Genealogy of wine grape cultivars: "Pinot" is related to "Syrah"

Since the domestication of wild grapes ca 6000 years ago, numerous cultivars have been generated by spontaneous or deliberate crosses, and up to 10 000 are still in existence today. Just as in human paternity analysis, DNA typing can reveal unexpected parentage of grape cultivars. In this study, we have analysed 89 grape cultivars with 60 microsatellite markers in order to accurately calculate the identity-by-descent (IBD) and relatedness (r) coefficients among six putatively related cultivars from France ("Pinot", "Syrah" and "Dureza") and northern Italy ("Teroldego", "Lagrein" and "Marzemino"). Using a recently developed likelihood-based approach to analyse kinship in grapes, we provide the first evidence of a genetic link between grapes across the Alps: "Dureza" and "Teroldego" turn out to be full-siblings (FS). For the first time in grapevine genetics we were able to detect FS without knowing one of the parents and identify unexpected second-degree relatives. We reconstructed the most likely pedigree that revealed a third-degree relationship between the worldwide-cultivated "Pinot" from Burgundy and "Syrah" from the Rhone Valley. Our finding was totally unsuspected by classical ampelography and it challenges the commonly assumed independent origins of these grape cultivars. Our results and this new approach in grape genetics will (a) help grape breeders to avoid choosing closely related varieties for new crosses, (b) provide pedigrees of cultivars in order to detect inheritance of disease-resistance genes and (c) open the way for future discoveries of first- and second-degree relationships between grape cultivars in order to better understand viticultural migrations.     

Refined crystal structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin

"Aged" organophosphoryl conjugates of serine hydrolases differ from the corresponding "non-aged" conjugates in their striking resistance to nucleophilic reactivation. The refined X-ray structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin were compared in order to understand the molecular basis for this resistance of "aged" conjugates. "Aged" and "non-aged" crystalline organophosphoryl-gamma-chymotrypsin conjugates were obtained by prolonged soaking of native gamma-chymotrypsin crystals with appropriate organophosphates. Thus, a representative "non-aged" conjugate, diethylphosphoryl-gamma-chymotrypsin, was obtained by soaking native crystals with paraoxon (diethyl-p-nitrophenyl phosphate), and a closely related "aged" conjugate, monoisopropyl-gamma-chymotrypsin, was obtained by soaking with diisopropylphosphorofluoridate. In both crystalline conjugates, the refined structures clearly reveal a high occupancy of the active site by the appropriate organophosphoryl moiety within covalent bonding distance of Ser195 O gamma. Whereas in the "non-aged" conjugate both ethyl groups can be visualized clearly, in the putative "aged" conjugate, as expected, only one isopropyl group is present. There is virtually no difference between the "aged" and "non-aged" conjugates either with respect to the conformation of the polypeptide backbone as a whole or with respect to the positioning of the side-chains within the active site. In the "aged" conjugate, however, close proximity (2.6 A) of the negatively charged phosphate oxygen atom of the dealkylated organophosphoryl group to His57 N epsilon 2 indicates the presence of a salt bridge between these two moieties. In contrast, in the "non-aged" conjugate the DEP moiety retains its two alkyl groups; thus, lacking a negative oxygen atom, it does not enter into such a charge-charge interaction and its nearest oxygen atom is 3.6 A away from His57 N epsilon 2. It is suggested that steric constraints imposed by the salt bridge in the "aged" conjugate lie at the basis of its resistance to reactivation.     

UPGMA树的不惟一性问题及其解决方法

对于一组给定的DNA或蛋白质序列,UPGMA算法构建的二叉进化树可能是不惟一的,其具体拓扑结构与序列输入顺序相关,这一现象通常被称为"tied trees"。提出了UPGMA的一种改进算法——不加权算术平均组群方法(UMGMA),用以解决UPGMA树的不惟一问题。在UPGMA树惟一时,该方法产生的进化树与UPGMA树相同;而在UPGMA树不惟一时,该方法可以产生一棵惟一的、与序列输入顺序无关的多叉进化树,而且该算法还具有一个可调的容差参数,来控制生成进化树的主要分枝结构,这对于突出大规模进化树的总体脉络具有重要意义。     

The Promise of Particularism and the Theology of Culture: Limits and Lessons of "Neo-Boasianism"

This article compares the status of "culture" as a politically engaged concept in Franz Boas's time and in our own time. Taking a Boasian approach to "neo-Boasianism," I examine the limits of this comparability in order to shed light on the nature of public culture-talk today and to identify dimensions of the Boasian concept of "culture" particularly relevant to a contemporary anthropology.     

