Method and metaphysics in Clements's and Gleason's ecological explanations

To generate explanatory theory, ecologists must wrestle with how to represent the extremely many, diverse causes behind phenomena in their domain. Early twentieth-century plant ecologists Frederic E. Clements and Henry A. Gleason provide a textbook example of different approaches to explaining vegetation, with Clements allegedly committed, despite abundant exceptions, to a law of vegetation, and Gleason denying the law in favor of less organized phenomena. However, examining Clements's approach to explanation reveals him not to be expressing a law, and instead to be developing an explanatory structure without laws, capable of progressively integrating causal complexity. Moreover, Clements and Gleason largely agree on the causes of vegetation; but, since causal understanding here underdetermines representation, they differ on how to integrate recognized causes into general theory--that is, in their methodologies. Observers of the case may have mistakenly assumed that scientific representation across the disciplines typically aims at laws like Newton's, and that representations always reveal scientists' metaphysical commitments. Ironically, in the present case, this assumption seems to have been made even by observers who regard Clements as nai ve for his alleged commitment to an ecological law.     

Pathogenic chaperone-like RNA induces congophilic aggregates and facilitates neurodegeneration in Drosophila

Protein aggregation is a hallmark of many neurodegenerative diseases. RNA chaperones have been suggested to play a role in protein misfolding and aggregation. Noncoding, highly structured RNA recently has been demonstrated to facilitate transformation of recombinant and cellular prion protein into proteinase K-resistant, congophilic, insoluble aggregates and to generate cytotoxic oligomers in vitro. Transgenic Drosophila melanogaster strains were developed to express highly structured RNA under control of a heat shock promoter. Expression of a specific construct strongly perturbed fly behavior, caused significant decline in learning and memory retention of adult males, and was coincident with the formation of intracellular congophilic aggregates in the brain and other tissues of adult and larval stages. Additionally, neuronal cell pathology of adult flies was similar to that observed in human Parkinson's and Alzheimer's disease. This novel model demonstrates that expression of a specific highly structured RNA alone is sufficient to trigger neurodegeneration, possibly through chaperone-like facilitation of protein misfolding and aggregation.     

Unraveling the Morphology of High Efficiency Polymer Solar Cells Based on the Donor Polymer PBDTTT‐EFT

The microstructure of the polymer PBDTTT‐EFT and blends with the fullerene derivative PC₇₁BM that achieve solar conversion efficiencies of over 9% is comprehensively investigated. A combination of synchrotron techniques are employed including surface‐sensitive near‐edge X‐ray absorption fine structure (NEXAFS) spectroscopy and bulk‐sensitive grazing‐incidence wide angle X‐ray scattering (GIWAXS). A preferential “face‐on” orientation of PBDTTT‐EFT is observed in the bulk of both pristine and blend thin films, with π–π stacking largely normal to the substrate, which is thought to be beneficial for charge transport. At the surface of the blend, a slight “edge‐on” structure of the polymer is observed with side‐chains aligned normal to the substrate. The effect of the solvent additive 1,8‐diiodooctane (DIO) on solar cell efficiency and film microstructure is also investigated, where the addition of 3 vol% DIO results in an efficiency increase from ≈6.4% to ≈9.5%. GIWAXS studies indicate that the addition of DIO improves the crystallization of the polymer. Furthermore, atomic force microscopy and transmission electron microscopy are employed to image surface and bulk morphology revealing that DIO suppresses the formation of large PC₇₁BM aggregates.     

Cytometry‐based single‐cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF‐α‐induced apoptosis in vivo

Understanding heterogeneous cellular behaviors in a complex tissue requires the evaluation of signaling networks at single-cell resolution. However, probing signaling in epithelial tissues using cytometry-based single-cell analysis has been confounded by the necessity of single-cell dissociation, where disrupting cell-to-cell connections inherently perturbs native cell signaling states. Here, we demonstrate a novel strategy (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue—DISSECT) that preserves native signaling for Cytometry Time-of-Flight (CyTOF) and fluorescent flow cytometry applications. A 21-plex CyTOF analysis encompassing core signaling and cell-identity markers was performed on the small intestinal epithelium after systemic tumor necrosis factor-alpha (TNF-α) stimulation. Unsupervised and supervised analyses robustly selected signaling features that identify a unique subset of epithelial cells that are sensitized to TNF-α-induced apoptosis in the seemingly homogeneous enterocyte population. Specifically, p-ERK and apoptosis are divergently regulated in neighboring enterocytes within the epithelium, suggesting a mechanism of contact-dependent survival. Our novel single-cell approach can broadly be applied, using both CyTOF and multi-parameter flow cytometry, for investigating normal and diseased cell states in a wide range of epithelial tissues.     

