Hommes et environnements au Paléolithique supérieur en Ukraine continentale et en Crimée : introduction

Research, conducted under the ANR project “Mammouths”, on “the end of the mammoth steppe: Man/Environment relationship during late Pleniglacial in Eastern Europe”, is the subject of several contributions, a part of them is published in this volume, under the heading “Humans and environments during Upper Paleolithic in mainland Ukraine and Crimea”, in the French journal L’anthropologie.     

“Protoisochores” in certain archaeal species are formed by replication-associated mutational pressure

This report shows that isochore-like structures can be found not only in warm-blooded animals, some reptiles, fishes and yeast, but also in certain archaeal species. In perfectly shaped isochore-like structures (in “protoisochores”) from Sulfolobus acidocaldarius and Thermofilum pendens genomes the difference in 3GC levels between genes from different “protoisochores” is about 30%. In these archaeal species GC-poor “protoisochores” are situated near the origin of replication, while GC-rich “protoisochores” are situated near the terminus of replication. There is a strong linear dependence between position of a gene and its 3GC level in S. acidocaldarius (an average difference in 3GC per 100?000 base pairs is equal to 3.6%). Detailed analyses of nucleotide usage biases in genes from leading and lagging strands led us to the suggestion that 3GC in genes situated near terminus of replication grows due to higher rates of thymine oxidation producing T to C transitions in lagging strands.     

Romancing The Celluloid Nature: A Review of American Zoo Exhibits, Part I

Zoos have gone through metamorphosis in recent decades, largely in response to the changing tide of the society. The central theme for the modern zoo is Conservation. Zoo exhibitry has been evolving accordingly toward a more “naturalistic” trend, symbolized by the landscape immersion method. This approach, however, has a built-in dilemma since nature cannot be duplicated in captivity. Animals are often concealed from the visiting public, generating complaints. At its core, currently common exhibit schemes are anthropomorphic as well as anthropocentric. Animals’ sensory faculties are ignored during the design process. In terms of taxonomy, distributions of the species in zoo collections are biased toward large mammals, and as resources are allocated toward species with public appeal, often left behind are smaller species of mammals and birds and lower vertebrates. There exists a need to turn a critical eye on today's zoo exhibits from all aspects.     

Configural processing of different topologically structured figures: an ERP Study

According to Chen’s theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without “holes”. An ERP experiment was conducted utilizing a passive paradigm to investigate the differences in perceiving figures with “hole” and with “no-hole”. The results showed differences in N170 components between figures with “holes” and with “no-holes”. The inversion of the “hole” could influence the latency of N170, but the inversion of the “no-hole” could not, which indicated that global features are processed first in the “hole” perception whilst local features are given priority to the “no-hole” perception. This result was similar to studies concerning face and non-face objects, suggesting a configural processing of the “hole”.     

The behavior of the domestic dog (Canis familiaris) during separation from and reunion with the owner: A questionnaire and an experimental study

We have constructed a questionnaire to investigate the separation behavior in a sample of family dogs (Canis familiaris) (N = 45) and in parallel we have observed dogs’ separation-related behavior in a simple behavioral test (Separation and greeting test, S&G). We recorded the dogs’ behavior during the separation from and reunion (greeting) with the owner. We investigated whether owners’ report about their dogs’ separation behavior reflected the separation behavior under controlled testing conditions. Furthermore, we wanted to find out whether the duration of separation affected the behavior of dogs and whether there was some relationship between separation and greeting behavior.Dogs that were rated by their owner to be more “anxious” during separation and “happier” at reunion, showed more activity and stress-related behavior during separation, and more affection toward the owner during greeting. Dogs with owner-reported separation-related disorder (SRD) showed more stress-related behavior, they spent less time near the owner's chair during separation, and were more active during greeting than dogs without SRD. The two groups of dogs did not differ in affectionate behavior shown toward the owner. Non-affected dogs’ activity decreased with increasing separation duration, but dogs with SRD did not show this change in their separation behavior.Our results show that owners’ have a realistic view on their dogs’ separation behavior. In addition, dogs with SRD may not be “hyper-attached” to their owners because they do not show more affection during greeting. Moreover, dogs with SRD do not show preference for the owners’ objects left behind and they cannot be easily calmed by the returning owner.Our questionnaire and the Separation and greeting test could be used for screening dogs with suspected separation-related behavior problems.     

