scholarly journals Racemate Resolution of Alanine and Leucine on Homochiral Quartz, and Its Alteration by Strong Radiation Damage

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1222
Author(s):  
Adrien D. Garcia ◽  
Cornelia Meinert ◽  
Friedrich Finger ◽  
Uwe J. Meierhenrich ◽  
Ewald Hejl
Keyword(s):  
Amino Acids ◽  
Radiation Damage ◽  
Mirror Symmetry ◽  
Near Surface ◽  
Racemate Resolution ◽  
Previous Hypothesis ◽  
Enantioselective Adsorption ◽  
Domains Of Life ◽  
Induced Fission ◽  
Strong Radiation

Homochiral proteins orchestrate biological functions throughout all domains of life, but the origin of the uniform l-stereochemistry of amino acids remains unknown. Here, we describe enantioselective adsorption experiments of racemic alanine and leucine onto homochiral d- and l-quartz as a possible mechanism for the abiotic emergence of biological homochirality. Substantial racemate resolution with enantiomeric excesses of up to 55% are demonstrated to potentially occur in interstitial pores, along grain boundaries or small fractures in local quartz-bearing environments. Our previous hypothesis on the enhanced enantioselectivity due to uranium-induced fission tracks could not be validated. Such capillary tubes in the near-surface structure of quartz have been proposed to increase the overall chromatographic separation of enantiomers, but no systematic positive correlation of accumulated radiation damage and enantioselective adsorption was observed in this study. In general, the natural l-quartz showed stronger enantioselective adsorption affinities than synthetic d-quartz without any significant trend in amino acid selectivity. Moreover, the l-enantiomer of both investigated amino acids alanine and leucine was preferably adsorbed regardless of the handedness of the enantiomorphic quartz sand. This lack of mirror symmetry breaking is probably due to the different crystal habitus of the synthetic z-bar of d-quartz and the natural mountain crystals of l-quartz used in our experiments.

Specimen Preparation of Near Surface Ion Irradiated Samples

1985 ◽  
Vol 43 ◽  
pp. 170-171
Author(s):  
K. F. Russell ◽  
L. L. Horton
Keyword(s):  
Radiation Damage ◽  
Heavy Ions ◽  
Target Material ◽  
Metal Alloys ◽  
Specimen Surface ◽  
Specimen Preparation ◽  
Particle Accelerators ◽  
Near Surface ◽  
Graaff Accelerator ◽  
Van De Graaff

Beams of heavy ions from particle accelerators are used to produce radiation damage in metal alloys. The damaged layer extends several microns below the surface of the specimen with the maximum damage and depth dependent upon the energy of the ions, type of ions, and target material. Using 4 MeV heavy ions from a Van de Graaff accelerator causes peak damage approximately 1 μm below the specimen surface. To study this area, it is necessary to remove a thickness of approximately 1 μm of damaged metal from the surface (referred to as “sectioning“) and to electropolish this region to electron transparency from the unirradiated surface (referred to as “backthinning“). We have developed electropolishing techniques to obtain electron transparent regions at any depth below the surface of a standard TEM disk. These techniques may be applied wherever TEM information is needed at a specific subsurface position.

scholarly journals Genetic code as an image of the mirror image. Supplement 1

2019 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Binary Tree ◽  
Mirror Symmetry ◽  
Essential Feature ◽  
Binary Sequence ◽  
Number System ◽  
Mirror Image ◽  
Chemical Similarity ◽  
Decimal Number

Searching for the answer to the question why – in the generating of the genetic code – only mirror symmetrical left and not right amino acids (AAs) were selected, in a previous work we showed the existence of a double Boolean "triangle" in mirror symmetry, with superposition of the top vertices: 00 -11-22 / 22-11-00 → 00-11-22-11-00 [0 as 000; 1 as 001; 2 as 010] (Rakočević, 2019a). The resulting sequence, summed with the binary sequence of a 6-bit binary tree, split with a mirror in the middle (101/010) [as in Dirac's positron / electron mirror], results in a sequence of decimal number system: 02-13-24-16-05, where a smaller number (010 = 2) was added three times and a larger number (101 = 5) twice (Survey 1). The mirror image of the obtained decimal sequence (20-31-42-61-50) is 100% consistent with the arrangement of protein AAs, arranged according to strict chemical similarity (Rakočević, 2019a, Table 3). Starting from this result, the paper of which this is a supplement, presents new insights and new examples of mirror symmetry valid for the genetic code, showing that mirror symmetry is also in other respects an essential feature of the genetic code. In this Supplement are given the further new insights.

