The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapping RT-PCR or nested PCR were subjected to direct sequencing. In total, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Non-KSB sequences were retrieved from the Los Alamos National Laboratory HIV Database. Phylogenetic analysis indicated that within KSB, 2 FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed signature nucleotide residues at 1.05%, compared with local controls. Additionally, in-depth FLs sequence analysis over 30 years in KSB indicates that the KSB FL significantly increases over time before combined antiretroviral therapy (cART) and decreases on cART. Furthermore, the increase in FLs over time significantly occurred in the subtypes B, C and G, but, there was no increase in the subtypes D, A, and F1. Consequently, subtypes F1 and D had the shortest sequence length. Our analysis was extended to compare HIV-1 with HIV-2 and SIVs. Essentially, the longer the sequence length (SIVsm > HIV-2 > SIVcpz > HIV-1), the longer the survival period. The increase in the length of the HIV-1 sequence over time suggests that it might be an evolutionary direction toward attenuated pathogenicity.

Centromeres are among the fastest evolving genomic regions in a diverse array of organisms. The evolutionary process driving this rapid evolution has not been unambiguously established. Here I integrate diverse information to motivate a model in which centromeres evolve rapidly because of their intrinsic molecular phenotype: they tightly bind centromeric proteins throughout the cell cycle. DNA-bound proteins have been shown to cause stalling and collapse of DNA replication forks in many genomic regions, including centromeres. Collapsed replication forks generate one-sided double strand breaks (DSBs) that are repaired by the Break-Induced Repair (BIR) pathway. Here I show why this repair is expected to generate tandem repeat structure and three key features at centromeres: i) increased nucleotide substitution mutation rates, ii) out-of- register re-initiation of replication that leads to indels spanning one or more repeat units, and iii) elevated rates of large and small transpositions within centromeres and between genomic regions. These phenotypes lead to: i) a rapid rate of nucleotide substitutions within a clade of centromeric sequences, ii) continual turnover of monomers within centromeres that fosters molecular-drift and molecular-drive, and iii) recurrent quantum leaps in centromere sequence due to the formation of mosaic monomers and new sequences transposed into non-homologous centromeres. These features are plausibly the major reason centromeres evolve so rapidly. I also speculate on how the DNA sequence of centromeres might perpetually coevolve with the protein sequence of histone CENH3 –the major epigenetic mark of centromeres.

Many positive sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model, and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolate viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution, and inspire new solutions to virus disease mitigation.

Cells occupy a prominent place in the history of life on planet Earth. The central role of cellular organization is observed by the fact that “cellular life” is often used as a synonym for life itself. Thus, most characteristics used to define cells overlap with the ones used to define life. Notwithstanding, new scenarios about the origin of life are bringing alternative views to describe how cells may have evolved from the open biological systems named progenotes. Here, using a logical and conceptual analysis, we re-evaluate the characteristics used to infer a single origin for cells. We argue that some evidences used to support cell monophyly, such as the presence of elements from both the translation mechanism and the universality of the genetic code, actually indicate a unique origin for all “biological systems”, a term used to define not only cells, but also virus and progenotes. Besides, we present evidence that at least two biochemical pathways as important as (i) DNA replication and (ii) lipid biosynthesis may not homologous between Bacteria and Archaea. The identities observed between the proteins involved in those pathways along representatives of these two ancestral Domains are too low to indicate common genic ancestry. Altogether these facts can be seen as an indication that cellular organization has possibly evolved two or more times and that LUCA (the Last Universal Common Ancestor) might not have existed as a cellular entity. Thus, we aim to consider the possibility that different strategies acquired by biological systems to exist, such as viral, bacterial and archaeal were originated independently from the evolution of different progenote populations.

In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve a SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.

This study analyzed the structural changes of semicrystalline polylactide (PLA) in the form of spun-bonded mulching nonwoven, during outdoor composting. The investigation was carried out at the microstructural, supramolecular and molecular levels using scanning electron microscopy (SEM), wide-angle X-ray diffraction (WAXD) and the viscosity method, respectively. The results showed the varying degree of influence of the climatic condition, prepared compost mixtures and time on the molecular, supramolecular and micromorphological structure of PLA spun-bonded mulching nonwoven and its degradation rate. The obtained experimental results revealed how the popular outdoor composting method, realized under two different European climatic conditions (in Poland and in Bulgary), affects the degradation of PLA nonwoven, designed for agriculture use.

For decades, sepsis research has been motivated by the idea of a dangerous overreaction of the immune system in sepsis. But is it true that the response to sepsis is dysregulated? This review surveys the history of sepsis trials and found that evidence for dysregulation does not exist in many of the physiologic mechanisms of sepsis. It is time to consider the alternative hypothesis, that sepsis traits are often functional, and do more harm than good. This review discusses the implications of this perspective for the future of sepsis research

The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence is a major factor influencing the position of nucleosomes on genomes. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

We develop and apply new physics theory. The theory suggests specific unfound elementary particles. The theory suggests specific constituents of dark matter. We apply those results. We explain ratios of dark matter amounts to ordinary matter amounts. We suggest details about galaxy formation. We suggest details about inflation. We suggest aspects regarding changes in the rate of expansion of the universe. The theory points to relationships between masses of elementary particles. We show a relationship between the strength of electromagnetism and the strength of gravity. The mathematics basis for matching known and suggesting new elementary particles extends mathematics for harmonic oscillators.

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host adhesion like type 1 fimbriae. The extent to which non-pathogenic gut E. coli and infectious ST131 share AMR genes and key associated plasmids remains understudied at a genomic level. Here, we examined AMR gene sharing between gut E. coli and ST131 to discover an extensive shared preterm infant resistome. In addition, individual ST131 show extensive AMR gene diversity highlighting that analyses restricted to the core genome may be limiting and could miss AMR gene transfer patterns. We show that pEK499-like segments are ancestral to most ST131 Clade C isolates, contrasting with a minority with substantial pEK204-like regions encoding a type IV fimbriae operon. Moreover, ST131 possess extensive diversity at genes encoding type 1, type IV, P and F17-like fimbriae, particular within subclade C2. The type, structure and composition of AMR genes, plasmids and fimbriae varies widely in ST131 and this may mediate pathogenicity and infection outcomes.

Galls are characteristic plant structures formed by cell size enlargement and/or cell proliferation induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to insects. To form unique gall structures, gall-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development remain largely unknown due to the difficulties associated with the study of non-model plants in the wild. Recent advances in next-generation sequencing have allowed us to determine the biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the adaptive significance of galls for insects and plants. Thereafter, we summarize recent progress regarding the molecular aspects of insect gall formation.

Epoxy asphalt (EA) concrete is widely used in constructing long-span steel bridge pavements (SBDPs). This study aims to derive a fatigue damage evolution law, conducting an experimental investigation of SBDP. First, a general theoretical form of the fatigue damage evolution law of materials is established based on the thermal motion of atoms. Then, fatigue experiments demonstrate that this evolution law well represents the known damage–life relationships of SBDP. Taking into account the experimental relationships between damage and fatigue life under symmetrical cyclic loadings with different overload amplitudes and temperature variations, a detailed damage evolution law is deduced. Finally, the role of damage accumulation is discussed on the basis of the proposed damage evolution law for the extreme situation of heavy overload and severe environments. The results show that both heavy loading and falling temperatures increase the fatigue damage of SBDP considerably; therefore, SBDP should avoid heavy loading combined with winter temperatures. EA shows a fatigue life two to three times longer than that of modified matrix asphalt (SMA) or guss asphalt (GA). For the same thickness, EA pavement is demonstrated to be more suitable for an anti-fatigue design of large-span SBDP under high traffic flows and low temperatures.

In this paper we first provide a primer on SARS-CoV-2 and Covid-19 delineating the etiopathogenesis, epidemiology, clinical manifestations and the natural history of the disease. We then trace the evolution of the Covid-19 pandemic highlighting the characteristics of the epidemic in China where the pandemic originated, select countries of Europe which peaked during April, and Brazil, US and India where the pandemic has taken serious turns recently. We also project some possible trajectories for the mega cities of India based on the demographic characteristics of these cities in comparison to New York city. This is an updated version of the article from mid-April published online.

Space-time evolution is briefly explained by using the 3-dimensional quantized space model (TQSM) based on the 4-dimensional (4-D) Euclidean space. The energy (E=cDtDV), charges (|q|= cDt) and absolute time (ct) are newly defined based on the 4-D Euclidean space. The big bang is understood by the space-time evolution of the 4-D Euclidean space but not by the sudden 4-D Minkowski space-time creation. The big bang process created the matter universe with the positive energy and the partner anti-matter universe with the negative energy from the CPT symmetry. Our universe is the matter universe with the negative charges of electric charge (EC), lepton charge (LC) and color charge (CC). This first universe is made of three dark matter -, lepton -, and quark - primary black holes with the huge negative charges which cause the Coulomb repulsive forces much bigger than the gravitational forces. The huge Coulomb forces induce the inflation of the primary black holes, that decay to the super-massive black holes. The dark matter super-massive black holes surrounded by the normal matters and dark matters make the galaxies and galaxy clusters. The spiral arms of galaxies are closely related to the decay of the 3-D charged normal matter black holes to the 1-D charged normal matter black holes. The elementary leptons and quarks are created by the decay of the normal matter charged black holes, that is caused by the Coulomb forces much stronger than the gravitational forces. The Coulomb forces are very weak with the very small Coulomb constants (k₁(EC) = k_dd(EC) ) for the dark matters and very strong with the very big Coulomb constants (k₂(EC) = k_nn(EC)) for the normal matters because of the non-communication of the photons between the dark matters and normal matters. The photons are charge dependent and mass independent. But the dark matters and normal matters have the similar and very weak gravitational forces because of the communication of the gravitons between the dark matters and normal matters. The gravitons are charge independent and mass dependent. Note that the three kinds of charges (EC, LC and CC) and one kind of mass (m) exist in our matter universe. The dark matters, leptons and quarks have the charge configurations of (EC), (EC,LC) and (EC,LC,CC), respectively. Partial masses of elementary fermions are calculated, and the proton spin crisis is explained. The charged black holes are not the singularities.

The probability of the evolution of a character depends on two factors: the probability of moving from one character state to another character state and the probability of the new character state fixation. More the evolution of a character is probable more convergent evolution will be witnessed, consequently, convergent evolution could mean that the convergent character evolution result as a combination of these two factors. We investigate this phenomenon by studying the convergent evolution of biochemical functions. We use for the investigation the case of β-lactamases. β-lactamases hydrolyzes β-lactams which are antimicrobials able to block the DD-peptidases involved in bacterial cell wall synthesis. β-lactamase activity is present in two different superfamilies: the metallo-β-lactamase and the serine β-lactamase superfamily. The mechanism used to hydrolyze the β-lactam is different for the two superfamilies. We named this kind of evolution an allo-convergent evolution. We further show that the β-lactamase activity evolved several times within each superfamily, a convergent evolution type that we named iso-convergent evolution. Both types of convergent evolution can be explained by the two evolutionary mechanisms discussed above. The probability of moving from one state to another is explaining the promiscuous β-lactamase activity present in the ancestral sequences of each superfamily, while the probability of fixation is explained in part, by positive selection as the organisms having β-lactamase activity allows them to resist to organism secreting β-lactams. Indeed a mutation increasing the β-lactamases activity will be selected as the organisms having this activity will have an advantage over the others.

