Abiotic Ribose Synthesis Under Aqueous Environments with Various Chemical Conditions.

Ribose is the defining sugar in ribonucleic acid (RNA), which is often proposed to have carried the genetic information and catalyzed the biological reactions of the first life on Earth. Thus, abiological processes that yield ribose under prebiotic conditions have been studied for decades. However, aqueous environments required for the formation of ribose from materials available in quantity under geologically reasonable models, where the ribose formed is not immediately destroyed, remain unclear. This is due in large part to the challenge of analysis of carbohydrates formed under a wide range of aqueous conditions. Thus, the formation of ribose on prebiotic Earth has sometimes been questioned. We investigated the quantitative effects of pH, temperature, cation, and the concentrations of formaldehyde and glycolaldehyde on the synthesis of diverse sugars, including ribose. The results suggest a range of conditions that produce ribose and that ribose could have formed in constrained aquifers on prebiotic Earth.

Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores.

Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.

Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses.

Reported here are experiments that show that ribonucleoside triphosphates are converted to polyribonucleic acid when incubated with rock glasses similar to those likely present 4.3-4.4 billion years ago on the Hadean Earth surface, where they were formed by impacts and volcanism. This polyribonucleic acid averages 100-300 nucleotides in length, with a substantial fraction of 3',-5'-dinucleotide linkages. Chemical analyses, including classical methods that were used to prove the structure of natural RNA, establish a polyribonucleic acid structure for these products. The polyribonucleic acid accumulated and was stable for months, with a synthesis rate of 2 × 10-3 pmoles of triphosphate polymerized each hour per gram of glass (25°C, pH 7.5). These results suggest that polyribonucleotides were available to Hadean environments if triphosphates were. As many proposals are emerging describing how triphosphates might have been made on the Hadean Earth, the process observed here offers an important missing step in models for the prebiotic synthesis of RNA.

Leriche Syndrome Misdiagnosed as Complex Regional Pain Syndrome in a Patient with Neuropathic Pain Caused by a Chip Fracture: A Case Report.

INTRODUCTION: Leriche syndrome is an aortoiliac occlusive disease caused by atherosclerotic occlusion. We report a case of Leriche syndrome with a fracture that was suspected as complex regional pain syndrome (CRPS), as the post-traumatic pain gradually worsened in the form of excruciating neuropathic pain. CASE REPORT: A 52-year-old woman with a history of hypertension was referred to the Department of Pain Medicine from a local orthopedic clinic because of suspected CRPS for excruciating neuropathic pain for one month. She complained of gait dysfunction and severe pain in the right foot following an incident of trauma with the right first toe. The average pain intensity assessed using the visual analog scale (VAS) was 90 (0: no pain, 100: the worst pain imaginable), and the neuropathic pain was evident as a score of 6/10 on Douleur neuropathique 4. Allodynia, hyperalgesia, blue discoloration of the skin, asymmetric temperature change (1.38 °C), and edematous soft tissue changes were observed. Ultrasonography showed a chip fracture in the first distal phalanx of the right first toe. The diagnosis was most probably CRPS type I according to the Budapest research criteria for CRPS. However, multiple pain management techniques were insufficient in controlling the symptoms. A month and a half later, an ankle-brachial index score of less than 0.4 suggested severe peripheral artery disease. Computed tomography angiography showed total occlusion between the infrarenal abdominal aorta and the bilateral common iliac arteries. Therefore, she underwent aortic-bifemoral bypass surgery with a diagnosis of Leriche syndrome. Three months after the surgery, the average pain intensity was graded as 10 on the VAS (0-100), the color of the skin of the right first toe improved and no gait dysfunction was observed. CONCLUSION: A chip fracture in a region with insufficient blood flow could manifest as excruciating neuropathic pain in Leriche syndrome.

Abiotic Synthesis of Nucleoside 5'-Triphosphates with Nickel Borate and Cyclic Trimetaphosphate (CTMP).

