental tissues, and some of them can be isolated and detected in peripheral blood and urine in patients with preeclampsia. Studying the miRNA types will allow for determining the most significant prognostic markers for early detection of preeclampsia and developing non-invasive tests.

THE COMPLETE NUCLEOTIDE SEQUENCE OF THE GENOMIC RNA OF BEAN COMMON MOSAIC VIRUS STRAIN NL4

The complete nucleotide sequence of the genomic RNA of the NL4 strain of Bean common mosaic virus (BCMV-NL4) was determined. The viral genome is 10037 nucleotides in length, excluding the 3’ terminal poly (A) tail, and contains a single open reading frame (ORF) of 9666 nucleotides encoding a polyprotein of 3222 amino acids. The ORF is flanked by 5’ and 3’ untranslated regions (UTRs) of 133 and 235 nucleotides, respectively. Comparative analyses of the predicted BCMV-NL4 polyprotein with other species of the genus Potyvirus revealed nine cleavage sites resulting in ten functional proteins. Nucleotide and amino acid sequence identities indicated a close relationship between BCMV-NL4 and BCMV-NL1. Blast comparisons using coat protein (CP) and 3’UTR sequences showed 100% identity between BCMV-NL4 and the Mexican variant (US6) of this strain.

Antisense oligonucleotides: a novel Frontier in pharmacological strategy.

Antisense oligonucleotides (ASOs) are short single stranded synthetic RNA or DNA molecules, whereas double-stranded RNA nucleotide sequences are called small interfering RNA (siRNA). ASOs bind to complementary nucleic acid sequences impacting the associated functions of the targeted nucleic acids. They represent an emerging class of drugs that, through a revolutionary mechanism of action, aim to directly regulate disease-causing genes and their variants, providing an alternative tool to traditional "protein-specific" therapies. The majority of the ASOs are designed to treat orphan genetic disorders that in most of the cases are seriously disabling and still lacking an adequate therapy. In order to translate ASOs into clinical success, constant technological advances have been instrumental in overcoming several pharmacological, toxicological and formulation limitations. Accordingly, chemical structures have been recently implemented and new bio-conjugation and nanocarriers formulation strategies explored. The aim of this work is to offer an overview of the antisense technology with a comparative analysis of the oligonucleotides approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA).

MRNA decoding in human is kinetically and structurally distinct from bacteria

In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems1. Although key features are conserved across evolution2, eukaryotes achieve higher-fidelity mRNA decoding than bacteria3. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment4–6. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.

Automating microbial taxonomy workflows with PHANTASM: phylogenomic analyses for the taxonomy and systematics of microbes.

The nucleotide sequences of 16S ribosomal RNA (rRNA) genes have been used to inform the taxonomic placement of prokaryotes for several decades. Whole-genome approaches can better resolve evolutionary relationships of organisms, but these analyses often require computational proficiencies that are uncommon among microbiologists. PHANTASM is a new tool capable of automating these workflows. This tool was designed to work for a wide range of prokaryotes and is the first example of an automated reconciliation of NCBI's Taxonomy database with that of the List of Prokaryotic names with Standing in Nomenclature (LPSN). In this study, we describe the workflow of PHANTASM and provide several examples of results generated by it. The source code is freely-available on GitHub. In order to facilitate the ease-of-access for researchers, PHANTASM is also available as a Docker image. While other tools exist to facilitate starting points for these analyses, PHANTASM provides users with a greater degree of control and produces outputs that can be used to make publication-quality figures.

Alkaline Protease Production by Immobilized Klebsiella aerogenes Cells from Dairy Effluent Sludge

This study investigated the screening of alkaline protease microorganism from diary effluent sludge and identified by 16S ribosomal RNA nucleotide sequence as Klebsiella aerogenes with accession number MF156964.1 and maximum identity 95.45%. The cells were immobilized with coconut pod husks and optimization studies such as the effects of particle sizes, pH, temperature, agitation speed, and incubation time were determined. Out of twenty three microorganisms screened, three were potential protease producers. K. aerogenes gave the highest zone of hydrolysis (35 mm) on the skimmed milk agar plate. The particle size (0.075 mm2) of the immobilization agent gave the highest enzyme activity 176.83 U/mL. The optimum incubation time for the production of protease was 48 h with enzyme activity 143.054 U/mL which further declined. The optimum pH of the protease was pH 9.0 with activity 209.61 U/mL which made it alkaline. The agitation speed 150 rpm resulted in a protease activity 175.83 U/mL and reduced by 56.5% at 250 rpm. The optimal temperature 35 ºC was 183.78 U/mL. This study also confirmed the stability and reusability of the immobilized cells using the coconut pod husks matrix by maintaining from 100% to 76.2% up to six times recycle. Conclusively, the study established the efficiency of low cost, readily available matrix and reusability potentials of coconut pod husks for cells immobilization technology through entrapment at optimal conditions for protease production.

