bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Transmigration of Souls: Reincarnation Into Animal Bodies in Pythagoras, Empedocles, and Plato
Authors: Osborne Catherine
Published: May 2008

This chapter considers what is involved in the claim that some species are ‘similar to’ or ‘different from’ ourselves, and what role such claims play in moral discourse. Examples are taken from the reincarnation theories of Pythagoreans, Empedocles, and Plato, which suggest that animal souls are in some way the same as human souls. Texts discussed include Xenophanes (on Pythagoras and the puppy), Empedocles (on animal sacrifice), and Plato's Timaeus (on the creation of all animals as human animals in the first generation). The chapter argues that moral philosophy is not grounded in biology, but rather that the psychological and biological agenda is motivated by prior commitment to the truth of a certain moral outlook.
On Language, Concepts, and Automata: Rational and Irrational Animals in Aristotle and Descartes
Authors: Osborne Catherine
Published: May 2008

This chapter considers whether language or concepts are necessary for intelligent purposive agency, and argues that neither humans nor animals require propositional thought or concepts for normal decisions and purposive behaviour. The idea that second order reflection on reasons and intentions is additionally available to humans is shown to be irrelevant to first order intention. Descartes' mechanistic account of human and animal behaviour is inspired by Aristotle's discussion in De motu animalium, but deliberately rejects ‘imagination’ (phantasia), which served for Aristotle to secure intelligent agency by means of stored perceptions, without mental concepts or complex propositions. Aristotle's account (including Posterior Analytics B19) is compared to Plato's notion of recollection (anamnesis) as a source of concepts in humans and animals, with a view to illustrating the similarity of the two models, and the relative merits of the Platonic one.
On the Vice of Sentimentality: Androcles and the Lion and Some Extraordinary Adventures in the Desert Fathers
Authors: Osborne Catherine
Published: May 2008

This chapter investigates the notion of sentimentality and the vice of excessive sentimental attachment. It reviews a number of fables from the classical tradition and from the stories of the desert fathers, to explore the limits of realism and sentimentality and to consider what purpose is served by such fabulous tales in which the beasts are portrayed as more intelligent and morally superior to the human subjects. It suggests that the tales are designed to engineer a change in moral outlook on the part of the readers, and to open their eyes to the moral corruption of human society, and to present an image of heaven (an ideal society in which human corruption is absent).
On the Notion of Natural Rights: Defending the Voiceless and Oppressed in the Tragedies of Sophocles
Authors: Osborne Catherine
Published: May 2008

The chapter asks about the idea of animal rights and seeks to show that talk of ‘natural rights’ in general, where it is coherent at all, is designed to express moral outrage on the part of a third party against the abuse of the vulnerable and voiceless. This being so, it cannot be the case that to have a natural right one must have a voice or language. Quite the reverse is the case. The chapter also shows that the appeal to moral absolutes on behalf of the oppressed in respect of their most basic needs, for which ‘natural rights’ talk is currently the favoured discourse, is a longstanding part of traditional moral thinking and can be traced in the tragedies of Sophocles.
Man's Wars
Authors: Donagan Barbara
Published: May 2008

This chapter focuses on English views about war. Despite its absence from English soil, war was present in English minds through stories about political and military operations, and the horrors and atrocities committed in the continental war. English knowledge of the continental war formed expectations as to the nature of war and contributed to the anxiety and nervousness of civilians as war approached home. Sensational news from Germany may have conditioned the English public to a heightened response to reports of cruelty, sexual outrage, and broken taboos, and contributed to the violence of the reaction to the Irish rebellion of 1641, which in turn cast a long shadow over the civil war years.
Boarstall House 1645–1646
Authors: Donagan Barbara
Published: May 2008

This chapter details the siege of Boarstall House, a small-scale military event that dragged on to the middle of 1646. By then, the defenders' obstinate refusal to admit that their party had been defeated and that further resistance was futile frustrated and irritated the parliamentarian enemy.
Colchesters Teares: Fire, Hunger, and Atrocity
Authors: Donagan Barbara
Published: May 2008

This chapter focuses on the outcome of the siege of the city of Colchester. The siege of Colchester was uncommonly harsh in the suffering it brought to soldiers and civilians. Much in the military management and the treatment accorded civilians at Colchester was nonetheless the ordinary stuff of sieges, but much was also exceptional and was seen to be so by contemporaries. Some claimed not only that European levels of starvation and destruction had been introduced into England, but that the codes of war had been abandoned. Each side accused the other of being the instigator of civilian suffering and at the same time legalistically justified its draconian interpretation of the laws of war.
Conclusion
Authors: Donagan Barbara
Published: May 2008

This concluding chapter presents a synthesis of discussions in the preceding chapters. The preceding chapters have attempted to convey something of the actuality of the civil war, and the responses of soldiers and civilians to its professional, moral, and material demands. Study of the war reveals, alongside occasional atrocities, frequent cruelties, and vituperative narratives, the attempt to restrain conduct within bounds that would make it possible to preserve a recognizable — and, structurally, a fundamentally unchanged — English society.
The world outside thepolis
Authors: Clarke Katherine
Published: May 2008

