A decimal code describing the developmental stages of head cabbage (Brassica oleracea var. capitata)

The developmental stages of head cabbage (Brassica oleracea var. capitata) as a vegetable have been characterised by a decimal code. Five primary stages are recognised: germination, emergence and establishment, leaf formation, head formation and maturity. Each primary stage is divided into secondary stages, which apply both to single plants and to crops. Maturity is defined as the head having obtained a marketable weight and density. The standing ability is defined as the number of days from 90% of the crop being marketable to 25% of the crop having become unmarketable.     

An alternative explanation for plant growth promotion by bacteria of the genus Azospirillum

Experiments were performed to identify the substances that are excreted by the soil bacterium Azospirillum brasilense Sp7 and that were reported to stimulate the formation of lateral roots and of root hairs of grasses. Azospirillum forms indole-3 acetic acid (IAA) but only in the late stationary growth phase or when tryptophan is present in the medium, but not in continuous cultures or in the logarithmic growth phase of batch cultures. Formation of IAA by Azospirillum requires aerobic conditions. Nitrite can replace IAA in several phytohormone assay, and is even more active than IAA in a test with wheat root segments in which the increase of wet weight is determined. Higher amounts of nitrite are necessary for activity in other classical auxin assays. Nitrite shows 40–60% of the activity of IAA in the straight-growth test of Avena coleoptiles and in the formation of C₂H₄ by pea epicotyl segments. Like IAA, nitrite is inactive in promoting C₂H₄ formation by ripe apple tissues. Since nitrite alone can hardly exert phytohormonal effects, it is postulated that nitrite reacts with a substance in the cells and that a product formed by this reaction functions as auxin. Such a substance could be ascorbate. Exogenously added ascorbate enhances the rate of nitrite-dependent C₂H₄ formation by pea epicotyl sections and the nitrite-dependent increase in the wet weight of wheat root segments. Nitrite is formed by nitrate respiration of Azospirillum. The findings that nitrite can have phytohormonal effects offers an alternative explanation of the promotion of the growth of roots and the enhancement of mineral uptake of grasses by Azospirillum. Indole-acetic acid completely and nitrite partly substitute for an inoculation with Azospirillum in an assay where the increase of the dry weight of intact wheat roots is determined after an incubation for 10 d. Nitrite and IAA are, therefore, possibly the only factors causing an enhancement of the growth of roots of grasses.Abbreviations HPLC high-performance liquid chromatography - IAA indole-3-acetic acid     

An explanation of the inhibition of root growth caused by indole-3-acetic Acid

Low concentrations of indole-3-acetic acid inhibit the growth of pea root sections by inducing the formation of the growth regulator, ethylene gas. Ethylene is produced within 15 to 30 minutes after indole-3-acetic acid is applied and roots begin to swell immediately after they are exposed to the gas. Carbon dioxide competitively inhibits ethylene action in roots, impedes their geotropic response, and partially reinstates auxin inhibited growth. It is concluded that ethylene participates in the geotropic response of roots, but not that of stems.     

An explanation for negligible senescence in animals

Negligible or negative senescence occurs when mortality risk is stable or decreases with age, and has been observed in some wild animals. Age‐independent mortality in animals may lead to an abnormally long maximum individual lifespans and be incompatible with evolutionary theories of senescence. The reason why there is no evidence of senescence in these animals has not been fully understood. Recovery rates are usually very low for wild animals with high dispersal ability and/or small body size (e.g., bats, rodents, and most birds). The only information concerning senescence for most of these species is the reported lifespan when individuals are last seen or caught. We deduced the probability density function of the reported lifespan based on the assumption that the real lifespan corresponding to Weibull or Gompertz distribution. We show that the magnitude of the increase in mortality risk is largely underestimated based on the reported lifespans with low recovery probability. The risk of mortality can aberrantly appear to have a negative correlation with age when it actually increases with increasing lifespan. We demonstrated that the underestimated aging rate for wild animals with low recovery probability can be generalizable to any aging models. Our work provides an explanation for the appearance of negligible senescence in many wild animals. Humans attempt to obtain insights from other creatures to better understand our own biology and its gain insight into how to enhance and extended human health. Our advice is to take a second glance before admiring the negligible senescence in other animals. This ability to escape from senescence is possibly only as beautiful illusion in animals.     

