Rachel Walker

BIODIVERSITY OF CORALLINE ALGAE IN THE NORTHEASTERN ATLANTIC INCLUDING CORALLINA CAESPITOSA SP. NOV. (CORALLINOIDEAE, RHODOPHYTA)(1).

The Corallinoideae (Corallinaceae) is represented in the northeastern Atlantic by Corallina officinalis L.; Corallina elongata J. Ellis et Sol.; Haliptilon squamatum (L.) H. W. Johans., L. M. Irvine et A. M. Webster; and Jania rubens (L.) J. V. Lamour. The delimitation of these geniculate coralline red algae is based primarily on morphological characters. Molecular analysis based on cox1 and 18S rRNA gene phylogenies supported the division of the Corallinoideae into the tribes Janieae and Corallineae. Within the Janieae, a sequence difference of 46–48 bp (8.6%–8.9%) between specimens of H. squamatum and J. rubens in the cox1 phylogeny leads us to conclude that they are congeneric. J. rubens var. rubens and J. rubens var. corniculata (L.) Yendo clustered together in both phylogenies, suggesting that for those genes, there was no genetic basis for the morphological variation. Within the Corallineae, it appears that in some regions, the name C. elongata has been misapplied. C. officinalis samples formed two clusters that differed by 45–54 bp (8.4%–10.0%), indicating species‐level divergence, and morphological differences were sufficient to define two species. One of these clusters was consistent with the morphology of the type specimen of C. officinalis (LINN 1293.9). The other species cluster is therefore described here as Corallina caespitosa sp. nov. This study has demonstrated that there is a clear need for a revision of the genus Corallina to determine the extent of “pseudocryptic” diversity in this group of red algae.

Evolutionary Analysis of the MIXTA Gene Family Highlights Potential Targets for the Study of Cellular Differentiation

Differentiated epidermal cells such as trichomes and conical cells perform numerous essential functions in plant biology and are important for our understanding of developmental patterning and cell shape regulation. Many are also commercially significant, such as cotton fibers and trichomes that secrete pharmaceutically useful or herbivore-deterring compounds. Here, we focus on the phylogeny and evolution of the subgroup 9 R2R3 MYB gene transcription factors, which include the MIXTA gene, and that are important for the specification and regulation of plant cellular differentiation. We have sequenced 49 subgroup 9 R2R3 MYB genes from key experimental taxa and combined these sequences with those identified by an exhaustive bioinformatic search, to compile a data set of 223 subgroup 9 R2R3 MYB genes. Our phylogenetic analyses demonstrate, for the first time, the complex evolutionary history of the subgroup 9 R2R3 MYB genes. A duplication event is inferred before the origin of seed plants giving rise to two major gene lineages, here termed SBG9-A and SBG9-B. The evolutionary conservation of the SBG9-B gene lineage has not been previously recognized and its role in cellular differentiation is unknown, thus an entire clade of potential candidate genes for epidermal cell regulation remains to be explored. Using a heterologous transformation bioassay, we provide functional data that implicate members of the SBG9-B lineage in the specification of epidermal projections. Furthermore, we reveal numerous putative duplication events in both SBG9-A and SBG9-B lineages, resolving uncertainty about orthology and paralogy among the subgroup 9 R2R3 MYB genes. Finally, we provide a robust framework over which to interpret existing functional data and to direct ongoing comparative genetic research into the evolution of plant cellular diversity.

Epitypification and Redescription of Corallina officinalis L., the Type of the Genus, and C. elongata Ellis et Solander (Corallinales, Rhodophyta)

Abstract Corallina L. is the type genus of the subfamily Corallinoideae (Aresch.) Foslie and Corallina officinalis L. is the type species of the genus. This name has been applied worldwide, particularly in temperate waters. An attempt to obtain sequence data from the lectotype specimen was not successful. In order to establish a species concept for C. officinalis based on molecular sequence data as well as morphology, an epitype was selected from Devon, England within the vague type locality ‘in O [Oceano] Europaeo’, and from which mitochondrial (cox1) and plastid (rbcL) data were obtained. A second species, Corallina elongata Ellis et Solander (type locality Cornwall, England), was shown previously to include at least two species based on DNA sequences. The lectotype of C. elongata is an illustration and therefore an epitype was selected to provide molecular sequence data, using the same markers as for C. officinalis. These molecular sequences for C. officinalis and C. elongata are compared with those of a third, recently described species from Great Britain, Corallina caespitosa R.H. Walker, J. Brodie et L.M. Irvine: these data provide an example for studying Corallina species taxonomy and diversity in other parts of the world. The implications of this work are discussed in relation to concepts of species distribution.