scholarly journals Identification of novel translated small ORFs in Escherichia coli using complementary ribosome profiling approaches

2021 ◽  
Author(s):  
Anne Stringer ◽  
Carol Smith ◽  
Kyle Mangano ◽  
Joseph T. Wade
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
High Sensitivity ◽  
Purifying Selection ◽  
Ribosome Profiling ◽  
Small Subset ◽  
Stop Codons ◽  
Small Proteins ◽  
Domains Of Life ◽  
Short Orfs

Small proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Ribosome profiling has been used to infer the existence of small proteins by detecting the translation of the corresponding open reading frames (ORFs). Detection of translated short ORFs by ribosome profiling can be improved by treating cells with drugs that stall ribosomes at specific codons. Here, we combine the analysis of ribosome profiling data for Escherichia coli cells treated with antibiotics that stall ribosomes at either start or stop codons. Thus, we identify ribosome-occupied start and stop codons with high sensitivity for ∼400 novel putative ORFs. The newly discovered ORFs are mostly short, with 365 encoding proteins of <51 amino acids. We validate translation of several selected short ORFs, and show that many likely encode unstable proteins. Moreover, we present evidence that most of the newly identified short ORFs are not under purifying selection, suggesting they do not impact cell fitness, although a small subset have the hallmarks of functional ORFs. IMPORTANCE Small proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Recent studies have discovered small proteins by mapping the location of translating ribosomes on RNA using a technique known as ribosome profiling. Discovery of translated sORFs using ribosome profiling can be improved by treating cells with drugs that trap initiating ribosomes. Here, we show that combining these data with equivalent data for cells treated with a drug that stalls terminating ribosomes facilitates the discovery of small proteins. We use this approach to discover 365 putative genes that encode small proteins in Escherichia coli .

scholarly journals Microstructure Evolution in ZrCx with Different Stoichiometries Irradiated by Four MeV Au Ions

Materials ◽  
2019 ◽  
Vol 12 (22) ◽  
pp. 3768
Author(s):  
Boxin Wei ◽  
Dong Wang ◽  
Yujin Wang ◽  
Haibin Zhang
Keyword(s):  
Radiation Damage ◽  
Microstructure Evolution ◽  
Vacancy Concentration ◽  
Ion Beam ◽  
Grazing Incidence ◽  
Dislocation Loops ◽  
Black Dot ◽  
X Ray Diffraction ◽  
Near Surface ◽  
Transmission Electron

ZrCx ceramics with different stoichiometries were irradiated under a four MeV Au ion beam in doses of 2 × 1016 ions/cm2 at room temperature, corresponding to ~130 dpa. Grazing incidence, X-ray diffraction and transmission electron microscopy were performed to study the radiation damage and microstructure evolution in ZrCx ceramics. With the decrease in C/Zr ratio, the expansion of ZrCx lattice became smaller after irradiation. Some long dislocation lines formed at the near-surface, while, in the area with the greatest damage (depth of ~400 nm), large amounts of dislocation loops formed in ZrC, ZrC0.9 and ZrC0.8. With the increase in carbon vacancy concentration, the size of the dislocation loops gradually decreased. Few dislocation loops were found in ZrC0.7 after irradiation, and only black-dot defects were found in the area with the greatest damage. For the non-stoichiometric ZrCx, with the increase of the intrinsic vacancies, the number of C interstitials caused by irradiation decreased, and the recombination barrier of C Frenkel pairs reduced. The above factors will reduce the total number of C interstitials after cascade cooling, suppressing the formation and growth of dislocation loops, which is significant for the enhancement of the tolerance of radiation damage.