This chapter explores the expression of time in non-polis historiography in order to highlight distinctive features of city-histories. In particular, it examines the synthetic temporal frameworks and strategies of Olympiadic dating and synchronism which were developed by universal historians, such as Ephorus, Timaeus, Polybius, and Diodorus, to overcome the fact that different poleis had different calendars and different histories. It takes Strabo as an example of an author whose presentation of the past spans both local and universal frameworks. It also looks at the way in which time is configured by Greek authors writing about the non-Greek world in order to discern trends and recurring themes in the treatment of time, which throw into relief the Greek city-histories.
EPILOGUE
Authors: Clarke Katherine
Published: May 2008

This chapter stresses the significance of time not only to professional chronographers and historians, but also to the polis. Articulating and expressing time effectively and plausibly, particularly in local history, mattered. The historian, the orator, or the artist used the same frameworks as the chronographers but to serve the polis; he linked the formal manipulation of time and the life of the city. Tragic and comic dramatists, orators, native and visiting historians, rhapsodes, exegetae, and statesmen all offered versions of the past for the polis to reject or to accept.
4 Consonant Epenthesis: Natural and Unnatural Histories
Authors: Blevins Juliette
Published: May 2008

This chapter argues that there are clear natural and unnatural histories for patterns of consonant insertion which make no reference to syllable onset or segmental markedness. It offers new ways of understanding the typology of C-epenthesis. Within the realm of natural history, glide epenthesis and laryngeal epenthesis are two distinct subtypes with different phonetic and phonological profiles. In the domain of unnatural histories, significant correlations are observed between consonants subject to coda weakening and those involved in epenthesis. This finding follows from our understanding of rule inversion as part of phonological acquisition. Finally, a mix of natural and unnatural history characterizes the analysis of Oceanic j-accretion and Ritwan l-sandhi.
Dispersal in Plants
Authors: Cousens Roger , Dytham Calvin , Law Richard
Published: May 2008

Ecologists, both practical and theoretical, now appreciate that to understand biological systems they must consider the spatial dimension. Consequently, dispersal has become one of the hottest topics in plant ecology. However, in the midst of so much research output on dispersal, there is a need for a stock-take to determine the needs of future research: what has been achieved to date, where do current studies fit in, and what still needs to be determined? What are the implications of dispersal for those engaged in managing plant populations and communities? This is the first book for many years to present a synthesis of research on dispersal and its implications for plant population dynamics. The book consists of three sections: Section A reviews information on the biological and environmental processes that determine the path of an individual dispersing propagule, usually a seed, and the theory that has been developed to predict these trajectories; Section B discusses the distributions of seeds resulting from dispersal from an entire plant, theoretical research predicting the shapes of these distributions and design issues for future dispersal studies; Section C explores the implications of dispersal for expansion of populations, structure within existing populations and communities, and the evolution of dispersal traits.
5 The International Mobility of Entrepreneurs and Regional Upgrading in India and China
Authors: Saxenian AnnaLee
Published: May 2008

By 2000, over one-third of Silicon Valley's high-skilled workers were foreign-born, and overwhelmingly from Asia. These US-educated engineers are transforming developmental opportunities for formerly peripheral regions as they build professional and business connections to their home countries. In a process more akin to ‘brain circulation’ than ‘brain drain’, these engineers and entrepreneurs, aided by the lowered transaction costs associated with digitization, are transferring technical and institutional know-how between distant regional economies faster and more flexibly than most large corporations. This chapter examines how Chinese and Indian-born engineers are contributing to highly localized processes of entrepreneurial experimentation in their home countries, while maintaining close ties to the technology and markets in Silicon Valley.
10 International Organizations as a Profession: Professional Mobility and Power Distribution
Authors: Coicaud Jean‐Marc
Published: May 2008

The role of international organizations grows with the acceleration of globalization and the increasing importance of global governance. However, thus far, only limited and rather narrow research has been generated on the subject. It is a state of affairs that reflects on international studies, as well as on the power realities of the world. By assessing international organizations through the career prospects that they offer to skilled professionals, this chapter is an attempt to remedy this situation. As such it unveils some of the internal dynamics of international organizations and explores their external consequences in terms of the relations between international organizations, the people employed by these, and the power play (economic, social, political, and even cultural) at the national and international level.
5 Practical Politics
Authors: Black Antony
Published: May 2008

Muslim Advices-to-Kings took into account Realpolitik in a way that European political writings did not, until Machiavelli. They were handbooks of political management and social psychology with a prudential, utilitarian approach. Muslims saw ruthless force applied for the right ends as legitimate. The idea of ‘the circle of power’ embodied an Iranian view of the relationship between power and justice. Ibn Khaldun saw the caliphate and 'umma as subject to the same universal pattern as other states, in which tribal groups, nurtured in the wilderness and inspired by collective loyalty ('asabiyya), take over civilization and then themselves become decadent. His thought partly anticipated the sociological theories of Hegel and Marx.
7 Changes in Religion and Politics
Authors: Black Antony
Published: May 2008