Hypothetical stages in the mutational evolution of the present-day genetic code from its RNY,comma-free ancestor

The primitive comma-free genetic code may have had 16 triplets of the form RNY, where R = purine, N = purine or pyrimidine, and Y = pyrimidine, specifying eight (present-day) amino acids. Calculations reveal that in this primitive code all transition changes (A?G, C?U) are either silent or missense i.e. result in the same or another one of these particular eight amino acids. There are no single transitions to non-RNY codons. Single transversions in the primitive codons can, individually, generate new (present-day) codons for four or eight amino acids. Present-day glutamine, tryptophan and stop (UGA, UAA, UAG) codons cannot be so derived., by single transversions, from any of the eight primitive codons. The modern initiation codons, AUG and GUG, can however be generated by both C → G and U → G single transversions in primitive codons. Overall, a total of 32 modern sense codons, not represented in the primitive RNY code, can be derived from this code by single transversions. Many modern codons, including all those not generated by single transversions in the primitive code, can also be produced by either of the two types of frameshift possible in runs of U- or C-rich primitive codons. Present-day stop codons are generated by +1 (-2) type frameshifts in U-rich primitive runs; AUG and GUG initiation codons are produced by the other type, +2 (-1), frameshifts in U-rich runs.     

Orthogenesis and progressive appearance of early-ontogenetic form relations in the adult stages during human evolution with a possible explanation for them

Summary The orthogenetic development of some characteristic features during the evolution of the Hominidae has been pointed out. Especially brain- and skull development have been dwelt on (see Fig. 1). A parallel has been drawn with the orthogenetic development of some characteristic features during the evolution of the Equidae. It appears that during human evolution early-ontogenetic features come more and more to the front whereas during the evolution of Horses these characters are more and more pushed back in ontogeny. By this, human evolution, at least as concerns the orthogenetically developing features which happen to be very characteristic of the organisation of Man, shows a generalising developmental tendency whereas that of Horses shows on the whole a specialising tendency.Some modes in which early-ontogenetic characters can be present in the adult stages are dealt with such asBolk's theory of retardation andSchindewolf's theory of proterogenesis which are considered not to differ very much in essentials. Also the principle of development along a roundabout way (Prinzip der umwegigen Entwicklung. ofNauck) is mentioned in this connection and some examples are given.A better understanding of orthogenetic evolution and of the differences existing between that of the Hominidae and that of the Equidae is found in the principle of heterochronic development, the change of developmental intensity and the rate of growth of features in the ontogenies of allied forms. This is illustrated by the two diagrams of Fig. 2. Here we also established connection with the science of genetics which can explain experimentally the heterochronous shifting of features in compared ontogenies by difference in rate of action and quantitative action value of genes or sets of genes.