In this study the processes taking place on the surfaces of nanostructurized Cu/CuO and Cu/CuO/Pd electrodes at different potential, $E$, values in the solutions of 0.1 M KOH in H$_2$O and D$_2$O (heavy water) were probed by the surface enhanced Raman spectroscopy (SERS) and analysis of electrochemical reactions occurring under experimental conditions is presented. Bands of the SERS spectra of Cu/CuO/Pd electrode observed in the range of $E$ values from +0.3~V to 0 V~(SHE) at 1328 - 1569~cm$^{-1}$ are consistent with the existence of species which are adsorbed or weakly bound to the surface with the energy of interaction close to 15 - 21~kJ mol$^{-1}$. These bands can be attributed to the ad(ab)sorbed (H$_3$O$^+$)$\rm{_{ad}}$, (H$_2^+$)$\rm{_{ab}}$ and (H$_2^+$)$\rm{_{ad}}$ ions as intermediates in reversible HER/HOR processes taking place on Cu/CuO/Pd electrode. There was no isotopic effect observed; this is consistent with a dipole nature of electron-ion pair formation of adsorbed (H$_3$O$^+$)$\rm{_{ad}}$ and (H$_2^+$)$\rm{_{ad}}$ or (D$_3$O$^+$)$\rm{_{ad}}$ and (D$_2^+$)$\rm{_{ad}}$. In accordance with literature data SERS bands at 125-146~cm$^{-1}$ and $\sim 520-565$~cm$^{-1}$ were assigned to Cu(I) and Cu(II) oxygen species. These findings corroborate the mechanism of cascading reduction of water.

In million years, under the pressure of natural selection, hominins acquired vocal learning, music, language, and intense cooperation, thanks to the efficacy of music in enhancing sociality. Thus, early in human evolution music became part of human life, a relevant activity, which required sophisticated perceptual and motor skills. It contributed to developing cultures and history, social bonding, and from the beginning of life strengthens the mother-baby relation while within the mother’s womb. Music existed in all known human cultures, although it varies in rhythmic and melodic complexity. It is art made of sounds capable of arousing emotions, evokes memories, engages multiple cognitive functions, and promotes attention, concentration, stimulates the imagination, creativity, and harmony of movement. Music and language share the same complex neural network. Music changes the chemistry of the brain activating the reward and prosocial systems, altruism, and allowing its use in therapy. This review explores "what" is music and illustrates the neural circuits that allow the production of music and language and those that transduce the sounds perceived by the ear, localize and archive them, allowing to recall them. Interestingly, songbirds share many commonalities with human music:, common neural pathways that shape vocal learning, and how they make sounds.

In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic ‘structural capacitance elements’. Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance – that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (DO) transition in previously disordered regions of proteins. Here we propose that the DO transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.

This work is mainly focused on improving the differential evolution algorithm with the utilization of shadowed and general type 2 fuzzy systems to dynamically adapt one of the parameters of the evolutionary method. In this case, the mutation parameter is dynamically moved during the evolution process by using a shadowed and general type-2 fuzzy systems. The main idea of this work is to make a performance comparison between using shadowed and general type 2 fuzzy systems as controllers of the mutation parameter in differential evolution. The performance is compared with the problem of optimizing fuzzy controllers for a D.C. Motor. Simulation results show that general type-2 fuzzy systems are better when higher levels of noise are considered in the controller.

Malignant tumors behave dynamically as cell communities governed by ecological principles. Massive sequencing tools are unveiling the true dimension of the heterogeneity of these communities along their evolution in most human neoplasms, clear cell renal cell carcinomas (CCRCC) included. Although initially thought to be purely stochastic processes, very recent genomic analyses have shown that temporal tumor evolution in CCRCC may follow some deterministic pathways that give rise to different clones and sub-clones randomly spatially distributed across the tumor. This fact makes each case unique, unrepeatable and unpredictable. Precise and complete molecular information is crucial for patients with cancer since it may help in establishing a personalized therapy. Intratumor heterogeneity (ITH) detection relies on the correctness of tumor sampling and this is part of the pathologist’s daily work. International protocols for tumor sampling are insufficient today. They were conceived decades ago, when ITH was not an issue, and have remained unchanged until now. Noteworthy, an alternative and more efficient sampling method for detecting ITH has been developed recently. This new method, called multisite tumor sampling (MSTS), is specifically addressed to large tumors that are impossible to be totally sampled, and represent an opportunity to improve ITH detection without extra costs.

We aimed to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among pa-tients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB) was performed. Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed 91 signature nucleotide residues (1.05%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Only six positions contained 100% specific nucleotide(s) in clusters O and P. Additionally, in-depth FL analysis over 30 years indicates that the KSB FL significantly increased over time before combined antiretroviral therapy (cART) and decreased with cART. The increase occurred due to a significant increase in env and nef genes, originating in the variable regions of both genes. The increase in the sequence length of HIV-1 over time suggests that it has an evolutionary direction.

Surface finishing is challenging for additively manufactured components with complex geometries. Magnetic abrasive finishing (MAF) is a promising surface finishing technology that can refine the surface quality of components with complex shapes produced by additive manufacturing. However, there is insufficient study regarding the impact of MAF on microstructure-property relationships for additively manufactured builds, which is critical for evaluating the mechanical performance. Furthermore, although MAF is usually used as the final step of post-processing, it remains unclear whether adjusting the sequence between MAF and other processes, e.g., heat treatment, can potentially improve the mechanical performance. In this work, the effects of MAF on the microstructure and mechanical property evolution of Inconel 718 superalloys made by laser powder bed fusion (LPBF) were studied. The application of MAF was found to significantly reduce the surface roughness of alloys and refine the grain size of aged samples. Moreover, MAF is able to increase the elongation of materials, which can be further influenced by the sequence of MAF and different heat treatments. The highest elongation can be achieved when MAF is performed between homogenization and aging processes. This work demonstrated a promising solution to improving the performance of LPBF Inconel 718 by combining MAF and heat treatment, which provides new perspectives on the post-processing development of additively manufactured alloys for advanced mechanical properties.

Many studies deal synthesis of carbon because of its versatility but lack the arresting of understanding at convincing and compelling levels. A binding energy shape-like parabola is linked to state of handing over electron to state of taking over electron at each opposite side of the atom maintaining the equilibrium of resulting new state of the carbon atom. Through this mechanism of transferring electrons for the gas state carbon atom, it converts into graphitic state, nanotube state, fullerene state, diamond state, lonsdaleite state and graphene state carbon atom. Forces of relevant poles remain neutral at instant of transferring electrons to attain specific state of their carbon atom. Structure evolutions in graphitic, nanotube and fullerene state carbon atoms are remained one-dimensional, two-dimensional and four-dimensional, respectively, where energy shape-like parabola is also involved along the relevant quadrant executing electron-dynamics to engage neutral behavior of exerting relevant poles forces. A graphite structure when develops under attained dynamics of atoms and their binding is under a bit difference of involved opposite pole forces, it develops in two-dimensional also. Evolution of structure in diamond, lonsdaleite and graphene state carbon atoms is under involving potential energy of electrons dealing double clamping of energy knot where relevant poles forces exerted in the orientationally controlled manner. Growth of diamond is south to ground, but binding of atoms is ground to south, so, it is a tetra-electrons ground to south topological structure. Lonsdaleite is a bi-electrons ground to just-south topological structure. Growth of graphene is just-north to ground, but binding of atoms is ground to just-north, so, it is a tetra-electrons ground to just-north topological structure. Glassy carbon is related to a layered-topological structure where successive tri-layers of gas, graphitic and lonsdaleite state atoms bind in the repetition manner. In glassy carbon, pairs of orientated electrons of gas and lonsdaleite state carbon atoms deal double clamping of energy knot by entering from the rear-side and front-side, respectively, to bind to intermediate layers of graphitic state atoms. Different carbon atoms develop amorphous structures when they bind under frustrating amalgamation. Hardness of carbon-based materials is also sketched in the light of different force-energy behaviors of different state carbon atoms. Here, structure evolution in each carbon state atom explores its own science.

Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 genomes in Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species and performed a phylogenetic analysis to determine their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasica and Apis mellifera mellifera and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD30D/Tigger, DD33D/Tigger and DD34D/mariner may have experienced horizontal transfer events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

A modern definition of “deep sleep” is elusive despite being ubiquitously appreciated as an important physiological state supporting health and homeostasis. In modern times, human deep sleep is identified by specific bioelectric signatures in the electroencephalogram (EEG) emerging somewhere between periods of wakefulness. However, deep sleep has been used to describe states of quiescence well before the first electrical brain recordings in the late 1800s, highlighting its own evolution in both lay and medical literature. Furthermore, EEG states are not only ill-defined in most mammals outside of humans and laboratory rodents, but non-existent in some invertebrates. Given that all organisms rest and do so with seemingly well-defined utility, it remains a challenge linguistically, scientifically, and comparatively define what “deep sleep” means—or what it should—in a research context. Here, I explore standard definitions of deep sleep from a modern, comparative perspective, and discuss potential problems of using a strict and narrow definition of such a fleeting concept that has historically undergone significant updates. Finally, I suggest a path towards resolving inconsistencies around the meaning of “deep sleep” and consider whether it is truly reflected by any one measure.

A supernova close enough to the Earth is a spectacular event: it can appear as a \new star" as luminous as Venus, or even more, visible for several days. The rate of Galactic supernovae is expected to be of about one in 30 years, with a fraction visible at naked eye; however in all the history of human civilization only seven supernovae in the Milky Way have been reported, the last two (1572 and 1604) during Galilei's life. The supernova of 1604, today called Kepler's Supernova, was observed by Galilei, Kepler and other astronomers in Europe, Korea, and China. Like the supernova SN1572, today called Tycho's supernova, it has been the subject of extensive studies, and inspired observational measurements and philosophical considerations on the nature of the heavens. The remnant of SN1604 has been indicated by recent X- and gamma-ray data to be a likely site of cosmic ray acceleration. The first recorded data of optical observations, together with new data, can still tell us a lot about the early evolution of this supernova.

Jingmen viruses are newly described segmented flavi-like viruses that have a worldwide distribution in ticks and have been associated with febrile illnesses in humans. Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and short alpha-helices, a fusion peptide with interfacial hydrophobicity and a three domain architecture. Jingmen flavi-like virus glycoproteins have a sequence enriched in serine, threonine and proline at the amino terminus, which is a feature of mucin-like domains. Several of the serines and threonines are predicted be modified by the addition of O-linked glycans. Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices. The flavivirus envelope protein and Jingmen flavi-virus glycoproteins may have diverged from a common class II precursor glycoprotein with a mucin-like domain or domains acquired after divergence.

Here, I present an alternate solution for the dark matter problem. I show that the stars of a galaxy’s arm attract each other with a force other than gravity, producing a chain of stars. We already have an abundance of data (ring and multiring galaxies) as proof for the existence of this strong stars’ chain. This attraction force does not end at the galaxy’s boundaries but gets deeper into the cosmos, and it may explain the dark-energy problem. This attraction force affects only stars and seems to have no effect on planets. I also offer a novel timeline order for the well-known galaxies using Hubble classification. I nominate entangled particles for the role that causes this phenomenon.