While nucleoside 5'-triphosphates are precursors for RNA in modern biology, the presumed difficulty of making these triphosphates on Hadean Earth has caused many prebiotic researchers to consider other activated species for the prebiotic synthesis of RNA. We report here that nickel(II), in the presence of borate, gives substantial amounts (2-3%) of nucleoside 5'-triphosphates upon evaporative heating in the presence of urea, salts, and cyclic trimetaphosphate (CTMP). Also recovered are nucleoside 5'-diphosphates and nucleoside 5'-monophosphates, both likely arising from 5'-triphosphate intermediates. The total level of 5'-phosphorylation is typically 30%. Borate enhances the regiospecificity of phosphorylation, with increased amounts of other phosphorylated species seen in its absence. Experimentally supported paths are already available to make nucleosides in environments likely to have been present on Hadean Earth soon after a midsized 1021 to 1023 kg impactor, which would also have delivered nickel to the Hadean surface. Further, sources of prebiotic CTMP continue to be proposed. Thus, these results fill in one of the few remaining steps needed to demystify the prebiotic synthesis of RNA and support a continuous model from atmospheric components to oligomeric RNA that is lacking only a mechanism to obtain homochirality in the product RNA.

Prebiotic Chemistry that Could Not Not Have Happened.

We present a direct route by which RNA might have emerged in the Hadean from a fayalite-magnetite mantle, volcanic SO2 gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH3, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., lüneburgite) and/or trimetaphosphate-borate with Ni2+ catalysis to give nucleoside 5'-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (1023-1020 kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday.

Hachimoji DNA and RNA: A genetic system with eight building blocks.

We report DNA- and RNA-like systems built from eight nucleotide "letters" (hence the name "hachimoji") that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

A Prebiotic Synthesis of Canonical Pyrimidine and Purine Ribonucleotides.

The "RNA first" model for the origin of life holds that RNA emerged spontaneously on early Earth and developed into life through its dual capabilities for genetics and catalysis. The model's central weakness is the difficulty of making its building blocks, in particular, the glycosidic bond joining nucleobases to ribose. Thus, the focus of much of the modern literature on the topic is directed toward solving this difficulty and includes elegant, though indirect, methods for making this bond. Here, we report that the glycosidic bond in canonical pyrimidine and purine ribonucleotides can be formed by direct coupling of cyclic carbohydrate phosphates with free nucleobases, all reported to be available by experimentally supported pathways that might have operated on early Earth.

Molybdenum(VI)-Catalyzed Rearrangement of Prebiotic Carbohydrates in Formamide, a Candidate Prebiotic Solvent.

It has been four decades since formamide was first suggested to perform roles as a precursor and/or a solvent in prebiotic chemistry. However, little work has sought to integrate formamide into larger prebiotic schemes that might create prebiotic RNA, often proposed to have been the first Darwinian biopolymer. Here, we report that formamide can be used as a solvent to perform the Bílik reaction, which uses molybdenum(VI) oxo species as catalysts at near-neutral pH to rearrange branched carbohydrates to give linear carbohydrates; the branched carbohydrates are produced from formaldehyde (HCHO) in alkaline mixtures containing borate, whereas the linear carbohydrates are the precursors needed for ribonucleosides and ribonucleotides. Under conditions wherein the Bílik reaction does this rearrangement, carbohydrate reaction products do not require stabilization by borate. These results, therefore, connect aqueous and formamide-based processes for the prebiotic formation of RNA components. Based on data from Hadean zircons that show that the mantle of the early Earth was near the fayalite-quartz-magnetite fugacity, molybdenum in its 6+ oxidation state was likely available in the Hadean. Together, these allow us to conjecture a process that delivers ribonucleosides and ribonucleotides from hydrogen cyanide and HCHO from a Hadean atmosphere on a Hadean geosphere, without needing precisely timed transitions from one solvent system to the other.

"Skinny" and "Fat" DNA: Two New Double Helices.

According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.

Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection.

Described here are the synthesis, enzymology and some applications of a purine nucleoside analog (H) designed to have two tautomeric forms, one complementary to thymidine (T), the other complementary to cytidine (C). The performance of H is compared by various metrics to performances of other 'biversal' analogs that similarly rely on tautomerism to complement both pyrimidines. These include (i) the thermodynamic stability of duplexes that pair these biversals with various standard nucleotides, (ii) the ability of the biversals to support polymerase chain reaction (PCR), (iii) the ability of primers containing biversals to equally amplify targets having polymorphisms in the primer binding site, and (iv) the ability of ligation-based assays to exploit the biversals to detect medically relevant single nucleotide polymorphisms (SNPs) in sequences flanked by medically irrelevant polymorphisms. One advantage of H over the widely used inosine 'universal base' and 'mixed sequence' probes is seen in ligation-based assays to detect SNPs. The need to detect medically relevant SNPs within ambiguous sequences is especially important when probing RNA viruses, which rapidly mutate to create drug resistance, but also suffer neutral drift, the second obstructing simple methods to detect the first. Thus, H is being developed to detect variants of viruses that are rapidly mutating.