Reply to “Mirror Symmetry Breaking” of the Centrosymmetric CaCO3 Crystals with Amino Acids

2008 ◽  
Vol 120 (20) ◽  
pp. 3741-3744
Author(s):  
Niklas Loges ◽  
Stephan E. Wolf ◽  
Martin Panthöfer ◽  
Lars Müller ◽  
Marc-Christopher Reinnig ◽  
...  
Keyword(s):  
Amino Acids ◽  
Symmetry Breaking ◽  
Mirror Symmetry

Milk Protein Precursors in the Goat During Late Lactation

1993 ◽  
Vol 1993 ◽  
pp. 1-1
Author(s):  
B.J. Bequette ◽  
F.R.C. Backwell ◽  
A.G. Calder ◽  
J.A. Metcalf ◽  
D. Wray-Cahen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Mammary Gland ◽  
Milk Protein ◽  
Protein S ◽  
Dairy Goats ◽  
Protein Precursor ◽  
Previous Hypothesis ◽  
Casein Protein ◽  
Isotope Kinetics

Previously, we have reported on work in dairy goats using stable isotope kinetics to examine the precursors for milk protein synthesis (1). Contrary to a previous hypothesis (2), these results suggested that blood free amino acids (AA) are not simply transported into the mammary gland and incorporated directly into milk protein. Although the latter may still occur, a substantial amount of the AA for milk protein synthesis appears to be channelled through constitutive mammary gland protein(s) first. Moreover, the data indicated that a proportion (12-20%) of the casein protein precursor may be derived from extra-mammary sources other than blood free AA, e.g. peptides and/or proteins. It may be possible therefore to alter milk protein synthesis by the provision of different forms of precursor amino acids. Since the previous study was in goats during early lactation (day 61 ± 11), the present study reports on the precursors for milk protein synthesis in goats during late lactation, and allows a comparison between stages of lactation.

scholarly journals Orientation of palmitoylated CaVβ2a relative to CaV2.2 is critical for slow pathway modulation of N-type Ca2+ current by tachykinin receptor activation

2009 ◽  
Vol 134 (5) ◽  
pp. 385-396 ◽  
Author(s):  
Tora Mitra-Ganguli ◽  
Iuliia Vitko ◽  
Edward Perez-Reyes ◽  
Ann R. Rittenhouse
Keyword(s):  
Amino Acids ◽  
Arachidonic Acid ◽  
Palmitic Acid ◽  
Receptor Activation ◽  
Slow Pathway ◽  
Channel Activity ◽  
Tachykinin Receptor ◽  
Previous Hypothesis ◽  
Inhibitory Site ◽  
Neurokinin 1

The Gq-coupled tachykinin receptor (neurokinin-1 receptor [NK-1R]) modulates N-type Ca2+ channel (CaV2.2 or N channel) activity at two distinct sites by a pathway involving a lipid metabolite, most likely arachidonic acid (AA). In another study published in this issue (Heneghan et al. 2009. J. Gen Physiol. doi:10.1085/jgp.200910203), we found that the form of modulation observed depends on which CaVβ is coexpressed with CaV2.2. When palmitoylated CaVβ2a is coexpressed, activation of NK-1Rs by substance P (SP) enhances N current. In contrast, when CaVβ3 is coexpressed, SP inhibits N current. However, exogenously applied palmitic acid minimizes this inhibition. These findings suggested that the palmitoyl groups of CaVβ2a may occupy an inhibitory site on CaV2.2 or prevent AA from interacting with that site, thereby minimizing inhibition. If so, changing the orientation of CaVβ2a relative to CaV2.2 may displace the palmitoyl groups and prevent them from antagonizing AA's actions, thereby allowing inhibition even in the presence of CaVβ2a. In this study, we tested this hypothesis by deleting one (Bdel1) or two (Bdel2) amino acids proximal to the α interacting domain (AID) of CaV2.2's I–II linker. CaVβs bind tightly to the AID, whereas the rigid region proximal to the AID is thought to couple CaVβ's movements to CaV2.2 gating. Although Bdel1/β2a currents exhibited more variable enhancement by SP, Bdel2/β2a current enhancement was lost at all voltages. Instead, inhibition was observed that matched the profile of N-current inhibition from CaV2.2 coexpressed with CaVβ3. Moreover, adding back exogenous palmitic acid minimized inhibition of Bdel2/β2a currents, suggesting that when palmitoylated CaVβ2a is sufficiently displaced, endogenously released AA can bind to the inhibitory site. These findings support our previous hypothesis that CaVβ2a's palmitoyl groups directly interact with an inhibitory site on CaV2.2 to block N-current inhibition by SP.