Hymenoscyphus albidus is a native fungus in Europe where it behaves as a harmless decomposer of leaves of common ash. Its close relative Hymenoscyphus fraxineus was introduced into Europe from Asia and currently threatens ash (Fraxinus sp.) stands all across the continent causing ash dieback. H. fraxineus isolates from Europe were previously shown to harbor a mycovirus named Hymenoscyphus fraxineus Mitovirus 1 (HfMV1). In the present study, we describe a conspecific mycovirus that we detected in H. albidus. HfMV1 was consistently identified in H. albidus isolates (mean prevalence: 49.3%) which were collected in the sampling areas before the arrival of ash dieback. HfMV1 strains in both fungal hosts contain a single ORF of identical length (717 AA) for which a mean pairwise identity of 94.5% was revealed. The occurrence of a conspecific mitovirus in H. albidus and H. fraxineus is most likely the result of parallel virus evolution in the two fungal hosts. HfMV1 sequences from H. albidus showed a higher nucleotide diversity and a higher number of mutations compared to those from H. fraxineus, probably due to a bottleneck caused by the introduction of H. fraxineus in Europe. Our data also points to multiple interspecific virus transfers from H. albidus to H. fraxineus, which could have contributed to the intraspecific virus diversity found in H. fraxineus.

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans, and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational program, Domain Analysis and Motif Matcher (DAMM), that predicts target specificity in choanoflagellate PDZ domains by analyzing peptide-binding cleft sequence identity as compared to human PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 M affinity, a value commonly considered the threshold for cellular PDZ-peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contributes to investigations into choanoflagellate signaling and how it informs metazoan evolution.

Intelligence is a human construct to represent the ability to achieve goals. Given this wide berth, intelligence has been defined countless times, studied in a variety of ways and represented using numerous measures. Understanding intelligence ultimately requires theory and quantification, both of which have proved elusive. I develop a framework – the Theory of Intelligences (TIS) – that applies across all systems from physics, to biology, humans and AI. TIS likens intelligence to a calculus, differentiating, correlating and integrating information. Intelligence operates at many levels and scales and TIS distils these into a parsimonious macroscopic framework centered on solving, planning and their optimization to accomplish goals. Notably, intelligence can be expressed in informational units or in units relative to goal difficulty, the latter defined as complexity relative to system (individual or benchmarked) ability. I present general equations for intelligence and its components, and a simple expression for the evolution of intelligence traits. The measures developed here could serve to gauge different facets of intelligence for any step-wise transformation of information. I argue that proxies such as environment, technology, society and collectives are essential to a general theory of intelligence and to possible evolutionary transitions in intelligence, particularly in humans. I conclude with testable predictions of TIS and offer several speculations.

The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to pIgR of multiple teleost species belonging to five perciform sub-orders, including 11 Antarctic and one non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in less cold periantarctic sea. Antarctic pIgR genes displayed particularly long in-trons marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold adapted species pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.

Informational (Shannon) measures of symmetry are introduced and analyzed for the patterns built of 1D and 2D shapes. The informational measure of symmetry Hsym (G) characterizes the an averaged uncertainty in the presence of symmetry elements from the group G in a given pattern; whereas the Shannon-like measure of symmetry Ωsym (G) quantifies averaged uncertainty of appearance of shapes possessing in total n elements of symmetry belonging to group G in a given pattern. Hsym(G1)=Ωsym(G1)=0 for the patterns built of irregular, non-symmetric shapes. Both of informational measures of symmetry are intensive parameters of the pattern and do not depend on the number of shapes, their size and area of the pattern. They are also insensitive to the long-range order inherent for the pattern. Informational measures of symmetry of fractal patterns are addressed. The mixed patterns including curves and shapes are considered. Time evolution of the Shannon measures of symmetry is treated. The close-packed and dispersed 2D patterns are analyzed.

Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium with a robust ability to degrade lignocellulosic biomass complexes, including crystalline cellulose components, through a multienzyme cellulosomal system. In contrast, it exhibits poor growth on simple monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on monosaccharides have been poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium on monosaccharides, and genome resequencing was used to detect the genes that had mutated during adaptation. RNA-seq data of the 1st-generation culture growing on either fructose or glucose revealed that several glycolytic genes in the EMP pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After 8 generations of culture on fructose and glucose, the evolved H. thermocellum strains grew faster and yielded greater biomass than the nonadapted strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in genes responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as targets for further metabolic engineering to improve this bacterium for bioindustrial usage.

Although Darwin‘s evolutionary mutation theory has been widely accepted, many endeavors have been tried to challenge it. With more and more observation of successful hybridization and hybrids, the sexual isolation between species has become vague. The mechanism of evolution has been expanded from the classical model of evolution to multiple routes of speciation. Furthermore, a fundamental crossbreeding theory has been raised and proved by two lines of evidences: paleopolyploidy and fan-shaped spectrum of species. Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. The genome polyploidization, especially in the somatic cell hybridization, can break through the sexual incompatibility between diploid counterparts to hybridize and produce new species. By comparing characteristics, all species in every taxon, both in the extinct fossil and extant organisms, can be arranged into fan-shaped spectrum according to their similarity: left primitive type-middle advanced type-right primitive type. The species are primitive at the two ends and advanced at the middle. The primitive two species always resemble two types of more primitive species that can be confirmed as their ancestors respectively, and the middle species is half similar to the two ancestors respectively. These suggest that the species in the spectrum come from two different ancestors by crossbreeding and gene combination. As a sum, advanced species originated from crossbreeding of two primitive ancestors, by major method of polyploidization, and proved by results of fan-shaped spectrum of species. Then, sex is the cause, force and opportunity for evolution.

Crocodilepox virus (CRV) belongs to the Poxviridae family and mainly infects hatchling and juvenile Nile crocodiles. Most poxviruses encode inhibitors of the host antiviral protein kinase R (PKR), which is activated by viral double-stranded (ds) RNA formed during virus replication, resulting in the phosphorylation of eIF2 and subsequent shutdown of general mRNA translation. Because CRV lacks orthologs of known poxviral PKR inhibitors, we experimentally characterized one candidate (CRV157), which contains a predicted dsRNA-binding domain. Bioinformatic analyses indicated that CRV157 evolved independently from other poxvirus PKR inhibitors. CRV157 bound to dsRNA, co-localized with PKR in the cytosol, and inhibited PKR from various species. To analyze whether CRV157 could inhibit PKR in the context of a poxvirus infection, we constructed recombinant vaccinia virus strains that contain either CRV157 or a mutant CRV157 deficient in dsRNA binding in a strain that lacks PKR inhibitors. The presence of wild type CRV157 rescued vaccinia virus replication, while the CRV157 mutant did not. The ability of CRV157 to inhibit PKR correlated with virus replication and eIF2alpha phosphorylation. The independent evolution of CRV157 demonstrates that poxvirus PKR inhibitors evolved from a diverse set of ancestral genes in an example of convergent evolution.

The stellar winds of the central stars of planetary nebulae play an essential role in planetary nebulae shaping. In the interacting stellar winds model, the fast stellar wind injects energy and momentum which are transfered to the nebular envelope through an X-ray-emitting hot bubble. Together with other physical processes, such as the ionization of the nebular envelope, the asymmetrical mass-loss in the AGB, and the action of collimated outflows and magnetic fields, the presurized hot gas determines the expansion and evolution of planetary nebulae. \emph{Chandra} and \emph{XMM-Newton} have provided us with detailed information of this hot gas. Here in this talk I will review our current understanding of the effects of the fast stellar wind in the shaping and evolution of planetary nebulae and give some hints of the promissing future of this research.

Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called “extended evolutionary synthesis” (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding “modern evolutionary synthesis” by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of historical kinds. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate.

The acceleration of the universe is described as a consequence of the extrinsic curvature of the space-time embedded in a bulk space, defined by the Einstein-Hilbert. Using the linear approximation of Nash-Green theorem, we obtain the related perturbed equations in which just the gravitational-tensor field equations contribute to propagation of cosmological perturbations. In accordance with Big Bang Nucleosynthesis and solar constraints, we calculate numerically the effective Newtonian function Geff to constrain the related parameters of the model. We numerically solve the growth density equation for two possible family of solutions leading to an interesting overdensity and, in some cases, a mild damping of the growth profiles, with a top amplification of the growth perturbations around 14% in comparison with LCDM model and quintessence. The effective gravitational Phi and Newtonian curvature Psi are also analysed showing mild perturbations in early times induced only by the extrinsic curvature differently from the LambdaCDM standards.

Cannabis is among the oldest human domesticates and has been subjected to intensive artificial (human-mediated) selection throughout history to create a wide array of varieties and biotypes for diverse uses, including fibre, food, biofuel, medicine and drugs. This paper briefly reviews the available literature on the taxonomy, evolutionary origin and domestication of this plant, as well as its worldwide dispersal, in both its wild and cultivated forms. Emphasis is placed on Europe and especially on the Iberian Peninsula. Today, it is accepted that Cannabis is a monospecific genus with two subspecies, C. sativa subsp. sativa and C. sativa subsp. indica, originating in Europe and Asia, respectively, by allopatric differentiation after geographic isolation fostered by Pleistocene glacial-interglacial cycles. Palynological and phylogeographic evidence situates the Cannabis ancestor on the NE Tibetan Plateau during the mid-Oligocene. The timing and place of domestication is still a matter of debate between contrasting views that defend single or multiple Neolithic domestication centres situated in different parts of the Eurasian supercontinent, notably central/southeastern China and the Caucasus region. Recent meta-analyses have suggested that wild Cannabis may have already been spread across Europe in the Pleistocene, and its domestication could have occurred during the European Copper/Bronze ages. According to the available reviews and meta-analyses, pre-anthropic dispersal of Cannabis into the Iberian Peninsula seems to have occurred only in postglacial times, and the earlier signs of cultivation date to the Early Medieval Ages. However, the palynological and archaeological evidence used to date is insufficient for a sound assessment, and the development of thorough Iberian databases to address further meta-analysis is essential for more robust conclusions. Some clues are provided for these achievements to be fulfilled.

The C5-methylation of uracil to form 5-methyluracil (m⁵U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m⁵U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup, use the ancestral tetrahydrofolate-dependent TrmFO enzyme, to catalyze the formation of m⁵U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m⁵U1939 formation in 23S RNA. RlmFO has replaced the S-adenosyl-l-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m⁵U modifying enzymes that is highly dynamic and has undergone horizontal transfer. This emphasizes the necessity for combining bioinformatics predictions with empirical testing and structural information to get a reliable functional annotation of these enzymes.

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is the extent to which similar or different genes and regulatory interactions underlie similar complex systems across species. Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well-characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems - especially in non-model organisms - are beginning to highlight a “deep diversity” of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise complex systems of non-model groups to better understand biodiversity and its evolution.

Eutherians have 11 retrotransposon Gag-like (RTL)/sushi-ichi retrotransposon homolog (SIRH) genes presumably derived from a certain retrovirus. Accumulating evidence indicates that the RTL/SIRH genes play a variety of roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system in a eutherian-specific manner. It has been shown that the functional role of Paternally Expressed 10 (PEG10) in placental formation is unique to the therian mammals, as are the eutherian-specific roles of PEG10 and PEG11/RTL1 in maintaining the fetal capillary network and the endocrine regulation of RTL7/SIRH7 (aka Leucine Zipper Down-Regulated in Cancer 1 (LDOCK1)) in the placenta. In the brain, PEG11/RTL1 is expressed in the corticospinal tract and hippocampal commissure, mammalian-specific structures, and in the corpus callosum, a eutherian-specific structure. Unexpectedly, at least three RTL/SIRH genes, RTL5/SIRH8, RTL6/SIRH3 and RTL9/SIRH10, play important roles in combating a variety of pathogens, viruses, bacteria and fungi, respectively, suggesting that the innate immunity system of the brain in eutherians has been enhanced by the emergence of these new components. In this review, we will summarize the function of 10 out of the 11 RTL/SIRH genes and discuss their roles in eutherian development and evolution.