An analysis of the meaning of the concepts of "commitment" and "determination" in the study of patterns of development

The use of the term "commitment" by different authors was compared and the term itself was compared with the term "determination". Different authors understand the term "commitment" in different ways. It is proposed to preserve the terms "competence", "determination" (labile and stable) and "differentiation" in studies of normal development at stages preceding the appearance of organ rudiments in order to facilitate the use of the knowledge acquired by experimental embryology and to decipher these concepts at the molecular level. The meaning of the term "commitment" should be made more precise when describing the experimental results and also when assessing the results obtained by various authors and published in numerous papers and reviews.     

"Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as "ant" and "grasshopper" strategies of resource utilization. Interestingly, a strain may be "ant" in one medium and "grasshopper" in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective.     

The many-body problem for anisotropic membrane inclusions and the self-assembly of "saddle" defects into an "egg carton"

We calculate the many-body, nonpairwise interaction between N rigid, anisotropic membrane inclusions by modeling them as point-like constraints on the membrane's curvature tensor and by minimizing the membrane's curvature energy. Because multipolar distortions of higher-order decay on very short distances, our calculation gives the correct elastic interaction energy for inclusions separated by distances of the order of several times their size. As an application, we show by thermally equilibrating the many-body elastic energy using a Monte Carlo algorithm, that inclusions shaped as "saddles" attract each other and build an "egg-carton" structure. The latter is reminiscent of some patterns observed in membranes obtained from biological extracts, the origin of which is still mysterious.     

Relative contributions of "pressure pump" and "peristaltic pump" to gastric emptying

The relative contributions to gastric emptying from common cavity antroduodenal pressure difference ("pressure pump") vs. propagating high-pressure waves in the distal antrum ("peristaltic pump") were analyzed in humans by high-resolution manometry concurrently with time-resolved three-dimensional magnetic resonance imaging during intraduodenal nutrient infusion at 2 kcal/min. Gastric volume, space-time pressure, and contraction wave histories in the antropyloroduodenal region were measured in seven healthy subjects. The subjects fell into two distinct groups with an order of magnitude difference in levels of antral pressure activity. However, there was no significant difference in average rate of gastric emptying between the two groups. Antral pressure history was separated into "propagating high-pressure events" (HPE), "nonpropagating HPEs," and "quiescent periods." Quiescent periods dominated, and average pressure during quiescent periods remained unchanged with decreasing gastric volume, suggesting that common cavity pressure levels were maintained by increasing wall muscle tone with decreasing volume. When propagating HPEs moved to within 2-3 cm of the pylorus, pyloric resistance was found statistically to increase with decreasing distance between peristaltic waves and the pylorus. We conclude that transpyloric flow tends to be blocked when antral contraction waves are within a "zone of influence" proximal to the pylorus, suggesting physiological coordination between pyloric and antral contractile activity. We further conclude that gastric emptying of nutrient liquids is primarily through the "pressure pump" mechanism controlled by pyloric opening during periods of relative quiescence in antral contractile wave activity.     

The "Moi-peau"

