Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the "RNA world" hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme, belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the ultraconserved occurrence of HHR in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitously features of life. Those are the versatility and efficiency of small RNAs, viroids and ribozymes, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.

Nicotinamide is an important functional compound and, in the form of nicotinamide adenine dinucleotide (NAD), is used as a cofactor by protein-based enzymes to catalyze redox reactions. In the context of the RNA world hypothesis, it is therefore reasonable to assume that ancestral ribozymes could have used cofactors such as NAD or its simpler analog nicotinamide riboside (NAR) to catalyze redox reactions. The only described example of such an engineered ribozyme uses a nicotinamide moiety bound to the ribozyme through non-covalent interactions. Covalent attachment of NAR to RNA could be advantageous, but the demonstration of such scenarios to date has suffered from the chemical instability of both NAR and its reduced form NARH, making their use in oligonucleotide synthesis less straightforward. Here, we review the literature describing the chemical properties of the oxidized and reduced species of NAR, their synthesis, and previous attempts to incorporate either species into RNA. We discuss how to overcome the stability problem and succeed in generating RNA structures incorporating NAR.

Abstract: Chikungunya virus (CHIKV) is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates following the introduction of its major vector, Ae. albopictus. Recent cases have been documented in Europe, the Caribbean, and the Americas. CHIKV causes a disease frequently misdiagnosed as Dengue fever, with potentially life-threatening symptoms that can result in long term debilitating arthritis. There have been ongoing investigations of possible therapeutic interventions for both acute and chronic symptoms, but to date none have proven effective in reducing the severity or lasting effects of CHIKV disease. Recently, a promising vaccine candidate has received accelerated FDA approval, indicating the importance of remedies to this emerging worldwide health threat. Nonetheless, therapeutic interventions for CHIKV and other mosquito borne virus diseases are urgently needed yet remain elusive. The increasing risk of spread from endemic regions via human travel and commerce, coupled with the absence of a vaccine or FDA approved therapeutic, puts a significant proportion of the world population at risk for this disease. In this report we explore the possibility of using SOFA (Specific On/oFf Adapter) Hepatitis Delta Virus Ribozymes (HDV-Rzs) as antivirals in cells infected with CHIKV. The results we obtained suggest there could be some role in using these SOFA HDV molecules as antiviral therapies for not only CHIKV, but potentially other viruses as well.

There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes evolution of type I and type II tRNAs from ordered precursors (RNA repeats and inverted repeats). Despite diversification of tRNAome sequences, statistical tests overwhelmingly support the theorem. Furthermore, the theorem relates the dominant pathway for the origin of life on Earth, specifically, how tRNAomes and the genetic code may have coevolved. Alternate models for tRNA evolution (i.e., 2 minihelix, convergent and accretion models) are falsified. In the context of the pre-life world, tRNA was a molecule that via mutation could modify anticodon sequences and teach itself to code. We relate the clearest history to date of the chemical evolution of life on Earth. From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in evolution of complexity during the pre-life to life transition on Earth.

Background: In healthy children, the frequency of anomalous persistence of primitive reflexes (PRs) and craniosacral blocks (CBs) are unknown, as well as their impact on neurodevelopment, behaviour disorders and related consequences. We aim to know the prevalence of anomalous PRs and CBs in apparently healthy children and its relationships with behavior and neurodevelopment anomalies. Methods: Participants (n=120) were evaluated through physical examination to detect PRs and CBs, an ad hoc parent survey to collect perinatal events, and children behavior assessment by teachers using Battelle score. Results: PRs were present in 89.5%. Moro (70.8%), cervical asymmetric (78.3%) and cervical symmetric PRs (67.5%) were the most frequent observed PRs. CBs were found in 83.2%, and the most frequent CBs were dura mater (77.5%) and sphenoid bone (70%) blocks. Moro, cervical asymmetric and cervical symmetric active primitive reflexes are significantly associated to cranial blocks of dura mater, parietal zones, and sphenoid bone sway. Gestational disorders or perinatal complications were associated to a higher frequency of PRs and CBs. The presence of PRs and CBs were associated with abnormal Battelle scores and neurobehavioral problems. Conclusion: Presence of PRs and CBs in children without diagnosed diseases are frequent and related with disturbances in childhood neurodevelopment.

In this paper, we present the definition, some properties, and solve a problem on special primes. These properties help in providing us with a better understanding of the problem posed related to special primes on the open problem garden website. The problem involves finding all the primes q, given a prime p such that q≡1(mod p) and 2^((q−1)/p)≡1(mod q). We prove that a prime number q is a special prime of p if and only if the order of 2 in U(q) divides q−1p. Also, we prove that a prime number q is not a special prime for any prime number if 2 is a generator of the group U(q) and that there exist infinitely many special primes for any given prime number.

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.