The companion paper (Rice 2020) found that the centromeric repeats of the Western European house mouse (Mus musculus domesticus) have unusual structure: i) despite moderate pairwise sequence divergence (average = 5.9%), no monomer sequence was common and many hundreds of monomer sequences were observed, ii) local sequence divergence among neighboring monomers was nearly as high as genome-wide divergence, and iii) matching sequences were rare between side-by-side monomers. Here I integrate information from many published studies to formulate a hypothesis for the evolution of this structure. Non-matching sequences of neighboring centromeric monomers is hypothesized to be selectively favored in the context of molecular drive because it reduces the rate of monomer deletion during repair of double strand breaks (DSBs) via the Single Strand Annealing (SSA) pathway. The foundation for the hypothesis is the observation that centromeres of most populations of M. m. domestics reside close to the telomere, i.e., all their chromosomes are telocentrics. This proximity influences repair of centromeric DSBs because it places at least part of the centromere within the Telomere-Affected Repair Region (TARR; a location with increased concentrations of the shelterin-complex proteins that bind telomeres, especially TRF2). Shelterin proteins increase the level of 5’→3’ end resection at DSBs and thereby: i) decrease the frequency of repair via the c- NHEJ pathway, and ii) increase the frequency of homology-directed repair (HD-repair) –including the SSA repair pathway. It is hypothesized that certain ‘trigger’ events (e.g., sub-telomeric deletions) occur in local populations that increase the influence of TARR on the centromere. This increase elevates the occurrence of SSA repair of centromeric DSBs to a level that causes centromeres to begin to gradually shrink. Chronic shrinkage leads to coevolution between centromere size and karyotype number. Once centromeres shrink to a size below a critical minimum (that causes substantially reduced kinetochore size), fusions between non- homologous telocentrics with undersized centromeres produces metacentrics with an expanded centromere size (and a corresponding ‘quantum-jump’ in kinetochore size). These metacentrics: i) accumulate to fixation because they are favored by centromere drive, and ii) are released from the influence of TARR and thereby gradually recover larger centromere size. Fission of metacentrics with enlarged centromeres can next plausibly regenerate pairs of telocentrics with sufficiently large centromeres (which recruit normal-sized kinetochores) to be favored by centromere drive and accumulate to fixation. This fixation completes a cycle of coevolution within genomes that oscillate between two extremes: i) high karyotype number (2N = 40; all telocentrics) with larger centromeres, and ii) low karyotype number (2N << 40; mainly metacentrics) with initially small centromeres that gradually increase in size.

In this paper, I give readers an idea of what some scholars are interested in, what I found interesting, and what may be of future interest in the philosophy of emotion. I begin with a brief overview of the general topics of interests in the philosophy of emotion. I then discuss what I believe to be some of the most interesting topics in the contemporary discourse, including questions about how philosophy can inform the science of emotion, conceptions of the mind and the mind-body problem, concerns about perception, cognition, and emotion, along with questions about the place of 4E approaches and meta-semantic pluralist approaches in the embodied cognitive tradition. Finally, I discuss the emerging field of cultural evolution, the import of a dual-inheritance theory in this emerging field, and I propose a possible way to integrate the frameworks of dual-inheritance theory and meta-semantic pluralism to demonstrate at least one way in which the philosophy of emotion can contribute to the emerging field of cultural evolution.

The progesterone receptor (PR) mediates progesterone regulation of female reproductive physiology, as well as gene transcription in non-reproductive tissues, such as brain, bone, lung and vasculature, in both women and men. An unusual property of progesterone is its high affinity for the mineralocorticoid receptor (MR), which regulates electrolyte transport in the kidney in humans and other terrestrial vertebrates. In humans, rats, alligators and frogs, progesterone antagonizes activation of the MR by aldosterone, the physiological mineralocorticoid in terrestrial vertebrates. In contrast, in elephant shark, ray-finned fishes and chickens, progesterone activates the MR. Interestingly, cartilaginous fishes and ray-finned fishes do not synthesize aldosterone, raising the question of which steroid(s) activate the MR in cartilaginous fishes and ray-finned fishes. The simpler synthesis of progesterone, compared to cortisol and other corticosteroids, makes progesterone a candidate physiological activator of the MR in elephant sharks and ray-finned fishes. Elephant shark and ray-finned fish MRs are expressed in diverse tissues, including heart, brain and lung, as well as, ovary and testis, two reproductive tissues that are targets for progesterone, which together suggests a multi-faceted physiological role for progesterone activation of the MR in elephant shark and ray-finned fish. The functional consequences of progesterone as an antagonist of some terrestrial vertebrate MRs and as an agonist of fish and chicken MRs are not fully understood. Indeed, little is known of physiological activities of progesterone via any vertebrate MR.

Evolutionary ecologists seek to understand how phenotypic evolution relates to population level traits. To document that, we quantified functional traits (escape strategy, sprint speed and predatory performance) and population density across 10 lizard species representing the acquisition of burrowing snake-like morphs (BSLM), from Brazil. We used phylogenetic mixed models to test if: a) morph and substrate affects lizards’ flight strategy and speed, b) BSLM species get more access to different potential prey types than lacertoid ones, when in syntopy, and d) morph is correlated with population abundance and habitat use in a way expected from the output of the previous experiments. We found that BSLM rigidly relied on burrowing as flight strategy, while syntopic lacertoid species changed their strategy according to the substrate. Also, sand has opposite effects on sprint speed depending on morph, making lacertoids run slower and BSLM faster. Despite BSLM were overall slower than lacertoids, they were as good hunters of challengingly fast prey, and better hunters of underground prey. Further, in the sandy habitats where these morphs are syntopic, prey is most available at superficial leaf litter under vegetation, although there is a large stock of underground prey, under the vegetation, too. These results support our observed higher importance of sand for BSLM’s populations and the higher importance of vegetation for lacertoids’ population density. Finally, although BSLM species reached the highest populational densities among the studied species, a systematic effect of morphological evolution on abundance remains elusive.

The newly established virus family Phenuiviridae in Bunyavirales harbors viruses infecting three kingdoms of host organisms (animals, plants, and fungi), which is rare in known virus families. Many phenuiviruses are arboviruses and replicate in two distinct hosts (e.g., insects and humans or rice). Multiple phenuiviruses, such as Dabie bandavirus, Rift Valley fever phlebovirus, and Rice stripe tenuivirus, are highly pathogenic to humans, animals, or plants. They impose heavy global burdens on human health, livestock industry, and agriculture and are research hotspots. In recent years the taxonomy of Phenuiviridae has been expanded greatly, and researches on phenuiviruses have made significant progress. With these advances, this review drew a novel panorama regarding the biomedical significance, distribution, morphology, genomics, taxonomy, evolution, replication, transmission, pathogenesis, and control of phenuiviruses, to aid researchers in various fields to recognize this highly adaptive and very important virus family.

Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we have determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.

Proton exchange membrane water electrolyzers (PEMWEs) for water electrolysis have received tremendous attention due to their immediate response, high proton conductivity, low ohmic losses and gas crossover rate. However, design high activity, economical and long-term durable electrocatalysts in an acidic environment is still the bottleneck to realize the large-scale commercialization of PEMWEs. Iridium-based materials represent one of the most promising classes of oxygen evolution reaction (OER) catalysts due to their intrinsic stability in acid media over ruthenium-based counterparts. However, only a few innovative approaches have been developed to synthesizing iridium-based catalysts (IBCs) in the past decade, mainly due to achieving high activity may deteriorate the stability of IBCs. Accordingly, various engineering strategies of optimizing IBCs have been proposed to address this issue, including doping engineering, morphology engineering, crystal phase engineering and support engineering. Herein, a critical overview focusing on various synthesis and modulation strategies of IBCs is presented, based on an in-depth understanding of the relationship between electronic structures, charge redistribution and activity as well as stability of the electrocatalysts. In addition, the unprecedented achievements in PEMWEs are summarized. The reaction mechanisms and future perspectives are critically discussed to inspire more rational design of IBCs toward practical applications.

Physics lacks a confirmed description of dark matter, has yet to develop an adequate understanding of dark energy, and includes unverified conjectures regarding new elementary particles. This essay features modeling that addresses those problems and explains otherwise unexplained data. Our modeling starts from five bases – multipole expansions for the electromagnetic and gravitational fields associated with an object, the list of known elementary particles, some aspects of mathematics for isotropic harmonic oscillators, concordance cosmology, and a conjecture that the universe includes six isomers of most elementary particles. The multipole expansions – which have use in conjunction with Newtonian kinematics modeling, special relativity, and general relativity – lead to a catalog of kinematics properties such as charge, magnetic moment, mass, and repulsive gravitational pressure. The multipole expansions also point to all known elementary particles, some properties of those particles, and properties of some would-be elementary bosons and elementary fermions. The harmonic-oscillator mathematics points to Gauge symmetries regarding some elementary bosons. The would-be elementary fermions lack charge and would measure as dark matter. The conjecture regarding six isomers of most elementary particles rounds out and dominates our specification for dark matter. Five of the isomers form the basis for most dark matter. Our modeling explains ranges of observed ratios of dark matter effects to ordinary matter effects – for the universe, galaxy clusters, two sets of galaxies observed at high redshifts, three sets of galaxies observed at modest redshifts, and one type of depletion of cosmic microwave background radiation. Our description of repulsive gravitational pressure points toward resolution for tensions – between data and modeling – regarding the recent rate of expansion of the universe, resolution for possible tensions regarding large-scale clumping, and resolution for possible tensions regarding interactions between neighboring galaxies. Our work regarding gravity, dark matter, and elementary particles suggests characterizations for eras that might precede the inflationary epoch, a mechanism that might have produced baryon asymmetry, mechanisms that govern the rate of expansion of the universe, and insight about galaxy formation and evolution.

Ability of quantitative structure – property / activity relationships (QSPRs/QSARs) to serve for epistemological processes in natural sciences is discussed. Some weirdness of QSPR/QSAR state-of-art are listed. There are some contradictions in the research results in this area. Sometimes, these should be classified as paradoxes or weirdness. These points often are ignored. Here these are listed and briefly commented. In addition, hypothesises on the future evolution of the QSPR/QSAR theory and practice are suggested.

Using the 2011-2020 digital inclusive finance data released by Peking University and the index system constructed by the Blue Book of China Rural Revitalization and Development Index (2018), this paper analyzes the dynamic evolution of the digital inclusive finance and the rural revitaliza-tion from time and space dimensions with the help of kernel density estimation, Markov chain and Moran index. Using The Gini coefficient decomposition method to analyze the source of differ-ences in digital inclusive finance, and then using the spatial autoregressive (SAR) model and ge-ographically weighted regression (GWR) model to study the boosting effect of digital inclusive finance on rural revitalization from the perspective of spatial aggregation and spatial differentia-tion, respectively. The results show that: (1) The growth rate of China's digital inclusive finance slows down year by year, and the inter-provincial differences increase year by year and show gradient characteristics, indicating that there may be a trend of multipolar differentiation. The overall level of Rural Revitalization shows an increasing trend, and the gap between provinces is still apparent. (2) The evolution of digital inclusive finance and rural revitalization is a slow ad-justment process, and there has been no cross-level jump in the past ten years. In digital inclusive finance, the liquidity from the highest and lowest levels to the medium level is high. However, the liquidity in the states of rural revitalization development level is not high. (3) Rural revitalization has a positive spatial spillover effect. The level of rural revitalization in the western area is signif-icantly lower than in the eastern area. At the same time, there is no significant difference between the east and central areas. The depth of the use of digital inclusive finance has a significant positive impact on the revitalization and development of rural areas, indicating that the further promotion of digital inclusive finance business in rural areas can substantially boost the revitalization of rural areas. (4) The boosting effect of digital inclusive finance on rural revitalization shows prominent spatial differentiation characteristics. The depth of use and the degree of digitization generally show a positive impact. The central and eastern coastal cities have the highest impact, decreasing toward the southwest and northeast. The areas with the lowest usage depth impact are clustered in the northeast, and the areas with the lowest digitization impact are clustered in the southwest.