The papalist revolution of the 11th century led to greater divergence between the political thought of the West and of Islam and Byzantium. Pope Gregory VII's views on papal sovereignty provided a prototype for the modern Western state. He and his supporters desacralized kingship. Their attempt to subordinate the state to the church provoked a reaction which led to secular theories of the state. This ‘first European revolution’ coincided with the rise of city republics and economic development. Sunni Islam was consolidated through a firmer alliance between the sultans and the 'ulama. But the Mongol invasions hastened economic and cultural decline. The Shi'ite revolution in 16th-century Iran resulted in social dominance for the Shi'ite 'ulama. This laid a basis for their rise to political power in the 20th century. These changes in the relationship between religion and politics had the opposite results in the West and in Islam.
Towards a New Modus Operandi of the International Financial System
Authors: Cohen Daniel
Published: May 2008

The Bretton Woods system was conceived as a fixed exchange rate regime, allowing for a few devaluations, with the IMF supplying a line of credits to countries in ‘transitory’ difficulties. As capital mobility expanded, the system has radically changed. The role of the IMF is no longer to finance ‘transitory’ balance of payments disequilibria, which almost by definition can be dealt with by financial integration. As a result of capital mobility, however, orderly resolution of sovereign debt crises has also become more difficult in the past decade. The political difficulty of setting up an international court with authority over the handling of sovereign debt has also appeared be unattainable. This chapter reports a new modus operandi rather than a big bang approach to the reform of the system.
Spatio-temporal patterns of fishing pressure on UK marine landscapes, and their implications for spatial planning and management
Authors: Stelzenmüller Vanessa , Rogers Stuart I. , Mills Craig M.
Published: May 2008

Stelzenmüller, V., Rogers, S. I., and Mills, C. M. 2008. Spatio-temporal patterns of fishing pressure on UK marine landscapes, and their implications for spatial planning and management. – ICES Journal of Marine Science, 65: 1081–1091. The spatio-temporal distribution of fishing pressure on marine landscapes in offshore UK (England and Wales) waters is assessed, based on a time-series of fishing vessel monitoring system (VMS) data for UK and foreign fleets deploying beam and otter trawls, and scallop dredges. The results reveal that marine landscapes with coarse or mixed sediments and weak or moderate tide stress are heavily fished. Marine landscapes experienced different intensities of fishing pressure depending on their spatial location in UK offshore waters and the regional heterogeneity of landscape types. Spatial patterns of fishing pressure vary by region, but within regions, patches of high fishing pressure remain centred at the same locations. When designing marine management plans, it is important to take account of the spatial extent and patchiness of fishing activity, and the consistency with which areas are fished in the same region from year to year. Descriptions of the spatial distribution of fishing pressures will become more meaningful at a local level if they also reflect the sensitivity of the habitats to those pressures. The further development of such sensitivity analyses, using life-history traits or measures of benthic production, is now becoming a priority.
Orientation of eddy fluxes in geostrophic turbulence
Authors: Nadiga B.T
Published: May 2008

Given its importance in parametrizing eddies, we consider the orientation of eddy flux of potential vorticity (PV) in geostrophic turbulence. We take two different points of view, a classical ensemble- or time-average point of view and a second scale decomposition point of view. A net alignment of the eddy flux of PV with the appropriate mean gradient or the large-scale gradient of PV is required. However, we find this alignment to be very weak. A key finding of our study is that in the scale decomposition approach, there is a strong correlation between the eddy flux and a nonlinear combination of resolved gradients. This strong correlation is absent in the classical decomposition. This finding points to a new model to parametrize the effects of eddies in global ocean circulation.
PX-RICS mediates ER-to-Golgi transport of the N-cadherin/β-catenin complex
Authors: Nakamura Tsutomu , Hayashi Tomoatsu , Nasu-Nishimura Yukiko , Sakaue Fumika , Morishita Yasuyuki , Okabe Toshio , Ohwada Susumu , Matsuura Ken , Akiyama Tetsu
Published: May 2008

Cadherins mediate Ca2+-dependent cell–cell adhesion. Efficient export of cadherins from the endoplasmic reticulum (ER) is known to require complex formation with β-catenin. However, the molecular mechanisms underlying this requirement remain elusive. Here we show that PX-RICS, a β-catenin-interacting GTPase-activating protein (GAP) for Cdc42, mediates ER-to-Golgi transport of the N-cadherin/β-catenin complex. Knockdown of PX-RICS expression induced the accumulation of the N-cadherin/β-catenin complex in the ER and ER exit site, resulting in a decrease in cell–cell adhesion. PX-RICS was also required for ER-to-Golgi transport of the fibroblast growth factor-receptor 4 (FGFR4) associated with N-cadherin. PX-RICS-mediated ER-to-Golgi transport was dependent on its interaction with β-catenin, phosphatidylinositol-4-phosphate (PI4P), Cdc42, and its novel binding partner γ-aminobutyric acid type A receptor-associated protein (GABARAP). These results suggest that PX-RICS ensures the efficient entry of the N-cadherin/β-catenin complex into the secretory pathway, and thereby regulates the amount of N-cadherin available for cell adhesion and FGFR4-mediated signaling.
Fibronectin fibrillogenesis regulates three-dimensional neovessel formation
Authors: Zhou Xiaoming , Rowe R. Grant , Hiraoka Nobuaki , George Jerry P. , Wirtz Denis , Mosher Deane F. , Virtanen Ismo , Chernousov Michael A. , Weiss Stephen J.
Published: May 2008

