Scared and less noisy: glucocorticoids are associated with alarm call entropy

The nonlinearity and arousal hypothesis predicts that highly aroused mammals will produce nonlinear, noisy vocalizations. We tested this prediction by measuring faecal glucocorticoid metabolites (GCMs) in adult yellow-bellied marmots (Marmota flaviventris), and asking if variation in GCMs was positively correlated with Wiener entropy-a measure of noise. Contrary to our prediction, we found a significant negative relationship: marmots with more faecal GCMs produced calls with less noise than those with lower levels of GCMs. A previous study suggested that glucocorticoids modulate the probability that a marmot will emit a call. This study suggests that, like some other species, calls emitted from highly aroused individuals are less noisy. Glucocorticoids thus play an important, yet underappreciated role, in alarm call production.     

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.     

High-resolution 2-dimensional protein mapping of "diploid" and "aneuploid" mammary adenocarcinomas

Two-dimensional-electrophoretic analysis has been applied to non-neoplastic mammary epithelium from eight healthy women, tumor tissue from eight "diploid" mammary adenocarcinomas, and tumor tissue from eight "aneuploid" mammary adenocarcinomas. Compared with non-neoplastic mammary epithelium, a slight numerical net non-neoplastic mammary epithelium, a slight numerical net increase of the protein spots was detected in "diploid" tumors and a marked increase in "aneuploid" tumors. Two prominent spots were present in all 16 malignant tissues examined and absent in all eight non-neoplastic tissues (silver staining method). The results suggest that a difference in the composition of cellular proteins exists both between non-neoplastic mammary cells and malignant tumor cells, and between "diploid" and "aneuploid" tumors.     

Human body mass estimation: a comparison of "morphometric" and "mechanical" methods

In the past, body mass was reconstructed from hominin skeletal remains using both "mechanical" methods which rely on the support of body mass by weight-bearing skeletal elements, and "morphometric" methods which reconstruct body mass through direct assessment of body size and shape. A previous comparison of two such techniques, using femoral head breadth (mechanical) and stature and bi-iliac breadth (morphometric), indicated a good general correspondence between them (Ruff et al. [1997] Nature 387:173-176). However, the two techniques were never systematically compared across a large group of modern humans of diverse body form. This study incorporates skeletal measures taken from 1,173 Holocene adult individuals, representing diverse geographic origins, body sizes, and body shapes. Femoral head breadth, bi-iliac breadth (after pelvic rearticulation), and long bone lengths were measured on each individual. Statures were estimated from long bone lengths using appropriate reference samples. Body masses were calculated using three available femoral head breadth (FH) formulae and the stature/bi-iliac breadth (STBIB) formula, and compared. All methods yielded similar results. Correlations between FH estimates and STBIB estimates are 0.74-0.81. Slight differences in results between the three FH estimates can be attributed to sampling differences in the original reference samples, and in particular, the body-size ranges included in those samples. There is no evidence for systematic differences in results due to differences in body proportions. Since the STBIB method was validated on other samples, and the FH methods produced similar estimates, this argues that either may be applied to skeletal remains with some confidence.     

Motile plant cell body: a "bug" within a "cage"

Analysis of the cytoskeleton in morphogenetically active plant cells allows us to propose a unified concept for the structural organization of eukaryotic cells. Their cytoarchitecture is determined by two principal structural complexes: nucleus-microtubule-based cell bodies ("bugs") and plasma-membrane-F-actin-based cell periphery complexes ("cages"). There are dynamic interactions between each of these entities in response to extracellular and intracellular signals. In the case of the cell body, these signals determine its polarization, rotation and migration. Interactions between cell body and cell periphery complexes determine cell growth polarity and morphogenesis throughout the eukaryotic kingdom.     

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.     

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.     

Taking the "I" out of IRB--and putting "community" in

If one looks back on the history of American research ethics, a bold pattern emerges. Since World War II, about every twenty years or so a breach of the social contract between investigators and human research subjects galvanizes public and professional interest in the ethical foundations and oversight mechanisms governing research with humans.     

