The animal origin of SARS-CoV

The first case of severe acute respiratory syndrome(SARS)in Guangdong province was reported on2Jan2003,whileretrospective survey has datedthe first index case on16Nov2002.In months that followed,pandemic of SARS widelyspread over the world until July2003,infecting8454people and claiming908deathsin39countries andregions global-ly.On16Dec2003,a32years old photographerlivinginsuburban Guangzhou presented withsymptoms of SARSinfec-tion.There were3other ensuing cases betweenthe end of2003and…     

Eogenesis — The origin of animal forms

Zusammenfassung Alle Formen von Leben entstanden aus der primitiven Zelle, betrachtet eher als eine Art denn als ein Individuum, welches die Fähigkeit für ununterbrochene Selbst-Teilung besass. Fortgesetzte Vermehrung der Zellen mag eins von drei verschiedenen Verfahren folgen: 1. Die zwei Zellen von jeder Teilung hervorgehend, mögen sich vollständig von einander trennen; diese Linie der Entwicklung der primitiven Zelle rief die Protozoa hervor. 2. Während die Zellen sich teilen, mögen sie mehr oder weniger unregelmässig zusammen hängen. Diese Linie rief die Porifera (Schwämme) hervor. 3. Die sich teilenden Zellen mögen regelmässig zusammenhängen, eine Blastula und eine Gastrula bildend. Die Gastrula ist fähig eine unbestimmte Anzahl von Variationen hervorzubringen, und durch diese Variationen in der Gastrula entstanden alle Tier-Typen ausser der Protozoa und der Porifera.Diese Linien der Entwicklung von der einzelnen Zelle stellen alle die physischen und geometrischen entfaltungsfähigen Möglichkeiten, denkbar im Falle von Zellen, dar, die die Kraft besitzen sich durch Selbst-Teilung zu vermehren. Da diese entfaltungsfähigen Linien einfach mechanische Antworten auf die geometrischen und physischen Eigentümlichkeiten sind, eigen der Vermehrung der sich selbst teilenden Zellen, so gibt es keine Rechtfertigung für die Annahme einer bestimmten Ordnung in ihrem Vorkommen. Es ist logischer anzunehmen, dass die primitive Zelle gleich nach ihrem Erscheinen sich nach jeder möglichen Richtung gleichzeitig entwickelte, kurz, dass alle die Haupttypen des Tierlebens gleichzeitig erschienen.Es gibt keinen Beweis gegen diese Annahme, welche in Übereinstimmung mit dem geologischen Hintergrund des Lebens ist, wie wir es verstehen; mit der Fossilien-Urkunde, wie illustriert durch Fossilien von genau vergleichbaren Umgebungen; und mit der angenommenen Nötigkeit für ein System von Kontrolle und Ausgleich zwischen den verschiedenen Typen von Leben.

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Résumé Toutes les formes de la vie proviennent d'une cellule primitive unique, considérée comme espèce plutôt que comme individu, possédant le pouvoir de se multiplier par bi-partition répétée. La propagation continue de cellules peut avoir lieu de trois façons différentes: 1. Les deux cellules, après la division, peuvent se séparer complètement l'une de l'autre; cette forme de propagation de la cellule primitive a donné lieu aux Protozoaires. 2. Les cellules, en se divisant, peuvent rester liées plus ou moins irrégulièrement; cette forme de propagation caractérise les Porifères (spongiées). 3. Les cellules, en se divisant, peuvent rester liées selon un arrangement régulier, en formant une blastula et une gastrula; la gastrula peut être formée selon un infinité de modalités, et c'est à ces différences de la formation de la gastrula que sont dues toutes les espèces animales exceptés les Protozoaires et les spongiées.Ces formes de propagation de la cellule unique représentent la somme des possibilités d'arrangement permises par les lois de la géométrie et de la physique. Du moment que ces procédés de propagation sont soumis à un arrangement mécanique gouverné par des lois physiques et géométriques, il n'y a pas lieu d'admettre qu'il y ait, dans leur succession, d'ordre déterminé. Il est plus logique de supposer qu'aussitôt parue la cellule primitive se soit propager simutanément dans toutes les directions concevables, en d'autres mots que toutes les phyla animales se soient différenciées au même moment.Aucune preuve ne démont cette hypothèse qui, d'ailleurs, concorde avec les prémises géologiques de la vie telles que nous les comprenons, avec les vestiges fossilisés de couches géologiques strictément comparable, et avec la théorie qui admet l'établissement de l'équilibre entre les différentes espèces animales au moyen d'un contrôle et de limitations mutuelles.

     

The origin of recent introns: transposons?

The long-standing question of how genes acquire introns has provoked much debate. A recent study makes considerable progress by identifying numerous recently gained introns in nematodes - although it remains difficult to distinguish definitively between models of intron gain.     

Biochemical characteristics and fermentation of glucose and starch by rabbit cæcal strains ofBifidobacterium globosum

Two strains ofBifidobacterium globosum were isolated from cæcal contents of rabbits in a search for potential probiotics. Both strains fermented glucose, galactose, pentoses, maltose, raffinose and starch. Common coccidiostats (monensin, salinomycin) and antimicrobial growth promotors (avoparcin, bacitracin, nitrovin, virginiamycin) supplied at 10 mg/L inhibited their growth in cultures with glucose. Fermentation parameters of bifidobacteria on glucose and starch. When growing on starch, the two strains of bifidobacteria produced 1 mol lactate per 5.6 and 5.7 mol acetate, respectively. Corresponding values during growth on glucose were 17.3 and 8.4 mol of acetate per mol of lactate. Starch-grown cells accumulated more saccharides than cells grown on glucose (1.48vs. 0.41 and 3.12vs. 1.18 mmol glucose units per 1 g of dry matter, respectively).     