Photogrammetry involves aerial photography of the earth’s surface and subsequently processing the images to provide a more accurate depiction of the area (Orthophotography). It’s used by the Spanish Instituto Geográfico Nacional to update road cartography but requires a significant amount of manual labor due to the need to perform visual inspection of all tiled images. Deep Learning techniques (artificial neural networks with more than one hidden layer) can perform road detection but it is still unclear how to find the optimal network architecture. Our system applies grammar guided genetic programming to the search of deep neural network architectures. In this kind of evolutive algorithm all the population individuals (here candidate network architectures) are constrained to rules specified by a grammar that defines valid and useful structural patterns to guide the search process. Grammar used includes well-known complex structures (e.g. Inception-like modules) combined with a custom designed mutation operator (dynamically links the mutation probability to structural diversity). Pilot results show that the system is able to design models for road detection that obtain test accuracies similar to that reached by state of the art models when evaluated over a dataset from the Spanish National Aerial Orthophotography Plan.

The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 “Kraken” variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.

Either stereo reactants or stereo catalysis from achiral or chiral molecules are prerequisite to obtain pure enantiomeric lipid derivatives. We reviewed a few plausible organic syntheses of phospholipids under prebiotic conditions with a special attention to the starting materials as pro-chiral dihydroxyacetone and dihydroxyacetone phosphate (DHAP), which are the key molecules to break symmetry in phospholipids. The advantages of homochiral membranes compared to those of heterochiral membranes were analysed in term of specific recognition, optimal functions of enzymes, membrane fluidity and topological packing. All biological membranes contain enantiomeric lipids in modern bacteria, eukarya and archaea. The contemporary archaea, comprising of methanogens, halobacteria and thermoacidophiles are living under extreme conditions reminiscent of primitive environment and may indicate the origin of one ancient evolution path of lipid biosynthesis. The analysis of lipid metabolism reveals that all modern cells including archaea synthetize enantiomeric lipid precursors from prochiral DHAP. sn-glycerol-1-phosphate dehydrogenase (G1PDH), usually found in archaea, catalyses the formation of sn-glycerol-1-phosphate (G1P), while sn-glycerol-3-phosphate dehydrogenase (G3PDH) catalyses the formation of sn-glycerol-3-phosphate (G3P) in bacteria and eukarya. The selective enzymatic activity seems to be the main strategy that evolution retained to obtain enantiomeric pure lipids. The occurrence of two genes encoding for G1PDH and G3PDH, served to build up an evolution tree and the basis of our review focusing on the evolution of these two genes. Gene encoding for G3PDH in Eukarya may originate from G3PDH gene found in rare archaea indicating that archaea appeared earlier in the evolution tree than eukarya. Archaea and bacteria evolved probably separately, due to their distinct respective genes coding for G1PDH and G3PDH. The suggested hypothesis is that catalysis of homochiral G1P or G3P from DHAP are more efficient than those leading to racemic G1P and G3P, since there are no enzymes able to synthesize racemic G1P and G3P from DHAP. We propose that G1PDH or G3DPH, which are not “image mirror enzymes” but belonging to distinct family of proteins, emerged separately during evolution. They were probably selected for their efficient catalytic activities during evolution from large libraries of vesicles containing various biopolymers, including amino acids, carbohydrates, nucleic acids, lipids, and meteorite components to induce chemical imbalance.

Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex metabolic disorder that manifests in genetically susceptible women following a range of negative exposures to nutritional and environmental factors related to contemporary lifestyle. The hypothesis that PCOS phenotypes are derived from a mismatch between ancient genetic survival mechanisms and modern lifestyle practices is supported by a diversity of research findings. The proposed evolutionary model of the pathogenesis of PCOS incorporates evidence related to evolutionary theory, genetic studies, in-utero developmental epigenetic programming, transgenerational inheritance, metabolic features including insulin resistance, obesity and the apparent paradox of lean phenotypes, reproductive effects and subfertility, the impact of the microbiome and dysbiosis, endocrine disrupting chemical exposure, and the influence of lifestyle factors such as poor quality diet and physical inactivity. Based on these premises, the diverse lines of research are synthesized into a composite evolutionary model of the pathogenesis of PCOS. It is hoped that this model will assist clinicians and patients to understand the importance of lifestyle interventions in the prevention and management of PCOS and provide a conceptual framework for future research. It is appreciated that this theory represents a synthesis of the current evidence and that it is expected to evolve and change over time.

A small phylogenetically conserved sequence of 11,231 bp termed FAM247 is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, the long non-coding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionary conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it are presented.

Evolution by natural selection is often viewed as an optimisation process where an organism's phenotypic traits are adapted gradually to improve its fitness. Because of the many different traits with potentially conflicting requirements, among other factors, this optimisation process may appear onerous. Building on recent mathematical work connecting optima and simplicity, we here show that for certain generic phenotype fitness requirements --- those based on physics and engineering principles --- optimal phenotypic shapes will tend to `simple', in the sense of low algorithmic or descriptional complexity. As a result, we argue that adapting to these types of generic fitness requirements will be a much `easier' task for natural selection, compared to a null expectation based on arbitrary optimisation requirements. Further, selection's task may be easier still due to the fact that optimal phenotypes for one set of generic fitness constraints may also be close to optimal for other generic constraints, such that adapting to one constraint yields the other `for free'.

This feature study attempts on setting a granules involving mesoscopic matter-aggregation context as a problem of passing locally by the matter-aggregating system from classical stochastic (mesoscopic limit) to a quantum description (nanoscale quantum-size effect limit). A d-dimensional entropy-production aggregation of the granules-involving matter is considered in terms of a (sub)diffusive realization. It turns out that when taking a full d-dimensional pathway of the aggregation toward the nanoscale, one is capable of disclosing a Heisenberg type (diffusional) relation, setting up an upper uncertainty bound for the (sub)diffusive very slow granules-including environment that matches the quantum limit of h/2pm (m– average mass of a granule; h – the Planck’s constant) for the diffusion coefficient of the aggregation, likely first proposed by Fürth in 1933, and qualitatively foreseen by Schrödinger some years before, both in the context of a diffusing particle cluster. The classical-quantum passage uncovered here, also termed insightfully the quantum-size effect (as borrowed from the quantum dots’ parlance), works properly for the three-dimensional (d=3) case, making use of a substantial physical fact that the (nano)granules interact readily via their surfaces with the also granular surroundings in which they are immersed. This natural observation is embodied in the basic averaging construction of the diffusion coefficient of the aggregation of interest. Certain, possibly biomedical, applications of the model can also be viewed by prospective inspection of tiny inhomogeneities in nanofibrillar and/or lamellar matter for which certain numerical realizations are plausible to prepare based on thorough nanoscale experiments.

Aptamers have a well-earned place in therapeutic, diagnostic, and sensor applications, and we now show that they provide an excellent foundation for education, as well. Within the context of the Freshman Research Initiative (FRI) at The University of Texas at Austin, students have used aptamer selection and development technologies in a teaching laboratory to build technical and 21st century skills appropriate for research scientists. One of the unique aspects of this course-based undergraduate research experience is that students develop their own projects, and take ownership of their own science in what would otherwise be a traditional teaching lab setting. Of the many successes, this work includes the isolation and characterization of novel calf intestinal alkaline phosphatase (anti-CIAP) RNA aptamers by an undergraduate researcher. Further, preliminary survey data suggest that students who participate in the aptamer research experience express significant gains in their self-efficacy to conduct research, and their perceived ability to communicate scientific results, as well as organize and interpret data. This work will describe the use of aptamers in an educational setting, highlight the positive student outcomes of the aptamer research experience, and more particularly present the research findings relative to the anti-CIAP aptamer.

A general procedure is described, to generate material parameter sets to simulate fire propagation in horizontal cable tray installations. Cone Calorimeter test data is processed in an inverse modelling approach. Here, parameter sets are generated procedurally and serve as input for simulations conducted with the Fire Dynamics Simulator (FDS). The simulation responses are compared with the experimental data and ranked based on their fitness. The best fitness was found for a test condition of \SI{50}{\kilo\watt\per\meter^2}. Low flux conditions \SI{25}{\kilo\watt\per\meter^2} and less exhibited difficulties to be simulated accurately. As a validation step, the best parameter sets are then utilised to simulate fire propagation within a horizontal cable tray installation and are compared with experimental data. It is important to note, the inverse modelling process is focused on the Cone Calorimeter and not aware of the actual validation step. Despite this handicap, the general features in the fire development can be reproduced, however not exact. The fire in the tray simulation extinguishes earlier and the total energy release is slightly higher as compared to the experiment. The responses of the material parameter sets are briefly compared with a selection of state of the art procedures.

As a special class of “green” elastomers, thermoplastic vulcanizates (TPVs) have been widely used in industries due to the combination of the excellent resilience of conventional elastomers and the easy recyclability of thermoplastics. Here, the morphology evolution of TPVs based on polyamide 6/ethylene-propylene-diene rubber (PA6/EPDM) blends was investigated by varying the content of the curing agent, phenolic resin (PF). With the incorporation of 6 wt% PF, the gel content of the EPDM phase reaches a high value of 49.6wt% and a typical sea-island structure is formed with EPDM domain in a micro-nano size. The dynamic rheology behaviors of TPVs showed that with the curing degree of EPDM phase increasing, a denser network of EPDM particles is formed in PA6 matrix. Also, a lower crystal degree and crystal peak temperature are observed, indicating that the presence of a growth restriction of PA6 crystal plate induced by a thinner plastic layer between the adjacent EPDM particles. However, the crystal form of PA6 is not changed with the increasing curing degree of the EPDM phase. This study provides an effective strategy to realize a new kind of TPVs, which can be easily introduced into industrial applications.

Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and glycinergic or glutamatergic neurons, respectively. Glycinergic neurotransmission in invertebrates has so far only been investigated in a very limited number of species, and, although it was suggested that its functions are to some extent conserved with vertebrates, the evolution of glycinergic neurotransmission remains very poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possesses three glycine transporter genes, two of which (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, while the other (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. While expression of GlyT2.2 is predominantly non-neural, GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are characterized by differential expression in neurons and glia, respectively. However, in vertebrates, glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by complex genetic remodeling leading to the paralog-specific inversion of gene expression. Albeit this genetic divergence between amphioxus and vertebrates, we found strong evidence for a general conservation of the role of glycinergic neurotransmission during larval swimming, allowing us to hypothesize that the neural networks controlling the rhythmic movement of chordate bodies are homologous.