Ticks Infesting Dogs in Khyber Pakhtunkhwa, Pakistan: Detailed Epidemiological and Molecular Report.

Ticks and tick-borne diseases are considered a major challenge for human and animal health in tropical, sub-tropical, and temperate regions of the world. However, only scarce information is available on the characterization of tick species infesting dogs in Pakistan. In this study, we present a comprehensive report on the epidemiological and phylogenetic aspects of ticks infesting dogs in Pakistan using the mitochondrial markers i.e. Cytochrome c oxidase subunit 1 (cox1) and 16S ribosomal RNA (16S rRNA) nucleotide sequences. A total of 300 dogs were examined and 1150 ixodid ticks were collected across central Khyber Pakhtunkhwa, Pakistan. The morpho-molecular characterization of hard ticks revealed the presence of two ixodid tick genera on dogs, i.e., Hyalomma and Rhipicephalus, including six tick species viz. Hyalomma dromedarii (15.9%), Hyalomma excavatum (3%), Rhipicephalus sanguineus s.l. (41.3%), Rhipicephalus turanicus s.s. (28.7%), Rhipicephalus haemaphysaloides (10.2%), and Rhipicephalus microplus (2%). The total prevalence of tick infestation in dogs was 61%. The district with the highest tick prevalence rate in dogs was Mardan (14.7%), followed by Peshawar (13%), Swabi (12%), Charsadda (11%), and Malakand (10.3%), respectively. Risk factors analysis indicated that some demographic and host management-associated factors such as host age, breed, exposure to acaricides treatment, and previous tick infestation history were associated with a higher risk of tick infestation on dogs. This is the first molecular report confirming the infestation of Hyalomma and Rhipicephalus tick species in the dog population from the study area. The present study also reported a new tick−host association between Hy. excavatum, Hy. dromedarii, and dogs. Phylogenetic analysis revealed that cox1 partial nucleotide sequences of Hy. excavatum in our dataset were 100% identical to similar tick specimens identified in Turkey, and those of Hy. dromedarii were identical to tick specimens from Iran. Whereas, Rh. haemaphysaloides and Rh. microplus’ cox1 partial nucleotide sequences were identical to sequences previously published from Pakistan. Rhipicephalus turanicus s.s. ‘s cox1 isolates from the present study were 99.8−100% identical to Pakistani-reported isolates, and those of Rh. sanguineus s.l. were 100% identical to Chinese specimens. Results on the genetic characterization of ticks were further confirmed by 16S rRNA partial nucleotide sequences analysis, which revealed 100% identity between the tick isolates of this study and those of Hy. excavatum reported from Turkey; Hy. dromedarii specimens reported from Senegal; Rh. haemaphysaloides, Rh. microplus, and Rh. turanicus s.s., previously published from Pakistan, and Rh. sanguineus s.l., published from China. Furthermore, phylogenetic analysis showed that the Rh. sanguineus s.l. isolates of this study clustered with specimens of the tropical lineage with 7.7−10% nucleotide divergence from the specimens of the temperate lineage. Further molecular works need to be performed throughout Pakistan to present a more detailed map of tick distribution with information about dog host associations, biological characteristics, and pathogen competence.

Morphological and molecular characterization of Eurytrema spp. Looss, 1907 detected in domestic water buffaloes and cattle in northern Vietnam.

Eurytrema spp. are pancreatic flukes belonging to the Dicrocoeliidae family. They are the cause of neglected diseases in Vietnam and are responsible for economic losses in ruminant production, particularly in water buffaloes and cattle. Eurytrema spp. have been widely reported in several Asian countries. Recently, morphological and molecular analyses to discriminate Eurytrema spp. have been conducted in Brazil, China, Bangladesh, Nepal, and Indonesia; however, similar analyses have not been performed in Vietnam. In the present study, we identified Eurytrema flukes collected from water buffaloes and cattle in northern Vietnam based on their morphology. Morphometric analyses were conducted on 15 samples each of Eurytrema cladorchis and Eurytrema coelomaticum. Representative samples from both species were selected for molecular analyses, and the nucleotide sequences of the 18S ribosomal RNA (18S rRNA) gene and internal transcribed spacer 2 (ITS2) were determined. Phylogenetic analyses based on 18S rRNA sequences revealed that E. cladorchis from Vietnam belongs to the same clade as that from Bangladesh. Similarly, E. coelomaticum isolates from Vietnam and China belonged to the same clade. Both clades were isolated from E. pancreaticum. This is the first study to describe the coexistence of E. cladorchis and E. coelomaticum in Vietnam and the first report of the ITS2 nucleotide sequence for E. coelomaticum, which can be used for molecular species discrimination.

