bluuebunny/crossref_metadata_2025 huggingface dataset:
Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies
Authors: Fortunato Laura , Jordan Fiona
Published: November 2010

Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship ‘facts’. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families.
Transmission coupling mechanisms: cultural group selection
Authors: Boyd Robert , Richerson Peter J.
Published: November 2010

The application of phylogenetic methods to cultural variation raises questions about how cultural adaption works and how it is coupled to cultural transmission. Cultural group selection is of particular interest in this context because it depends on the same kinds of mechanisms that lead to tree-like patterns of cultural variation. Here, we review ideas about cultural group selection relevant to cultural phylogenetics. We discuss why group selection among multiple equilibria is not subject to the usual criticisms directed at group selection, why multiple equilibria are a common phenomena, and why selection among multiple equilibria is not likely to be an important force in genetic evolution. We also discuss three forms of group competition and the processes that cause populations to shift from one equilibrium to another and create a mutation-like process at the group level.
Measuring the diffusion of linguistic change
Authors: Nerbonne John
Published: November 2010

We examine situations in which linguistic changes have probably been propagated via normal contact as opposed to via conquest, recent settlement and large-scale migration. We proceed then from two simplifying assumptions: first, that all linguistic variation is the result of either diffusion or independent innovation, and, second, that we may operationalize social contact as geographical distance. It is clear that both of these assumptions are imperfect, but they allow us to examine diffusion via the distribution of linguistic variation as a function of geographical distance. Several studies in quantitative linguistics have examined this relation, starting with Séguy (Séguy 1971Rev. Linguist. Romane35, 335–357), and virtually all report a sublinear growth in aggregate linguistic variation as a function of geographical distance. The literature from dialectology and historical linguistics has mostly traced the diffusion of individual features, however, so that it is sensible to ask what sort of dynamic in the diffusion of individual features is compatible with Séguy's curve. We examine some simulations of diffusion in an effort to shed light on this question.
Language shift, bilingualism and the future of Britain's Celtic languages
Authors: Kandler Anne , Unger Roman , Steele James
Published: November 2010

‘Language shift’ is the process whereby members of a community in which more than one language is spoken abandon their original vernacular language in favour of another. The historical shifts to English by Celtic language speakers of Britain and Ireland are particularly well-studied examples for which good census data exist for the most recent 100–120 years in many areas where Celtic languages were once the prevailing vernaculars. We model the dynamics of language shift as a competition process in which the numbers of speakers of each language (both monolingual and bilingual) vary as a function both of internal recruitment (as the net outcome of birth, death, immigration and emigration rates of native speakers), and of gains and losses owing to language shift. We examine two models: a basic model in which bilingualism is simply the transitional state for households moving between alternative monolingual states, and a diglossia model in which there is an additional demand for the endangered language as the preferred medium of communication in some restricted sociolinguistic domain, superimposed on the basic shift dynamics. Fitting our models to census data, we successfully reproduce the demographic trajectories of both languages over the past century. We estimate the rates of recruitment of new Scottish Gaelic speakers that would be required each year (for instance, through school education) to counteract the ‘natural wastage’ as households with one or more Gaelic speakers fail to transmit the language to the next generation informally, for different rates of loss during informal intergenerational transmission.
Phylogenetic analyses of Lapita decoration do not support branching evolution or regional population structure during colonization of Remote Oceania
Authors: Cochrane Ethan E. , Lipo Carl P.
Published: November 2010

Intricately decorated Lapita pottery (3100–2700 BP) was made and deposited by the prehistoric colonizers of Pacific islands, east of the main Solomon's chain. For decades, analyses of this pottery have focused on the ancestor–descendant relationships of populations and the relative degree of interaction across the region to explain similarities in Lapita decoration. Cladistic analyses, increasingly used to examine the evolutionary relationships of material culture assemblages, have not been conducted on Lapita artefacts. Here, we present the first cladistic analysis of Lapita pottery and note the difficulties in using cladistics to investigate datasets where a high degree of horizontal transmission and non-branching evolution may explain observed variation. We additionally present NeighborNet and phenetic distance network analyses to generate hypotheses that may account for Lapita decorative similarity.
Untangling cultural inheritance: language diversity and long-house architecture on the Pacific northwest coast
Authors: Jordan Peter , O'Neill Sean
Published: November 2010