The study of co-fusion was one of the essential topics in the history of metallurgy in China. Simulation experiments had been an essential concept in the study of the co-fusion steelmaking process. This paper mainly studied the simulation experiments of co-fusion from two aspects: the replication of co-fusion swords by three different methods, and the micro-analysis of the co-fusion samples. The experimental results indicated that several co-fusion swords could be made by different processes, but the carbon content and surface hardness were quite different. During repeated forging welded, the microstructure of the samples transformed from laminated to homogenized, finally the steel with a uniform carbon content was obtained. It was challenging to find the characteristics of co-fusion from the homogenized samples. The results prompted people to rethink the microstructure characteristics of ancient co-fusion artifacts.

Genome-scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre-recombinase mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimise genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (Rapid Evolution Detection), a simple colorimetric plate-assay procedure to rapidly quantify the degree of genomic rearrangements within a post-SCRaMbLE yeast population. RED-enabled semi-synthetic strains were mated with haploid progeny of industrial yeast strains to produce stress tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED-assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED-assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate optimal SCRaMbLE induction times of different Cre-recombinse expression systems for the development of industrial strains.

Magnesium transporters (MGTs) play a prominent role in the absorption, transport and storage of magnesium in plant cells. In the present study, MGT gene family members were identified and characterized in two species of cucurbitaceae, including C. sativus and C. lanatus. 20, 19, and 20 MGT genes were recognized in C. lanatus, C. sativus, and C. melo, respectively. According to physicochemical properties, the members of each sub-class of MGTs in the species of cucurbitaceae showed the close relationship. Proteins from NIPA were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, MGT family members were classified into three groups, and NIPAs showed more diversity. Besides, duplication events were not identified between the MGT members in C. lanatus, and C. sativus. According to pocket analysis, residues such as L, V, S, I, and A were frequently observed in the binding sites of MGT proteins in both species. The prediction of post-translation modifications revealed that MSR2 proteins have high phosphorylation potential than other sub-classes in both studied plants. The expression profile of MGTs showed that MGTs are more expressed in root tissues. In addition, MGTs showed differential expression in response to abiotic/biotic stresses as well as hormone application and NIPAs were more induced in response to stimuli in watermelon. The results of this study, as the primary work of MGT gene family, can be used in programs related to cucurbitaceae breeding.

Acknowledging the diverse perceptions about science-religion relationships among learners who come from various religious environments may increase learners’ willingness to learn about evolution. This study is based on a zoology course designed for in-service teachers, which aimed to provide basic scientific knowledge about evolution using the Religious Cultural Competence in Evolution Education framework. The study explores whether learners who were resistant to evolution modify their attitudes and willingness to learn about it, and whether they develop respect toward learners who hold contradicting views. Using qualitative methods, the findings indicate that using the Religious Cultural Competence in Evolution Education framework increased some formerly "resistant" learners’ willingness to learn about evolution and include it in their own teaching, albeit in varying degrees and with various reservations. The learners appreciated the freedom to express their challenges concerning evolution learning or teaching and became more willing to respect opposing perspectives, even though not all the religious learners accepted evolution as an explanation for the development of organisms. This study has international implications for bridging the gap between science and religion, thus reducing resistance to learning and teaching about evolution.

Cellular communications play pivotal roles in multi-cellular species, but they do so also in uni-cellular species. Moreover, cells communicate with each other not only within the same individual but also with cells in other individuals belonging to the same or other species. These communications occur between two unicellular species, two multicellular species, or between unicellular and multicellular species. The molecular mechanisms involved exhibit diversity and specificity, but they share common basic features which allow common pathways of communication between different, and sometimes very different species. These interactions have been made possible by the high degree of conservation of the basic molecular mechanisms of interaction of many ligand-receptor pairs in evolutionary remote species. These inter-species cellular communications played crucial roles during Evolution and must have been positively selected, particularly when collectively beneficial in hostile environments. We think that communications between cells did not arise after their emergence but was part of the very nature of first cells. Synchronization of populations of non-living protocells through chemical communications may have been a mandatory step towards their emergence as populations of living cells and explain the large commonality of cell communication mechanisms among microorganisms, plants, and animals.

Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high quality primate genomes warrants a study of the characteristics, evolution and distribution of SERV proviruses; (2) Methods: Cercopithecinae OWM genomes from public databases were queried for the presence of full length SERV proviruses. A dataset of 81 Cer-SERV genomes was generated and analyzed; (3) Results: Full length Cer-SERV proviruses were mainly found in terrestrial OWM, and less so in arboreal, forest- dwelling monkeys. Phylogenetic analysis confirmed the existence of two genotypes, Cer-SERV-1 and Cer-SERV-2, with Cer-SERV-1 showing evidence of recent germ line expansions. Long Terminal Repeat (LTR) variation indicated that most proviruses were of a similar age, and were estimated to be between &lt;0.3 and 10 million years old. Integrations shared between species were relatively rare. Sequence analysis further showed extensive CpG methylation-associated mutation, variable Primer Binding Site (PBS) use with Cer-SERV-1 using PBSlys3 and Cer-SERV-2 using PBSlys1,2, and the recent gain of LTR motifs for transcription factors active during embryogenesis in Cer-SERV-1; (4) Conclusions: sequence analysis of 81 SERV proviruses from Cercopithecinae OWM genomes provides evidence for the adaptation of this retrovirus to germ line reproduction.

PD-1/PD-L1 axis is one key therapeutic target against tumor cell immune escape. Structurally essential to the PD-1/PD-L1-linked immune escape is the binding interface of the PD-1/PD-L1 complex structure. Incorporating currently available PD-1/PD-L1-related experimental structures, this article unveils two sets of experimentally observed inter-molecular electrostatic interactions which stabilize the binding interface of the PD-1/PD-L1 complex structure. For the first time, this article proposes an evolutionary structural hypothesis that, as a result of natural selection, PD-1 is able to genetically mutate itself to structurally disrupt the PD-1/PD-L1 axis towards the restoration of T cell-mediated anti-tumor immunity.

Seemingly normal tissues progressively become populated by mutant clones over time. Most of these clones bear mutations in well-known cancer genes but only rarely do they transform into cancer. This poses questions on what triggers cancer initiation and what implications somatic variation has for cancer early detection. We analysed recent mutational screens of healthy and cancer-free diseased tissues to compare somatic drivers and the causes of somatic variation across tissues. We then reviewed the mechanisms of clonal expansion and their relationships with age and diseases other than cancer. We finally discussed the relevance of somatic variation for cancer initiation and how it can help or hinder cancer detection and prevention. The extent of somatic variation is highly variable across tissues and depends on intrinsic features, such as tissue architecture and turnover, as well as the exposure to endogenous and exogenous insults. Most somatic mutations driving clone expansion are tissue-specific and inactivate tumour suppressor genes involved in chromatin modification and cell growth signalling. Some of these genes are more frequently mutated in normal tissues than cancer, indicating a context-dependent cancer promoting or protective role. Mutant clones can persist over a long time or disappear rapidly, suggesting that their fitness depends on the dynamic equilibrium with the environment. The disruption of this equilibrium is likely responsible for their transformation into malignant clones and knowing what triggers this process is key for cancer prevention and early detection. Somatic variation should be considered in liquid biopsy, where it may contribute cancer-independent mutations, and in the identification of cancer drivers, since not all mutated genes favouring clonal expansion also drive tumourigenesis. Somatic variation and the factors governing homeostasis of normal tissues should be taken into account when devising strategies for cancer prevention and early detection.

Delve into the ebb and flow of human ingenuity as the researcher traces the evolution of writing from papyrus to pixels. Discover how humble instruments like quill pens and typewriters have propelled human into the digital frontier, forever reshaping the art of expression in the modern age. This article examines the evolution of writing tools from traditional pen and paper to digital writing in the modern age. It explores the development of writing materials such as papyrus, parchment, and paper, as well as the invention of writing tools including quill pens, fountain pens, and typewriters. The rise of digital writing tools, including word processing software and smartphones, is also discussed, along with their benefits such as increased efficiency and productivity, enhanced collaboration and sharing capabilities, and greater accessibility and flexibility. However, the article also highlights the challenges of writing in the digital age, including the impact of digital distractions on writing focus and quality, the issue of online plagiarism and copyright infringement, and the potential loss of traditional writing skills. The article concludes with recommendations for educators, school administrators, students, and researchers to strike a balance between digital and traditional writing practices, to embrace digital writing tools while preserving traditional writing skills, and to understand the importance of the evolution of writing. The theoretical frameworks of Social Construction of Technology (SCOT) Theory, Media Ecology Theory, and Activity Theory are also discussed in relation to the evolution of writing tools. Overall, this article provides valuable insights into the history, benefits, and challenges of writing in the digital age, as well as suggestions for navigating the future of writing and its tools.

The microstructure of Al-5Fe-1.5Er alloy was characterized and analyzed by using XRD, SEM, TEM and EDS. The effect of microstructure on the behavior of crack initiation and propagation was investigated by in situ tensile testing. Results show that the microstructure consists of α-Al matrix, Al₃Fe, Al₄Er, eutectic phase Al₃Fe + Al₄Er, while the 1.5 wt.% Er was added in Al-5Fe alloy. The twin structure of the Al₃Fe phase was observed, and the twin plane is {001}. Moreover, a continuous concave and convex interface structure of the Al₄Er has been found. Al₃Fe is in the form of a sheet with a clear gap inside.In situ tensile tests of the alloy at room temperature show that the crack initiation occured mainly in the Al₃Fe phase, and that the crack propagation modes include intergranular and transgranular expansion. Crack transgranular expansion is due to the strong binding ability between Al₄Er phases and surrounding organization, and the continuous concave and convex interface structure of the Al₄Er provides a significant meshing effect on the matrix and eutectic structure.

We provide a biochronology of Jurassic planktonic foramininfera, using first order linkage to ammonite and nannofossil stratigraphy and geochronology. This enigmatic and understudied group of microfossils occurred from middle Toarcian through Tithonian time, from ~180 to ~143 Ma; its origin is unknown. There are three genera: Globuligerina, Conoglobigerina and Petaloglobigerina. The genus Globuligerina, with a smooth to pustulose test surface texture appeared in Toarcian (late Early Jurassic) and Conoglobigerina, with a rough reticulate test surface texture in Oxfordian (early Late Jurassic) time. The genus Petaloglobigerina, with a petaloid last whorl and one or more twisted and claviform chambers evolved in early Kimmeridgian time from Globuligerina balakhmatovae. We recognize stratigraphic events from eleven species across four evolutionary lineages, calibrated to Geologic Time Scale 2020. A dramatic faunal change over, which is not well documented led to the survival of only one taxon, most likely Gobuligerina oxfordiana in the Tithonian. During the Berriasian several new taxa appeared.

Evolution of cooperation has traditionally been studied by assuming that individuals adopt either of two pure strategies, to cooperate or defect. Recent work have considered continuous cooperative investments, turning full cooperation and full defection into two opposing ends of a spectrum and sometimes allowing for the emergence of the traditionally-studied pure strategies through evolutionary diversification. These studies have typically assumed a well-mixed population in which individuals are encountered with equal probability, Here, we allow for the possibility of assortative interactions by assuming that, with specified probabilities, an individual interacts with one or more other individuals of the same strategy. A closely related assumption has previously been made in evolutionary game theory and has been interpreted in terms of relatedness. We systematically study the effect of relatedness and find, among other conclusions, that the scope for evolutionary branching is reduced by either higher average degree of, or higher uncertainty in, relatedness with interaction partners. We also determine how different types of non-linear dependencies of benefits and costs constrain the types of evolutionary outcomes that can occur. While our results overall corroborate the conclusions of earlier studies, that higher relatedness promotes the evolution of cooperation, our investigation gives a comprehensive picture of how relatedness affects the evolution of cooperation with continuous investments.