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Zusammenfassung Es wird gezeigt wie die phylogenetische Entwicklung einiger charakteristischen Merkmale bei den Hominiden orthogenetisch verläuft. Vor allem werden Gehirn- und Schädelentwicklung (s. Fig. 1) in dieser Weise betrachtet. Vergleichenderweise wird die orthogenetische Entwicklung von einigen charakteristischen Merkmalen während der Phylogenie der Equidae besprochen. Es ergibt sich, dass während der menschlichen Evolution früh-ontogenetische Merkmale immer mehr in den Vordergrund treten während solche in der Phylogenie der Equiden immer mehr zurück treten in der Ontogenie. In dieser Weise zeigt sich die menschliche Evolution, wenigstens was den sich orthogenetisch entwickelnden Merkmalen anbelangt, welche gerade sehr charakteristisch für die Organisation des Menschen sind, eine verallgemeinerende Entwicklungstendenz, die der Equidae dagegen eine spezialisierende.Einige Möglichkeiten durch welche früh-ontogenetische Merkmale im erwachsenen Zustand auftreten können werden besprochen, so die Retardationstheorie vonBolk und die Proterogenesistheorie vonSchindewolf. Diese werden als nicht grundverschieden betrachtet. Auch das Prinzip der umwegigen Entwicklung vonNauck wird in diesem Zusammenhang genannt und einige Beispiele gegeben.Das Prinzip der heterochronischen Entwicklung, die Abänderung der Entwicklungsintensität und der Wachstumsgeschwindigkeit bei Merkmalen von verwandten Formen bietet uns einen besseren Begriff von der orthogenetischen Evolution und von dem oben angeführten Unterschied zwischen der menschlichen Phylogenie und der der Equidae. Dies wird näher ausgeführt und mit Beispielen belegt mit Hilfe der beiden Diagramme von Fig. 2. In dieser Weise wird auch eine Verbindung hergestellt mit der genetischen Wissenschaft, die in experimenteller Weise im Stande ist die heterochrone Verschiebung von Merkmalseigenschaften in vergleichbaren Ontogenesen durch Unterschiede in der Geschwindigkeit der Wirkung und in dem quantitativen Verwirklichungswert der Gene zu erklären.

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Résumé Il est démontré que le développement phylogénétique de certains caractères morphologiques chez les Hominides est orthogénétique. Principalement le développement du cerveau et du crâne (Fig. 1) est discuté dans cette connection. Comparativement le développement orthogénétique de certains caractères pendant la phylogénie des Equides est traité. Il résulte que pendant l'évolution humaine des caractères fetaux se misent progressivement en premier plan dans les ontogénèses pendant que ceux dans la phylogénie des Equides se misent de plus en plus en arrière-plan ontogénétiquement. Dans cette manière l'évolution humaine montre, aux moins relative aux caractères orthogénétiques, qui sont exactement très caractéristiques pour l'organisation de l'Homme, une tendence généralisante de développement, celle des Equides au contraire une tendence spécialisante.Quelques possibilités avec lesquelles des caractères fetaux peuvent paraître dans la phase adulte sont discutées comme la théorie de retardation deBolk et la théorie de développement proterogénétique deSchindewolf. Celles-ci sont regardées comme principalement pas différentes. Aussi le principe de développement selon un détour (Prinzip der umwegigen Entwicklung deNauck) est nommé dans cette connection et quelques exemples en sont donnés.Le principe du développement hétérochronique, le changement de l'intensité et de la vitesse du développement chez des caractères des formes alliés, nous donne un meilleur notion de l'évolution orthogénétique et de la différence, cité ci-dessus, entre la phylogénie humaine et celle des Equides. Ceci est démontré détaillé avec des exemples à l'aide des deux diagrammes de Fig. 2. Dans, cette façon une connection est mise avec la science génétique, qui peut expliquer expérimentalement le développement hétérochronique des caractères morphologiques dans des ontogénèses comparables par des différences dans la vitesse d'action et dans la réalisation quantitative des gènes.

     

An integrated,structure- and energy-based view of the genetic code

The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon–anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson–Crick pairs in the codon–anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon–anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids.     

An 11-space code for bacterial names

Citation of names of bacteria in records intended for storage and retrieval of information in computer files presents serious problems because of the variable lengths of the generic name and specific epithets. In this paper an eleven space alpha-numeric code is proposed for each valid species and subspecies, based on internationally approved documents, for use in computer filing.

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Un código de once espacios para nombres de bacterias

Resumen Las citas de nombres de bacterias en informaciones que han de ser almacenadas y utilizadas a través de un ordenador presentan serios problemas debido a la variación en longitud de su nombre genérico y al uso de espítetos específicos. Este trabajo propone la utilización de un código alfa-numérico de once espacios para cada especie y subespecie válida basado en regalamentaciones y documentos approbados internacionalmente que facilitaría la utilización de sistemas electrónicos de ficheros.

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Un code à onze espacements pour les noms de bactéries

Résumé La dénomination des bactéries pour conservation et récupération de l'information dans un ordinateur pose, à cause de la longueur variable du nom générique et des épithètes spécifiques, de sérieux problèmes. Dans cet article, il est proposé pour chaque espèce et sous-espèce valide un code alpha-numérique de onze espacements, basé sur des documents internationalement approuvés.