Floral trait variation and integration as a function of sexual deception in Gorteria diffusa

Phenotypic integration, the coordinated covariance of suites of morphological traits, is critical for proper functioning of organisms. Angiosperm flowers are complex structures comprising suites of traits that function together to achieve effective pollen transfer. Floral integration could reflect shared genetic and developmental control of these traits, or could arise through pollinator-imposed stabilizing correlational selection on traits. We sought to expose mechanisms underlying floral trait integration in the sexually deceptive daisy, Gorteria diffusa, by testing the hypothesis that stabilizing selection imposed by male pollinators on floral traits involved in mimicry has resulted in tighter integration. To do this, we quantified patterns of floral trait variance and covariance in morphologically divergent G. diffusa floral forms representing a continuum in the levels of sexual deception. We show that integration of traits functioning in visual attraction of male pollinators increases with pollinator deception, and is stronger than integration of non-mimicry trait modules. Consistent patterns of within-population trait variance and covariance across floral forms suggest that integration has not been built by stabilizing correlational selection on genetically independent traits. Instead pollinator specialization has selected for tightened integration within modules of linked traits. Despite potentially strong constraint on morphological evolution imposed by developmental genetic linkages between traits, we demonstrate substantial divergence in traits across G. diffusa floral forms and show that divergence has often occurred without altering within-population patterns of trait correlations.

Toward resolution of species diversity and distribution in the calcified red algal genera Corallina and Ellisolandia (Corallinales, Rhodophyta)

Abstract: Cryptic species diversity and the misapplication of names have restricted an understanding of species boundaries in the tribe Corallineae of the calcified red algal order Corallinales. Recent DNA sequencing of type material provided a framework facilitating further examination of genera within the tribe. A phylogenetic study of the genera Corallina and Ellisolandia, based on cytochrome c oxidase subunit 1 and ribulose-bisphosphate carboxylase gene sequences, was undertaken using Natural History Museum herbarium collections and contemporary samples to explore species diversity, geographic distributions and the extent to which names have been misapplied. Twenty Corallina clades likely corresponding to species were resolved, of which C. officinalis and C. caespitosa were confirmed, four were clades newly identified during the present study and 14 had been reported by other workers in previous studies. These data indicated considerable genetic diversity within the genus that was not readily apparent on the basis of morphology. The generitype C. officinalis was shown to have a predominantly North Atlantic Ocean, cool-temperate distribution, whereas the global distribution of C. caespitosa is confirmed for the first time, with samples from Asia, Australasia, Europe, Africa and America. Widespread misidentification of Corallina species was documented, as was the need for sequencing of type specimens to correctly apply names and for comparison with historical collections. The phylogeny reported here serves both as a baseline for future phylogenetic positioning of Corallina species and highlights the degree to which species concepts within this genus remain unresolved.

From concept to clinic: Mathematically informed immunotherapy.

To allow innovative, progressive treatments to make the transition from concept to clinic, experimentally calibrated and clinically motivated mathematical models are essential. To aid the development of well-informed clinical trials, collaboration between mathematicians, computational modelers, biologists, and clinicians is required to allow qualitative hypotheses to take on a quantitative dimension. Such interdisciplinary science can allow both personalization and optimization of dose and scheduling of immunotherapeutic protocols, both as an independent therapy and in conjunction with other more traditional therapies, to streamline the transition from innovative concept to clinical practice and improve clinical outcomes for individual patients.