Reduced Bacterial Wilt in Tomato Plants by Bactericidal Peroxyacetic Acid Mixture Treatment.

Peroxyacetic acid mixture Perosan, composed of peroxyacetic acid, hydrogen peroxide and acetic acid, was evaluated for eco-friendly management of tomato bacterial wilt by Ralstonia pseudosolanacearum. Perosan drastically suppressed in vitro growth of R. pseudosolanacearum in liquid cultures in dose- and incubation time-dependent manners. Higher perosan doses (0.1 and 1%) caused lowered pH and phytotoxicity to detached leaves of two tomato cultivars Cupirang and Benekia 220 in aqueous solution. Treatment with 0.01% of Perosan delayed wilting symptom significantly in the detached leaves of two cultivars inoculated with R. pseudosolanacearum (107 cfu/ml). Soil drenching of 5% Perosan solution in pots caused severe tissue collapse of tomato seedlings at the four-week-old stage of two tomato cultivars. Treatment with 1% Perosan by soil-drenching significantly reduced bacterial wilt in the tomato seedlings of two cultivars. These findings suggest that Perosan treatment can be applied to suppress bacterial wilt during tomato production.

A Direct Prebiotic Synthesis of Nicotinamide Nucleotide.

The "RNA World" hypothesis proposes an early episode of the natural history of Earth, where RNA was used as the only genetically encoded molecule to catalyze steps in its metabolism. This, according to the hypothesis, included RNA catalysts that used RNA cofactors. However, the RNA World hypothesis places special demands on prebiotic chemistry, which must now deliver not only four ribonucleosides, but also must deliver the "functional" portion of these RNA cofactors. While some (e.g., methionine) present no particular challenges, nicotinamide ribose is special. Essential to its role in biological oxidations and reductions, its glycosidic bond that holds a positively charged heterocycle is especially unstable with respect to cleavage. Nevertheless, we are able to report here a prebiotic synthesis of phosphorylated nicotinamide ribose under conditions that also conveniently lead to the adenosine phosphate components of this and other RNA cofactors.

Angiomyolipoma of the Glabellar Region.

Angiomyolipomas are hamartomatous lesions consisting of smooth muscle bundles, thick-walled blood vessels, and mature adipocytes. They are usually found in the kidneys of tuberous sclerosis patients and more rarely in other organs, such as the liver, the oral cavity, the sinonasal tract, the heart, the large intestines, the lungs, and the skin. Cutaneous angiomyolipoma has shown to be very rare and generally occurs at the ends of the digits, the elbows, the ears, and the nose. Herein, we report the first documented case of angiomyolipoma of the glabellar region.

Prebiotic stereoselective synthesis of purine and noncanonical pyrimidine nucleotide from nucleobases and phosphorylated carbohydrates.

According to a current "RNA first" model for the origin of life, RNA emerged in some form on early Earth to become the first biopolymer to support Darwinism here. Threose nucleic acid (TNA) and other polyelectrolytes are also considered as the possible first Darwinian biopolymer(s). This model is being developed by research pursuing a "Discontinuous Synthesis Model" (DSM) for the formation of RNA and/or TNA from precursor molecules that might have been available on early Earth from prebiotic reactions, with the goal of making the model less discontinuous. In general, this is done by examining the reactivity of isolated products from proposed steps that generate those products, with increasing complexity of the reaction mixtures in the proposed mineralogical environments. Here, we report that adenine, diaminopurine, and hypoxanthine nucleoside phosphates and a noncanonical pyrimidine nucleoside (zebularine) phosphate can be formed from the direct coupling reaction of cyclic carbohydrate phosphates with the free nucleobases. The reaction is stereoselective, giving only the ß-anomer of the nucleotides within detectable limits. For purines, the coupling is also regioselective, giving the N-9 nucleotide for adenine as a major product. In the DSM, phosphorylated carbohydrates are presumed to have been available via reactions explored previously [Krishnamurthy R, Guntha S, Eschenmoser A (2000) Angew Chem Int Ed 39:2281-2285], while nucleobases are presumed to have been available from hydrogen cyanide and other nitrogenous species formed in Earth's primitive atmosphere.