Improvement of yield of Pleurotus eryngii var. eryngii by substrate supplementation and use of a casing overlay

Improved yield and biological efficiency (BE) of Pleurotus eryngii var. eryngii were achieved by supplementation of substrate with a commercial delayed-release nutrient and use of a casing overlay. Yield increases of 14% were achieved from cased substrates that were supplemented at time of casing with delayed-release nutrient (Remo’s). Use of a casing layer enhanced yield by 141% over non-cased substrates. When casing and substrate supplementation were combined, yield increased 179% over non-cased/non-supplemented substrates. Mushrooms harvested from cased substrates were darker in color and solids contents were lower compared to non-cased substrates. An additional break of mushrooms was harvested from non-cased “spent” substrate by fragmenting and re-supplementing the substrate prior to the application of a casing overlay. Three production methods were compared for their effect on mushroom yield: “standard”, “casing” and “casing after first break”. Casing of the substrate before first break (“casing” production method) resulted in the highest yield and biological efficiency.     

Tug-of-war model for the two-bandit problem: Nonlocally-correlated parallel exploration via resource conservation

We propose a model - the “tug-of-war (TOW) model” - to conduct unique parallel searches using many nonlocally-correlated search agents. The model is based on the property of a single-celled amoeba, the true slime mold Physarum, which maintains a constant intracellular resource volume while collecting environmental information by concurrently expanding and shrinking its branches. The conservation law entails a “nonlocal correlation” among the branches, i.e., volume increment in one branch is immediately compensated by volume decrement(s) in the other branch(es). This nonlocal correlation was shown to be useful for decision making in the case of a dilemma. The multi-armed bandit problem is to determine the optimal strategy for maximizing the total reward sum with incompatible demands, by either exploiting the rewards obtained using the already collected information or exploring new information for acquiring higher payoffs involving risks. Our model can efficiently manage the “exploration-exploitation dilemma” and exhibits good performances. The average accuracy rate of our model is higher than those of well-known algorithms such as the modified ?-greedy algorithm and modified softmax algorithm, especially, for solving relatively difficult problems. Moreover, our model flexibly adapts to changing environments, a property essential for living organisms surviving in uncertain environments.     

The state transition mechanism—simply depending on light-on and -off in Spirulina platensis

The state transition in cyanobacteria is a long-discussed topic of how the photosynthetic machine regulates the excitation energy distribution in balance between the two photosystems. In the current work, whether the state transition is realized by “mobile phycobilisome (PBS)” or “energy spillover” has been clearly answered by monitoring the spectral responses of the intact cells of the cyanobacterium Spirulina platensis. Firstly, light-induced state transition depends completely on a movement of PBSs toward PSI or PSII while the redox-induced one on not only the “mobile PBS” but also an “energy spillover”. Secondly, the “energy spillover” is triggered by dissociation of PSI trimers into the monomers which specially occurs under a case from light to dark, while the PSI monomers will re-aggregate into the trimers under a case from dark to light, i.e., the PSI oligomerization is reversibly regulated by light switch on and off. Thirdly, PSI oligomerization is regulated by the local H⁺ concentration on the cytosol side of the thylakoid membranes, which in turn is regulated by light switch on and off. Fourthly, PSI oligomerization change is the only mechanism for the “energy spillover”. Thus, it can be concluded that the “mobile PBS” is a common rule for light-induced state transition while the “energy spillover” is only a special case when dark condition is involved.     

Peach fruit ripening: A proteomic comparative analysis of the mesocarp of two cultivars with different flesh firmness at two ripening stages

A proteomic analysis was conducted on peach fruit mesocarp in order to better elucidate the biochemical and physiological events which characterize the transition of fruit from the “unripe” to the “ripe” phase.The first goal of the present work was to set-up a protocol suitable for improving protein extraction from peach mesocarp. The use of freeze-dried powdered tissue, together with the addition of phenol prior to the extraction with an aqueous buffer, significantly increased the protein yield and the quality of 2-DE gels. The proteomic profiles of the mesocarp from peach fruit of a non-melting flesh (NMF; ‘Oro A’) and a melting flesh (MF; ‘Bolero’) cultivar, at “unripe” and “ripe” stages as defined by some parameters typical of ripening, were then analyzed.The comparative analysis of the 2-DE gels showed that in NMF and MF peaches the relative volumes of 53 protein spots significantly changed in relation to both the ripening stage (“unripe” versus “ripe”) and/or the genetic background of the cultivar (‘Oro A’ versus ‘Bolero’).Thirty out of the 53 differently abundant spots were identified by LC-ESI-MS/MS. The analysis revealed enzymes involved in primary metabolism (e.g. C-compounds, carbohydrates, organic acids and amino acids) and in ethylene biosynthesis as well as proteins involved in secondary metabolism and responses to stress.Among these, 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) appeared to be one of the proteins with the largest change in relative abundance during the fruit transition from the pre-climacteric (“unripe”) to the climacteric (“ripe”) phase. Other proteins, such as S-adenosylmethionine synthetase and β-cyanoalanine synthase involved in ethylene metabolism, were also identified. Moreover, the changes in the relative abundances of a sucrose synthase and an α-amylase suggested differences between the two cultivars in the carbohydrate import activity of ripe fruit. The different accumulation of a few typical ROS-scavenger enzymes suggested that a higher oxidative stress occurred in MF with respect to NMF fruit. This result, together with data concerning the levels of total proteins and free amino acids and those regarding proteins involved in the maintenance of tissue integrity, was consistent with the hypothesis that the last phase of ripening in MF fruit is characterized by the appearance of a senescence status.The present study appears to define well some of the biochemical and physiological events that characterize the ripening of peach and, at the same time, provides interesting indications that could be employed in future marker assisted selection (MAS) programmes aimed to obtain MF fruits with higher ability to preserve tissue functionality maintaining for a longer time their organoleptic characteristics.     