The study was conducted in coniferous and deciduous old growth forests in two forest complexes located in: i) the fenced area of the Popielno Research Station of the Polish Academy of Sciences, with free-living Polish pony [Polish primitive horse (Equus ferus caballus)], and ii) open Maskulińskie Forest District managed (harvested) forest, without horses. The impact of forest animals on ground cover layer as well as on understory shrub layer and undergrowth, in i) area (horses and other forest animals) was compared with the results in ii) area (forest animals without horses). Very significant differences in the understory and undergrowth (above 0,5 m) layer vegetation communities structure between both areas and type of stands were found. The results suggest that the presence of the Polish horse substantially changed the species composition and increased the species diversity of the ground layer and shrub layer both on coniferous forest and in the deciduous forest habitats. The height of the shrub layer trees was lower by 30% in the area with the Polish horse.

Geochemists disagree whether or not prebiotic chemistry has existed already during the Hadean Eon and whether the then terrestrial atmosphere has been strongly or weakly reduced. Here I argue that cellular life has existed already just after the end of the Hadean Eon and that terrestrial life has survived a number of cataclysms during the Earth's history. I argue that although organic molecules have been detected in meteorites that most organic molecules required for the formation of macromolecules must have been formed on Earth. Finally, I argue that the primitive terrestrial atmosphere during the Hadean Eon has been weakly reduced, so that amino acids and small nucleic acids could have been formed. I suggest that the first self-replicable macromolecules have been similar to viroids.

Physical Unclonable Functions (PUFs) based on the retention times of the cells of a Dynamic Random Access Memory (DRAM) can be utilised for the implementation of cost-efficient and lightweight cryptographic protocols. However, as recent work has demonstrated, the times needed in order to generate their responses may prohibit their widespread usage. In order to address this issue, the Row Hammer PUF has been proposed by Schaller et al. [1], which leverages the row hammer effect in DRAM modules to reduce the retention times of their cells and, therefore, significantly speed up the generation times for the responses of PUFs based on these retention times. In this work, we extend the work of Schaller et al. by presenting a run-time accessible implementation of this PUF and further reducing the time required for the generation of its responses. Additionally, we also provide a more thorough investigation of the effects of temperature variations on the the Row Hammer PUF and briefly discuss potential statistical relationships between the cells used to implement it. As our results prove, the Row Hammer PUF could potentially provide an adequate level of security for Commercial Off-The-Shelf (COTS) devices, if its dependency on temperature is mitigated, and, may therefore, be commercially adopted in the near future.

In vitro circular RNA (circRNA) preparation methods have been gaining a lot of attention recently as several reports suggest that circRNAs are more stable with better performances in cells and in vivo than linear RNAs in various biomedical applications. Self-splicing ribozymes are considered a major in vitro circRNA generation method for biomedical applications due to their simplicity and efficiency in circularization of gene of interest. This review summarizes updates and discusses recently developed self-circularization methods based on the self-splicing ribozyme such as group I and II intron ribozymes and pros and cons of each method to prepare circRNA in vitro.

Hepatitis D virus (HDV) infection represents the most severe form of chronic viral hepatitis. We have shown that the delivery of HDV replication-competent genomes to the hepatocytes using adenoassociated virus (AAV-HDV) as gene delivery vehicles offers a unique platform to investi-gate the molecular aspects of HDV and associated liver damage. Here, we generated HDV ge-nomes modified by site directed mutagenesis aimed to: i) prevent some post-translational modi-fications of HDV antigens (HDAgs) such as Large-HDAg (L-HDAg) isoprenylation or Short-HDAg (S-HDAg) phosphorylation ii) alter the localization of HDAgs within the subcellular compartments and iii) inhibit the right conformation of the delta ribozyme. First, the different HDV mutants were tested in vitro using plasmid-transfected Huh-7 cells and then in vivo in C57BL/6 mice using AAV vectors. We found that Ser 177 phosphorylation and the ribozymal ac-tivity are essential for HDV replication and HDAg expression. Mutation of the isoprenylation domain prevent the formation of infectious particles and increase cellular toxicity and liver dam-age. Finally, altering the intracellular localization od HDAg have a profound on viral replication in vivo but liver toxicity is maintained. Mutation in the nuclear export signal impair the for-mation of infectious viral particles. These findings contribute valuable insights into the intricate mechanisms of HDV biology and have implications for therapeutic considerations

Understanding the mechanism, how entirely new (EntNew) gene/protein or the first ancestral gene/protein of a family was created, should be one of the most important issues in the biological sciences. However, the mechanism is totally unknown still now. On the other hand, it is well known that mature protein is generally rigid and one catalytic center exists on the protein. Creation of such a mature EntNew gene/protein should be, of course, carried out through random process, because it cannot be designed in advance. However, the EntNew gene/protein never be created by random polymerization of the respective monomeric units, because of the extraordinary large sequence diversities of ~10¹⁸⁰ and ~10¹³⁰, respectively. Protein 0^th-order structure or a specific amino acid composition, in which immature but water-soluble protein can be produced even through random process, holds the key for solving the difficult problem. As it was fragmentally described in the previous papers how and where EntNew gene/protein was created, I describe in detail in this review three processes generating EntNew gene/protein with some flexibility under three genetic codes, the universal genetic code, SNS primitive code and GNC primeval code, and discuss why the mature gene/protein could be created through the processes.