Many recent studies of cultural inheritance have focused on small-scale craft traditions practised by single individuals, which do not require coordinated participation by larger social collectives. In this paper, we address this gap in the cultural transmission literature by investigating diversity in the vernacular architecture of the Pacific northwest coast, where communities of hunter–fisher–gatherers constructed immense wooden long-houses at their main winter villages. Quantitative analyses of long-house styles along the coastline draw on a range of models and methods from the biological sciences and are employed to test hypotheses relating to basic patterns of macro-scale cultural diversification, and the degree to which the transmission of housing traits has been constrained by the region's numerous linguistic boundaries. The results indicate relatively strong branching patterns of cultural inheritance and also close associations between regional language history and housing styles, pointing to the potentially crucial role played by language boundaries in structuring large-scale patterns of cultural diversification, especially in relation to ‘collective’ cultural traditions like housing that require substantial inputs of coordinated labour.
Splits or waves? Trees or webs? How divergence measures and network analysis can unravel language histories
Authors: Heggarty Paul , Maguire Warren , McMahon April
Published: November 2010

Linguists have traditionally represented patterns of divergence within a language family in terms of either a ‘splits’ model, corresponding to a branching family tree structure, or the wave model, resulting in a (dialect) continuum. Recent phylogenetic analyses, however, have tended to assume the former as a viable idealization also for the latter. But the contrast matters, for it typically reflects different processes in the real world: speaker populations either separated by migrations, or expanding over continuous territory. Since history often leaves a complex of both patterns within the same language family, ideally we need a single model to capture both, and tease apart the respective contributions of each. The ‘network’ type of phylogenetic method offers this, so we review recent applications to language data. Most have used lexical data, encoded as binary or multi-state characters. We look instead at continuous distance measures of divergence in phonetics. Our output networks combine branch- and continuum-like signals in ways that correspond well to known histories (illustrated for Germanic, and particularly English). We thus challenge the traditional insistence on shared innovations, setting out a new, principled explanation for why complex language histories can emerge correctly from distance measures, despite shared retentions and parallel innovations.
On the shape and fabric of human history
Authors: Gray Russell D. , Bryant David , Greenhill Simon J.
Published: November 2010

In this paper we outline two debates about the nature of human cultural history. The first focuses on the extent to which human history is tree-like (its shape), and the second on the unity of that history (its fabric). Proponents of cultural phylogenetics are often accused of assuming that human history has been both highly tree-like and consisting of tightly linked lineages. Critics have pointed out obvious exceptions to these assumptions. Instead ofa prioridichotomous disputes about the validity of cultural phylogenetics, we suggest that the debate is better conceptualized as involving positions along continuous dimensions. The challenge for empirical research is, therefore, to determine whereparticularaspects of culture lie on these dimensions. We discuss the ability of current computational methods derived from evolutionary biology to address these questions. These methods are then used to compare the extent to which lexical evolution is tree-like in different parts of the world and to evaluate the coherence of cultural and linguistic lineages.
Evolutionary approaches to cultural and linguistic diversity
Authors: Steele James , Jordan Peter , Cochrane Ethan
Published: November 2010

Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a ‘grand synthesis’ is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely ‘cultural’ fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.
Running hot and cold: behavioral strategies, neural circuits, and the molecular machinery for thermotaxis in C. elegans and Drosophila
Authors: Garrity Paul A. , Goodman Miriam B. , Samuel Aravinthan D. , Sengupta Piali
Published: November 2010

Like other ectotherms, the roundworm Caenorhabditis elegans and the fruit fly Drosophila melanogaster rely on behavioral strategies to stabilize their body temperature. Both animals use specialized sensory neurons to detect small changes in temperature, and the activity of these thermosensors governs the neural circuits that control migration and accumulation at preferred temperatures. Despite these similarities, the underlying molecular, neuronal, and computational mechanisms responsible for thermotaxis are distinct in these organisms. Here, we discuss the role of thermosensation in the development and survival of C. elegans and Drosophila, and review the behavioral strategies, neuronal circuits, and molecular networks responsible for thermotaxis behavior.
Cytoplasmic ASPP1 inhibits apoptosis through the control of YAP
Authors: Vigneron Arnaud M. , Ludwig Robert L. , Vousden Karen H.
Published: November 2010