To construct a coherent identity, humans must distinguish what belongs to the external, perceived world from what belongs to their own inner world and the inner world of other individuals. Based on the theory developed by S. Freud and on work by ethologists, a number of psychoanalysts (J. Bowlby, R.A. Spitz, D.W. Winnicott, etc.) have underlined the importance of early tactile exchanges with the mother if a child is to become an autonomous individual who feels secure within what he or she perceives to be sound and reliable mental and physical boundaries. More recently, other psychoanalysts (E. Bick, W.R. Bion, etc.) have studied the fantasized mental structures that form the limits between an individual's inner mental space and the external world (including other individuals). As part of this theoretical psychoanalytical movement, Didier Anzieu, a French psychoanalyst, started to develop the concept of the "Moi-peau" in 1974. The "Moi-peau" designates a fantasized reality that a child uses during its early development to represent itself as "me", based on its experience of the body surface. The child, enveloped in its mother's care, fantasizes of a skin shared with its mother: on one side the mother (the outer layer of the "Moi-peau"), and on the other side the child (the inner layer of the "Moi-peau"). These two layers must separate gradually if the child is to acquire its own me-skin. D. Anzieu's work allowed dermatologists and other specialists, such as pediatricians, to focus on the quality of early tactile exchanges between a mother and her child, including the child with a chronic skin disorder. It also helped dermatologists to recognize patients with "borderline" states, which are particularly frequent in dermatology (ereutophobia, dysmorphophobia, tattooing, self-mutilation, artefacta dermatitis). These borderline patients are adults who, as a result of their mental conflicts, adopt defense mechanisms derived from both neurotic and psychotic functioning. Their complaints reflect difficulties with the solidity of their mental and physical limits: their real skin is metaphorically linked to the fantasized mental structure that delimits the individual mental space. Among other clinical characteristics, they have a "pathology of action" and frequently attack their own skin, paradoxically, in order to test the solidity and reliability of their own limits. Finally, D. Anzieu's work encouraged dermatologists to use psychotherapeutic approaches in parallel to classical dermatologic approaches, when necessary, and helped them better understand how psychoanalysts work with patients who have not yet acquired their own "Moi-peau". As a result, D. Anzieu was among the first to reconcile dermatologists and psychoanalysts.     

"Sweeping up after the parade": professional, ethical, and patient care implications of "turfing"

"Turfing" denotes a patient transfer or triage from one physician to another when the care of that patient feels more troublesome than it is worth. A widespread phenomenon in medical training programs, turfing appears to allocate patient care to meet physicians' rather than patients' needs. Although turfing reportedly causes inter-physician discord and inter-specialty stereotyping, its deeper consequences are poorly understood. Turfing is an interpersonal conflict masquerading as a medical issue. After examining turfing alongside other patient-related slang, I analyze the distinction between "the turf," a person, and "to turf," a practice. Several explanatory models from medical practice are explored in order to illuminate turfing's implications for medical professionalism, ethics, and patient care. I suggest that a physician's medical specialty or practice type--that is, professional culture--may link to that physician's degree of altruism. If so, then what it means fundamentally to be a physician might vary across medical specialties. Such a link calls for a new notion of cultural competence, one that physicians may apply not to patients but to each other.     

"Brother" and "Uncle": An Analysis of Rules, Structural Contradictions, and Meaning in Vietnamese Kinship

This paper analyzes the meanings of Vietnamese kinship terms on the basis of the rules that regulate their referential and nonreferential uses. These rules are not completely consistent with one another. They constitute contradictory models of and for sociocultural reality at a certain level. The structural contradictions among these models render "fuzzy" even the definitions of the prototypical uses of Vietnamese kin terms. The coexistence of alternative models makes the use of a linguistic form both a goal-directed action and the representation of an order.     

Once again about "Gregg paradox" and its solution

"Gregg paradox" means that monotypical groups containing the same species (or groups of species) will be equal each other although systematics considers them as different taxa. Thus if the order of placental mammalia Tubilidentata includes one species aardvark Orycteropus after, the order itself, its single family Orycteropodiaceae, single genus of the family Orycteropus and the single species Orycteropus after can be considered as equal to each other. To solve this disagreement the author asserts that taxa of any level can be regarded as an individual according to the taxa of higher rank. Possibility of such interpretation was already suggested by Georg Cantor (1985). He supposed that a set (class) can be regarded as unity by itself. In this case connections between taxa of different levels can be realized by Peano ratio of intrasitive conformities. In this model a genus will consist of species but not individuals, a type--of classes, etc. Thus, if a taxon x as an individual is an element of taxon y, and taxon y as an individual is an element of taxon z, then z according to x will be not only logical class, but class of classes and, hence we could not consider x as an element of z, because the latter consists of indecomposable individual-class y or some similar classes. In this situation "Gregg paradox" does not arise.     

A case of terminal renal insufficiency revealing a "charge" association in an adult

A case report: Different abnormalities suggesting a "Charge" association were recognized in a 23-year-old man, as an end-stage renal disease was discovered. Though its undetermined cause(s), this association needs to be evoked in order to detect and to manage occult visceral anomalies and to evaluate for a familial form.     

