Stable transformation of papaya via microprojectile bombardment

Summary Stable transformation of papaya (Carica papaya L.) has been achieved following DNA delivery via high velocity microprojectiles. Three types of embryogenic tissues, including immature zygotic embryos, freshly explanted hypocotyl sections, and somatic embryos derived from both, were bombarded with tungsten particles carrying chimeric NPTII and GUS genes. All tissue types were cultured prior to and following bombardment on half-strength MS medium supplemented with 10 mg 1^–1 2,4-D, 400 mg 1^–1 glutamine, and 6% sucrose. Upon transfer to 2,4-D-free medium containing 150 mg 1^–1 kanamycin sulfate, ten putative transgenic isolates produced somatic embryos and five regenerated leafy shoots. Leafy shoots were produced six to nine months following bombardment. Tissues from 13 of these isolates were assayed for NPTII activity, and 10 were positive. Six out of 15 isolates assayed for GUS expression were positive. Three isolates were positive for both NPTII and GUS,Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - GUS -glucuronidase - X-gluc 5-Br-4-Cl-3-indolyl--D-glucuronic acid - CaMV cauliflower mosaic virus - NOS nopaline synthase - NPTII neomycin phosphotransferase II Journal Series no. 3448 of the Hawaii Institute of Tropical Agriculture and Human Resources     

Versatility and specialization in labrid fishes: ecomorphological implications

Summary The term specialized has been used to describe species that possess unique functional attributes and/or a narrow, stereotyped range of attributes, but there are few comparative functional analyses of specialists and generalists. If species with functional morphological specializations are capable of functioning over a broad range, the link between morphology and ecology may be relaxed under certain environmental conditions. In this study, high-speed films of jaw movements during prey capture were compared statistically for three coexisting coral reef fish species in the family Labridae, one trophic specialist and two trophic generalists. The trophic specialist possessed a unique functional feature related to the movement of the hyoid in the floor of the mouth, while the trophic generalists were not observed to possess any functional specializations. All three species showed functional versatility in that they were able to adjust their prey capture mechanism in response to the evasive potential of the prey. The functional versatility of trophic specialists has implications for ecomorphological studies, since species characterized as possessing unique functional or morphological features may demonstrate marked flexibility in ecological variables such as diet or foraging behavior, decreasing the likelihood of identifying correlations between morphology and ecology.     

The roles of integration in molecular systems biology

A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.     

Molecular Mechanisms of Ischemia–Reperfusion Injury in Brain: Pivotal Role of the Mitochondrial Membrane Potential in Reactive Oxygen Species Generation

Stroke and circulatory arrest cause interferences in blood flow to the brain that result in considerable tissue damage. The primary method to reduce or prevent neurologic damage to patients suffering from brain ischemia is prompt restoration of blood flow to the ischemic tissue. However, paradoxically, restoration of blood flow causes additional damage and exacerbates neurocognitive deficits among patients who suffer a brain ischemic event. Mitochondria play a critical role in reperfusion injury by producing excessive reactive oxygen species (ROS) thereby damaging cellular components, and initiating cell death. In this review, we summarize our current understanding of the mechanisms of mitochondrial ROS generation during reperfusion, and specifically, the role the mitochondrial membrane potential plays in the pathology of cerebral ischemia/reperfusion. Additionally, we propose a temporal model of ROS generation in which posttranslational modifications of key oxidative phosphorylation (OxPhos) proteins caused by ischemia induce a hyperactive state upon reintroduction of oxygen. Hyperactive OxPhos generates high mitochondrial membrane potentials, a condition known to generate excessive ROS. Such a state would lead to a “burst” of ROS upon reperfusion, thereby causing structural and functional damage to the mitochondria and inducing cell death signaling that eventually culminate in tissue damage. Finally, we propose that strategies aimed at modulating this maladaptive hyperpolarization of the mitochondrial membrane potential may be a novel therapeutic intervention and present specific studies demonstrating the cytoprotective effect of this treatment modality.     

Prokaryotic evolution and the tree of life are two different things

Background

The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.

Results

It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.

Conclusion

Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.

Reviewers

This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.     

AMPA receptor-dependent clustering of synaptic NMDA receptors is mediated by Stargazin and NR2A/B in spinal neurons and hippocampal interneurons

Under standard conditions, cultured ventral spinal neurons cluster AMPA- but not NMDA-type glutamate receptors at excitatory synapses on their dendritic shafts in spite of abundant expression of the ubiquitous NMDA receptor subunit NR1. We demonstrate here that the NMDA receptor subunits NR2A and NR2B are not routinely expressed in cultured spinal neurons and that transfection with NR2A or NR2B reconstitutes the synaptic targeting of NMDA receptors and confers on exogenous application of the immediate early gene product Narp the ability to cluster both AMPA and NMDA receptors. The use of dominant-negative mutants of GluR2 further showed that the synaptic targeting of NMDA receptors is dependent on the presence of synaptic AMPA receptors and that synaptic AMPA and NMDA receptors are linked by Stargazin and a MAGUK protein. This system of AMPA receptor-dependent synaptic NMDA receptor localization was preserved in hippocampal interneurons but reversed in hippocampal pyramidal neurons.     

Detection and Structural Characterization of Ether Glycerophosphoethanolamine from Cortical Lysosomes Following Traumatic Brain Injury Using UPLC‐HDMSE

The use of ultra performance liquid chromatography coupled to data independent tandem mass spectrometry with traveling wave ion mobility for detection and structural identification of ether‐linked glycerophosphoethanolamine is described. The experimental design generates 4D data (chromatographic retention time, precursor accurate mass, drift time with associated calculated collisional cross‐section, and time‐aligned accurate mass diagnostic product ions) for each ionization mode. Confident structure identification depends on satisfying 4D data confirmation in both positive and negative ion mode. Using this methodology, a number of ether‐linked glycerophosphoethanolamine lipids are structurally elucidated from mouse brain lysosomes. It is further determined that several ether‐linked glycerophosphoethanolamine structures are differentially abundant between lysosomes isolated from mouse cortex following traumatic brain injury as compared to that of sham animals. The combined effort of aligning multi‐dimensional mass spectrometry data with a well‐defined traumatic brain injury model lays the foundation for gaining mechanistic insight in the role lysosomal membrane damage plays in neuronal cell death following brain injury.     

Effects of plant odor on oviposition by the black swallowtail butterfly,Papilio polyxenes (Lepidoptera: Papilionidae)

Black swallowtail females laid more eggs on plant models treated with contact stimulants and volatiles from carrot leaves than on models treated only with contact stimulants. The volatiles enhanced landing rates and females alighted more frequently on artificial leaves treated with host volatiles than on adjacent control leaves. Volatiles from cabbage, a nonhost, inhibited landing rates on artificial leaves treated with carrot contact stimulants. Examination of antennae revealed two major types of sensilla, believed to be olfactory in function. Electroantennogram preparations responded more strongly to carrot volatiles than to cabbage volatiles and several shared responses at particular retention times to carrot volatile components eluting from a gas chromatograph. Our results are consistent with a long-standing hypothesis that behavioral responses to essential oil components characteristic of the larval food plants have facilitated host shifts in the genus Papilio.     

Deriving phylogenetic trees from the similarity analysis of metabolic pathways

MOTIVATION: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree. RESULTS: We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms.