Pathologies of non‐marine bivalve shells from the Late Triassic of Poland

Gorzelak, P., Nied?wiedzki, G. & Skawina, A. 2010: Pathologies of non‐marine bivalve shells from the Late Triassic of Poland. Lethaia, Vol. 43, pp. 285–289. Shells of Late Triassic non‐marine bivalves from Lisowice (Lipie ?l?skie clay pit, southern Poland), which co‐occur with remains of several vertebrate taxa (mammal‐like reptiles, carnivorous dinosaurs, pterosaurs, temnospondyl amphibians, hybodont sharks, dipnoan and ganoid fish), bear evidence of pathologies. Distribution, dimension and shape of some of these injuries (radiate tooth marks) closely match the dental morphology of lungfish (here probably represented by the genus Ceratodus). Thus, we interpret these pathologies as evidence of unsuccessful predatory attack on bivalves by this fish. This interpretation is also consistent with modern examples of such behaviour among lungfish. The feasibility that other culprits caused other pathologies (shell scarring and wedges) on the bivalves analysed is also discussed. Discovery of these traces constitutes important evidence of predator–prey interaction, which provides ‘fingerprints’ of trophic structure within this Late Triassic freshwater ecosystem. □Freshwater bivalves, lungfish, pathologies, predation, Triassic.     

Image analysis tools and emerging algorithms for expression proteomics

Since their origins in academic endeavours in the 1970s, computational analysis tools have matured into a number of established commercial packages that underpin research in expression proteomics. In this paper we describe the image analysis pipeline for the established 2-DE technique of protein separation, and by first covering signal analysis for MS, we also explain the current image analysis workflow for the emerging high-throughput 'shotgun' proteomics platform of LC coupled to MS (LC/MS). The bioinformatics challenges for both methods are illustrated and compared, whereas existing commercial and academic packages and their workflows are described from both a user's and a technical perspective. Attention is given to the importance of sound statistical treatment of the resultant quantifications in the search for differential expression. Despite wide availability of proteomics software, a number of challenges have yet to be overcome regarding algorithm accuracy, objectivity and automation, generally due to deterministic spot-centric approaches that discard information early in the pipeline, propagating errors. We review recent advances in signal and image analysis algorithms in 2-DE, MS, LC/MS and Imaging MS. Particular attention is given to wavelet techniques, automated image-based alignment and differential analysis in 2-DE, Bayesian peak mixture models, and functional mixed modelling in MS, and group-wise consensus alignment methods for LC/MS.     

High levels of genetic diversity in populations of Iris aphylla L. (Iridaceae), an endangered species in Poland

We used RAPDs (Random Amplified Polymorphic DNAs) to investigate genetic diversity and its partition within and between three populations of Iris aphylla in Poland. Analysis of Molecular Variance (AMOVA) of 84 distinct RAPD multiband genotypes revealed higher variation within populations (77.2%) than genetic differentiation between them (22.8%, P  < 0.002). Values of genetic diversity indices ( H ) were similar in all three sites (0.21–0.24). The differentiation of the populations corresponded to low average gene flow ( Nm  = 0.81). Our results indicated that genetic diversity was independent of population size. We concluded that although sexual reproduction and gene flow between populations of I. aphylla were very limited, they preserved high levels of genetic diversity. Relatively large number of seeds, which migrated in the past to populations, as well as patterns of reproduction and life history of I. aphylla may explain this situation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 65–72.     

To sink or float: the fate of dormant offspring is determined by maternal behaviour in Daphnia

• 1 As the ephippia (chitinous shells enclosing diapausing eggs) of pelagic crustaceans of the genus Daphnia have been occasionally reported to float at the water surface, we considered that this might be an adaptation promoting their passive dispersal. We investigated the mechanisms by which ephippia appear at the water surface.
• 2 While field surveys revealed that floating Daphnia ephippia are often numerous in various freshwater habitats, laboratory tests showed that newly formed ephippia are not buoyant initially. Once transferred to the surface by whatever means, however, they may remain there due either to surface tension or gas absorption.
• 3 Video recordings showed that all ephippia at the water surface in laboratory vessels were shed there by ephippial females when moulting (despite the attendant risk of exposure to UV radiation). This implies that the moulting behaviour of female Daphnia may determine the fate of their dormant offspring, predetermining whether they remain in the natal environment (when the ephippium is released into the water column) or disperse (when it is deposited at the water surface).
• 4 Our findings reveal a potential mechanism underlying the high dispersal capacity of freshwater cladocerans inhabiting island‐like aquatic habitats.

     

The role of bioinformatics in two-dimensional gel electrophoresis

Over the last two decades, two-dimensional electrophoresis (2-DE) gel has established itself as the de facto approach to separating proteins from cell and tissue samples. Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research topic. The results of these analyses include accurate protein quantification, isoelectric point and relative molecular mass estimation, and the detection of differential expression between samples run on different gels. Systematic errors such as current leakage and regional expression inhomogeneities are corrected for, followed by each protein spot in the gel being segmented and modelled for quantification. To assess differential expression of protein spots in different samples run on a series of two-dimensional gels, a number of image registration techniques for correcting geometric distortion have been proposed. This paper provides a comprehensive review of the computation techniques used in the analysis of 2-DE gels, together with a discussion of current and future trends in large scale analysis. We examine the pitfalls of existing techniques and highlight some of the key areas that need to be developed in the coming years, especially those related to statistical approaches based on multiple gel runs and image mining techniques through the use of parallel processing based on cluster computing and the grid technology.     