During vasculogenesis and angiogenesis, endothelial cell responses to growth factors are modulated by the compositional and mechanical properties of a surrounding three-dimensional (3D) extracellular matrix (ECM) that is dominated by either cross-linked fibrin or type I collagen. While 3D-embedded endothelial cells establish adhesive interactions with surrounding ligands to optimally respond to soluble or matrix-bound agonists, the manner in which a randomly ordered ECM with diverse physico-mechanical properties is remodeled to support blood vessel formation has remained undefined. Herein, we demonstrate that endothelial cells initiate neovascularization by unfolding soluble fibronectin (Fn) and depositing a pericellular network of fibrils that serve to support cytoskeletal organization, actomyosin-dependent tension, and the viscoelastic properties of the embedded cells in a 3D-specific fashion. These results advance a new model wherein Fn polymerization serves as a structural scaffolding that displays adhesive ligands on a mechanically ideal substratum for promoting neovessel development.
Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease
Authors: Cloos Paul A.C. , Christensen Jesper , Agger Karl , Helin Kristian
Published: May 2008

The enzymes catalyzing lysine and arginine methylation of histones are essential for maintaining transcriptional programs and determining cell fate and identity. Until recently, histone methylation was regarded irreversible. However, within the last few years, several families of histone demethylases erasing methyl marks associated with gene repression or activation have been identified, underscoring the plasticity and dynamic nature of histone methylation. Recent discoveries have revealed that histone demethylases take part in large multiprotein complexes synergizing with histone deacetylases, histone methyltransferases, and nuclear receptors to control developmental and transcriptional programs. Here we review the emerging biochemical and biological functions of the histone demethylases and discuss their potential involvement in human diseases, including cancer.
Regulation of alternative polyadenylation by genomic imprinting
Authors: Wood Andrew J. , Schulz Reiner , Woodfine Kathryn , Koltowska Katarzyna , Beechey Colin V. , Peters Jo , Bourc’his Deborah , Oakey Rebecca J.
Published: May 2008

Maternally and paternally derived alleles can utilize different promoters, but allele-specific differences in cotranscriptional processes have not been reported. We show that alternative polyadenylation sites at a novel murine imprinted gene (H13) are utilized in an allele-specific manner. A differentially methylated CpG island separates polyA sites utilized on maternal and paternal alleles, and contains an internal promoter. Two genetic systems show that alleles lacking methylation generate truncated H13 transcripts that undergo internal polyadenylation. On methylated alleles, the internal promoter is inactive and elongation proceeds to downstream polyadenylation sites. This demonstrates that epigenetic modifications can influence utilization of alternative polyadenylation sites.
Making and Diluting Stock Solutions
Authors: Adams Dany Spencer
Published: May 2008

INTRODUCTION

For particular experiments, certain solutions are used frequently and are therefore made up in large quantities. To minimize the volume actually occupied by these solutions, they are often made at a higher concentration than that which will be used. These concentrated solutions are referred to as stock solutions. Stock solutions save time in addition to space; when you need a solution of a given concentration, you need only dilute the stock rather than starting from scratch. This article describes the steps necessary to make and dilute stock solutions appropriately.
Dissection of Larval Salivary Glands and Polytene Chromosome Preparation: Figure 1.
Authors: Kennison James A.
Published: May 2008

INTRODUCTION

Although the large polytene chromosomes of diptera were originally described in the late 1880s, it was not until the early 1930s that their significance to the study of the genome of Drosophila was realized. Polytene chromosomes are found in several larval and adult tissues, but preparations are usually made of the chromosomes in the larval salivary glands, because the glands are easily dissected and the polytene chromosomes are large.
Phenotypic Analysis of Arabidopsis Mutants: Gibberellin/Abscisic Acid/Paclobutrazol Hormone Response
Authors: Blázquez Miguel
Published: May 2008

INTRODUCTION

Seed germination requires breaking the dormancy that is maintained by abscisic acid (ABA) and involves the activation of gibberellin (GA) biosynthesis and signaling. Mutants with low germination rates may be defective in GA biosynthesis and/or signaling and often require exogenous GAs for efficient germination. Conversely, mutants with either increased GA signaling or reduced signaling by the GA antagonist ABA are resistant to GA-biosynthesis inhibitors or ABA, respectively. Mutants with enhanced GA signaling or decreased ABA content are also more resistant to inhibition of germination by Paclobutrazol (PAC), a GA biosynthesis inhibitor. This protocol describes the measurement of the germination rate of Arabidopsis seeds in the presence of GA, ABA, or PAC.
Hematoxylin and Eosin Staining of Tissue and Cell Sections
Authors: Fischer Andrew H. , Jacobson Kenneth A. , Rose Jack , Zeller Rolf
Published: May 2008