Prevalence and Molecular Characterization of Four Enteric Protozoa in Dromedary Camels (Camelus Dromedarius)

Enteric protozoa are major causes of economic losses in dromedary camels due to clinical and subclinical diseases. The study investigated the prevalence of enteric protozoal parasites in dromedary camels using parasitological and molecular techniques. Besides, the molecular characterization of selected enteric protozoa was performed by nucleotide sequencing and phylogenetic analysis. One hundred and twenty-one fecal samples were collected from dis-eased (49) and apparently healthy (72) dromedary camels during December 2020 - November 2021. Overall, 57.02% of the fecal samples were positive for enteric protozoa with the B. coli, Eimeria spp., Giardia spp., Cryptosporidium spp. were detected in 32.23%, 8.26%, 2.48%,3.30% fecal samples, respectively, while 10.74% samples had mixed infection. While the PCR technique revealed the overall prevalence of 69.56%, 13.04% and 10.14% for the B. coli, Giardia spp. and Cryptosporidium spp., respectively in the study areas. Phylogenetic analysis based on the partial nucleotide sequences of the small subunit ribosomal RNA, B beta giardin (bg) and Cryptosporidium parvum precursor of oocyst wall protein (COWP) genes of B. coli, Giardia spp. and Cryptosporidium spp., respectively revealed that the enteric proto-zoa from camels had high genetic similarities with strains detected from other animals and humans in Egypt and different parts of the world. This study suggests that the camels may act a potential source of infection of the studied enteric protozoa for other livestock and humans.

Set-Theoretical Data Models in the Problem of Calculating Secondary Structures of RNA

The tasks of counting the secondary structures of nucleotide sequences are a special case of combinatorial problems of high complexity (NP-problems) that can be solved by logic-heuristic methods. In addition, it is possible to use special software programs to solve the calculation of secondary structures of RNA nucleotide sequences for phylogenetic analysis (recovery of all mutations from an ancestor to the next one). In this paper, we propose more general means of data presentation and more powerful algorithms for calculating the secondary structures of RNA nucleotide sequences than in previous works of the author. In addition, we note that the software has great flexibility to solve problems of phylogenetic analysis. Computational experiments, the results of which are presented in this work, were carried out on the primary data taken from the website www.ncbi.nlm.nih.gov. In addition, data were also taken from the GenBank (USA) and EMBL (Europe) nucleotide sequence banks. The adaptation of the developed methods for calculating secondary structures was first carried out by searching for the full range of perfect repeats in genetic texts (the genomes of Bradyrhizobium japonicum (BA0000040_GR), Streptomyces avermitilis (BA0000030_GR)). As a result, a program was created that is customizable in many ways, including working in the alphabet, with extended consensus symbols (for more details, see the introduction).

Molecular characterization of a novel mitovirus from Rhizoctonia solani AG-4 HGIII strain XMC-IF.

The nucleotide sequence of a viral double-stranded RNA (dsRNA) from Rhizoctonia solani AG-4 HGIII strain XMC-IF (designated as "Rhizoctonia solani mitovirus 106", RsMV-106) was determined. The complete sequence was 2794 bp in length with a 57.50% A + U content and contained a large open reading frame (ORF) when the fungal mitochondrial genetic code was used. The ORF potentially encodes a 95.76-kDa protein containing a conserved domain of an RNA-dependent RNA polymerase (RdRp). BLASTp analysis revealed that the RdRp domain of RsMV-106 shared 47.52-73.24% sequence identity with those of viruses of the genus Duamitovirus and was most similar (73.24% identity) to that of Alternaria alternata mitovirus 1 (AaMV1). Phylogenetic analysis showed that RsMV-106 is a novel member of the genus Duamitovirus, family Mitoviridae. This is the first report of the full genome sequence of a mitovirus associated with R. solani AG-4 HGIII.

Algorithmic Design of 3D Wireframe RNA Polyhedra.

We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.

Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism

Nanopore sequencing (ONT) is a new and rapidly developing method for determining nucleotide sequences in DNA and RNA. It serves the ability to obtain long reads of thousands of nucleotides without assembly and amplification during sequencing compared to next-generation sequencing. Nanopore sequencing can help for determination of genetic changes leading to antibiotics resistance. This study presents the application of ONT technology in the assembly of an E. coli genome characterized by a deletion of the tolC gene and known single-nucleotide variations leading to antibiotic resistance, in the absence of a reference genome. We performed benchmark studies to determine minimum coverage depth to obtain a complete genome, depending on the quality of the ONT data. A comparison of existing programs was carried out. It was shown that the Flye program demonstrates plausible assembly results relative to others (Shasta, Canu, and Necat). The required coverage depth for successful assembly strongly depends on the size of reads. When using high-quality samples with an average read length of 8 Kbp or more, the coverage depth of 30× is sufficient to assemble the complete genome de novo and reliably determine single-nucleotide variations in it. For samples with shorter reads with mean lengths of 2 Kbp, a higher coverage depth of 50× is required. Avoiding of mechanical mixing is obligatory for samples preparation. Nanopore sequencing can be used alone to determine antibiotics-resistant genetic features of bacterial strains.

Cellular sentience as the primary source of biological order and evolution

All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative adaptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.