Making Forest of Bliss: The Film, the Book, the DVD, and the Breakthrough

Robert Gardner's and Àkos Östör's Making of Forest of Bliss (2002) is a combination book and DVD that contains eight teaching tools for better understanding Gardner's celebrated film Forest of Bliss. After the film was shot in 1985, filmmaker Gardner and anthropologist Östör recorded a conversation about each image and sound of the film while they screened it again in 1987, and remembered their filmmaking process on location in Benares, India. The feature length (89 minute) documentary about death ritual, reincarnation, the sacred Ganges River, and the very atmosphere of Benares is included as DVD, as are teaching tools such as frame grabs (still images from the film), a mathematically precise shot list, bibliography, important criticism and essays about the film, and the featured in-depth conversation between filmmaker Gardner and anthropological advisor Östör. This essay articulates the unique breakthroughs in pedagogy, cross-cultural studies, and multidisciplinary analysis such hybrid technology provides.     

Citing a Data Repository: A Case Study of the Protein Data Bank

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB’s large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.     

Change of insulin-like growth factor gene expression in Chinese hamster ovary cells cultured in serum-free media

Although the sera used in animal cell culture media provide the macromolecules, nutrients, hormones, and growth factors necessary to support cell growth, it could also be an obstacle to the production of recombinant proteins in animal cell culture systems used in many sectors of the biotechnology industry. For this reason, many research groups, including our laboratory, have been trying to develop serum-free media (SFM) or serum-supplemented media (SSM) for special or multi-purpose cell lines. The Chinese hamster ovary (CHO) cell, for example, is frequently used to produce proteins and is especially valuable in the large-scale production of pharmaceutically important proteins, yet information about its genome is lacking. Also, SFMs have only been evaluated by comparing growth patterns for cells grown in SFMs with those grown in SSM or by measuring the titer of the target protein obtained from cells grown in each type of medium. These are not reliable methods of obtaining the type of information needed to determine whether an SFM should be replaced with an SSM. We carried out a cDNA microarray analysis to evaluate MED-3, an SFM developed in our laboratory, as a CHO culture medium. When CHO cells were cultured in MED-3 instead of an SSM, several genes associated with cell growth were down-regulated, although this change diminished over time. We found that the insulin-like growth factor (IGF) gene was representative of the proteins that were down-regulated in cells cultured in MED-3. When several key supplements-including insulin, transferrin, ethanolamine, and selenium-were removed from MED-3, theIGF expression was consistently down-regulated and cell growth decreased proportionately. Based on these results, we concluded that when an SFM is used as a culture medium, it is important to supplement it with substances that can help the cells maintain a high level ofIGF expression. The data presented in this study, therefore, might provide useful information for the design and development of SFM or SSM, as well as for the design of genome-based studies of CHO cells to determine how they can be used optimally for protein production in pharmaceutical and biomedical research.     

Inferring gene networks from steady-state response to single-gene perturbations

Inferring gene networks from gene expression data is an important step in understanding the molecular machinery of life. Three methods for establishing and quantifying causal relationships between genes based on steady-state measurements in single-gene perturbation experiments have recently been proposed: the regulatory strength method, the local regulatory strength method, and Gardner's method. The theoretical basis of these methods is presented here in a thorough and consistent fashion. In principle, for the same data set all three methods would generate identical networks, but they would quantify the strengths of connections in different ways. The regulatory strength method is shown here to be topology-dependent. It adopts the format of the data collected in gene expression microarray experiments and therefore can be immediately used with this technology. The regulatory strengths obtained by this method can also be used to compute local regulatory strengths. In contrast, Gardner's method requires both measurements of mRNA concentrations and measurements of the applied rate perturbations, which is not usually part of a standard microarray experimental protocol. The results generated by Gardner's method and by the two regulatory strengths methods differ only by scaling constants, but Gardner's method requires more measurements. On the other hand, the explicit use of rate perturbations in Gardner's approach allows one to address new questions with this method, like what perturbations caused given responses of the system. Results of the application of the three techniques to real experimental data are presented and discussed. The comparative analysis presented in this paper can be helpful for identifying an appropriate technique for inferring genetic networks and for interpreting the results of its application to experimental data.     

Evolutionary naturalistic justifications of morality: A matter of faith and works

Robert Richards has presented a detailed defense of evolutionary ethics, a revised version of Darwin's views and a major modification of E. O. Wilson's. He contends that humans have evolved to seek the community welfare by acting altruistically. And since the community welfare is the highest moral good, humans ought to act altruistically. Richards asks us to take his empirical premises on faith and aims to show how they can justify an ethical conclusion. He identifies two necessary conditions for a naturalistic justification of morality (NJ): its premises (1) must be empirical and (2) concerned with morally relevant causal factors. I argue that these two conditions are insufficient. An NJ must also appeal to teleogical or teleonomic laws which identify proper effects and reliable causes of these effects. So I supplement biological faith with an NJ that I believe has a better chance of working since faith without works is dead.     

Dead Birds Migrating: DVD Reinvigorates Classic Ethnographic Film

The DVD release of Robert Gardner's Dead Birds exemplifies the added value of extra features and the improvement in viewing quality when existing ethnographic films are distributed in this new medium. Whereas in the past, ethnographic films have been experienced as transitory performances, a nonlinear medium like DVD makes it possible to read a film the way one reads a book, stopping, reflecting, and reviewing. The inclusion of multiple soundtracks, additional sequences, and associated texts affords a density of content that has not previously been possible in either films or books.     

Iron (III) citrate inhibits polyethylenimine-mediated transient transfection of Chinese hamster ovary cells in serum-free medium

Recent advances in transient transfection protocols using polyethylenimine (PEI) as a transfection reagent have led to the development of economical methods that provide yields sufficient for industrial production of proteins for many preclinical needs. There are many variables that can be optimized to improve protein expression in transient transfection, and one of the most critical is the medium in which the cells are grown. While transfection with PEI works well in media containing serum, the biopharmaceutical industry is moving away from animal-derived components in media. A number of serum-free media have been found to allow transient transfection, but many others do not for reasons that are not clear. Thus, knowledge of the components of serum-free media that can cause inhibition of PEI-mediated transient transfection would be useful for media development. In this study, an analysis was performed of various components of a serum-free medium used for Chinese hamster ovary cells in which PEI-mediated transient transfection was inhibited. We found that an iron supplement added to the medium was responsible for the inhibition. Further investigation showed that iron (III) citrate, a common iron chelator found in serum-free medium, was the specific component that caused the effect. Further, we showed that inhibition of transient transfection was caused by iron (III) citrate specifically, rather than citrate or iron alone. Finally, we showed that various iron chelators in serum-free media other than iron (III) citrate do not inhibit antibody expression.     

Mass Production of the Beneficial Nematode Heterorhabditis bacteriophora and Its Bacterial Symbiont Photorhabdus luminescens

Entomoparasitic nematodes (EPNs) are being commercialized as a biocontrol measure for crop insect pests, as they provide advantages over common chemical insecticides. Mass production of these nematodes in liquid media has become a major challenge for commercialization. Producers are not willing to share the trade secrets of mass production and by doing so, have made culturing EPNs extremely difficult to advance existing technologies. Theoretically, mass production in liquid media is an ideal culturing method as it increases cost efficiency and nematode quantity. This paper will review current culturing methodologies and suggest basic culturing parameters for mass production. This review is focused on Heterorhabditis bacteriophora; however, this information can be useful for other nematode species.     

Investigations into the etiology of neural tube defects

Neural tube defects (NTDs) are serious malformations affecting approximately 1 per 1000 births, yet the mechanisms by which they arise are unknown. There have been consistent efforts in many fields of research to elucidate the etiology of this multifactorial condition. While no single gene has been identified as a major independent risk factor for NTDs, candidate genes have been proposed that may modify the effects of maternal and/or embryonic exposures. Folate supplementation effectively reduces the occurrence of NTDs and, consequently, has focused much research on metabolism of folate-related pathways during pregnancy and development. Further understanding of normal development and how teratogens can perturb these orchestrated processes also remains at the fore of modern scientific endeavors. The composite of these factors remains fragmented; the aim of this review is to provide the reader with a summary of sentinel and current works in the body of literature addressing NTD disease etiology.     