INTRODUCTION

Hematoxylin and eosin (H&E) stains have been used for at least a century and are still essential for recognizing various tissue types and the morphologic changes that form the basis of contemporary cancer diagnosis. The stain has been unchanged for many years because it works well with a variety of fixatives and displays a broad range of cytoplasmic, nuclear, and extracellular matrix features. Hematoxylin has a deep blue-purple color and stains nucleic acids by a complex, incompletely understood reaction. Eosin is pink and stains proteins nonspecifically. In a typical tissue, nuclei are stained blue, whereas the cytoplasm and extracellular matrix have varying degrees of pink staining. Well-fixed cells show considerable intranuclear detail. Nuclei show varying cell-type- and cancer-type-specific patterns of condensation of heterochromatin (hematoxylin staining) that are diagnostically very important. Nucleoli stain with eosin. If abundant polyribosomes are present, the cytoplasm will have a distinct blue cast. The Golgi zone can be tentatively identified by the absence of staining in a region next to the nucleus. Thus, the stain discloses abundant structural information, with specific functional implications. A limitation of hematoxylin staining is that it is incompatible with immunofluorescence. It is useful, however, to stain one serial paraffin section from a tissue in which immunofluorescence will be performed. Hematoxylin, generally without eosin, is useful as a counterstain for many immunohistochemical or hybridization procedures that use colorimetric substrates (such as alkaline phosphatase or peroxidase). This protocol describes H&E staining of tissue and cell sections.
Paraffin Embedding Tissue Samples for Sectioning
Authors: Fischer Andrew H. , Jacobson Kenneth A. , Rose Jack , Zeller Rolf
Published: May 2008

INTRODUCTION

This protocol describes a method for embedding tissues in paraffin blocks for sectioning. Paraffin sections require extensive fixation and processing steps, but provide superior morphology compared with other sectioning methods.
Decalcifying Tissues for Paraffin Embedding
Authors: Fischer Andrew H. , Jacobson Kenneth A. , Rose Jack , Zeller Rolf
Published: May 2008

INTRODUCTION

Paraffin sections of bone usually require a decalcification step after fixation before sectioning. This protocol describes a method for decalcifying fixed tissue.
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase
Authors: Liu Chih Long , Bernstein Bradley E. , Schreiber Stuart L.
Published: May 2008

INTRODUCTION

T7-based linear amplification of DNA (TLAD) uses a linear amplification approach based on in vitro transcription (IVT) of template DNA by RNA polymerase from T7 phage. TLAD was designed for use with the ChIP-chip method (whereby DNA recovered from chromatin immunoprecipitation [ChIP] of cell lysate is used for subsequent analysis on DNA microarrays) and requires nanogram quantities of dsDNA to generate microgram amounts of amplified RNA. In Part I of the method, described here, a 3′ conserved end is added to the template dsDNA, using terminal deoxynucleotidyl transferase (TdT) tailing. The initial treatment with calf intestinal phosphatase (CIP) is optional but strongly recommended for removing 3′ phosphate groups, because most genomic DNA fragmentation methods (i.e., sonication, micrococcal nuclease digestion, and certain restriction digests) produce a significant proportion of 3′ phosphate groups within the mixture of fragmented genomic DNA. This protocol is compatible with the presence of RNase A and can be carried out immediately after digestion of RNA carried over from ChIP, without any intermediate clean-up step. The tailing reaction involves the addition of a short (20-40 nucleotide [nt]) poly(dT) tail to the template DNA. The included dideoxynucleotide acts as a tail terminator in the reaction mixture and is necessary to maintain a tight size distribution. This poly(dT) tail provides a conserved 3′ element that permits the addition of a T7 promoter sequence in the subsequent second-strand synthesis step. IVT can then use this newly appended T7 promoter and linearly amplify the template dsDNA, producing amplified RNA product.
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification
Authors: Liu Chih Long , Bernstein Bradley E. , Schreiber Stuart L.
Published: May 2008

INTRODUCTION

T7-based linear amplification of DNA (TLAD) uses a linear amplification approach based on in vitro transcription (IVT) of template DNA by RNA polymerase from the T7 phage. TLAD was designed primarily for use with the ChIP-chip method (whereby DNA recovered from chromatin immunoprecipitation [ChIP] of cell lysate is used for subsequent analysis on DNA microarrays) and requires nanogram quantities of dsDNA to generate microgram amounts of amplified RNA. Briefly, the strategy is to add a 3′ conserved end to the template dsDNA, using terminal deoxynucleotidyl transferase (TdT) tailing, which permits the addition of a T7 promoter sequence in the subsequent second-strand synthesis step. IVT can then use this newly appended T7 promoter and linearly amplify the template dsDNA, producing antisense RNA (aRNA) product. After the IVT reaction is complete, the aRNA is cleaned up using the QIAGEN RNeasy Kit. This protocol for RNA sample purification is based on the manufacturer’s protocol for cleaning up RNA reactions, with minor modifications.
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview
Authors: Liu Chih Long , Bernstein Bradley E. , Schreiber Stuart L.
Published: May 2008

INTRODUCTION

T7-based linear amplification of DNA (TLAD) was designed primarily to overcome the shortcomings of exponential amplification approaches. TLAD uses a linear amplification method based on the in vitro transcription (IVT) of template DNA by RNA polymerase from the T7 phage, a common strategy used in RNA amplification protocols. The TLAD protocol introduced here successfully addresses amplification fidelity issues encountered with use of random PCR (R-PCR) with the ChIP-chip method (whereby DNA recovered from chromatin immunoprecipitation [ChIP] of cell lysate is used for subsequent analysis on DNA microarrays). Thus, optimizations have been done with this particular application in mind. For other applications that require DNA instead of RNA to be the end point, reverse transcription is a necessary step that increases the cost and complexity of necessary molecular biological manipulations to the sample, when compared with PCR. However, IVT amplification does offer improved fidelity and a much higher maximum yield per single reaction. Thus, other techniques that require amplification of complex mixtures of randomly fragmented genomic DNA can also benefit from this method.
Fungal Effector Protein AVR2 Targets Diversifying Defense-Related Cys Proteases of Tomato
Authors: Shabab Mohammed , Shindo Takayuki , Gu Christian , Kaschani Farnusch , Pansuriya Twinkal , Chintha Raju , Harzen Anne , Colby Tom , Kamoun Sophien , van der Hoorn Renier A.L.
Published: May 2008