Genetic evidence of "American" and "European" type symbiotic algae of Paramecium bursaria Ehrenberg

Paramecium bursaria is composed of a "host" ciliate and a "symbiont" green alga. Based upon physiology, DNA hybridization and virus infection, two types of symbionts, called "American" type and "European" type, have been reported to date. Here, we determined the 18S rDNA and internal transcribed spacer 2 (ITS2) regions for both "American" and "European" types. Sequence features clearly separated into two lineages; NC64A (USA), Syngen 2-3 (USA), Cs2 (Chinese), MRBG1 (Australian), and Japanese strains belong to the "American", whereas PB-SW1 (German) and CCAP 1660/11 (British) strains belong to the "European". In "American" 18S rDNA, three introns were inserted in the same positions as for previously described Japanese symbionts. In "European" 18S rDNA, a single intron occurred in a different position than in the "American". Between the types, sequence differences were seven or eight nucleotides (0.39 %) in the 18S rDNA exon, and more than 48 nucleotides (19.2 %) in ITS2 regions. We subsequently sequenced the host 18S rDNA. As a result, two groups: Cs2, MRBG1, and Japanese strains, and PB-SW1 and CCAP 1660/11 strains, were separated (with 23 substitutions and 4 insertions or deletions between the groups). The congruent separations between hosts and symbionts may imply that the type of symbiont depends on the host type.     

A comparative study of allogenic "first set" and "second set" skin rejection in mice.

In our case, where the difference between donor WHT/Ht(H--2d) and recipient C57B1/6 (H--2b) was at the H--2 locus of histocompatibility, the FSg rejection occurred between the 6th and the 10th day, while the SSg rejection was two days earlier. The morphological study emphasized that the cellular infiltrate in the FSg is predominantly lymphocytic, while in the SSg it is predominantly granulocytic. The vascularization settles on the second day postgrafting in the FSg as well as in the SSg, but is scarce and quickly destroyed in the SSg, thus being explained the scanty supply of lymphocytes in the latter graft type. The histochemical reactions demonstrated an increase of the NMPS in skin allograft from the moment of settling till the end of the rejection and a decrease of AMPS, till the complete disappearance, in the rejected graft. Little morphological differences were found between colateral draining nodes and contralateral ones during the reaction to the graft. An important feature described is the presence at the bed graft level of some cells morphologically identical to the IB encountered in great number in the TDA of lymph nodes in the allograft-bearing mice.     

Technical note: Dental microwear textures of "Phase I" and "Phase II" facets

The power stroke of mastication has been traditionally divided into two parts, one which precedes centric occlusion, and the other which follows it-"Phase I" and "Phase II," respectively. Recent studies of primate mastication have called into question the role of Phase II in food processing, as they have found little muscle activity or accompanying bone strain following centric occlusion. That said, many researchers today look to Phase II facets to relate diet to patterns of dental microwear. This suggests the need to reevaluate microwear patterns on Phase I facets. Here we use texture analysis to compare and contrast microwear on facets representing both phases in three primate species with differing diets (Alouatta palliata, Cebus apella, and Lophocebus albigena). Results reaffirm that microwear patterns on Phase II facets better distinguish taxa with differing diets than do those on Phase I facets. Further, differences in microwear textures between facet types for a given taxon may themselves reflect diet. Some possible explanations for differences in microwear textures between facet types are proposed.     

"I" becomes "L": modification of vertical mammaplasty

The problems of the vertical mammaplasty by Lejour (i.e., gathering the skin envelope in one vertical suture, frequent secondary healing problems, and later sagging of the inferior glandular part in the case of large and very large breasts) are well known. A simple modification of the Lejour technique, that is, adding a lateral inframammary scar to shorten the vertical scar length, is presented. The modified L technique was used in 45 patients (90 breasts) between October of 1999 and August of 2001. With an average follow-up of 13 months, the jugular notch-to-nipple distance was 21 cm, the vertical scar length was 8.4 cm, the lateral inframammary scar length was 11 cm, and the average resection weight was 625 g per breast (range, 200 g to 2080 g). Even among patients who had very large glandular bases and resection weights it was possible to achieve a breast base reduction, modeling the glandular corpus to a harmonic, well-projecting, and youthful shape. Slight wound-healing problems with spontaneous cicatrization within 2 weeks occurred in six patients. In two patients who exhibited gigantomastia up to 2080 g per breast, partial mamilla necrosis occurred on one side. Ninety-one percent of the patients reported being "very satisfied" with the outcome, and 9 percent reporting being "satisfied." The authors' modification of the vertical mammaplasty to an L-shaped scar technique enables the surgeon to apply the principles of the Lejour technique for higher resection weights and diminishes wound-healing problems, and it is still a scar-minimizing technique that results in a scar-free cleavage. It is easy to learn and an ideal standard technique for a teaching hospital.     