Go forth,evolve and prosper: the genetic basis of adaptive evolution in an invasive species

Invasive species stand accused of a familiar litany of offences, including displacing native species, disrupting ecological processes and causing billions of dollars in ecological damage (Cox 1999 ). Despite these transgressions, invasive species have at least one redeeming virtue – they offer us an unparalleled opportunity to investigate colonization and responses of populations to novel conditions in the invaded habitat (Elton 1958 ; Sakai et al. 2001 ). Invasive species are by definition colonists that have arrived and thrived in a new location. How they are able to thrive is of great interest, especially considering a paradox of invasion (Sax & Brown 2000 ): if many populations are locally adapted (Leimu & Fischer 2008 ), how could species introduced into new locations become so successful? One possibility is that populations adjust to the new conditions through plasticity – increasing production of allelopathic compounds (novel weapons), or taking advantage of new prey, for example. Alternatively, evolution could play a role, with the populations adapting to the novel conditions of the new habitat. There is increasing evidence, based on phenotypic data, for rapid adaptive evolution in invasive species (Franks et al. 2012 ; Colautti & Barrett 2013 ; Sultan et al. 2013 ). Prior studies have also demonstrated genetic changes in introduced populations using neutral markers, which generally do not provide information on adaptation. Thus, the genetic basis of adaptive evolution in invasive species has largely remained unknown. In this issue of Molecular Ecology, Vandepitte et al. ( 2014 ) provide some of the first evidence in invasive populations for molecular genetic changes directly linked to adaptation.     

A reflection of the lasting contributions from Dr. Robert Bittman to sterol trafficking,sphingolipid and phospholipid research

With the passing of Dr. Robert Bittman from pancreatic cancer on the 1st October 2014, the lipid research field lost one of the most influential and significant personalities. Robert Bittman's genius was in chemical design and his contribution to the lipid research field was truly immense. The reagents and chemicals he designed and synthesised allowed interrogation of the role of lipids in constituting complex biophysical membranes, sterol transfer and in cellular communication networks. Here we provide a review of these works which serve as a lasting memory to his life.     

Characterization of intermediate phenotypes induced by chemically undefined laboratory media in virulent Bordetella bronchiseptica strains

The expression of many virulence factors of Bordetella bronchiseptica is regulated by the bvgAS locus and reduced in response to environmental signals called modulators. Virulent strains can alternate between virulent (Bvg(+)), intermediate (Bvg(i)), and modulated (Bvg(+)mod) phenotypes. Potential vaccine antigens can be expressed by Bvg1 strains grown only in the absence of modulators. In the present study we evaluated filamentous hemagglutinin (FHA) and outer membrane protein (OMP) expression in Bvg(+) B. bronchiseptica strains grown in chemically undefined media: nutrient agar (NA), tryptic soy agar (TSA), tryptose phosphate broth (TPB), and brain-heart infusion (BHI). Our results suggest that TSA and TPB usually induce semimodulation, since Bvg(+) strains cultured in these media retained the expression of FHA and virulence-associated OMPs in the 30 kDa region, but failed to express other virulence markers such as OMPs in the regions of 90 and 200 kDa, though they expressed flagellin (avirulence marker). On the other hand, NA and BHI usually induce modulation. Thus the assayed chemically undefined media should not be used in vaccine production. Semimodulation induced by TSA and TPB can be accurately detected by SDS-PAGE Sarkosyl-insoluble OMP-enriched profiles. The reduction or absence of OMPs in the regions of 90 and 200 kDa is the most sensitive marker, and in some cases the presence of flagellin in intermediate profiles is another trait of the Bvg(i) phenotypes. Therefore these markers could be useful for selecting media for vaccine production. We also characterized the phenotype of Bvg(+) strains grown in Stainer-Scholte broth, an expensive medium, with and without glutathione, and we have detected no differences; this is the first attempt to reduce the cost of a Bordetella growth medium for veterinary vaccine production.     

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics.     