Fish otoliths from the Priabonian (Late Eocene) of North Italy and South-East France - Their paleobiogeographical significance

The study of the Late Eocene (Priabonian) otolith associations from Possagno, North-East Italy, and from the Synclinal d’Allons in Haute Provence, South-East France, allows for the reconstruction of a teleost fauna of 55 taxa, which is the most diversified assemblage presently known from the Upper Eocene Paleo-Mediterranean basin. Thirty-six taxa are identified at the species level, and five of those are new: “genus Alepocephalidarum” astrictus, “genus Lophiiformorum” canovae, “genus Agonidarum” sudans, “genus Uranoscopidarum” cochlearis and Aseraggodes laganum. In the Synclinal d’Allons, the otolith associations reflect a tropical to subtropical neritic environment with a few mesopelagic fishes. At Possagno, the associations indicate an environment that changed from one that was deep and exposed to the pelagic realm and then evolved to a more shallow sea with a well-diversified benthic life and less mesopelagic fishes. A paleobiogeographical analysis of all known data on Priabonian otoliths, worldwide, shows clearly a western Atlantic (Louisiana) and an eastern Atlantic-Paleomediterranean association. In the eastern Atlantic-Paleomediterranean association, the Aquitaine association not only differs from the Possagno-Allons association in function of its more distant geographical position, but also by its stronger oceanic character in the southern part of the basin, and by the occurrence in the north, of a very shallow water facies (Saint-Estephe Formation) that contains some taxa which are known nowhere else in the Priabonian. The Ukraine fauna is characterized by a high number of species, which have an Oligocene record in other European sites. The northern geographic location of Ukraine, combined with the good connections to both the North Sea Basin and the Turgai street can provide the explanation. Many Oligocene species (or their close relatives) probably already existed at Eocene times in more northern regions, but could penetrate only in more southern European seas since the strong cooling at the beginning of the Oligocene.     

Survivor's dilemma: Defend the group or flee?

We consider a survival game of gregarious individuals, in which the aim of the players is survival to reproductive age under predator attacks. The survivor’s dilemma (shortly: SVD) game consists in the following: a group member either surely survives alone by fleeing, while its defensive mate may be killed; or tries to save its mate’s life, risking to get killed. The dilemma is that, in every single attack, fleeing ensures maximal survival probability, but if its mate survives by fighting both, and they remain together, its risk to be killed at the next attack will be lower. We show that, if defense is successful enough, then the one-attack game is a prisoner’s dilemma (PD), where fleeing is the strict ESS. We have additively decomposed the SVD game, according to the survival of the group mate of the focal prey, into two games: the aim of the “collective game” is survival of the group of prey. Counter-wise, the aim of the “hostile game” is survival alone (focal prey survives and its mate is killed by the predator). We obtain the following results: if the attack number is large enough, the multi-attack SVD game is dominated by the “collective game” in the sense that each individual can ensure its own maximal survival probability by maximizing the group survival probability in each attack. In the hostile game, the only strict ESS is the fleeing strategy. In the collective game there are two different cases: either defense is a unique strict ESS, or the collective game is bistable, i.e. fleeing and defense are local strict ESS’s. If defense is the only strict ESS in the collective game, and the attack number is large enough, defense replaces fleeing strategy in the multi-attack SVD game. However, in the bistable case, defense cannot invade into the fleeing population. It is shown that, if the interaction between relatives is frequent enough, than defense can replace fleeing strategy, in spite of the fact that in the well-mixed population the collective game is bistable.     

Darwin's apes and “savages”

Since his visit to Tierra del Fuego in the 1830s, Darwin had been fascinated by the “savages” that succeeded in surviving on such a “broken beach”, and because they were certainly similar in behaviour to our ancestors. However, he was also fascinated by baboons’ behaviour, according to Brehm's accounts: hamadryas baboons showed a strong altruism to the point of risking their own lives in order to save their infants from attack by dogs. In 1871, he mentions he would rather have descended from brave baboons than from “savages”, considered egoistic. We study the two sources of these ideas and try to show how Darwin's comparative reflections on apes and “savages” made him the first evolutionist anthropologist.     