The ASPP (apoptosis-stimulating protein of p53) family of proteins can function in the nucleus to modulate the transcriptional activity of p53, with ASPP1 and ASPP2 contributing to the expression of apoptotic target genes. In this study, we describe a new function for cytoplasmic ASPP1 in controlling YAP (Yes-associated protein)/TAZ. ASPP1 can inhibit the interaction of YAP with LATS1 (large tumor suppressor 1), a kinase that phosphorylates YAP/TAZ and promotes cytoplasmic sequestration and protein degradation. This function of ASPP1 therefore enhances nuclear accumulation of YAP/TAZ and YAP/TAZ-dependent transcriptional regulation. The consequence of YAP/TAZ activation by ASPP1 is to inhibit apoptosis, in part through the down-regulation of Bim expression, leading to resistance to anoikis and enhanced cell migration. These results reveal a potential oncogenic role for cytoplasmic ASPP1, in contrast to the tumor-suppressive activity described previously for nuclear ASPP1.
The Lats2 tumor suppressor augments p53-mediated apoptosis by promoting the nuclear proapoptotic function of ASPP1
Authors: Aylon Yael , Ofir-Rosenfeld Yaara , Yabuta Norikazu , Lapi Eleonora , Nojima Hiroshi , Lu Xin , Oren Moshe
Published: November 2010

Apoptosis is an important mechanism to eliminate potentially tumorigenic cells. The tumor suppressor p53 plays a pivotal role in this process. Many tumors harbor mutant p53, but others evade its tumor-suppressive effects by altering the expression of proteins that regulate the p53 pathway. ASPP1 (apoptosis-stimulating protein of p53-1) is a key mediator of the nuclear p53 apoptotic response. Under basal conditions, ASPP1 is cytoplasmic. We report that, in response to oncogenic stress, the tumor suppressor Lats2 (large tumor suppressor 2) phosphorylates ASPP1 and drives its translocation into the nucleus. Together, Lats2 and ASPP1 shunt p53 to proapoptotic promoters and promote the death of polyploid cells. These effects are overridden by the Yap1 (Yes-associated protein 1) oncoprotein, which disrupts Lats2–ASPP1 binding and antagonizes the tumor-suppressing function of the Lats2/ASPP1/p53 axis.
Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged
Authors: David Charles J. , Manley James L.
Published: November 2010

Alternative splicing of mRNA precursors is a nearly ubiquitous and extremely flexible point of gene control in humans. It provides cells with the opportunity to create protein isoforms of differing, even opposing, functions from a single gene. Cancer cells often take advantage of this flexibility to produce proteins that promote growth and survival. Many of the isoforms produced in this manner are developmentally regulated and are preferentially re-expressed in tumors. Emerging insights into this process indicate that pathways that are frequently deregulated in cancer often play important roles in promoting aberrant splicing, which in turn contributes to all aspects of tumor biology.
The U2AF35-related protein Urp contacts the 3′ splice site to promote U12-type intron splicing and the second step of U2-type intron splicing
Authors: Shen Haihong , Zheng Xuexiu , Luecke Stephan , Green Michael R.
Published: November 2010

The U2AF35-related protein Urp has been implicated previously in splicing of the major class of U2-type introns. Here we show that Urp is also required for splicing of the minor class of U12-type introns. Urp is recruited in an ATP-dependent fashion to the U12-type intron 3′ splice site, where it promotes formation of spliceosomal complexes. Remarkably, Urp also contacts the 3′ splice site of a U2-type intron, but in this case is specifically required for the second step of splicing. Thus, through recognition of a common splicing element, Urp facilitates distinct steps of U2- and U12-type intron splicing.
Dok-7 regulates neuromuscular synapse formation by recruiting Crk and Crk-L
Authors: Hallock Peter T. , Xu Chong-Feng , Park Tae-Ju , Neubert Thomas A. , Curran Tom , Burden Steven J.
Published: November 2010