The interaction between the fungal pathogen Cladosporium fulvum and its host tomato (Solanum lycopersicum) is an ideal model to study suppression of extracellular host defenses by pathogens. Secretion of protease inhibitor AVR2 by C. fulvum during infection suggests that tomato papain-like cysteine proteases (PLCPs) are part of the tomato defense response. We show that the tomato apoplast contains a remarkable diversity of PLCP activities with seven PLCPs that fall into four different subfamilies. Of these PLCPs, transcription of only PIP1 and RCR3 is induced by treatment with benzothiadiazole, which triggers the salicylic acid–regulated defense pathway. Sequencing of PLCP alleles of tomato relatives revealed that only PIP1 and RCR3 are under strong diversifying selection, resulting in variant residues around the substrate binding groove. The doubled number of variant residues in RCR3 suggests that RCR3 is under additional adaptive selection, probably to prevent autoimmune responses. AVR2 selectively inhibits only PIP1 and RCR3, and one of the naturally occurring variant residues in RCR3 affects AVR2 inhibition. The higher accumulation of PIP1 protein levels compared with RCR3 indicates that PIP1 might be the real virulence target of AVR2 and that RCR3 acts as a decoy for AVR2 perception in plants carrying the Cf-2 resistance gene.
Interspecific variation in avian blood parasites and haematology associated with urbanization in a desert habitat
Authors: Bobby Fokidis H. , Greiner Ellis C. , Deviche Pierre
Published: May 2008

Many avian species are negatively impacted by urbanization, but other species survive and prosper in urbanized areas. One factor potentially contributing to the success of some species in urban areas is the reduced presence of predators or parasite vectors in urban compared to rural areas. In addition, urban areas may provide increased food and water resources, which can enhance immune capacity to resist infection and the ability to eliminate parasites. We determined patterns of blood parasitism, body condition, and immune cell profiles in urban and rural populations of five adult male songbird species that vary in their relative abundance within urban areas. Urban birds generally exhibited less blood parasitism than rural birds. This difference was particularly evident for the urban‐adaptable Abert's towheePipilo aberti. In contrast, no difference in haemoparasitism was seen between urban and rural populations of the curve‐billed thrasherToxostoma curvirostre, a less‐urban adaptable species. In two closely related species, the curve‐billed thrasher and the northern mockingbirdMimus polyglottos, urban birds had a higher leukocyte count and a higher heterophil to lymphocyte ratio, which is often associated with chronic stress or current infection, than rural birds. Urban northern mockingbirds were in better condition than rural counterparts, but no habitat‐related differences in condition were detected for other species. Parasitic infection was correlated with body condition in only one species, the canyon towheePipilo fuscus. Parasitic infection in most species was correlated with changes in leukocyte abundance and profile. The findings suggest that interspecific differences in parasitic infection cannot be attributed entirely to differences in vector abundance or body condition. Interactions between immune function, parasite infection risk, and resource availability may contribute to determining the relative ability of certain species to adapt to cities.
Ultraviolet‐blue reflectance of some nestling plumage patches mediates parental favouritism in great tits Parus major
Authors: Galván Ismael , Amo Luisa , Sanz Juan J.
Published: May 2008

The colouration exhibited by nestling birds is generally cryptic, but in some species it has a conspicuous appearance. The adaptive function of these nestling displays is poorly known, especially in altricial species. We performed an experimental study in which the ultraviolet‐blue reflectance of the carotenoid‐based plumage of great tit Parus major nestlings was reduced in order to find possible evidence of parental favouritism. Tarsus length increment in a three‐day period was significantly lower in manipulated nestlings than in their control siblings. As tarsus length may be a good predictor of survival, the parents may increase their fitness return by investing more in those nestlings reflecting more in the UV‐blue spectral region. Interestingly, this effect was only found in a yellow patch located at the nape of nestlings that has been previously overlooked, as all the studies on plumage colouration in this species have focused on the breast plumage. Some quality indicators are proposed for the colour of nestling plumage, though the possibility exists that selection may operate through aspects of signal efficacy instead of aspects of signal content.
A NEW METHOD OF ESTIMATING THE CELL CYCLE TIME IN EPITHELIAL TISSUES OF LONG GENERATION TIME
Authors: Brown J. M. , Oliver R.
Published: May 2008

1. Using standard autoradiographic techniques, the percentage of labelled mitoses and the numbers of labelled cells in the various layers of the epithelium of the hamster cheek pouch have been studied at various times after a single injection of [3H]thymidine.

2. A new method for determining the cell cycle time of the basal layer cells is described and compared with the techniques previously used. This method is based on the rate at which labelled cells leave the basal layer and enter the spinous layer above it.

