Opinion: Can coalescent models explain deep divergences in the diatoms and argue for the acceptance of paraphyletic taxa at all taxonomic hierarchies?

Although ancestral polymorphisms and incomplete lineage sorting are commonly used at the population level, increasing reports of these models have been invoked and tested to explain deep radiations. Hypotheses are put forward for ancestral polymorphisms being the likely reason for paraphyletic taxa at the class level in the diatoms based on an ancient rapid radiation of the entire groups. Models for ancestral deep coalescence are invoked to explain paraphyly and molecular evolution at the class level in the diatoms. Other examples at more recent divergences are also documented. Discussion as to whether or not paraphyletic groups seen in the diatoms at all taxonomic levels should be recognized is provided. The continued use of the terms centric and pennate diatoms is substantiated with additional evidence produced to support their use in diatoms both as descriptive terms for both groups and as taxonomic groups for the latter because new morphological evidence from the auxospores justifies the formal classification of the basal and core araphids as new subclasses of pennate diatoms in the Class Bacillariophyceae. Keys for higher levels of the diatoms showing how the terms centrics and araphid diatoms can be defined are provided.

Biomarker Geochemistry of Core Sediments in the Mangrove Ecosystems along Northern Kerala Coast

Mangroves are diverse group of trees, palms, shrubs, and ferns that share a common ability to live in waterlogged saline soils exposed to regular flooding, and are highly specialised plants which have developed unusual adaptations to the unique environmental conditions. They are sites of accumulation and preservation of both allochthonous and autochthonous organic matter owing to their strategic loction at the interface between land and sea and prevailing reducing environment. They are among the most productive ecosystems and are efficient carbon sinks with most of the carbon stored in sediments.Mangrove ecosystems play a significant role in global carbon cycle and hence the knowledge on the processes controlling the delivery of organic matter to coastal sediments, and how these signatures are preserved in the sediment is a prerequisite for the understanding of biogeochemical cycles. The evaluation of nature and sources of organic matter can be accomplished by the determination of biochemical constituents like carbohydrates, proteins and lipids. When characterised at molecular level, lipids provide valuable information about the sources of organic matter, even though they account only small fraction of organic matter. They are useful for the paleo-environmental reconstruction because of their low reactivity, high preservation potential and high source specificity relative to other organic class of compounds. The application of recent analytical techniques has produced a wealth of useful information but has also indicated the gaps in our knowledge on cycling of organic matter in the coastal ecosystems. The quantity and quality of organic matter preserved in sediments vary depending up on the nature of material delivered to the sediment and on the depositional environment. The input from both autochthonous and allochthonous sources sharpens the complexity of biogeochemistry of mangrove ecosystem and hence bulk sedimentary parameters are not completely successful in evaluating the sources of organic matter in mangrove sediments. An effective tool for the source characterisation of organic matter in coastal ecosystems is biomarker approach. Biomarkers are chemical "signatures" present in environmental samples whose structural information can be linked to its biological precursor. The usefulness of molecular biomarkers depends on high taxonomic specificity, potential for preservation, recalcitrant against geochemical changes, easily analysable in environmental samples and should have a limited number of well-defined sources.