Agrin, released by motor neurons, promotes neuromuscular synapse formation by stimulating MuSK, a receptor tyrosine kinase expressed in skeletal muscle. Phosphorylated MuSK recruits docking protein-7 (Dok-7), an adaptor protein that is expressed selectively in muscle. In the absence of Dok-7, neuromuscular synapses fail to form, and mutations that impair Dok-7 are a major cause of congenital myasthenia in humans. How Dok-7 stimulates synaptic differentiation is poorly understood. Once recruited to MuSK, Dok-7 directly stimulates MuSK kinase activity. This unusual activity of an adapter protein is mediated by the N-terminal region of Dok-7, whereas most mutations that cause congenital myasthenia truncate the C-terminal domain. Here, we demonstrate that Dok-7 also functions downstream from MuSK, and we identify the proteins that are recruited to the C-terminal domain of Dok-7. We show that Agrin stimulates phosphorylation of two tyrosine residues in the C-terminal domain of Dok-7, which leads to recruitment of two adapter proteins: Crk and Crk-L. Furthermore, we show that selective inactivation of Crk and Crk-L in skeletal muscle leads to severe defects in neuromuscular synapses in vivo, revealing a critical role for Crk and Crk-L downstream from Dok-7 in presynaptic and postsynaptic differentiation.
The Hippo signaling pathway restricts the oncogenic potential of an intestinal regeneration program
Authors: Cai Jing , Zhang Nailing , Zheng Yonggang , de Wilde Roeland F. , Maitra Anirban , Pan Duojia
Published: November 2010

Although a developmental role for Hippo signaling in organ size control is well appreciated, how this pathway functions in tissue regeneration is largely unknown. Here we address this issue using a dextran sodium sulfate (DSS)-induced colonic regeneration model. We find that regenerating crypts express elevated Yes-associated protein (YAP) levels. Inactivation of YAP causes no obvious intestinal defects under normal homeostasis, but severely impairs DSS-induced intestinal regeneration. Conversely, hyperactivation of YAP results in widespread early-onset polyp formation following DSS treatment. Thus, the YAP oncoprotein must be exquisitely controlled in tissue regeneration to allow compensatory proliferation and prevent the intrinsic oncogenic potential of a tissue regeneration program.
Δ40p53 controls the switch from pluripotency to differentiation by regulating IGF signaling in ESCs
Authors: Ungewitter Erica , Scrable Heidi
Published: November 2010

Δ40p53 is a transactivation-deficient isoform of the tumor suppressor p53. We discovered that Δ40p53, in addition to being highly expressed in embryonic stem cells (ESCs), is the major p53 isoform during early stages of embryogenesis in the mouse. By altering the dose of Δ40p53 in ESCs, we identified a critical role for this isoform in maintaining the ESC state. Haploinsufficiency for Δ40p53 causes a loss of pluripotency in ESCs and acquisition of a somatic cell cycle, while increased dosage of Δ40p53 prolongs pluripotency and inhibits progression to a more differentiated state. Δ40p53 controls the switch from pluripotent ESCs to differentiated somatic cells by controlling the activity of full-length p53 at critical targets such as Nanog and the IGF-1 receptor (IGF-1R). The IGF axis plays a central role in the switch between pluripotency and differentiation in ESCs—and Δ40p53, by controlling the level of the IGF-1R, acts as a master regulator of this switch. We propose that this is the primary function of Δ40p53 in cells of the early embryo and stem cells, which are the only normal cells in which this isoform is expressed.
Disruption of Cultured Cells by Nitrogen Cavitation: Figure 1.
Authors: Simpson Richard J.
Published: November 2010