Sipunculan larvae and "cosmopolitan" species

Sipuncula is a relatively small taxon with roughly 150 recognized species. Many species are geographically widespread or "cosmopolitan." The pelagosphera larvae of some species are estimated to spend several months in the plankton. However, recent molecular evidence suggests that many of the "cosmopolitan" species actually represent species-complexes, some not even monophyletic. Herein, we present data on three sipunculan species with different developmental modes that occur both in the Sea of Japan and in the Northeast Pacific. The development of the three species-Phascolosoma agassizii, Thysanocardia nigra, and Themiste pyroides-is exceptionally well studied in both regions of the Pacific. Significant differences have been observed between the two regions with respect to egg size, developmental mode, and developmental timing. In general, eggs are larger and development slower in the Northeast Pacific when compared with the Sea of Japan. These differences have been explained as a result of phenotypic plasticity exhibited under different environmental conditions, in particular temperature, but we show that the populations of all three species are also remarkably distinct genetically and that gene flow between the two regions is extremely unlikely. In Thysanocardia nigra, we even found two very distinct genetic lineages within the same location in the Northeast Pacific. The amount of genetic divergence between populations from the Sea of Japan and those from the Northeast Pacific is not correlated with developmental mode. Themiste pyroides, the species with the most abbreviated development, actually has the least degree of genetic divergence between the regions. Analyses of molecular variance show that the majority of the observed variation in all three species is between the regions. We conclude that all three "cosmopolitan" species actually represent complexes of cryptic or pseudo-cryptic species. These examples demonstrate that a solid taxonomic framework based on molecular and morphological evidence is a prerequisite for evaluating relationships between dispersal capabilities, species' ranges, and the connectivity of populations.     

"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.     

"Necking" behaviour in the giraffe

Previous references to "necking" behaviour, and the main features of the study area are briefly outlined.
"Necking" behaviour in giraffe takes place only in all male herds. When the animals are in a head to head posture the intensity is either high or low, but when animals take up a head to tail posture the actions are always of high intensity and appear to have greater sexual significance.
The significance of "necking" is discussed, and it is suggested that these ritualized actions form an important sexuo-social bonding mechanism whereby a hierarchy is created amongst the males, and movement between strictly bachelor and mixed herds helps to maintain contact between the sexes in this polygamous mammal.     

"Necking" behaviour in the giraffe

Previous references to "necking" behaviour, and the main features of the study area are briefly outlined.
"Necking" behaviour in giraffe takes place only in all male herds. When the animals are in a head to head posture the intensity is either high or low, but when animals take up a head to tail posture the actions are always of high intensity and appear to have greater sexual significance.
The significance of "necking" is discussed, and it is suggested that these ritualized actions form an important sexuo-social bonding mechanism whereby a hierarchy is created amongst the males,and movement between strictly bachelor and mixed herds helps to maintain contact between the sexesin this polygamous mammal.     

"Timer" and "scanner" neurons in the cat visual cortex with low stimulus-background contrast

The response pattern and orientation detection of "timer" and "scanner" neurons were investigated in awake, immobilized cats with reduced contrast (2.3 and 10.0) between the light stimulus and the background. These two divisions had already been made [3, 5] at a high contrast level of 100. During this action, all scanners were found to retain their properties: they did not change into timers. The number of timers, however, dropped to 40% of their original total. The relationship between the properties of neurons belonging to these groups remained as it was during maximum contrast: with timers, response began and peaked earlier; it was also of higher frequency and briefer, while its capacity for orientation detection was far inferior to that of scanners. The neurons leaving the timer group following a reduction in contrast manifested a pattern somewhere between timer and scanner cells, resembling the latter in a number of parameters. Findings confirmed the deduction that both timer and scanner neurons are present and operate consistently under a wide range of conductions in the cat visual cortex; the former fulfill the functions of synchronizers and the latter of directional filters which are rearranged in time [5].Institute of Higher Nervous Activity and Neurophysiology, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 18, No. 6, pp. 805–812, November–December, 1986.     

Analyzing the "degree of humanness" of antibody sequences

Genetically engineered mouse antibodies are now commonly in clinical use. However, their development is limited because the human immune system tends to regard them as foreign and this triggers an immune response. The solution is to make engineered antibodies appear more human. Here, we propose a method to assess the "degree of humanness" of antibody sequences providing a tool that may contribute to predictions of antigenicity. We analyzed sequences of antibodies belonging to various chains/classes in human and mouse. Our analysis of metrics based on percentage sequence identity between antibody sequences shows distinct differences between human and mouse sequences. Based on mean sequence identity and standard deviation, we calculated Z-scores for data sets of antibody sequences extracted from the Kabat database. We applied the analysis to a set of humanized and chimeric antibodies and to human germline sequences. We conclude that this approach may aid in the selection of more suitable mouse variable domains for antibody engineering to render them more human but in general, we find that typicality of a sequence compared with the expressed human repertoire is not well correlated with antigenicity. We have provided a Web server allowing humanness to be assigned for a sequence.