The Chemical Synthesis of DNA/RNA: Our Gift to Science

It is a great privilege to contribute to the Reflections essays. In my particular case, this essay has allowed me to weave some of my major scientific contributions into a tapestry held together by what I have learned from three colleagues (Robert Letsinger, Gobind Khorana, and George Rathmann) who molded my career at every important junction. To these individuals, I remain eternally grateful, as they always led by example and showed many of us how to break new ground in both science and biotechnology. Relative to my scientific career, I have focused primarily on two related areas. The first is methodologies we developed for chemically synthesizing DNA and RNA. Synthetic DNA and RNA continue to be an essential research tool for biologists, biochemists, and molecular biologists. The second is developing new approaches for solving important biological problems using synthetic DNA, RNA, and their analogs.     

Modelling Production and Biomasses of Prey and Predatory Fish in Lakes

This work presents a new dynamic model to predict two fundamental functional categories of fish in lakes, prey and predatory fish. The model has been developed within the framework of a more comprehensive lake ecosystem model, LakeWeb, which also accounts for phytoplankton, bacterioplankton, two types of zooplankton (herbivorous and predatory), zoobenthos, macrophytes and benthic algae. The new fish model gives seasonal variations (the calculation time is 1 week). It is meant to account for all factors regulating the production of fish for lakes in general. The model has not been calibrated and tested in the traditional way using data from a few well investigated lakes. Instead, it has been tested using empirical data and regressions based on data from many lakes. The basic aim of the model is that it should capture typical functional and structural patterns in many lakes. It accounts in a relatively simple manner for many complicated processes, like fishing (by birds, animals and man), fish migration to and from lakes and how macrophyte cover gives shelter to small fish and reduces predation pressure. Food choices are handled by distribution coefficients regulating how much of the different available food sources a given organism would consume. Beside these distribution coefficients, and the way the food choices are structured (the food choice panel), fundamental concepts in the fish model are: (1) metabolic efficiency ratios, which express how much of the food consumed by the predator that will increase the biomass of the predator and how much that will be lost by respiration and faeces, (2) actual consumption rates, which are defined from the ratio between the actual biomass of the predator and the normal biomass of the predator, and the normal consumption rates, which are related to the turnover time of the predator. We have demonstrated that the new model gives predictions which agree well with the values given by the empirical regressions, and also expected and requested divergences from these regression lines when they do not provide sufficient resolution.     

The impact of flooding on aquatic ecosystem services

Flooding is a major disturbance that impacts aquatic ecosystems and the ecosystem services that they provide. Predicted increases in global flood risk due to land use change and water cycle intensification will likely only increase the frequency and severity of these impacts. Extreme flooding events can cause loss of life and significant destruction to property and infrastructure, effects that are easily recognized and frequently reported in the media. However, flooding also has many other effects on people through freshwater aquatic ecosystem services, which often go unrecognized because they are less evident and can be difficult to evaluate. Here, we identify the effects that small magnitude frequently occurring floods (<?10-year recurrence interval) and extreme floods (>?100-year recurrence interval) have on ten aquatic ecosystem services through a systematic literature review. We focused on ecosystem services considered by the Millennium Ecosystem Assessment including: (1) supporting services (primary production, soil formation), (2) regulating services (water regulation, water quality, disease regulation, climate regulation), (3) provisioning services (drinking water, food supply), and (4) cultural services (aesthetic value, recreation and tourism). The literature search resulted in 117 studies and each of the ten ecosystem services was represented by an average of 12?±?4 studies. Extreme floods resulted in losses in almost every ecosystem service considered in this study. However, small floods had neutral or positive effects on half of the ecosystem services we considered. For example, small floods led to increases in primary production, water regulation, and recreation and tourism. Decision-making that preserves small floods while reducing the impacts of extreme floods can increase ecosystem service provision and minimize losses.     