INTRODUCTION

Cell disruption by nitrogen decompression from a pressurized vessel is a rapid and effective way to homogenize cells and tissues, to release intact organelles, and to prepare cell membranes. Cells are placed in a pressure vessel and large quantities of oxygen-free nitrogen are dissolved in the cells under high pressure (~5500 kilopascals [kPa], equivalent to 800 pounds per square inch [psi]). When the pressure is released suddenly, the nitrogen bubbles out of solution, rupturing the cell membrane and releasing the cell contents. Nitrogen cavitation is well suited for mammalian and plant cells and fragile bacteria, but is less effective with yeast, fungi, spores, or other cell types with tough cell walls. The chemical and physical stresses imposed by nitrogen cavitation on enzymes and subcellular compartments are minimized compared with ultrasonic and mechanical homogenizing methods. Unlike lysis methods relying on shear stresses and friction, there is no heat damage to proteins and organelles during nitrogen cavitation. Indeed, the method is accompanied by an adiabatic expansion that cools the sample instead. Also, labile cell components are protected from oxidation by the inert nitrogen gas. Furthermore, nitrogen does not alter the pH of the suspending medium. The process is fast and uniform because the same disruptive forces are applied within each cell and throughout the sample, ensuring reproducible cell-free homogenates. Finally, variable sample sizes (e.g., from ~1 mL to 1 L or more) can be accommodated with most commercial systems.
DNA Extraction from Freeze-Dried Plant Tissue with CTAB in a 96-Well Format
Authors: Hsia An-Ping , Chen Hsin D. , Ohtsu Kazuhiro , Schnable Patrick S.
Published: November 2010

INTRODUCTION

This protocol is a modified version of DNA isolation using cetyltrimethylammonium bromide (CTAB) and 96-well plates. It is high-throughput, which facilitates the analysis of large mapping populations. The DNA yield is adequate for at least 100-500 polymerase chain reaction (PCR) procedures.
Transfection of Mammalian Cells with Fluorescent Protein Fusions
Authors: Spector David L. , Goldman Robert D.
Published: November 2010

INTRODUCTION

Fluorescent protein fusions (FPFs) have been used to address a wide range of questions in individual cells as well as in specific tissues of particular organisms. However, investigators must take extreme care when using FPFs to ensure that the resultant fusion protein is expressed at or close to the endogenous level of the parent protein, and also that it is full length, localizes correctly, and behaves normally once incorporated in the cell. Although transient transfection methods can be used to introduce DNA coding for FPFs, in many cases it is beneficial and/or essential to develop stable cell lines expressing the fusion protein of interest. In addition to providing more native levels of expression, the individual clones can be generated from single cells, the integration site of the plasmid can be mapped, and the copy number can be determined. Moreover, because every cell in the population is expressing the fusion protein, cell cycle analyses and biochemical fractionation are significantly easier to accomplish. This article presents a protocol for generating, selecting, and screening stable cell lines expressing FPFs.
Locomotor Activity Level Monitoring Using the Drosophila Activity Monitoring (DAM) System: Figure 1.
Authors: Pfeiffenberger Cory , Lear Bridget C. , Keegan Kevin P. , Allada Ravi
Published: November 2010

INTRODUCTION

Adult behavioral assays have been used with great success in Drosophila melanogaster to identify circadian rhythm genes. In particular, the locomotor activity assay can identify altered behavior patterns over the course of several days in small populations, or even individual flies. Commercially available, highly efficient automated systems allow for continuous data collection from large numbers of individuals, and analytical tools make it possible to quickly analyze multiple aspects of circadian behavior from each experiment. These features make the locomotor activity assay useful for high-throughput analyses, leading to the rapid discovery and functional characterization of many Drosophila circadian rhythm genes. The locomotor assay described here can simultaneously assess both circadian and sleep behavior, and several methods can be used to analyze the data generated from such assays. This protocol details the use of the Drosophila Activity Monitoring (DAM) System from TriKinetics. Briefly, the system records activity from individual flies maintained in sealed tubes placed in activity monitors. An infrared beam directed through the midpoint of each tube measures an “activity event” each time a fly crosses the beam. Events detected over the course of each consecutive sampling interval are summed and recorded over the course of the experiment for each fly. The general approaches described here can be applied to a wide range of behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity.
Processing Circadian Data Collected from the Drosophila Activity Monitoring (DAM) System: Figure 1.
Authors: Pfeiffenberger Cory , Lear Bridget C. , Keegan Kevin P. , Allada Ravi
Published: November 2010

