Criteria for assessing maturity of skulls in the common dolphin,Delphinus sp., from New Zealand waters

Knowledge about the maturity status of specimens included in evolutionary, taxonomic or life history investigations is fundamentally important. This study investigated the use of the degree of cranial suture fusion, the developmental status of cranial bones, and the degree of tooth wear as indicators for cranial maturity status in Delphinus sp. from New Zealand waters. In total, 15 sutures, one joint and three nonmetric characters were assessed on 66 skulls obtained from stranded and bycaught individuals sampled between 1932 and 2011. A suture index (SI) was computed based on 10 sutures, in which degree of fusion was correlated with age and the three misclassification indices (MI), calculated for a given suture, were <50%. In addition to these, five premaxilla‐maxilla fusion and seven tooth wear categories were assessed. Results suggest that New Zealand Delphinus sp. skulls should be regarded as cranially mature if at least two of the following criteria are met: (1) individuals assessed as sexually mature, (2) aged ≥ 11 yr, (3) SI ≥ 8, and (4) premaxilla‐maxilla fusion ≥ 75% of the length of the dorsal side of the rostrum. Presence of any number of rostral teeth worn to the gum line provided further evidence for cranial maturity.     

Divergent evolution of a bifunctional de novo protein

Primordial proteins, the evolutionary ancestors of modern sequences, are presumed to have been minimally active and nonspecific. Following eons of selective pressure, these early progenitors evolved into highly active and specific proteins. While evolutionary trajectories from poorly active and multifunctional generalists toward highly active specialists likely occurred many times in evolutionary history, such pathways are difficult to reconstruct in natural systems, where primordial sequences are lost to time. To test the hypothesis that selection for enhanced activity leads to a loss of promiscuity, we evolved a de novo designed bifunctional protein. The parental protein, denoted Syn‐IF, was chosen from a library of binary patterned 4‐helix bundles. Syn‐IF was shown previously to rescue two different auxotrophic strains of E. coli: ΔilvA and Δfes. These two strains contain deletions for proteins with very different biochemical functions; IlvA is involved in isoleucine biosynthesis, while Fes is involved in iron assimilation. In two separate experiments, Syn‐IF, was evolved for faster rescue of either ΔilvA or Δfes. Following multiple rounds of mutagenesis, two new proteins were selected, each capable of rescuing the selected function significantly faster than the parental protein. In each case, the evolved protein also lost the ability to rescue the unselected function. In both evolutionary trajectories, the original bifunctional generalist was evolved into a monofunctional specialist with enhanced activity.     

Patterning of the early Middle Paleolithic occupations at Douara Cave and its implications for settlement dynamics in the Palmyra basin,Syria

This paper examines spatial patterning and settlement dynamics of early Middle Paleolithic hominins at Douara Cave, located on the northern edge of the Syrian Desert. The analyzed material came from our 1984 excavations of Horizons IVB–IVD, techno-typologically assigned to the Tabun D-type Levantine Mousterian (ca. 250 to 130 ka). Two findings are reported. One is the existence of spatial organization in the cave interior. Analysis of the field records shows that the occupation floor of the early Middle Paleolithic at Douara was well-organized into specific activity areas with a focal area of intensive activities close to the back wall. This suggests that the organized use of space known at late Middle Paleolithic sites like Tor Faraj, Jordan, is also applicable to the early Middle Paleolithic. Second, this paper discusses the functional role of this cave within the regional settlement system. A range of features characterizing its living floor(s) point to a very low occupational intensity, undoubtedly reflecting adaptation and particular land use patterns in the arid environments of this region. Moreover, this pattern, along with the division of interior space, seems to have remained consistent through multiple early Middle Paleolithic levels (IVB–IVD). These observations suggest that Douara Cave was a short-term camp embedded in a regional settlement system in the arid environments of this period.     

Positional Information,Positional Error,and Readout Precision in Morphogenesis: A Mathematical Framework

The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail.     

Impact of the terrestrial-aquatic transition on disparity and rates of evolution in the carnivoran skull

Background

Which factors influence the distribution patterns of morphological diversity among clades? The adaptive radiation model predicts that a clade entering new ecological niche will experience high rates of evolution early in its history, followed by a gradual slowing. Here we measure disparity and rates of evolution in Carnivora, specifically focusing on the terrestrial-aquatic transition in Pinnipedia. We analyze fissiped (mostly terrestrial, arboreal, and semi-arboreal, but also including the semi-aquatic otter) and pinniped (secondarily aquatic) carnivorans as a case study of an extreme ecological transition. We used 3D geometric morphometrics to quantify cranial shape in 151 carnivoran specimens (64 fissiped, 87 pinniped) and five exceptionally-preserved fossil pinnipeds, including the stem-pinniped Enaliarctos emlongi. Range-based and variance-based disparity measures were compared between pinnipeds and fissipeds. To distinguish between evolutionary modes, a Brownian motion model was compared to selective regime shifts associated with the terrestrial-aquatic transition and at the base of Pinnipedia. Further, evolutionary patterns were estimated on individual branches using both Ornstein-Uhlenbeck and Independent Evolution models, to examine the origin of pinniped diversity.