Through Class Darkly: Class in the British TV Noir

Class has always been at the heart of the television crime drama. Whether it is the post-war paternalism of Dixon of Dock Green (1955 – 1976), the harsh social realism of The Sweeney (1975-1978), or the almost mythical evocations of Britain in Heartbeat (1992 – 2010) and Midsomer Murders (1997- present), class and crime have always been seen as being inextricably linked. Since the 1990s, the British crime drama has been influenced by successive waves of cultural imports from, firstly, the US and then from Scandinavia. There is now a recognisable ‘genre’ for what we might think of as British TV Noir. Beginning with shows such as Cracker (1993 – 2006), Prime Suspect (1991 – 2006) and Messiah (2001) and continuing with dramas like Red Riding (2008), Southcliffe (2013) and Hinterland (2013 – present), the British TV Noir employs narratives and stylistic tropes that might usually be associated with the cinema of the 1940s. Although drawing influence from high profile shows such as Twin Peaks (1990 – 1991), Millennium (1996) and (latterly) The Wire (2002 – 2008), CSI (2000 – present) and The Killing (2007) these British Noir shows also articulate the nation’s shifting class system. As Susan Sydney-Smith has ably demonstrated, the crime drama is “historically contingent” (Sydney-Smith, 2002, p. 5) and shaped by the surrounding socio-political, as well aesthetic, context. To this end, this chapter traces the depiction of class in three key crime series – Prime Suspect, Red Riding and Southcliffe - and explores how social class, and more importantly, its changing face provides a constant background to the narratives and characterisations. These three texts were each produced at pivotal moments in Britain’s relationship to class – Prime Suspect was shown 6 months after Margaret Thatcher vacated office; Red Riding was produced in the midst of the global recession in 2008 and Southcliffe was made in the shadows of stringing welfare and immigration reforms. These texts span three successive political administrations and over two decades of social and political change. Understanding the relationship between criminal activity and class in these dramas however is far more complicated than simply reading the historical context through the text. Commensurate with its cinematic incarnation, TV Noir is both reflective and productive, employing visual and narrative tropes to manipulate, as well reflect, its audience’s moral and social positioning. The picture that emerges from an examination of class and the British TV Noir is one of suspicion and discontent. As Andrew Spicer suggests (with reference to British cinema) the Noir sensibility both depicts and critiques a society that it sees as being “class-ridden, racist and misogynist” (Spicer, 2002, p.202). This is certainly the case with the texts that are being examined here, as social positions and taxonomies are constantly being redefined and renegotiated.

Cultivating Subjectivities: The Class Politics of Convivial Labor in the Interstitial Spaces of Neoliberal Neglect

Thesis (Ph.D.)--University of Washington, 2016-08

Functions of the SLC36 transporter Pathetic in growth control of Drosophila sensory neurons

Thesis (Ph.D.)--University of Washington, 2016-08

Series representations of the remainders in the expansions for certain functions with applications

We present a summary of the series representations of the remainders in the expansions in ascending powers of t of 2/(et+1)2/(et+1) , sech t and coth t and establish simple bounds for these remainders when t>0t>0 . Several applications of these expansions are given which enable us to deduce some inequalities and completely monotonic functions associated with the ratio of two gamma functions. In addition, we derive a (presumably new) quadratic recurrence relation for the Bernoulli numbers Bn.

Studies on the Gospels in harmony: being the fourth or Bible-class grade in the series of lessons on the life of Christ. Harmonized from the four evangelists.

Mode of access: Internet.

Influence of socio-cultural identity of ase foundation adolescent students in their participation and attitude in the english class

Tesis (Licenciado en Lenguas Castellana, Inglés y Francés).--Universidad de La Salle. Facultad de Ciencias de La Educación. Licenciatura en Lengua Castellana, Inglés y Francés, 2014