INTRODUCTION

Adult behavioral assays have been used with great success in Drosophila melanogaster to identify circadian rhythm genes. In particular, the locomotor activity assay can identify altered behavior patterns over the course of several days in small populations, or even individual flies. Generally, circadian behavior is assayed during a period of 12 h light:12 h dark cycling (LD entrainment) followed by conditions of constant darkness (DD). LD activity profiles provide a qualitative image of daily activity bouts, and the data can be used to quantitatively assess the phase and/or amplitude of particular bouts. Additional activity assessments made from entrained flies that have been shifted to constant darkness can provide insight into the state of internal clocks and the ability of these clocks to drive rhythmic outputs. Typical LD DD runs assess both free-running rhythmicity and period length with χ2 periodogram (P’gram) analysis. This protocol describes the use of ClockLab (a MATLAB-based program) and the Counting Macro (an Excel-based program) to analyze circadian locomotor activity data collected using the Drosophila Activity Monitoring (DAM) System from TriKinetics. Specific procedures are described to analyze free-running rhythmicity and period length for individual flies, and assess group activity plots during both entrainment and constant conditions.
Delivery of Small Interfering RNA (siRNA) Using the Sleeping Beauty Transposon: Figure 1.
Authors: Fletcher Bradley S.
Published: November 2010

INTRODUCTION

RNA interference (RNAi) is an evolutionarily conserved process that silences gene expression through double-stranded RNA species in a sequence-specific manner. Small interfering RNAs (siRNAs) can promote sequence-specific degradation and/or translational repression of target RNA by activation of the RNA-induced silencing complex (RISC). Traditionally, silencing in mammalian cells had been achieved by transfection of synthetically derived siRNA duplexes, resulting in transient gene suppression of the target sequence. As the technology was advanced, inhibitory short-hairpin-shaped RNAs (shRNAs) could be produced by transcription from RNA polymerase-III (pol-III)-driven promoters, such as H1, U6, or cytomegalovirus (CMV)-enhanced pol III promoters. Following transcription, the shRNAs are processed by the enzyme Dicer into active siRNA. This approach allows for the continuous production of siRNA within cells using a DNA template and offers increased options for delivery of the pol-III-driven transcriptional units. A number of different viral vectors, as well as plasmid DNAs, have been utilized to deliver shRNA to mammalian cells. Here, the Tc1/mariner DNA transposon Sleeping Beauty (SB) is used as a tool to deliver shRNA-encoding transcriptional units. The SB transposon system uses a “cut-and-paste” mechanism to insert the transposon into random TA dinucleotides within the target genome. The shRNAs are then processed and used for gene knockdown.
Culturing the Antarctic Nematode Plectus murrayi
Authors: Adhikari Bishwo N. , Tomasel Cecilia M. , Li Grace , Wall Diana H. , Adams Byron J.
Published: November 2010

INTRODUCTION

The Antarctic terrestrial nematode Plectus murrayi is an excellent model organism for the study of stress response mechanisms in various types of environmental conditions. In this procedure, we describe a method for culturing P. murrayi extracted from soil and sediment samples from the McMurdo (MCM) Dry Valleys of Antarctica. Nematodes are cultured on sand agar plates and incubated at various temperatures, and feed on bacteria growing on the agar media. They can be subcultured and stored at 15°C for >2 mo. This method is easy to carry out and can produce nematodes in quantities sufficient for ecological and molecular studies.
Array Tomography: Rodent Brain Fixation and Embedding
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J.
Published: November 2010

INTRODUCTION

Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. This protocol describes the fixation and processing required to prepare tissues for immunofluorescence array tomography.
Array Tomography: Production of Arrays
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J.
Published: November 2010

INTRODUCTION

Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time consuming and require some practice to perfect. This protocol describes the sectioning of embedded tissues and the mounting of the serial arrays. The procedures require some familiarity with the techniques used for ultramicrotome sectioning for electron microscopy.
Array Tomography: Immunostaining and Antibody Elution
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J.
Published: November 2010

INTRODUCTION

Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are prepared for imaging by tagging with primary antibodies against specific cellular targets, followed by labeling with fluorescent secondary antibodies. Alternatively, fluorescent proteins that have been introduced into the tissue before dissection can be used.
Array Tomography: Semiautomated Image Alignment
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J.
Published: November 2010