Arguments justifying the acception of the notion "sublobular artery" in the nomenclature of renal vessels: the "conical" architectonics of the renal cortex

The corrosion technique was used to demonstrate the presence of the "sublobular artery", a constant vessel with a special profile of the dog kidney, generating after two divisions the so-called interlobular arteries as a third generation of branches. More rarely arteriae interlobulares emerge also directly from the arcuate artery. The sublobular arteries (= parent vessels of the interlobular arteries) are characterized by their particular origin, branching type, and by having no or sporadically disposed glomeruli. For this reason, the authors suggest the acception of the term "arteria sublobularis" in the international nomenclature of renal vessels. According to authors' opinion the dog kidney is composed of a number of conical vascular-parenchymatous units, each containing in their axis a sublobular artery of the second order ("conical" architectonics of the renal cortex).     

Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB

The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.     

Coming changes in accepted wisdom about "osteoporosis"

Here a voice from the past suggests 28 changes that will affect how people study, manage, classify and think about "osteoporoses" today. Those changes depend mainly on two things: (i) "Connecting the dots" between diverse evidence and ideas from many fields and sources in order to find larger "messages" hidden in mountains of often poorly-organized lesser details, (ii) and features of the still-evolving Utah paradigm of skeletal physiology. That paradigm sums contributions from many people who worked in many fields for over 100 years. In one view it is the most important development in skeletal physiology since Rudolf Virchow and others realized approximately 150 years ago that cells provide the basis for human physiology and diseases. This article emphasizes the above messages instead of the details. The messages affect ideas about the nature, pathogenesis, diagnosis, classification, study and management of osteopenias and osteoporoses, as well as some roles of muscle, drugs, hormones, other agents and fatigue damage, in those disorders. Those larger messages also concern how to classify "osteoporosis fractures", how to define bone health, the choice of absorptiometric methods for noninvasive evaluations of bones, osteopenias and muscle strength, and new criteria for selecting patient cohorts for "risk-of-fracture" analyses and in searches for genetic roles in "osteoporoses". Finally, those larger messages identify many new targets for research that should prove unusually useful in clinical and pharmaceutical domains and work.     

Parent-offspring conflicts, "optimal bad motherhood" and the "mother knows best" principles in insect herbivores colonizing novel host plants

SPECIALIZATION OF INSECT HERBIVORES TO ONE OR A FEW HOST PLANTS STIMULATED THE DEVELOPMENT OF TWO HYPOTHESES ON HOW NATURAL SELECTION SHOULD SHAPE OVIPOSITION PREFERENCES: The "mother knows best" principle suggests that females prefer to oviposit on hosts that increase offspring survival. The "optimal bad motherhood" principle predicts that females prefer to oviposit on hosts that increase their own longevity. In insects colonizing novel host plants, current theory predicts that initial preferences of insect herbivores should be maladaptive, leading to ecological traps. Ecological trap theory does not take into account the fact that insect lineages frequently switch hosts at both ecological and evolutionary time scales. Therefore, the behavior of insect herbivores facing novel hosts is also shaped by natural selection. Using a study system in which four Cephaloleia beetles are currently expanding their diets from native to exotic plants in the order Zingiberales, we determined if initial oviposition preferences are conservative, maladaptive, or follow the patterns predicted by the "mother knows best" or the "optimal bad motherhood" principles. Interactions with novel hosts generated parent-offspring conflicts. Larval survival was higher on native hosts. However, adult generally lived longer on novel hosts. In Cephaloleia beetles, oviposition preferences are usually associated with hosts that increase larval survival, female fecundity, and population growth. In most cases, Cephaloleia oviposition preferences follow the expectations of the "mothers knows best" principle.     

A brainstem "mini-discharge" syndrome (anesthesia dolorosa)

Chronic pain consisting of anesthesia dolorosa secondary to bilateral interruption of the trigeminal nerves is presented as a brain stem reticular denervation syndrome. Electrothalamograms revealed fast frequency discharges in the mesothalamic prerubral and centermedian reticular formation. Mesothalamic electrical stimulation attenuated the discharges. Pain and other symptoms presumably of brainstem origin also were attenuated or abolished by therapeutic electrical stimulation twice daily. It is postulated that brain stem-represented behavioral generators are implicated by the reticular discharges in order to produce the complex symptomatology. Consequently the symptom complex is collectively identified as a brainstem "mini-discharge" syndrome. A theoretical discussion is presented to defend the thesis that reticular denervation-induced low threshold discharge system accounts for the episodic states of pain, dyskinesia, mood, and memory disturbances.