Stretchable Ag electrodes with mechanically tunable optical transmittance on wavy-patterned PDMS substrates.

We report on semi-transparent stretchable Ag films coated on a wavy-patterned polydimethylsiloxane (PDMS) substrate for use as stretchable electrodes for stretchable and transparent electronics. To improve the mechanical stretchability of the Ag films, we optimized the wavy-pattern of the PDMS substrate as a function of UV-ozone treatment time and pre-strain of the PDMS substrate. In addition, we investigated the effect of the Ag thickness on the mechanical stretchability of the Ag electrode formed on the wavy-patterned PDMS substrate. The semi-transparent Ag films formed on the wavy-patterned PDMS substrate showed better stretchability (strain 20%) than the Ag films formed on a flat PDMS substrate because the wavy pattern effectively relieved strain. In addition, the optical transmittance of the Ag electrode on the wavy-patterned PDMS substrate was tunable based on the degree of stretching for the PDMS substrate. In particular, it was found that the wavy-patterned PDMS with a smooth buckling was beneficial for a precise patterning of Ag interconnectors. Furthermore, we demonstrated the feasibility of semi-transparent Ag films on wavy-patterned PDMS as stretchable electrodes for the stretchable electronics based on bending tests, hysteresis tests, and dynamic fatigue tests.

Ectopic Preauricular Sinus in a Facial Cleft and Microtia Patient.

Preauricular sinus is a congenital malformation that is very commonly encountered among the general population and it has especially high prevalence among Asians when compared to other ethnic groups. It can often go unnoticed or easily overlooked by the patient or even by doctors because most of them are asymptomatic and is most of the time only a tiny pit that can be trivial in terms of aesthetics. We report a very rare and unique case that has no precedence what so ever; hence no reported case in the literature: an ectopic preauricular sinus in a facial cleft and microsomia patient.

Crystal structures of deprotonated nucleobases from an expanded DNA alphabet.

Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(µ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3-·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.

Evaporite Borate-Containing Mineral Ensembles Make Phosphate Available and Regiospecifically Phosphorylate Ribonucleosides: Borate as a Multifaceted Problem Solver in Prebiotic Chemistry.

RNA is currently thought to have been the first biopolymer to support Darwinian natural selection on Earth. However, the phosphate esters in RNA and its precursors, and the many sites at which phosphorylation might occur in ribonucleosides under conditions that make it possible, challenge prebiotic chemists. Moreover, free inorganic phosphate may have been scarce on early Earth owing to its sequestration by calcium in the unreactive mineral hydroxyapatite. Herein, it is shown that these problems can be mitigated by a particular geological environment that contains borate, magnesium, sulfate, calcium, and phosphate in evaporite deposits. Actual geological environments, reproduced here, show that Mg2+ and borate sequester phosphate from calcium to form the mineral lüneburgite. Ribonucleosides stabilized by borate mobilize borate and phosphate from lüneburgite, and are then regiospecifically phosphorylated by the mineral. Thus, in addition to guiding carbohydrate pre-metabolism, borate minerals in evaporite geoorganic contexts offer a solution to the phosphate problem in the "RNA first" model for the origins of life.

Tin doped indium oxide anodes with artificially controlled nano-scale roughness using segregated Ag nanoparticles for organic solar cells.

Nano-scale surface roughness in transparent ITO films was artificially formed by sputtering a mixed Ag and ITO layer and wet etching of segregated Ag nanoparticles from the surface of the ITO film. Effective removal of self-segregated Ag particles from the grain boundaries and surface of the crystalline ITO film led to a change in only the nano-scale surface morphology of ITO film without changes in the sheet resistance and optical transmittance. A nano-scale rough surface of the ITO film led to an increase in contact area between the hole transport layer and the ITO anode, and eventually increased the hole extraction efficiency in the organic solar cells (OSCs). The heterojunction OSCs fabricated on the ITO anode with a nano-scale surface roughness exhibited a higher power conversion efficiency of 3.320%, than that (2.938%) of OSCs made with the reference ITO/glass. The results here introduce a new method to improve the performance of OSCs by simply modifying the surface morphology of the ITO anodes.