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga

The living prokaryotic microbiome of the calcified geniculate (articulated) red alga, Corallina officinalis from the intertidal seashore is characterised for the first time based on the V6 hypervariable region of 16S rRNA. Results revealed an extraordinary diversity of bacteria associated with the microbiome. Thirty-five prokaryotic phyla were recovered, of which Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Verrucomicrobia, Firmicutes and Chloroflexi made up the core microbiome. Unclassified sequences made up 25% of sequences, suggesting insufficient sampling of the worlds oceans/macroalgae. The greatest diversity in the microbiome was on the upper shore, followed by the lower shore then the middle shore, although the microbiome community composition did not vary between shore levels. The C. officinalis core microbiome was broadly similar in composition to those reported in the literature for crustose coralline algae (CCAs) and free-living rhodoliths. Differences in relative abundance of the phyla between the different types of calcified macroalgal species may relate to the intertidal versus subtidal habit of the taxa and functionality of the microbiome components. The results indicate that much work is needed to identify prokaryotic taxa, and to determine the nature of the relationship of the bacteria with the calcified host spatially, temporally and functionally.

Structural colour in Chondrus crispus

The marine world is incredibly rich in brilliant and intense colours. Photonic structures are found in many different species and provide extremely complex optical responses that cannot be achieved solely by pigments. In this study we examine the cuticular structure of the red alga Chondrus crispus (Irish Moss) using anatomical and optical approaches. We experimentally measure the optical response of the multilayer structure in the cuticle. Using finite-difference time-domain modelling, we demonstrate conclusively for the first time that the dimensions and organisation of lamellae are responsible for the blue structural colouration on the surface of the fronds. Comparison of material along the apical-basal axis of the frond demonstrates that structural colour is confined to the tips of the thalli and show definitively that a lack of structural colour elsewhere corresponds with a reduction in the number of lamellae and the regularity of their ordering. Moreover, by studying the optical response for different hydration conditions, we demonstrate that the cuticular structure is highly porous and that the presence of water plays a critical role in its ability to act as a structural light reflector.

Predicting Patient-Specific Radiotherapy Protocols Based on Mathematical Model Choice for Proliferation Saturation Index

Radiation is commonly used in cancer treatment. Over 50% of all cancer patients will undergo radiotherapy (RT) as part of cancer care. Scientific advances in RT have primarily focused on the physical characteristics of treatment including beam quality and delivery. Only recently have inroads been made into utilizing tumor biology and radiobiology to design more appropriate RT protocols. Tumors are composites of proliferating and growth-arrested cells, and overall response depends on their respective proportions at irradiation. Prokopiou et al. (Radiat Oncol 10:159, 2015) developed the concept of the proliferation saturation index (PSI) to augment the clinical decision process associated with RT. This framework is based on the application of the logistic equation to pre-treatment imaging data in order to estimate a patient-specific tumor carrying capacity, which is then used to recommend a specific RT protocol. It is unclear, however, how dependent clinical recommendations are on the underlying tumor growth law. We discuss a PSI framework with a generalized logistic equation that can capture kinetics of different well-known growth laws including logistic and Gompertzian growth. Estimation of model parameters on the basis of clinical data revealed that the generalized logistic model can describe data equally well for a wide range of the generalized logistic exponent value. Clinical recommendations based on the calculated PSI, however, are strongly dependent on the specific growth law assumed. Our analysis suggests that the PSI framework may best be utilized in clinical practice when the underlying tumor growth law is known, or when sufficiently many tumor growth models suggest similar fractionation protocols.

Fighting Cancer with Mathematics and Viruses

After decades of research, oncolytic virotherapy has recently advanced to clinical application, and currently a multitude of novel agents and combination treatments are being evaluated for cancer therapy. Oncolytic agents preferentially replicate in tumor cells, inducing tumor cell lysis and complex antitumor effects, such as innate and adaptive immune responses and the destruction of tumor vasculature. With the availability of different vector platforms and the potential of both genetic engineering and combination regimens to enhance particular aspects of safety and efficacy, the identification of optimal treatments for patient subpopulations or even individual patients becomes a top priority. Mathematical modeling can provide support in this arena by making use of experimental and clinical data to generate hypotheses about the mechanisms underlying complex biology and, ultimately, predict optimal treatment protocols. Increasingly complex models can be applied to account for therapeutically relevant parameters such as components of the immune system. In this review, we describe current developments in oncolytic virotherapy and mathematical modeling to discuss the benefit of integrating different modeling approaches into biological and clinical experimentation. Conclusively, we propose a mutual combination of these research fields to increase the value of the preclinical development and the therapeutic efficacy of the resulting treatments.