INTRODUCTION

Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving.
Constructing and Expressing Fluorescent Protein Fusions
Authors: Spector David L. , Goldman Robert D.
Published: November 2010

INTRODUCTION

Fluorescent protein fusions (FPFs) have been used to address a wide range of questions in individual cells as well as in specific tissues of a particular organism. However, investigators must take extreme care when using FPFs to ensure that the resultant fusion protein is expressed at or close to the endogenous level of the parent protein, and also that it is full length, localizes correctly, and behaves normally once incorporated in the cell. Because the molecular mass of the fluorescent protein (FP) itself is 27 kDa, one must consider the potential effects of placing such a large tag in association with a protein under investigation. This article discusses how these goals can be achieved and provides examples to assist the investigator in designing and implementing experiments using FPFs.
Spinning-Disk Microscopy Systems
Authors: Wilson Tony
Published: November 2010

INTRODUCTION

The popularity of the confocal microscope in life science laboratories around the world is undoubtedly due to its ability to permit volume objects to be imaged and to be rendered in three dimensions. It is important to realize that the confocal microscope itself does not produce three-dimensional images. Indeed, it does the opposite. The critical property that the confocal microscope possesses, which the conventional microscope does not, is its ability to image efficiently (and in-focus) only those regions of a volume specimen that lie within a thin section in the focal region of the microscope. In other words, it is able to reject (i.e., vastly attenuate) light originating from out-of-focus regions of the specimen. To image a three-dimensional volume of a thick specimen, it is necessary to take a whole series of such thin optical sections as the specimen is moved axially through the focal region. Once this through-focus series of optically sectioned images has been recorded, it is a matter of computer processing to decide how the three-dimensional information is to be presented. There are many methods for producing optical sections, of which the confocal optical system is just one. This article reviews these methods and describes a number of convenient methods of implementation that can lead to, among other things, real-time image formation.
Array Tomography: High-Resolution Three-Dimensional Immunofluorescence
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J.
Published: November 2010

INTRODUCTION

Array tomography, which is described in this article, is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Although the fabrication procedures can be relatively difficult, the high resolution, depth invariance, and molecular discrimination offered by array tomography justify the effort involved. Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture.
Novel method for cleaning a vacuum chamber from hydrocarbon contamination
Authors: Wanzenboeck H. D. , Roediger P. , Hochleitner G. , Bertagnolli E. , Buehler W.
Published: November 2010

A novel method for cleaning a high vacuum chamber is presented. This method is based on concurrent in situ high-energetic UV light activation of contaminants located in the residual gas and at the vacuum chamber surfaces as well as the in situ generation of highly reactive ozone. Ozone oxidizes the contaminants to volatile species. Investigations by energy-dispersive x-ray analysis of residual gas depositions and mass-spectroscopy measurements of the residual gas in the vacuum chamber identify the contaminant species as hydrocarbons. After a cleaning period of 8 h, a decrease in measured chamber contamination by about 90% could be achieved according to atomic force microscope analysis. Mass spectroscopy measurements using a residual gas analyzer indicate the creation of volatile, carbonaceous species during the cleaning process.
Comparison of Ti-Zr-V nonevaporable getter films deposited using alloy or twisted wire sputter-targets
Authors: Valizadeh R. , Malyshev O. B. , Colligon J. S. , Hannah A. , Vishnyakov V. M.
Published: November 2010

A comparison of the performance of nonevaporable getter (NEG) films deposited using two different types of targets has been made to find the one that has the best pumping properties. For the first time, the NEG coating was deposited using a preformed Ti-Zr-V alloy target. The NEG film characterization and pumping properties have been studied in comparison with a film deposited using the commonly used three-wire twisted target. It was demonstrated that the alloy target produces a NEG coating with uniform composition both laterally and in depth. The composition of the film was found to be the same as the target. Film topography and microstructure with 5 nm grain sizes were found to be the same for both targets. The main result is that the activation temperature of the NEG coating deposited using the Ti-Zr-V alloy target is 160 °C, which is 20 °C lower than for NEG coatings deposited using three twisted wires.
High-current electron optical design for reflective electron beam lithography direct write lithography
Authors: McCord Mark , Kojima Shinichi , Petric Paul , Brodie Alan , Sun Jeff
Published: November 2010