Reply to “Mirror Symmetry Breaking” of the Centrosymmetric CaCO3 Crystals with Amino Acids

2008 ◽  
Vol 47 (20) ◽  
pp. 3683-3686 ◽  
Author(s):  
Niklas Loges ◽  
Stephan E. Wolf ◽  
Martin Panthöfer ◽  
Lars Müller ◽  
Marc-Christopher Reinnig ◽  
...  
Keyword(s):  
Amino Acids ◽  
Symmetry Breaking ◽  
Mirror Symmetry

Investigation of the mode of nuclear control over protein synthesis in early development of loach and sea urchin

Development ◽  
1972 ◽  
Vol 28 (3) ◽  
pp. 491-509
Author(s):  
Maya R. Krigsgaber ◽  
A. A. Neyfakh
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Ionizing Radiation ◽  
Radiation Damage ◽  
Sea Urchin ◽  
Rna Synthesis ◽  
Developmental Stages ◽  
Subsequent Development ◽  
Long Term Treatment ◽  
Androgenetic Haploid

It is shown that in loach embryos the incorporation of precursors into protein takes place in the blastoderm cells only. The change of the rate of incorporation of labelled amino acids into protein of the blastoderm separated from the yolk at successive developmental stages reflects the changes in the level of protein synthesis in intact embryos of the same developmental stages. Typical periodic changes of the intensity of protein synthesis in early embryo-genesis of the loach are detected: low incorporation of amino acids at blastula stages is followed by an increase of synthesis during gastrulation and by a decrease with the onset of organogenesis. To study the genetic control over protein synthesis at various developmental stages of loach and sea-urchin embryos the effects of ionizing radiation and long-term treatment with actinomycin D have been examined. X-Irradiation doses produce an insignificant direct effect on protein synthesis, while radiation damage of the nuclear apparatus results in a gradual but ever increasing inhibition of protein synthesis. The inhibition of RNA synthesis with actinomycin or ionizing radiation damage of the nuclei produce essentially the same effect on the intensity of protein synthesis. Protein synthesis in androgenetic haploid hybrid embryos (loach ♀ × goldfish ♂) and in loach androgenetic haploid embryos after producing a partial elimination of chromosomes does not differ from ‘enucleated’ loach embryos completely deprived of chromosomes. These data suggest that high-polymeric RNA formed after the elimination of some chromsomes is unable to provide a normal level of protein synthesis. Protein synthesis is not controlled by the nuclei up to the stages of early blastula (sea urchin) and of late blastula (loach), being evidently programmed in oogenesis. To provide a rapid activation of protein synthesis in the course of gastrulation in the loach the function of the nuclei has to be realized during mid-blastula stages. An increase of the rate of the incorporation of amino acids at the stages of mesenchyme blastula in the sea urchin depends on the synthesis of RNA at the early blastula. At the same time protein synthesis during gastrulation in the loach and at mesenchyme blastula in the sea urchin is much less dependent on the simultaneous RNA synthesis. Protein synthesis at these stages seems to be provided by the long-living templates and controlled by non-gene mechanisms of the regulation of translation. Thus early embryonic differentiation in the loach and sea-urchin development is related to the activation of protein synthesis. The latter is provided by the preceding morphogenetic nuclear function, which makes protein synthesis relatively independent of simultaneous synthesis of templates that ensures subsequent development stages.

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