Societal views and animal welfare science: understanding why the modified cage may fail and other stories

The innovations developed by scientists working on animal welfare are often not adopted in practice. In this paper, we argue that one important reason for this failure is that the solutions proposed do not adequately address the societal concerns that motivated the original research. Some solutions also fail because they do not adequately address perceived constraints within the industry. Using examples from our own recent work, we show how research methods from the social sciences can address both of these limitations. For example, those who persist in tail-docking cattle (despite an abundance of evidence showing that the practice has no benefits) often justify their position by citing concern for cow cleanliness. This result informs the nature of new extension efforts directed at farmers that continue to tail dock, suggesting that these efforts will be more effective if they focus on providing producers with methods (of proven efficacy) for keeping cows clean. Work on pain mitigation for dehorning shows that some participants reluctant to provide pain relief believe that the pain from this procedure is short lasting and has little impact on the calf. This result informs the direction of new biological research efforts to understand both the magnitude and duration of any suffering that result from this type of procedure. These, and other examples, illustrate how social science methodologies can document the shared and divergent values of different stakeholders (to ensure that proposed solutions align with mainstream values), beliefs regarding the available evidence (to help target new scientific research that meets the perceived gaps), and barriers in implementing changes (to ease adoption of ideas by addressing these barriers).     

Water column contributions to coral reef productivity: overcoming challenges of context dependence

Coral reefs are declining at an unprecedented rate. Effective management and conservation initiatives necessitate improved understanding of the drivers of production because the high rates found in these ecosystems are the foundation of the many services they provide. The water column is the nexus of coral reef ecosystem dynamics, and functions as the interface through which essentially all energy and nutrients are transferred to fuel both new and recycled production. Substantial research has described many aspects of water column dynamics, often focusing on specific components because water column dynamics are highly spatially and temporally context dependent. Although necessary, a cost of this approach is that these dynamics are often not well linked to the broader ecosystem or across systems. To help overcome the challenge of context dependence, we provide a comprehensive review of this literature, and synthesise it through the perspective of ecosystem ecology. Specifically, we provide a framework to organise the drivers of temporal and spatial variation in production dynamics, structured around five primary state factors. These state factors are used to deconstruct the environmental contexts in which three water column sub-food webs mediate ‘new’ and ‘recycled’ production. We then highlight critical pathways by which global change drivers are altering coral reefs via the water column. We end by discussing four key knowledge gaps hindering understanding of the role of the water column for mediating coral reef production, and how overcoming these could improve conservation and management strategies. Throughout, we identify areas of extensive research and those where studies remain lacking and provide a database of 84 published studies. Improved integration of water column dynamics into models of coral reef ecosystem function is imperative to achieve the understanding of ecosystem production necessary to develop effective conservation and management strategies needed to stem global coral loss.     

Introduction: gender,migration and the media

Abstract

Mediated representations of gender, ethnicity and migration play an increasingly important role in the way these categories are understood in the public sphere and the private realm. As media often intervene in processes of individual and institutional communication, they provide frameworks for the production and consumption of representations of these categories. Thus media – in their production, representations and consumption – need to be analysed, not only as reflections as pre-existing socio-political realities, but also as constitutive elements in the production of meanings of the self and the Other. This special issue includes a number of articles that examine the articulations of gendered ethnic identities and of gendered citizenship as these are shaped in media production, media representations and media consumption.     

Fine control of call frequency by horseshoe bats

The auditory system of horseshoe bats is narrowly tuned to the sound of their own echoes. During flight these bats continuously adjust the frequency of their echolocation calls to compensate for Doppler-effects in the returning echo. Horseshoe bats can accurately compensate for changes in echo frequency up to 5 kHz, but they do so through a sequence of small, temporally-independent, step changes in call frequency. The relationship between an echo's frequency and its subsequent impact on the frequency of the very next call is fundamental to how Doppler-shift compensation behavior works. We analyzed how horseshoe bats control call frequency by measuring the changes occurring between many successive pairs of calls during Doppler-shift compensation and relating the magnitude of these changes to the frequency of each intervening echo. The results indicate that Doppler-shift compensation is mediated by a pair of (echo)frequency-specific sigmoidal functions characterized by a threshold, a slope, and an upper limit to the maximum change in frequency that may occur between successive calls. The exact values of these parameters necessarily reflect properties of the underlying neural circuitry of Doppler-shift compensation and the motor control of vocalization, and provide insight into how neural feedback can accommodate the need for speed without sacrificing stability.