Interpretation of Changes in Circulating Tumor Cell Counts

The presence of circulating tumor cells (CTCs) in the blood of cancer patients may guide the use of therapy. We investigated how to evaluate a reduction in the number of CTCs after administration of therapy. CTCs were enumerated with the CellSearch system in 111 metastatic breast and 185 metastatic prostate cancer patients before start of a new line of chemotherapy and after initiation of therapy. Different means to express changes in CTC counts were evaluated with respect to overall survival (OS). A static CTC cutoff is the best method to determine whether a therapy is effective. This is exemplified by the highest Cox hazard ratio of 2.1 for OS; three methods to express relative differences performed worse. A lookup table is provided from which the significance of a change in CTCs can be derived. The aim of therapy should be the elimination of all CTCs. A period of 10 to 12 weeks of therapy is needed to reach the treatment effect on CTCs.     

Chilled Galleria mellonella larvae: mechanism of supernumerary moulting

ABSTRACT. Supernumerary larval instars were produced when Galleria mellonella L. (Lepidoptera) larvae were chilled at 0°C. Although sensitivity to cooling stress of the last instar and younger larvae were generally the same, only penultimate and the last instar larvae showed a significant correlation between their age and the number of additional larval moults. Chilling stress induced a rapid and persistent increase in the JH titre of the last instar larvae. Severing the ventral nerve cord resulted in a predictable loss of the ability to produce supernumerary moults in chilled last instar larvae. The data suggest that sensory input stimulates allatotropic hormone secretion by the brain of chilled larvae. The possible mechanism controlling supernumerary moulting is discussed.     

Serotonin modulates a photic response in circadian locomotor rhythmicity of adults of the blow fly, Calliphora vicina

Abstract. The present experiments were undertaken to explore a role for serotonin (5-hydroxytryptamine, 5-HT) in modulating photic signal transduction in photoreceptors of the blow fly, Calliphora vicina. Injection of p-chlorophenylalanine (pCPA) into the haemolymph appeared to reduce sensitivity to the photic effects of constant ‘bright’ light (LL hyperactivity and circadian arrhythmicity). After drug injection in bright LL, flies continued with a free-running rhythm as in constant darkness (DD) or with a lengthened period τ as in ‘dim’ LL. When 5-HT was injected into flies kept in dim LL, they became hyperactive and arrhythmic as in bright LL. This finding suggests a potential role for serotonin as mediator of circadian changes in the insect visual system including extraretinal photoreceptors.     

PHYTOALEXIN DEFICIENT 4 affects reactive oxygen species metabolism,cell wall and wood properties in hybrid aspen (Populus tremula L. × tremuloides)

The PHYTOALEXIN DEFICIENT 4 (PAD4) gene in Arabidopsis thaliana (AtPAD4) is involved in the regulation of plant – pathogen interactions. The role of PAD4 in woody plants is not known; therefore, we characterized its function in hybrid aspen and its role in reactive oxygen species (ROS)‐dependent signalling and wood development. Three independent transgenic lines with different suppression levels of poplar PAD expression were generated. All these lines displayed deregulated ROS metabolism, which was manifested by an increased H₂O₂ level in the leaves and shoots, and higher activities of manganese superoxide dismutase (MnSOD) and catalase (CAT) in the leaves in comparison to the wild‐type plants. However, no changes in non‐photochemical quenching (NPQ) between the transgenic lines and wild type were observed in the leaves. Moreover, changes in the ROS metabolism in the pad4 transgenic lines positively correlated with wood formation. A higher rate of cell division, decreased tracheid average size and numbers, and increased cell wall thickness were observed. The results presented here suggest that the Populus tremula × tremuloides PAD gene might be involved in the regulation of cellular ROS homeostasis and in the cell division – cell death balance that is associated with wood development.     

Tuberculosis is associated with expansion of a motile,permissive and immunomodulatory CD16+ monocyte population via the IL-10/STAT3 axis

The human CD14⁺ monocyte compartment is composed by two subsets based on CD16 expression. We previously reported that this compartment is perturbed in tuberculosis (TB) patients, as reflected by the expansion of CD16⁺ monocytes along with disease severity. Whether this unbalance is beneficial or detrimental to host defense remains to be elucidated. Here in the context of active TB, we demonstrate that human monocytes are predisposed to differentiate towards an anti-inflammatory (M2-like) macrophage activation program characterized by the CD16⁺CD163⁺MerTK⁺pSTAT3⁺ phenotype and functional properties such as enhanced protease-dependent motility, pathogen permissivity and immunomodulation. This process is dependent on STAT3 activation, and loss-of-function experiments point towards a detrimental role in host defense against TB. Importantly, we provide a critical correlation between the abundance of the CD16⁺CD163⁺MerTK⁺pSTAT3⁺ cells and the progression of the disease either at the local level in a non-human primate tuberculous granuloma context, or at the systemic level through the detection of the soluble form of CD163 in human sera. Collectively, this study argues for the pathogenic role of the CD16⁺CD163⁺MerTK⁺pSTAT3⁺ monocyte-to-macrophage differentiation program and its potential as a target for TB therapy, and promotes the detection of circulating CD163 as a potential biomarker for disease progression and monitoring of treatment efficacy.