Neurogenesis in the Adult Avian Song-Control System

New neurons are added throughout the forebrain of adult birds. The song-control system is a model to investigate the addition of new long-projection neurons to a cortical circuit that regulates song, a learned sensorimotor behavior. Neuroblasts destined for the song nucleus HVC arise in the walls of the lateral ventricle, and wander through the pallium to reach HVC. The survival of new HVC neurons is supported by gonadally secreted testosterone and its downstream effectors including neurotrophins, vascularization, and electrical activity of postsynaptic neurons in nucleus RA (robust nucleus of the arcopallium). In seasonal species, the HVC→RA circuit degenerates in nonbreeding birds, and is reconstructed by the incorporation of new projection neurons in breeding birds. There is a functional linkage between the death of mature HVC neurons and the birth of new neurons. Various hypotheses for the function of adult neurogenesis in the song system can be proposed, but this remains an open question.Song behavior in oscine birds is regulated by a network of pallial and striatal nuclei. The song-control system shows extensive plasticity in adults, including ongoing neurogenesis in several nuclei (Brenowitz 2008). The addition of new neurons to the adult brain of higher vertebrates was first suggested by the pioneering studies of Altman and Das (1965) and Kaplan and Hinds (1977). They reported that labeled cells were present in the dentate gyrus (DG) of rats following the injection of ³H-thymidine. Their claims, however, met with skepticism and the neuronal identity of the new cells that they observed was called into question (Gross 2000). In an influential study, Rakic (1985) injected adult rhesus monkeys with ³H-thymidine and reported that, “all neurons of the rhesus monkey brain are generated during prenatal and early postnatal life.” The study of neuronal addition to the adult brain, was subsequently dropped for ∼20 years in the face of the dogma that neurogenesis was largely completed by birth (Gross 2000). This prevailing view only started to be overturned when Nottebohm and colleagues published a series of studies showing that new cells are added to the cortical-like song nucleus HVC (Fig. 1) of adult canaries (Serinus canarius) (Goldman and Nottebohm 1983). These new cells have neuronal morphology, some of these cells fire action potentials in response to sound (Paton and Nottebohm 1984), receive synaptic input (Burd and Nottebohm 1985), may synapse on neurons in the efferent robust nucleus of the arcopallium (RA) (Alvarez-Buylla et al. 1990), and express neuron-specific proteins (Barami et al. 1995). Together, these studies in songbirds showed that new neurons are born and incorporated into functional circuits in the brains of adults of higher vertebrates (Nottebohm 2004). This research on adult neurogenesis in songbirds stimulated investigators to re-examine this topic in mammals. It soon became clear that new neurons are added throughout life to the DG and olfactory bulb of mammals including humans (Cameron and Gould 1994; Gould et al. 1997, 1999a; Lim et al. 1997; Eriksson et al. 1998). Because of these initial confirmatory reports, there has been explosive growth in study of the mechanisms and functions of adult neurogenesis in the mammalian DG and olfactory bulb.Open in a separate windowFigure 1.A schematic of the neurogenic regions in the avian brain overlaid on the avian song circuits. Neurogenic regions are shown in red. Note the proximity of HVC (and hippocampus [HC]) to the ventricular zone (VZ). A schematic version of the motor pathway for song production is shown in blue. A schematic of the ascending auditory pathway is shown in green. The dotted line indicates an indirect route through many nuclei of the ascending auditory pathway leading to field L in the telencephalon. The anterior forebrain circuit for song learning and plasticity is shown in yellow. NCM, Caudomedial nidopallium; RA, arcopallium; LMAN, lateral magnocellular nucleus of the anterior neostriatum; OB, olfactory bulb; DLM, dorsolateral medial; PAm, parambigualis; RAm, retroambigualisBirds continue to be a productive model for the study of neurogenesis in the adult brain, as discussed below. In this article, we will focus on neurogenesis in the song-control system as this is the most intensively studied model in birds. (For a review of neurogenesis in the avian hippocampus [HC], see Barnea and Pravosudov 2011.) We will discuss the mechanisms of neurogenesis in the song system, intrinsic and extrinsic factors that influence neuronal addition, a linkage between cell death and neurogenesis, seasonal plasticity, and consider potential functions of adult neurogenesis.     

The impact of plant biotechnology on food allergy

Concerns about food allergy and its societal growth are intertwined with the growing advances in plant biotechnology. The knowledge of plant genes and protein structures provides the key foundation to understanding biochemical processes that produce food allergy. Biotechnology offers the prospect of producing low-allergen or allergen null plants that could mitigate the allergic response. Modified low-IgE binding variants of allergens could be used as a vaccine to build immunotolerance in sensitive individuals. The potential to introduce new allergens into the food supply by biotechnology products is a regulatory concern.