The origin of the Hominidae: Africa or Asia?

The authors review the evidence for the evolution of the apes and their geographical expansion out of Africa during the Miocene. The ecological background is discussed at each period.From this it is concluded that Dryopithecines in either Africa or Eurasia could have given rise to early Hominidae and that the ecological conditions in both continents were suitable for the appearance of Hominid adaptations.The evidence for early Hominids is at present more impressive in Eurasia than in Africa, though the African find from Fort Ternan, Kenya, is the earliest. On present evidence, neither continent can be precluded as the place of origin of the Hominidae and it appears to be a possibility that Hominidae evolved in both continents with intermittent gene exchange.     

The origin of adaptive mutants: Random or nonrandom?

Several recent reports have claimed that adaptive mutants in bacteria and yeast are induced by selective conditions. The results of these reports suggest that mutants can arise nonrandomly with respect to fitness, contrary to what has been widely accepted. In several cases that have received careful experimental reexamination, however, the detection of seemingly nonrandom mutation has been explained as an experimental artifact. In the remaining cases, there is no evidence to suggest that cells have the capacity to direct or choose which genetic variants will arise. Instead, current models propose processes by which genetic variants persist as mutations only if they enable cell growth and DNA replication. Most of these models are apparently contradicted by experimental data. One model, the hypermutable state model, has recently received limited circumstantial support. However, in this model the origin of adaptive mutants is random; the apparent nonrandomness of mutation is merely a consequence of natural selection. The critical distinction between the origin of genetic variation (mutation) and the possible consequence of that variation (selection) has been neglected by proponents of directed mutation.     

The origin of Darwin’s “abominable mystery”

The phrase “Darwin’s abominable mystery” is frequently used with reference to a range of outstanding questions about the evolution of the plant group today known as the angiosperms. Here, I seek to more fully understand what prompted Darwin to coin the phrase in 1879, and the meaning he attached to it, by surveying the systematics, paleobotanical records, and phylogenetic hypotheses of his time. In the light of this historical research, I argue that Darwin was referring to the origin only of a subset of what are today called angiosperms: a (now obsolete) group equivalent to the “dicotyledons” of the Hooker and Bentham system. To Darwin and his contemporaries, the dicotyledons’ fossil record began abruptly and with great diversity in the Cretaceous, whereas the gymnosperms and monocotyledons were thought to have fossil records dating back to the Carboniferous or beyond. Based on their morphology, the dicotyledons were widely seen by botanists in Darwin’s time (unlike today) as more similar to the gymnosperms than to the monocotyledons. Thus, morphology seemed to point to gymnosperm progenitors of dicotyledons, but this hypothesis made the monocotyledons, given their (at the time) apparently longer fossil record, difficult to place. Darwin had friendly disagreements about the mystery of the dicotyledons’ abrupt appearance in the fossil record with others who thought that their evolution must have been more rapid than his own gradualism would allow. But the mystery may have been made “abominable” to him because it was seen by some contemporary paleobotanists, most notably William Carruthers, the Keeper of Botany at the British Museum, as evidence for divine intervention in the history of life. Subsequent developments in plant systematics and paleobotany after 1879 meant that Darwin’s letter was widely understood to be referring to the abrupt appearance of all angiosperms when it was published in 1903, a meaning that has been attached to it ever since.     

The six editions of the ‘origin of species’ A comparative study

Comparison of the six editions of the Origin of Species reveals a definite change in Darwin's propounded theory.Although the tone of the statements seems to become more positive in later editions, the change of thought indicates a certain inability of the original theory to stand up to criticism.Up to the 5th edition, the alterations are mostly supportive to the theory of accumulation of modifications by natural selection, but in the last two editions non-selective forces come into play. Darwin himself was unwilling to admit a great structural change in his theory and although all the factors had been presented in earlier editions the importance of their role had so shifted by the 6th edition that it is difficult not to conclude that the basic axioms of the theory had changed.     

The origin of RNA interference: Adaptive or neutral evolution?

The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.

Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.     

The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009 ; Meyer 2011 ; Nosil 2012 ). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009 ), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009 ), or pollinator‐mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012 ), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011 ). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006 ), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011 ). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. ( 2014 ) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early‐stage divergence in Midas cichlids.     

The induction of autophagy in isolated insect fat body by β-ecdysone

The fat body in Calpodes undergoes sequential organelle specific autophagy as a first step in the cell remodeling process necessary for metamorphosis to the pupa. This autophagy begins at about 36 hr before pupation and coincides with a critical period after which an isolated abdomen will pupate without further influence from the prothoracic glands. This suggested that autophagy might be induced by ecdysone. Fat body taken before the critical period and cultured in a medium containing β-ecdysone undergoes autophagy. Fat body from the same animal maintained in hormone-free medium retains the pre-critical period morphology with no autophagy. Autophagy is therefore directly induced by β-ecdysone. Fat body taken soon after the critical period continues with the autophagic sequence in hormone-free medium. Therefore the entire autophagic sequence is induced and does not require the continuing presence of hormone. Protein storage granule formation and cell dissociation, which occur in fat body at metamorphosis, are also induced by β-ecdysone.