Results

Pinnipeds exhibit greater cranial disparity than fissipeds, even though they are less taxonomically diverse and, as a clade nested within fissipeds, phylogenetically younger. Despite this, there is no increase in the rate of morphological evolution at the base of Pinnipedia, as would be predicted by an adaptive radiation model, and a Brownian motion model of evolution is supported. Instead basal pinnipeds populated new areas of morphospace via low to moderate rates of evolution in new directions, followed by later bursts within the crown-group, potentially associated with ecological diversification within the marine realm.

Conclusion

The transition to an aquatic habitat in carnivorans resulted in a shift in cranial morphology without an increase in rate in the stem lineage, contra to the adaptive radiation model. Instead these data suggest a release from evolutionary constraint model, followed by aquatic diversifications within crown families.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0285-5) contains supplementary material, which is available to authorized users.     

A mysterious pacemaker suture: an uncommon foreign body reaction

Surgical suture material is usually inert and nontoxic and causes minimal inflammation of tissue. However, foreign body reactions to various suture types can lead to granuloma, abscess, or even sinus formation. We report an elderly female who was incidentally detected to have a mass protruding from the incision site which was confirmed histopathologically a chronic granulomatous reaction to non absorbable suture. The foreign body granulomatous reaction to suture material in the setting of pacemaker implantation has not been described in the literature. We also discuss the existing literature on this underrecognised entity.     

大鼠颈部自体静脉移植模型两种吻合方法的比较

目的比较间断吻合和连续吻合法建立静脉桥狭窄动物模型的优劣。方法SD大鼠20只,分成两组（间断吻合组和连续吻合组）,取颈外静脉与颈总动脉行端端吻合。术后4周取下静脉桥,观察桥管通畅性,分析新生内膜与中膜的厚度、面积比。结果连续组与间断组相比手术时间更短,出血更少,但桥管通畅率低,两组内膜增生程度没有显著差异。结论连续吻合用时短,出血少,对术者要求更高,较易形成吻合口狭窄。两者造模效果一样。     

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study

Ab initio structure prediction and de novo protein design are two problems at the forefront of research in the fields of structural biology and chemistry. The goal of ab initio structure prediction of proteins is to correctly characterize the 3D structure of a protein using only the amino acid sequence as input. De novo protein design involves the production of novel protein sequences that adopt a desired fold. In this work, the results of a double-blind study are presented in which a new ab initio method was successfully used to predict the 3D structure of a protein designed through an experimental approach using binary patterned combinatorial libraries of de novo sequences. The predicted structure, which was produced before the experimental structure was known and without consideration of the design goals, and the final NMR analysis both characterize this protein as a 4-helix bundle. The similarity of these structures is evidenced by both small RMSD values between the coordinates of the two structures and a detailed analysis of the helical packing.     

From larval bodies to adult body plans: patterning the development of the presumptive adult ectoderm in the sea urchin larva

Echinoderms are unique among bilaterians for their derived, nonbilateral adult body plan. Their radial symmetry emerges from the bilateral larval body plan by the establishment of a new axis, the adult oral–aboral axis, involving local mesoderm–ectoderm interactions. We examine the mechanisms underlying this transition in the direct-developing sea urchin Heliocidaris erythrogramma. Adult ectoderm arises from vestibular ectoderm in the left vegetal quadrant. Inductive signals from the left coelom are required for adult ectodermal development but not for initial vestibule formation. We surgically removed gastrula archenteron, making whole-ectoderm explants, left-, right-, and animal-half ectoderm explants, and recombinants of these explants with left coelom. Vestibule formation was analyzed morphologically and with radioactive in situ hybridization with HeET-1, an ectodermal marker. Whole ectodermal explants in the absence of coelom developed vestibules on the left side or ventrally but not on the right side, indicating that left–right polarity is ectoderm autonomous by the gastrula stage. However, right-half ectodermal explants robustly formed vestibules that went on to form adult structures when recombined with the left coelom, indicating that the right side retains vestibule-forming potential that is normally suppressed by signals from the left-side ectoderm. Animal-half explants formed vestibules only about half the time, demonstrating that animal–vegetal axis determination occurs earlier. However, when combined with the left coelom, animal-half ectoderm always formed a vestibule, indicating that the left coelom can induce vestibule formation. This suggests that although coelomic signals are not required for vestibule formation, they may play a role in coordinating the coelom–vestibule interaction that establishes the adult oral–aboral axis.