We present a Quantum Space Model (QSM) of cosmic evolution based on the theory that space consists of energy quanta which participates in the evolution of the universe. It shows that Dark Energy is the energy of space which causes its accelerating expansion. We used the Friedmann equations to trace the history of the cosmos from a time before the Big Bang to its ultimate end. The universe started from a quantum size volume of space with high energy density.Quantum fluctuations triggered the release of energy in a Big Bang at very high temperature and pressure. It then expanded and cooled undergoing phase transitions to radiation, fundamental particles, and matter. Matter grew into galaxies, and was further consolidated by gravity into Dark Energy Stars/Black Holes, ending in a Big Crunch at about 1.380 trillion years, thus bringing the universe back to its initial state. It can stay in a Deep Feeeze inside a Black Hole and through fluctuations or other mechanism may start a new cycle in its life with a new Bang. If the Law of Conservation of Energy is universal, then the cosmos is eternal. Space and energy are equivalent just as matter and energy are. This is well founded in Planck’s energy equation. They are the two most fundamental quantities in the universe that govern cosmic evolution. The two principal long range forces are the gravitational force and the space force.The latter could be the fifth force in the universe. They may provide the clockwork mechanism that operates our eternal cyclic universe.

A new type of ordinary differential equation is introduced and discussed, namely, the time-dependent order ordinary differential equations. These equations can be solved via fractional calculus and are mapped into Volterra integral equations of second kind with singular integrable kernel. The solutions of the time-dependent order differential equations smoothly deforms solutions of the classical integer order ordinary differential equations into one-another, and can generate or remove singularities. An interesting symmetry of the solution in relation to the Riemann zeta function and Harmonic numbers was also proved.

The COVID-19 pandemic has been met with an unprecedented response from the scientific community leading to the development, study, and authorization of vaccines and antivirals, ultimately reducing the impact of SARS-CoV-2 on global public health. However, SARS-CoV-2 is far from being eradicated, continues to evolve, and causes substantial health and economic burdens. In this paper, we posit essential points on SARS-CoV-2 and its management during the transition from the acute phase of the COVID-19 pandemic. As discussed, despite Omicron (sub)variant(s) causing clinically milder infections, SARS-CoV-2 is far from being a negligible pathogen. It requires continued genomic surveillance, particularly if one considers that its future (sub)lineages do not necessarily have to be milder. Antivirals and vaccines remain the essential elements in COVID-19 management. However, the former could benefit from further development and improvements in dosing, while the seasonal administration of the latter requires simplification to increase interest and tackle vaccine hesitancy. It is also essential to ensure accessibility of COVID-19 pharmaceuticals and vaccines in low-income countries and improve the understanding of their use in the context of long-term goals of SARS-CoV-2 management. Regardless of location, the primary role of COVID-19 awareness and education must be played by healthcare workers who directly communicate with patients and serve as role models for healthy behaviors.

Infectious bronchitis virus (IBV) is a highly variable RNA virus that affects chickens worldwide. Due to its inherited tendency to suffer point mutations and recombination events during viral replication, emergent IBV strains have been linked to nephropathogenic and reproductive disease that are more severe than the typical respiratory disease, leading, in some cases, to mortality, severe production losses, and/or unsuccessful vaccination. QX and DMV/1639 strains are examples of the above-mentioned IBV evolutionary pathway and clinical outcome. In this study, our purpose was to systematically compare whole genomes of QX and DMV strains looking at each IBV gene individually. Phylogenetic analyses and amino acid site searches were performed in datasets obtained from GenBank accounting for all IBV genes and using our own relevant sequences as a basis. The QX dataset studied is more genetically diverse than the DMV dataset, partially due to the greater epidemiological diversity within the five QX strains used as a basis compared to the four DMV strains from our study. Historically, QX strains have emerged and spread earlier than DMV strains in Europe and Asia. Consequently, there are more QX sequences deposited in GenBank than DMV strains, assisting in the identification of a larger pool of QX strains. It is likely that a similar evolutionary pattern will be observed among DMV strains as they develop and spread in North America.

The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures and for this propose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanism leading to the creation of genomic heterogeneity by altering the number of chromosomes as well as changing their structures. In this review we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, human genome shows induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as whole genome doubling to more discrete changes as indels as well as the recent discovered complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double strand breaks (DSB) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar pattern observed during tumorigenesis. Then, we will also list several diseases associated to CIN resulting in fertility issue, miscarriage, genetic rare diseases and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.

Addressing global environmental problem, water splitting to produce hydrogen fuel by solar energy is getting so much attention. In the water splitting, the essential problem to solve is the development of efficient　catalysts for oxygen production. In this paper, having the prospect for a practical application of photocatalysts to artificial photosynthesis, molecular mechanisms in the current literature are briefly reviewed. At first, recent progress in the function of Mn cluster at the natural photosystem II is briefly described. The kinds of devices in which oxygen evolution reaction (OER) catalysts are used were designated; water electrolyzers, photoelectrodes, and photocatalysts. Some methods for analyzing molecular mechanism in OER catalysis, emphasized by FTIR method, are shown briefly. After describing common OER mechanisms, the molecular mechanisms are discussed for TiO2 and BiVO4 photoelectrodes with our novel data, followed by presenting of co-catalysts IrO2, RuO2, NiO2, and other metal oxides for OER catalysts. Recent reports describing OER catalysts of perovskites, layered double hydroxides (LDH), metal-organic frameworks (MOF), single atom catalysts, as well as metal complexes are reviewed. Finally, by comparing with natural photosystem, the requiring factors to improve the activity of the catalysts for artificial photosynthesis will be discussed.

This paper illustrates that the ROTASE model proposed by the author for the formation of spiral arms of galaxies is nicely demonstrated by the spirals generated by rockets venting fuel during free fall. The patterns of spirals by the falling rockets strongly support that the spiral galaxies with perfect central symmetry have to be originated from the galactic centers, and the spiral arms and the galactic bars are bound together as “rigid” body. The exclusive presence of a rear side trail effect in galaxies indicates the absence of co-rotation, and the rotation of spiral arms is faster than the galactic matters. The exact nature of X-matter remains an open question.

Many microbes live in habitats below their optimum temperature. Retention of metabolic heat by aggregation or insulation would boost growth. Generation of excess metabolic heat may also provide benefit. A cell that makes excess metabolic heat pays the cost of production, whereas the benefit may be shared by neighbors within a zone of local heat capture. Metabolic heat as a shareable public good raises interesting questions about conflict and cooperation of heat production and capture. Metabolic heat may also be deployed as a weapon. Species with greater thermotolerance gain by raising local temperature to outcompete less thermotolerant taxa. Metabolic heat may provide defense against bacteriophage attack, by analogy with fever in vertebrates. This article outlines the theory of metabolic heat in microbial conflict and cooperation, presenting several predictions for future study.

Translation of the genetic code into proteins is the main process across all life and ribosomes are ancient cellular machines uniquely enabling this information transformation. We provide a brief overview of the recent advances in linking the ribosomal structure and evolution. Based on these insights into ribosomal organisation across time, we propose that early replication and protein biosynthesis functions were inseparable and in fact were performed by the same ancient RNA molecule, the riboreplisome. Riboreplisome hypothesis helps to address issues of non-Darwinian evolution and complicated starting point that are characteristic to the RNA world, protein world and RNA:protein mixed co-development theories. We suggest that the riboreplisome is the missing link and a molecular machine connecting chemical and biological evolution paths, by being capable of basic genetic and feature selection functions in a cell- or cell-free setting. The riboreplisome hypothesis allows ease of sequential, genetically uninterrupted emergence and sophistication of the genetic code and its decoding machinery, and provides plausible explanations to the origins of the three main RNA types involved in the decoding: the ribosomal, transfer and messenger RNA. Furthermore, riboreplisome can help explaining the co-evolution of aminoacylation machinery, the driving force behind selective gene transcription and expression, and the cell-like compartmentalisation. While we may never find the original riboreplisome again, we might continue to discover different molecular remnants of its prior existence across the existing biological RNA, which, once identified or resurrected, can be useful in synthetic biology applications.

We review our theory of interdependence applied to autonomous human-machine teams, with which we have made several generalizations based on theory that have led to new discoveries, compared to social science which is struggling to break free of its validation crisis, but also has no generalizations to new discoveries with human teams, let alone to human-machine teams. In this invited article, based around the stability of a team, of our discoveries, we review the uncertainty between a team's structure and its performance, our first finding. We generalize that finding to deception, vulnerability, innovation and fittedness. From there, our next generalization is to the quantum likeness of interdependence and quantum mechanics; we move on to Shannon holes, knowledge, and conclude with the value of debate and the need for boundaries to contain debate, to reduce interference, and to protect states of interdependence. After the introduction, we extend our model in Section 2 to energy and time, and we close with a brief review of innovation and future plans.

During the last few decades bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent regions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroups II and III generates impetus for additional phylogenetic and virological research within this geographical region.

Microbial immune escape represents the primary cause of induced pathogenesis in humans, and it represents a pivotal method used by viral agents to increase their load and suppress key mechanisms of the innate and adaptive immune system. This phenomenon represents the primary factor that led to the onset of the 1918-1920 A(H1N1) Influenza and 2020-2022 COVID-19 pandemics, and it possibly played a major role in the onset of the AIDS pandemic as well. Moreover, repeated incidents of immune evasion could be associated with higher rates of cellular aging (Jackson et al., 2017), most likely due to the consequent increased demands of energy consumption. Highly developed viral immune evasion ultimately indicates the high inner intelligence of human immunity due to reflective and imitative characteristics of reactions that are produced against initial actions. Ribonucleic acid-based viral genomes contain open reading frames, which consist of genes producing sixteen non-structural proteins. Such proteins play a considerable role in desensitizing first-line immunity during cellular infection, and non-structural proteins 1, 10 and 16 have the strongest effects against a healthy expression rate of Type I and Type III Interferon-encoding genes. Type I Interferons consist of IFN-alpha, -beta, -delta, -epsilon, -omega, -tau and -zeta, whilst Type III Interferons consist of IFN-lambda1, -lambda2 and -lambda3, and they act as stimulators of intracellular signalling cascades that in turn lead to the activation and expression of interferon-stimulated genes (Brown et al., 2022). The earlier the interferon-stimulated genes are activated, the lower the extent of pro-inflammatory mediation and overall, the more effective the antiviral immune response will be, given the exponential nature of the viral load increase. Non-structural protein 16 methylates the 5’ cap of the virus, making the pathogen-associated molecular patterns less recognisable by pattern-recognition receptors, and it requires activation by bonding with non-structural protein 10. It is preserved in the S-Adenosyl-L-Methionine pocket of the SARS-CoV-2 genome. Non-structural protein 1 (NS1) directly cleaves the host cell mRNA producing Type I and possibly Type III Interferons, thereby preventing a translation process of the immune proteins. NS1 has recently been found to often be packaged into exosomes once secreted by the viral genome in the cytosol, meaning that exocytosis and paracrine signalling to neighbouring cells before their actual infection is possible. As a result, NS1 is highly capable of silencing the first-line immune responses of uninfected neighbouring cells as well, thereby highlighting the need to adjust the focus of therapeutics and vaccinology toward first-line immunity and further indicating its foundational importance in the support for the development of precise and balanced defenses against microbial agents of concern (EL SAFADI et al., 2022).