     

An information theory of the genetic code

An information theory of the genetic code is given, which deals with the process by which template codes (nucleotides or codons) choose substrate codes (nucleotides or anti-codons) in accordance with the base-pairing rules in the chain elongation phase of polynucleotide or polypeptide synthesis. A definite period of recognition time (τ) required for a template code to discriminate a substrate code is proposed, and an experimental method for determining the time is suggested. A substrate word is defined to be the sequence of substrate codes which have appeared at a recognition site in turn before a substrate code complementary to a template code first appears, and the mean length of substrate words (F) is derived from the mole fractions of template codes and substrate codes. The chain elongation rate is greatest when the mole fractions of template codes is proportional to the square of those of substrate codes to minimize the mean recognition time per word (Fτ). The uncertainty of a template (G) and the uncertainty of a medium (M) respectively are derived from the minimum of the function F. The amount of genetic information contained in a template is measured by the function G. The unit of the amount of genetic information is termed “cit”. The function M, the ratio of the number of all binary collisions to the number of homogeneous binary collisions in a mixture of different molecules, may be the new other “entropy” which represents informational properties of the mixture not represented by thermodynamic entropy of mixing. Both functions (G and M) have maxima when all random variables are equal and they are multiplicative in nature in contrast to entropy which is additive. The multiplicativity of the function G may contribute to the enormous informational capacity of genes.     

An axiomatic explanation of complete self-reproduction

A similarity between the concepts of reproduction and explanation is observed which implies a similarity between the less well understood concepts of complete self-reproduction and complete self-explanation. These latter concepts are shown to be independent from ordinary logical-mathematical-biological reasoning, and a special form of complete self-reproduction is shown to be axiomatizable. Involved is the question whether there exists a function that belongs to its own domain or range. Previously, Wittgenstein has argued, on intuitive grounds, that no function can be its own argument. Similarly, Rosen has argued that a paradox is implied by the notion of a function which is a member of its own range. Our result shows that such functions indeed are independent from ordinary logical-mathematical reasoning, but that they need not imply any inconsistencies. Instead such functions can be axiomatized, and in this sense they really do exist. Finally, the introduced notion of complete self-reproduction is compared with “self-reproduction” of ordinary biological language. It is pointed out that complete self-reproduction is primarily of interest in connection with formal theories of evolution.     

An alternative explanation for global trends in thermal tolerance

Ectotherms from higher latitudes can generally perform over broader temperature ranges than tropical ectotherms. This pattern is thought to reflect trends in temperature variability: tropical ectotherms evolve to be ‘thermal specialists’ because their environment is thermally stable. However, the tropics are also hotter, and most physiological rates increase exponentially with temperature. Using a dataset spanning diverse ectotherms, we show that the temperature ranges ectotherms tolerate (the difference between lower and upper critical temperatures, and between optimum and upper critical temperatures) generally represents the same range of equivalent biological rates (e.g. metabolism) for cool‐ and warm‐adapted species, and independent of latitude or elevation. This suggests that geographical trends in temperature variability may not be the ultimate mechanism underlying latitudinal and elevational trends in thermal tolerance. Rather, we propose that tropical ectotherms can perform over a narrower range of temperatures than species from higher latitudes because the tropics are hotter.     

不同生育期降低光强对烟草生长发育和品质的影响

2004-2005年在烤烟生长发育的不同时期进行遮荫降低光照强度的盆栽试验,研究了不同生育期降低光强对烤烟生长发育和品质的影响.结果表明:遮荫条件下烟株干物质积累下降,叶片组织变薄,色素含量升高,落黄成熟时间延长;转化酶活性降低,但遮荫解除后又开始升高;叶片烤后烟叶含梗率增加,叶片厚度和比叶质量降低,烟碱、总氮、钾和氯含量增加,总糖和还原糖含量降低,中性致香成分含量增加.不同时期遮荫的影响为成熟期＞旺长期＞伸根期＞对照.