3. Using this technique, the mean cell cycle time of the basal cells has been estimated as 130 ± 7 hr; a value which compares favourably with the estimate of 135 ± 17 hr determined with similar assumptions from the length of the S period and the labelling index.

4. The technique enables an estimate to be made of the fraction of cells in the basal layer that are proliferating (the growth fraction). This is found to be indistinguishable from 1.

5. The mean time taken by cells in travelling from the basal layer to the keratin, i.e. the transit time through the spinous layer, has been found to be approximately 186 hr.
THE RELATIONSHIP BETWEEN DIURNAL VARIATION OF THE NUMBER OF CELLS IN MITOSIS AND OF THE NUMBER OF CELLS SYNTHESIZING DNA IN THE EPITHELIUM OF THE HAMSTER CHEEK POUCH
Authors: Brown J. M. , Berry R. J.
Published: May 2008

1. The numbers of cells in mitosis and in DNA synthesis in the epithelium of the hamster cheek pouch have been studied at different times of the day and night.

2. By accumulation of mitotic cells using colcemid, both the rate of entry of cells into mitosis and the duration of mitosis have been estimated at two different times of day.

3. A diurnal variation has been demonstrated in both the mitotic index and in the tritiated thymidine labelling index. Although these variations are of different amplitude and timing, the experimental data fit closely to the hypothesis that the diurnal mitotic variation is the result of a partially synchronous population moving through the DNA synthetic period. No direct action on the mitotic process need be postulated.

4. From the results of mitotic accumulation, it is clear that the rate of entry of cells into mitosis depends on the time of day at which this is studied. There is also the possibility that the duration of mitosis is slightly longer when the mitotic index is high.

5. It is concluded that, at least in the epithelium of the hamster cheek pouch, the diurnal rhythm in the number of mitoses present is a reflection of the diurnal variation in the number of cells synthesizing DNA at some time earlier. Small fluctuations in the mitotic pattern imposed by this partially synchronous population moving from S into mitosis, could be caused by slight variations in the duration of mitosis.
CELL POPULATION KINETICS OF THE RECOGNIZABLE ERYTHROID CELLS IN THE RAT
Authors: Tarbutt R. G. , Blackett N. M.
Published: May 2008

The cell population kinetic parameters defining a simple model of the recognizable part of the erythroid system have been determined. Experimental results using tritiated thymidine and radioactive iron autoradiography have provided estimates of the number of cell divisions, transit times and flow rates for all the recognizable stages of the erythroid system. The accuracy of the estimates and the validity of the model employed are discussed.
CELL LOSS FROM EXPERIMENTAL TUMOURS
Authors: Steel G. Gordon
Published: May 2008

The rate of loss of cells from a tumour may be estimated by measuring the cell production rate and comparing this with the rate at which cells are observed to be added to the tumour volume. An attractive method of measuring cell production rate is by the simultaneous measurement of a thymidine‐labelling index and the duration of the DNA synthetic period. A theoretical treatment of this method in exponential populations is given and the necessary assumptions are indicated.

Estimates of cell loss have been made for a number of experimental tumours using available published data. It is shown that in some cases cell loss is an important, perhaps even dominant, factor determining tumour growth rate and the shape of tumour growth curves.
DISTURBANCES IN THE DEVELOPMENT OF SMALL COLONIES FOLLOWING THE IRRADIATION OF DIFFERENT PARTS OF SINGLE CELLS IN TISSUE CULTURE WITH A HETEROCHROMATIC MICROBEAM OF ULTRAVIOLET LIGHT
Authors: Smith C. L. , Dendy P. P.
Published: May 2008

Various sites in mouse L cells have been irradiated using an heterochromatic ultraviolet microbeam 3.5 μ in diameter, and the subsequent growth of the cells has been studied for 5–7 days after irradiation.

Modifications in the growth curves were recorded for the total number of cells in each radiation category and significant anomalies in the DNA metabolism of some of the progeny of irradiated cells were noted at the end of the post‐irradiaton incubation period. The frequency with which binucleate and giant cells were produced was also recorded and the results analysed.

For equivalent absorbed doses, the nucleus is more sensitive than the cytoplasm in experiments of this type and there was some evidence to suggest that the maximum sensitivity is achieved when some nucleolar material is irradiated.
ASSESSMENT OF VIABILITY OF FROZEN BONE MARROW CELLS USING A CELL‐CULTURE METHOD
Authors: Abrahams S. , Till J. E. , McCulloch E. A. , Siminovitch L.
Published: May 2008

The survival of mouse bone marrow after freezing and thawing was assessed using two methods: the spleen‐colony technique; and a cell‐culture method. The results of these experiments indicate that both methods yield similar estimates of marrow cell viability. It is suggested that the cell‐culture method be used as an assay of marrow‐cell viability in situations where the spleen‐colony technique is not applicable.
ENZYME PATTERNS DURING A SYNCHRONOUS GROWTH CYCLE OF CHLORELLA PYRENOIDOSA
Authors: Cole Francis E. , Blondin Joan , Temple Louise
Published: May 2008

There have been no studies in which a significant number of isozymes have been investigated during a synchronous growth cycle of any organism. The present study was designed to obtain information on the fluctuations of a broad spectrum of enzymes during a synchronous growth cycle of Chlorella pyrenoidosa.