Characterization and polymorphism of Keratin Associated Protein 1.4 gene in goats

Keratin-associated proteins (KAPs) are among the main structural components of the animal fibers and form semi-rigid matrix wherein the keratin intermediate filaments (KIFs) are embedded. Variation in the KAP genes has been reported to affect the structure of KAPs and hence fiber characteristics. As no information is available on this gene in Capra hircus therefore, present work was undertaken to characterize and explore the different polymorphic variants of KAP1.4 gene at DNA level in different breeds/genetic groups of goats of Kashmir. Cashmere (Changthangi, 30 animals) and non-Cashmere (Bakerwal and Kargil goats, 20 animals each) goats formed the experimental animals for the study. Single strand conformation polymorphism technique was employed for exploring variability at gene level. On exploring the size variability in KAP1.4 gene between Ovine and Caprine, it was concluded that sheep KAP1.4 gene has a deletion of 30 nucleotides. In comparison to published nucleotide sequences of sheep, goat sequences explored are differing at positions 174, 462 and 568 and at these positions “G”, “T” and “T” nucleotides are present in sheep, but are replaced by “A”, “C” and “C” respectively, in goats. By SSC studies, two genotypes were observed in each genetic group and in Bakerwal goats the genotypes were designated as A1A1 (0.40) and A1A2 (0.60) and were formed by two alleles A1 (0.70) andA2 (0.30). The different SSC patterns observed in Kargil goats were designated as B1B1 (0.35) and B1B2 (0.65) genotypes with frequencies of B1 and B2 alleles as 0.675 and 0.325, respectively. Similarly, two genotypes C1C1 (0.60) and C1C2 (0.40) were observed in Changthangi goats and the frequencies of C1 and C2 alleles were 0.80 and 0.20, respectively. These alleles were later confirmed by sequencing. The sequences of these alleles are available in NCBI under Acc. No's. JN012101.1, JN012102.1, JN000317.1, JN000318.1, JQ436929 and JQ627657. It was concluded that all the alleles observed in a breed were unique to the breed. The designated A1 and A2 alleles of Bakerwal goats differ from each other at positions 245 and the nucleotides observed were “C” or “A” and at position 605 of the nucleotide sequence “T” or “C”, were observed. The designated B1 and B2 alleles of Kargil goats differed from each other at positions 224, 374, 375 and 521. The nucleotides observed in two SSC pattern were C→G, A→G, G→A and T→C, respectively. The designated C1 and C2 alleles of Changthangi goats differed from each other at one position 440 with the change of “A”→“C”.     

Anglesites gen. nov. (Ammonoidea, Ancyloceratina), un nouveau genre d’ammonites hétéromorphes du Barrémien supérieur du Sud-Est de la France

The revision of the Crioceras puzosianum d’Orbigny, 1842 made during the revision of the Paléontologie Française of d’Orbigny, shows that this taxon belongs to a new genus: Anglesites gen. nov. This new genus, from upper Barremian age, is monospecific for the moment and is homeomorphic to the Leptoceratoides from the Lower Barremian. It is temporarily included in the subfamily of the Leptoceratoidinae. A neotype for the “Crioceras” puzosianum d’Orbigny, 1842 is herein designated.     

Epigenomic communication systems in humans and honey bees: From molecules to behavior

A 2010 Nature editorial entitled “Time for the Epigenome” trumpets the appearance of the International Human Epigenome Consortium and likens it to Biology's equivalent of the Large Hadron Collider. It strongly endorses the viewpoint that selective modifications of “marks” on DNA and histones constitute the crucial codes of life, a proposition which is hotly contested (Ptashne et al., in 2010). This proposition reflects the current mindset that DNA and histone modifications are the prime movers in gene regulation during evolution. This claim is perplexing, since the well characterized organisms, Drosophila melanogaster and Caenorhabditis elegans, lack methylated DNA “marks” and the DNA methytransferase enzymology. Despite their complete absence, D. melanogaster nevertheless has extensive gene regulatory networks which drive sophisticated development, gastrulation, migration of germ cells and yield a nervous system with significant neural attributes. In stark contrast, the honey bee Apis mellifera deploys its human-type DNA methyltransferase enzymology to “mark” its DNA and it too has sophisticated development. What roles therefore is DNA methylation playing in different animals? The honey bee brings a fresh perspective to this question. Its combinatorial chemistry of pheromones, tergal and cuticular exudates provide an exquisite communication system between thousands of individuals. The development of queen and worker is strictly controlled by differential feeding of royal jelly and their adult behaviors are accompanied by epigenomic changes. Their interfaces with different “environments” are extensive, allowing an evaluation of the roles of epigenomes in behavior in a natural environment, in the space of a few weeks, and at requisite levels of experimental rigor.