Combining geometric morphometrics and finite element analysis with evolutionary modeling:towards a synthesis

<p>Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static.</p> <p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p> <p>Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.</p

ANALYSIS OF THE DIURNAL EXPRESSION PATTERNS OF THE TOMATO CHLOROPHYLL alb BINDING PROTEIN GENES. INFLUENCE OF LIGHT and CHARACTERIZATION OF THE GENE FAMILY *

Steady-state mRNA levels of the chlorophyll alb binding ( cab ) proteins oscillate substantially during a diurnal cycle in tomato leaves. This accumulation pattern is also observed in complete darkness, supporting the hypothesis that the expression of cab genes is at least partially regulated by an endogenous rhythm (“biological clock”). The amplitude of the cab mRNA accumulation is dependent on the duration of illumination and the circadian phase in which light was applied to the tomato plants. These results at the molecular level correlate well with the photoperiodic phenomenon. The characterization of the expression pattern of individual members of the cab gene family was attempted. Distinct primer extension products were detected using specific oligonucleotides homologous to the cab 1, cab 4, cab 5 and cab 8 genes. Based on this analysis the transcription start sites of these genes were determined to be between position -70 and -9 upstream of the ATG codon. During the diurnal cycle the cab 1 and cab 4 genes exhibit the same expression pattern; no transcripts detected at 3 and 6 a.m., maximum mRNA levels were measured at noon and decreasing levels in the afternoon.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74852/1/j.1751-1097.1990.tb01752.x.pd

Internalization of novel non-viral vector TAT-streptavidin into human cells

BACKGROUND: The cell-penetrating peptide derived from the Human immunodeficiency virus-1 transactivator protein Tat possesses the capacity to promote the effective uptake of various cargo molecules across the plasma membrane in vitro and in vivo. The objective of this study was to characterize the uptake and delivery mechanisms of a novel streptavidin fusion construct, TAT(47–57)-streptavidin (TAT-SA, 60 kD). SA represents a potentially useful TAT-fusion partner due to its ability to perform as a versatile intracellular delivery vector for a wide array of biotinylated molecules or cargoes. RESULTS: By confocal and immunoelectron microscopy the majority of internalized TAT-SA was shown to accumulate in perinuclear vesicles in both cancer and non-cancer cell lines. The uptake studies in living cells with various fluorescent endocytic markers and inhibiting agents suggested that TAT-SA is internalized into cells efficiently, using both clathrin-mediated endocytosis and lipid-raft-mediated macropinocytosis. When endosomal release of TAT-SA was enhanced through the incorporation of a biotinylated, pH-responsive polymer poly(propylacrylic acid) (PPAA), nuclear localization of TAT-SA and TAT-SA bound to biotin was markedly improved. Additionally, no significant cytotoxicity was detected in the TAT-SA constructs. CONCLUSION: This study demonstrates that TAT-SA-PPAA is a potential non-viral vector to be utilized in protein therapeutics to deliver biotinylated molecules both into cytoplasm and nucleus of human cells

OXYGEN REACTIVE POLYMERS FOR TREATMENT OF TRAUMATIC BRAIN INJURY

Methods and compositions for treating traumatic brain injury . The methods and compositions utilize a multi - functional oxygen reactive polymer ( ORP ) that includes repeating units that include a reactive oxygen species ( ROS ) scavenging group and a polyalkylene oxide group . For theranostic applications , the oxygen reactive polymer fur ther includes a diagnostic group

Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity

Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation

Ecomorphology of Carnivora challenges convergent evolution

Convergent evolution is often reported in the mammalian order Carnivora. Their adaptations to particularly demanding feeding habits such as hypercarnivory and durophagy (consumption of tough food) appear to favour morphological similarities between distantly related species, especially in the skull. However, phylogenetic effect in phenotypic data might obscure such a pattern. We first validated the hypotheses that extant hypercarnivorous and durophagous large carnivorans converge in mandibular shape and form (size and shape). Hypercarnivores generally exhibit smaller volumes of the multidimensional shape and form space than their sister taxa, but this pattern is significantly different from random expectation only when hunting behaviour categorisations are taken into account. Durophages share areas of the morphospace, but this seems to be due to factors of contingency. Carnivorans that hunt in pack exhibit incomplete convergence while even stronger similarities occur in the mandible shape of solitary hunters due to the high functional demands in killing the prey. We identified a stronger phylogenetic signal in mandibular shape than in size. The quantification of evolutionary rates of changes suggests that mandible shape of solitary hunters evolved slowly when compared with other carnivorans. These results consistently indicate that the need for a strong bite force and robust mandible override sheer phylogenetic effect in solitary hunters

Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories

Recent advances in geometric morphometrics provide improved techniques for extraction of biological information from shape and have greatly contributed to the study of ecomorphology and morphological evolution. However, the vertebral column remains an under-studied structure due in part to a concentration on skull and limb research, but most importantly because of the difficulties in analysing the shape of a structure composed of multiple articulating discrete units (i.e. vertebrae). Here, we have applied a variety of geometric morphometric analyses to three-dimensional landmarks collected on 19 presacral vertebrae to investigate the influence of potential ecological and functional drivers, such as size, locomotion and prey size specialisation, on regional morphology of the vertebral column in the mammalian family Felidae. In particular, we have here provided a novel application of a method—phenotypic trajectory analysis (PTA)—that allows for shape analysis of a contiguous sequence of vertebrae as functionally linked osteological structures. Our results showed that ecological factors influence the shape of the vertebral column heterogeneously and that distinct vertebral sections may be under different selection pressures. While anterior presacral vertebrae may either have evolved under stronger phylogenetic constraints or are ecologically conservative, posterior presacral vertebrae, specifically in the post-T10 region, show significant differentiation among ecomorphs. Additionally, our PTA results demonstrated that functional vertebral regions differ among felid ecomorphs mainly in the relative covariation of vertebral shape variables (i.e. direction of trajectories, rather than in trajectory size) and, therefore, that ecological divergence among felid species is reflected by morphological changes in vertebral column shape

Development of a Tetrameric Streptavidin Mutein with Reversible Biotin Binding Capability: Engineering a Mobile Loop as an Exit Door for Biotin

A novel form of tetrameric streptavidin has been engineered to have reversible biotin binding capability. In wild-type streptavidin, loop3–4 functions as a lid for the entry and exit of biotin. When biotin is bound, interactions between biotin and key residues in loop3–4 keep this lid in the closed state. In the engineered mutein, a second biotin exit door is created by changing the amino acid sequence of loop7–8. This door is mobile even in the presence of the bound biotin and can facilitate the release of biotin from the mutein. Since loop7–8 is involved in subunit interactions, alteration of this loop in the engineered mutein results in an 11° rotation between the two dimers in reference to wild-type streptavidin. The tetrameric state of the engineered mutein is stabilized by a H127C mutation, which leads to the formation of inter-subunit disulfide bonds. The biotin binding kinetic parameters (koff of 4.28×10−4 s−1 and Kd of 1.9×10−8 M) make this engineered mutein a superb affinity agent for the purification of biotinylated biomolecules. Affinity matrices can be regenerated using gentle procedures, and regenerated matrices can be reused at least ten times without any observable reduction in binding capacity. With the combination of both the engineered mutein and wild-type streptavidin, biotinylated biomolecules can easily be affinity purified to high purity and immobilized to desirable platforms without any leakage concerns. Other potential biotechnological applications, such as development of an automated high-throughput protein purification system, are feasible

Molecular characterization and genetic mapping of DNA sequences encoding the Type I chlorophyll a/b-binding polypeptide of photosystem I in Lycopersicon esculentum (tomato)

We report the isolation and characterization of a tomato nuclear gene encoding a chlorophyll a/b-binding (CAB) protein of photosystem I (PSI). The coding nucleotide sequence of the gene, designated Cab -6B, is different at eight positions from that of a previously isolated cDNA clone derived from the Cab -6A gene, but the two genes encode identical proteins. Sequence comparison with the cDNA clone revealed the presence of three short introns in Cab -6B. Genetic mapping experiments demonstrate that Cab -6A and Cab -6B are tightly linked and reside on chromosome 5, but the physical distance between the two genes is at least 7 kilobases. Cab -6A and Cab -6B have been designated Type I PSI CAB genes. They are the only two genes of this branch of the CAB gene family in the tomato genome, and they show substantial divergence to the genes encoding CAB polypeptides of photosystem II. The Type I PSI CAB genes, like the genes encoding PSII CAB proteins, are highly expressed in illuminated leaf tissue and to a lesser extent in other green organs.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43459/1/11103_2004_Article_BF00166457.pd

Re-Evaluation of Sinocastor (Rodentia: Castoridae) with Implications on the Origin of Modern Beavers

The extant beaver, Castor, has played an important role shaping landscapes and ecosystems in Eurasia and North America, yet the origins and early evolution of this lineage remain poorly understood. Here we use a geometric morphometric approach to help re-evaluate the phylogenetic affinities of a fossil skull from the Late Miocene of China. This specimen was originally considered Sinocastor, and later transferred to Castor. The aim of this study was to determine whether this form is an early member of Castor, or if it represents a lineage outside of Castor. The specimen was compared to 38 specimens of modern Castor (both C. canadensis and C. fiber) as well as fossil specimens of C. fiber (Pleistocene), C. californicus (Pliocene) and the early castorids Steneofiber eseri (early Miocene). The results show that the specimen falls outside the Castor morphospace and that compared to Castor, Sinocastor possesses a: 1) narrower post-orbital constriction, 2) anteroposteriorly shortened basioccipital depression, 3) shortened incisive foramen, 4) more posteriorly located palatine foramen, 5) longer rostrum, and 6) longer braincase. Also the specimen shows a much shallower basiocciptal depression than what is seen in living Castor, as well as prominently rooted molars. We conclude that Sinocastor is a valid genus. Given the prevalence of apparently primitive traits, Sinocastor might be a near relative of the lineage that gave rise to Castor, implying a possible Asiatic origin for Castor