Of the thirty‐two enzymic activities investigated, seventeen could be localized on starch gels from a high temperature strain of Chlorella pyrenoidosa. Nine of these activities were found to possess more than one band of activity by starch gel electrophoresis. Seven of these activities were localized on starch gels throughout a synchronous growth cycle of C. pyrenoidosa grown in continuous light. Assay techniques are described. The fluctuations in enzyme activity are discussed with relation to concurrent metabolic and cytological changes during cell maturation in C. pyrenoidosa.
AN EARLY RESPONSE OF THE MORPHOLOGICALLY RECOGNIZABLE ERYTHROID PRECURSORS TO BLEEDING
Authors: Hanna Ismail R. A.
Published: May 2008

55Fe autoradiography of the peripheral red blood cells has been used to study the proliferation of the recognizable erythroid precursors in bled animals. The transit time of the recognizable erythroid precursors present in the bone marrow and labelled with 55Fe 6 hr before bleeding, remains unchanged, but the number of red cells produced by these precursors is significantly greater than normal. It is deduced that the increased red cell production is brought about by an increase in the number of divisions that the cells undergo during maturation and that a shortening in the red cell cycle time is implied. The possibility that the transit time of the progeny of cells differentiating into pro‐erythroblasts after bleeding may be shorter than the transit time of the precursors already differentiated before bleeding, is briefly discussed.
THE EFFECT OF NITROGEN MUSTARD ON THE HAEMOPOIETIC STEM CELLS OF THE BONE MARROW IN THE RAT
Authors: Harriss E. B. , Aponte L.
Published: May 2008

The sensitivity of haemopoietic stem cells to the action of nitrogen mustard has been investigated by transfusion of bone marrow from treated donor rats to recipients whose own haemopoiesis had been reduced to low levels by whole body X‐irradiation. By measurement of the resultant erythropoiesis in the recipients with radioactive iron, a comparison of the repopulating ability of nitrogen mustard treated bone marrow with that of normal bone marrow could be made. It was found that although a dose of 0.9 mg/kg body weight reduces bone marrow cellularity to less than 10% of normal, repopulating ability is not decreased to much less than half the normal level. This is in contrast to the effects of X‐radiation, which has a more marked effect on the stem cell population than on the differentiated marrow cells. Possible reasons for this difference are discussed. It could be that the proliferative or metabolic state of the cell plays a role, or that some repair mechanism is operative in the stem cells which does not exist in the differentiated cells.
FURTHER EVIDENCE FOR THE PRESENCE OF A PANETH CELL PROGENITOR IN MOUSE INTESTINE
Authors: Hampton J. C.
Published: May 2008

Photomicrographic evidence, mitotic figures and 3H‐thymidine labeling among Paneth cells, is presented in support of the hypothesis that Paneth cells are replaced by cells proliferating in the bottom of the intestinal crypt rather than by migration of cells from the mid‐crypt region.
FRACTIONATION OF SUSPENSIONS OF MOUSE SPLEEN CELLS BY COUNTER CURRENT DISTRIBUTION
Authors: Brunette D. M. , McCulloch E. A. , Till J. E.
Published: May 2008

Suspensions of mouse spleen cells were fractionated by means of counter current distribution in an aqueous two‐phase polymer system composed of 5% (w/w) dextran and 4% (w/w) polyethylene glycol. Counter current distribution in this combination of polymers was not toxic for hemopoietic colony‐forming units (CFU) and yielded a partial separation of CFU, granulocytes and antibody‐producing cells. The results obtained indicate that counter current distribution is a useful means for the separation of populations of intact, viable hemopoietic cells.
CONTROL OF GRANULOCYTE PRODUCTION
Authors: Rytöaa T. , Kiviniemi Kyllikki
Published: May 2008

It has previously been demonstrated that granulocyte production is controlled by a humoral feedback mechanism based on at least two tissue‐specific substances, granulocytic chalone and antichalone. It is now shown that the action of these regulators is almost instantaneous, reversible, short‐term, and at least in the case of chalone, followed by an overshoot during recovery.

It is also shown that both substances operate primarily, if not solely, in a phase prior to DNA synthesis: chalone prevents and antichalone promotes the entry of precursor cells into the DNA synthesis phase. These actions are based on a switch mechanism, apparently involving transient change in the synthesis of a short‐living RNA.

In addition to these results, a dose‐effect relationship is obtained for chalone, and continuous production of the inhibitor in mature granulocytes is indicated.
SEMIQUANTITATIVE CELL CYCLE MODEL FOR SLOW GROWING ESCHERICHIA COLI
Authors: Simon Z.
Published: May 2008

A cell cycle model for Escherichia coli is discussed. It is assumed that the DNA synthesis starts when a threshold dTTP concentration is reached, that the dTTP synthesis is subject to product inhibition and that the duration of DNA replication is given by the time necessary to synthesize the required quantity of dTTP. The model is compared with data for slow growth rates. The constancy of cell volume and of the quotient of presynthetic period per generation cycle is reproduced by the model. The calculated upper limit for the cell volume and lower limit for the quotient are about ten times higher and lower respectively than the real values.