In this paper, the lamellar structural evolution and microvoids variations of β-iPP during the processing of two different stretching methods, sequential biaxial stretching and simultaneous biaxial stretching, were investigated in detail. It was found that different stretching methods led to significantly different lamellae deformation modes, and the microporous membranes obtained from the simultaneous biaxial stretching exhibited better mechanical properties. For the sequential biaxial stretching, abundant coarse fibers originated from the tight accumulation of the lamellae parallel to the longitudinal stretching direction, whereas the lamellae perpendicular to the stretching direction were easily deformed and separated. Those coarse fibers were difficult to be separated to form micropores during the subsequent transverse stretching process, resulting in a poor micropores distribution. However, for the simultaneous biaxial stretching, the β crystal had the same deformation mode, that is, the lamellae distributed in different directions were all destroyed, forming abundant microvoids and little coarse fibers formation.

By combining general relativity and CPT symmetry, the theory of CPT gravity predicts gravitational repulsion between matter and CPT-transformed matter, i.e. antimatter inhabiting an inverted space-time. Such repulsive gravity turned out to be an excellent candidate for explaining the accelerated expansion of the Universe, without the need for dark energy. The recent results of the ALPHA-g experiment, which show gravitational attraction between antihydrogen atoms and the Earth, seem to undermine this success in the cosmological field. Analyzing the above theory, we find two solutions that can be consistent with the experimental results, while preserving the large-scale gravitational repulsion. The first highlights how repulsive gravity can be the result of the interaction with an inverted space-time, but occupied by matter and not antimatter, and therefore the antimatter present in our space-time has no reason to exhibit gravitational repulsion. The second retains the original CPT transformation, resulting in repulsive gravity between matter and antimatter, but with the caveat that antimatter immersed in our space-time cannot exhibit the PT transformation which is the cause of the repulsion. Finally, it is shown that, in a Newtonian approximation of the geodesic equation, time reversal is not a necessary operation for repulsive gravity, therefore opening the possibility of an expanding cosmos with a single time direction.

The application of evolutionary optimization algorithms in problem solving is currently gaining wide popularity. Use of Differential Evolution (DE) algorithm in obtaining analytically approximate solution of unstable second order initial value Ordinary Differential Equation (ODE) is presented in this work. The methodology involves solving an associated problem of optimization with con-strains to get an analytically approximate solution for the ODE under consider-ation. Three test cases were used to demonstrate the efficiency of our method. In comparison with other methods discussed in the literature, our method gave significant improvement on the accuracy of the obtained results.

Multisubunit RNA polymerases (RNAP) carry out transcription in all domains of life; during vi-rus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host-virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as they aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscil-lations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes of RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymer-ases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.

Antibiotic resistance has emerged as one of the major concerns to public human health due to issues in treatment and control of major infectious diseases. From discovery of penicillin in 1940, the antibiotic resistance originated and now developed the microorganisms as resistive strains to the major available antibiotics. Furthermore, studies on this captivating activity of the microbes provide insight into the complexities of microbial physiology and may offer some guidance in preventing the onset and consequent development of antibiotic resistance. Despite of initiatives taken in last few decades to overcome the issues, the trends of antibiotic resistance gained much peak. Antibiotic resistance appears to have emerged as a result of various factors including antibiotics being misused and overused in both the medical field and the agricultural sector. Important factors in the development of antibiotic resistance also include bacterial mutation, unplanned evolution, and horizontal gene transfers. In addition, antibiotics resistance imposed the financial consequences to public health and drug development research. Future advancements related to innovative antibiotics and molecular drug designing become challenge for researchers due to intensive multiple antibiotics resistance among human population. Many researches have been conducted on origin, evolutionary aspect of antibiotic resistance and mechanisms of antibiotics resistance, but its effect on future drug development is little understood. Therefore, the recent review will highlight the role of antibiotic resistance in drug designing and impacts of antibiotic resistance on drug development in future.

Iron-containing nickel sulfides, selenides, and sulfoselenides were synthesized via a simple two-step hydrothermal reaction (temperature 160 °C) for their application as electrocatalysts in the oxygen evolution reaction (OER) in an alkaline solution (1 mol L–1 KOH). The study demonstrated that iron-containing nickel cobalt sulfides and selenides exhibit superior OER performance with lower overpotentials compared to iron-free nickel cobalt sulfide and selenide, which highlights the significant role of iron in enhancing OER nickel cobalt electrocatalysts: Fe0.1Ni1.4Co2.9(S0.87O0.13)4, η50 = 318 mV; Fe0.2Ni1.5Co2.8(S0.9O0.1)4, η50 = 310 mV; Fe0.3Ni1.2Co2.5(S0.9O0.1)4, η50 = 294 mV; Fe0.6Ni1.2Co2.5(S0.83O0.17)4, η50 = 294 mV, Fe0.4Ni0.7Co1.6(Se0.81O0.19)4, η50 = 306 mV compared to Ni1.0Co2.1(S0.9O0.1)4, η50 = 346 mV and Ni0.7Co1.4(Se0.85O0.15)4, η50 = 355 mV (all values at current densities η50 of 50 mA cm–2). Furthermore, the iron-containing nickel cobalt sulfoselenide Fe0.5Ni1.0Co2.0(S0.57Se0.25O0.18)4 displayed exceptional OER performance with η50 = 277 mV, surpassing the benchmark RuO2 electrode with η50 = 299 mV. The superior performance of the sulfoselenide was attributed to its low charge transfer resistance (Rct) of 0.8 Ω at 1.5 V vs. the reversible hydrogen electrode (RHE). Moreover, the sulfoselenide demonstrated remarkable stability, with only a minimal increase in overpotential (η50) from 277 mV to 279 mV after a 20 h chronopotentiometry test. These findings suggest that trimetallic iron, nickel and cobalt sulfide, selenide and especially sulfoselenide materials hold promise as high-performance, cost-effective, and durable electrocatalysts for sustainable OER reactions. This study provides a valuable approach for the development of efficient electrocatalytic materials, contributing to the advancement of renewable energy technologies.

Evolutionary, sequence and structural analyses of tRNA variable (V) loops provides a new understanding. Type I tRNA V loops have a primordial length of 5 nt, and type II tRNA V loops have a primordial length of 14 nt. Sequence-based alignments of type I and type II V loops gave deceptive results. Type II V loops are characterized by the trajectory of the V arm, the size and sequence of the loop and the first and last V loop nucleotides and their known contacts. Depending on the V arm trajectory, type II V stems and loops can be interaction sites for aminoacyl-tRNA synthetases. So, type II V arms for tRNALeu, tRNASer and tRNATyr (found in Bacteria) were coevolved and selected to distinguish determinants to support cognate tRNA charging. The alignment of type I and type II V loops was adjusted based on tRNA evolution. Results are consistent with Archaea being an older and simpler life form than Bacteria. TRNAome sequences were derived from radiation of an ordered tRNAPri (Pri for primordial) sequence comprised of known RNA repeats and inverted repeats. V loop and tRNA sequences, therefore, convey a history of the primary successful pathway in the origin of life.

Polycystic ovary syndrome (PCOS) is increasingly being characterized as an evolutionary mismatch disorder that presents with a complex mixture of metabolic and endocrine symptoms. The Evolutionary Model proposes that PCOS arises from a collection of inherited polymorphisms that have been consistently demonstrated in a variety of ethnic groups and races. In-utero developmental programming of susceptible genomic variants are thought to predispose the offspring to develop PCOS. Postnatal exposure to lifestyle and environmental risk factors results in epigenetic activation of developmentally programmed genes and disturbance of the hallmarks of health. The resulting pathophysiological changes represent the consequences of poor-quality diet, sedentary behaviour, endocrine disrupting chemicals, stress, circadian disruption, and other lifestyle factors. Emerging evidence suggests that lifestyle-induced gastrointestinal dysbiosis plays a central role in the pathogenesis of PCOS. Lifestyle and environmental exposures initiate changes that result in disturbance of the gastrointestinal microbiome (dysbiosis), immune dysregulation (chronic inflammation), altered metabolism (insulin resistance), endocrine and reproductive imbalance (hyperandrogenism), and central nervous system dysfunction (neuroendocrine, autonomic nervous system). PCOS can be a progressive metabolic condition that leads to obesity, gestational diabetes, type 2 diabetes, metabolic-associated fatty liver disease, metabolic syndrome, cardiovascular disease, and cancer. This review explores the mechanisms that underpin the evolutionary mismatch between ancient survival pathways and contemporary lifestyle factors involved in the pathogenesis and pathophysiology of PCOS.

Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed enantiomerically enriched fractions as a basis for the origin of homochiral life forms. Numerous hypotheses have been put forward as to how preferentially homochiral molecules could have formed and accumulated on Earth. In this article, it is shown that homochirality of the abiotic organic pool at the time of formation of the first self-replicating molecules is not necessary and not even probable. It is proposed to abandon the notion of a molecular ensemble and to focus on the level of individual molecules. Although the formation of the first self-replicating, most likely homochiral molecule is a seemingly improbable event, on a closer look, it is almost inevitable that homochiral molecules have formed simply on a statistical basis. In this case, the non-selective leap to homochirality would be one of the first steps in chemical evolution directly out of a racemic “ocean”. Moreover, most studies focus on the chirality of the primordial monomers with respect to an asymmetric carbon atom. However, any polymer with a minimal size that allows folding to a secondary structure, would spontaneously lead to asymmetric higher structures (conformations). Most of the functions of these polymers would be influenced by this inherently asymmetric folding. To summarize, simple and universal mechanisms may have led to homochiral self-replicating systems in the context of chemical evolution. A homochiral monomer pool is deemed unnecessary and probably never existed on primordial Earth.

There is much concern about disruption of endocrine physiology regulated by steroid hormones in humans, other terrestrial vertebrates and fish by industrial chemicals, such as bisphenol A, and pesticides, such as DDT. These endocrine-disrupting chemicals influence steroid-mediated physiology in humans and other vertebrates by competing with steroids for receptor binding sites, disrupting diverse responses involved in reproduction, development and differentiation. Here I discuss that due to evolution of the progesterone receptor (PR) and mineralocorticoid receptor (MR) after ray-finned fish and terrestrial vertebrates diverged from a common ancestor, each receptor evolved to respond to different steroids in ray-finned fish and terrestrial vertebrates. In elephant shark, a cartilaginous fish, ancestral to ray-finned fish and terrestrial vertebrates, both progesterone and 17,20-beta-dihydroxy-progesterone activate the PR. During the evolution of ray-finned fish and terrestrial vertebrates, the PR in terrestrial vertebrates continued responding to progesterone and evolved to weakly respond to 17,20-beta-dihydroxy-progesterone. In contrast, the physiological progestin for the PR in zebrafish and other ray-finned fish is 17,20-beta-dihydroxy-progesterone, and ray-finned fish PR responds weakly to progesterone. The MR in fish and terrestrial vertebrates also diverged to have different responses to progesterone. Progesterone is a potent agonist for elephant shark MR, zebrafish MR and other fish MRs, in contrast to progesterone’s opposite activity as an antagonist for aldosterone, the physiological mineralocorticoid for human MR. These different physiological ligands for fish and terrestrial vertebrate PR and MR need to be considered in applying data for their disruption by chemicals in fish and terrestrial vertebrates to each other.