Development of dendritic cells in the intestine

The intestinal tract is exposed to a large variety of antigens such as food proteins, commensal bacteria and pathogens and contains one of the largest arms of the immune system. The intestinal immune system has to discriminate between harmless and harmful antigens, inducing tolerance to harmless antigens and active immunity towards pathogens and other harmful materials. Dendritic cells (DC) in the mucosal lamina propria (LP) are central to this process, as they sample bacteria from the local environment and constitutively migrate to the draining mesenteric lymph nodes (MLN), where they present antigen to naïve T cells in order to direct an appropriate immune response. Despite their crucial role, understanding the function and phenotype of LP DC has been hampered by the fact that they share phenotypic markers with macrophages (mφ), which are the dominant population of mononuclear phagocyte (MP) in the LP. Recent work in our own and other laboratories has established gating strategies and phenotyping panels that allow precise discrimination between intestinal DC and mφ using the mφ specific markers CD64 and F4/80. In this way four bona fide DC subsets with distinct functions have been identified in adult LP based on their expression of CD11b and CD103 and a major aim of my project was to understand how these subsets might develop in the neonatal intestine. At the beginning of my PhD, the laboratory had used these new methods to show that signal regulatory protein α (SIRPα), an inhibitory receptor expressed by myeloid cells, was expressed by mφ and most DC in the intestine, except for those expressing CD103 alone. In addition, mice carrying a non-signalling mutation in SIRPα (SIRPα mt) had a selective reduction in CD103+CD11b+ DC, a subset which is unique to the intestinal LP. This was the basis for the initial experiments of my project, described in Chapter 3, where I investigated if the phenotype in SIRPα mt mice was intrinsic to haematopoietic cells or not. To explore this, I generated bone marrow (BM) chimeric mice by reconstituting irradiated WT mice with SIRPα mt BM, or SIRPα mt animals with WT BM. These experiments suggested that the defect in CD103+CD11b+ DC was not replicated in DC derived from BM of SIRPα origin. However as this seemed inconsistent with other data, I considered the possibility that 18 the phenotype may have been lost with age, as the BM chimeric mice were considerably older than those used in the original studies of SIRPα function. However a comparison of DC subsets in the intestine of WT and SIRPα mt mice as they aged provided no conclusive evidence to support this idea. As these experiments did show age-dependent effects on DC subsets, in Chapter 4, I went on to investigate how the DC populations appeared in the intestine and other tissues in the neonatal period. These experiments showed there were few CD103+CD11b+ DC present in the LP and migratory DC compartment of the MLN in the neonate and that as this population gradually increased in proportion with age, there was a reciprocal decrease in the relative proportion of CD103-CD11b+ DC. Interestingly, most of the changes in DC numbers in the intestine were found during the second or third week of life when the weaning process began. To validate my findings that there were few CD103+CD11b+ DC in the neonate and that this was not merely an absence of CD103 upregulation, I examined the expression of CD101 and Trem-1, markers that other work in the laboratory had suggested were specific to the CD103+CD11b+ DC lineage. My work showed that CD101 and Trem-1 were co- expressed by most CD103+CD11b+ DC in small intestine (SI) LP, as well as a small subset of CD103-CD11b+ DC in this tissue. Interestingly, Trem-1 was highly specific to the SI LP and migratory DC in the MLN, but absent from the colon and other tissues. CD101 expression was also only found on CD11b+ DC, but showed a less restricted pattern of distribution, being found in several tissues as well as the SI LP. The relative timing of their development suggested there might be a relationship between CD103+CD11b+ and CD103-CD11b+ DC and this was supported by microarray analysis. I hypothesised that the CD103-CD11b+ DC that co-expressed CD101 and Trem-1 may be the cells that developed into CD103+CD11b+ DC. To investigate this I analysed how CD101 and Trem-1 expression changed with age amongst the DC subsets in SI LP, colonic LP (CLP) and MLN. The proportion of CD101+Trem-1+ cells increased amongst CD103+CD11b+ DC in the SI LP and MLN with age, while amongst CD103+CD11b+ DC in the CLP this decreased. This was not the same in CD103-CD11b+ DC, where CD101 and Trem-1 expression was more varied with age in all tissues. CD101 and Trem-1 were not expressed to any great extent on CD103+CD11b- or CD103-CD11b- DC. The phenotypic development of the 19 intestinal DC subsets was paralleled by the gradual upregulation of CD103 expression, while the production of retinoic acid (RA), as assessed by the AldefluorTM assay, was low early in life and did not attain adult levels until after weaning. Thus DC in the neonatal intestine take some time to acquire the adult pattern of phenotypic subsets and are functionally immature compared with their adult counterparts. In Chapter 5, I used CD101 and Trem-1 to explore the ontogeny of intestinal DC subsets in CCR2-/- and SIRPα mt mice, both of which have selective defects in one particular group of DC. The selective defect seen amongst CD103+CD11b+ DC in adult SIRPα mt mice was more profound in mice at D7 and D14 of age, indicating that it may be intrinsic to this population and not highly dependent on environmental factors that change after birth. The expression of CD101 and Trem-1 by both CD103+CD11b+ and CD103-CD11b+ DC was reduced in SIRPα mt mice, again indicating that this entire lineage was affected by the lack of SIRPα signalling. However there was also a generalised defect in the numbers of all DC subsets in many tissues from early in life, suggesting there was compromised development, recruitment or survival of DC in the absence of SIRPα signalling. In contrast to the findings in SIRPα mt mice, more CD103+CD11b+ DC co-expressed CD101 and Trem-1 in CCR2-/- mice, while there were no differences in the expression of these molecules amongst CD103-CD11b+ DC. This may suggest that CCR2+ CD103-CD11b+ DC are not the cells that express CD101 and Trem-1 that are predicted to be the direct precursors of CD103+CD11b+ DC. I also examined the expression of DC growth factor receptors on DC subsets from mice of different ages, but no clear age or subset- related patterns of the expression of mRNA for Csf2ra, Irf4, Tgfbr1 and Rara could be observed. Next, I investigated whether Trem-1 played any role in DC development. Preliminary experiments in Trem-1-/- mice show no differences between any of the DC subsets, nor were there any selective effects on individual subsets when DC development from Trem-1-/- KO and WT BM was compared in competitive chimeras. However these experiments were difficult to interpret due to viability problems and because I found an unexpected defect in the ability of Trem-1-/- BM to generate all DC, irrespective of whether they expressed Trem-1 or not. 20 The final experiments I carried out were to examine the role of the microbiota in driving the differentiation of intestinal DC subsets, based on the hypothesis that this could be one of the environmental factors that might influence events in the developing intestine. To this end I performed experiments in both antibiotic treated and germ free adult mice, both of which showed no significant phenotypic differences amongst any of the DC subsets. However the study of germ free mice was compromised by recent contamination of the colony and may not be the conclusive answer. Together the data in this thesis have shown that the population of CD103+CD11b+ DC, which is unique to the intestine, is not present at birth. These cells gradually increase in frequency over time and as this occurs there is a reciprocal decrease in the frequency of CD103-CD11b+ DC. Along with other results, this leads to the idea that there may be a linear developmental pathway from CD103-CD11b+ DC to CD103+CD11b+ DC that is driven by non-microbial factors that are located preferentially in the small intestine. My project indicates that markers such as CD101 and Trem-1 may assist the dissection of this process and highlights the importance of the neonatal period for these events.