The authors present the latest design and results for the second generation column used in the reflective electron beam lithography program. The previous magnetic prism based concept to separate the illumination and projection beams has been replaced with a Wien filter that allows the column to be shrunk in size by a factor of 3, resulting in reduced Coulomb blur and energy spread. Experimental data from the column are presented and compared to simulation. The authors also discuss design considerations for this and future columns, including beam voltage, numerical aperture selection, and cathode optimization.
Ni full-filling into Al2O3/Al film with etched tunnels using a polyethylene glycol solution bath in electroless-plating
Authors: Jang Joo-Hee , Lee Chang-Hyoung , Choi Woo-Sung , Kim Nam-Jeong , Kim Taek-You , Kim Tae-Yoo , Kim Jang-Hyun , Park Chan , Suh Su-Jeong
Published: November 2010

Ni / Al 2 O 3 / Al film was fabricated for a high performance capacitor using electrochemical etching, anodizing, and electroless-plating. The focus of this study was to form seamless and void-free Ni electrodes on Al2O3/Al with etched tunnels. The conventional deposition method of metal was limited to full-fill for the Al tunnel pits with a high aspect ratio, a depth of about 40 μm, and diameters of about 0.5–1 μm. Nevertheless, Ni filling in tunnel pits was achieved through electroless-plating for the first time, producing a seamless and void-free electrode. The authors used a polyethylene glycol solution bath to block the Pd on top of the tunnel prior to electroless-plating, which enabled the Ni to deposit preferentially at the bottom, leading to a filling from the bottom to the top. Finally, the capacitance density for the etched and Ni electroless plated films was 220 nF/cm2 while that for a film without any etch tunnel was 12.5 nF/cm2.
Antimonide-based depletion-mode metal-oxide-semiconductor field-effect transistors using small-bandgap InAs channel layers
Authors: Lin H.-K. , Liau G.-Y. , Liu H.-K.
Published: November 2010

Antimonide-based depletion-mode InAs channel metal-oxide-semiconductor field-effect transistors showing complete pinch-off characteristics are successfully demonstrated. The epitaxial antimonide materials are grown by molecular beam epitaxy and gate dielectrics are deposited by plasma-enhanced chemical vapor deposition. A device with a 2.0 μm gate length shows a drain current density of 600 mA/mm at VGS=0 V and a peak transconductance of 380 mS/mm at VDS=1.5 V. Charge trapping at the dielectric-semiconductor interface is observed using pulsed ID−VDS measurements and is explained as a primary cause for the degradation of frequency performance of the device.
Rigid adhesive strapping tape: the effect of storage conditions on load, elongation and stiffness
Authors: Gordon S , Mulligan J
Published: November 2010

A variety of rigid adhesive strapping tape is used widely for the prevention and conservative management of musculoskeletal injuries. There is limited information regarding intrinsic mechanical properties of different brands of tape and no information is available about the effect of storage temperature on these mechanical properties. Hence, comparison of intrinsic mechanical properties of currently available tape is required to assist consumers in the selection of tape storage conditions according to specific mechanical properties of tape. Six adhesive rigid tapes commonly available in Australia were selected. Two configurations of tape were tested to mimic an ankle strapping configuration. All testing was conducted in a climate and humidity controlled laboratory. At initial testing, eight samples of each configuration, of each tape were loaded-to-failure using a densitometer. A roll of each tape was then stored for 1 month under two conditions; in the refrigerator and in a sports bag in a car. All tapes were then retested. The intrinsic ability of each configuration to resist vertical tensile force was assessed by measuring tensile load and elongation at failure. Tape stiffness was determined using Young's modulus, the modulus of elasticity. Significant differences in tensile load and elongation to failure existed at initial testing and after storage when comparing different tapes. Significant changes in mechanical properties also occurred within tapes when comparing initial and post storage measures. To ensure tape quality is maintained, further research is needed to establish if the intrinsic mechanical properties of tape alter on-field tape performance and to determine how environmental and climatic storage variables influence the physical and chemical components of tape to enable selection of optimal storage conditions to maximise on-field performance.