Seafloor heterogeneity influences the biodiversity–ecosystem functioning relationships in the deep sea

Theoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale, and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystems.

Assessing land–ocean connectivity via submarine groundwater discharge (SGD) in the Ria Formosa Lagoon (Portugal): combining radon measurements and stable isotope hydrology

Natural radioactive tracer-based assessments of basin-scale submarine groundwater discharge (SGD) are well developed. However, SGD takes place in different modes and the flow and discharge mechanisms involved occur over a wide range of spatial and temporal scales. Quantifying SGD while discriminating its source functions therefore remains a major challenge. However, correctly identifying both the fluid source and composition is critical. When multiple sources of the tracer of interest are present, failure to adequately discriminate between them leads to inaccurate attribution and the resulting uncertainties will affect the reliability of SGD solute loading estimates. This lack of reliability then extends to the closure of local biogeochemical budgets, confusing measures aiming to mitigate pollution. Here, we report a multi-tracer study to identify the sources of SGD, distinguish its component parts and elucidate the mechanisms of their dispersion throughout the Ria Formosa – a seasonally hypersaline lagoon in Portugal. We combine radon budgets that determine the total SGD (meteoric + recirculated seawater) in the system with stable isotopes in water (δ2H, δ18O), to specifically identify SGD source functions and characterize active hydrological pathways in the catchment. Using this approach, SGD in the Ria Formosa could be separated into two modes, a net meteoric water input and another involving no net water transfer, i.e., originating in lagoon water re-circulated through permeable sediments. The former SGD mode is present occasionally on a multi-annual timescale, while the latter is a dominant feature of the system. In the absence of meteoric SGD inputs, seawater recirculation through beach sediments occurs at a rate of  ∼  1.4  ×  106 m3 day−1. This implies that the entire tidal-averaged volume of the lagoon is filtered through local sandy sediments within 100 days ( ∼  3.5 times a year), driving an estimated nitrogen (N) load of  ∼  350 Ton N yr−1 into the system as NO3−. Land-borne SGD could add a further  ∼  61 Ton N yr−1 to the lagoon. The former source is autochthonous, continuous and responsible for a large fraction (59 %) of the estimated total N inputs into the system via non-point sources, while the latter is an occasional allochthonous source capable of driving new production in the system.

Crystallization and preliminary X-ray diffraction analysis of a eumenine mastoparan toxin: a new class of mast-cell degranulating peptide in the wasp venom

Mastoparans are tetradecapeptides found to be the major component of vespid venoms. A mastoparan toxin isolated from the venom of Anterhynchium flavomarginatum micado has been crystallized and X-ray diffraction data collected to 2.7 Angstrom resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P6(2)22 (P6(4)22). This is the first mastoparan to be crystallized and will provide further insights into the conformational significance of mastoparan toxins with respect to their potency and activity in G-protein regulation.