The Origin of Life: Models and Data.

A general framework for conventional models of the origin of life (OOL) is the specification of a 'privileged function.' A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients. In Membrane Worlds, the privileged function is compartmentalization. In evaluating these models, we consider the contents and properties of the Universal Gene Set of life, which is the set of orthologous genes conserved throughout the tree of life and found in every living system. We also consider the components and properties of the Molecular Toolbox of Life, which contains twenty amino acids, eight nucleotides, glucose, polypeptide, polynucleotide, and several other components. OOL models based on privileged functions necessarily depend on "takeovers" to transition from previous genetic and catalytic systems to the extant DNA/RNA/protein system, requiring replacement of one Molecular Toolbox with another and of one Universal Gene Set with another. The observed robustness and contents of the Toolbox of Life and the Universal Gene Set over the last 3.7 billion years are thought to be post hoc phenomena. Once the takeover processes are acknowledged and are reasonably considered, the privileged function models are seen to be extremely complex with low predictive power. These models require indeterminacy and plasticity of biological and chemical processes

The Central Symbiosis of Molecular Biology: Molecules in Mutualism.

As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. Mutualisms (i) increase fitness, (ii) inspire robustness, (iii) are resilient and resistant to change, (iv) sponsor co-evolution, (v) foster innovation, and (vi) involve partners that are distantly related with contrasting yet complementary proficiencies. Previous to this work, mutualisms were understood to operate on levels of cells, organisms, ecosystems, and even societies and economies. Here, the concepts of mutualism are extended to molecules and are seen to apply to the relationship between RNA and protein. Polynucleotide and polypeptide are Molecules in Mutualism. RNA synthesizes protein in the ribosome and protein synthesizes RNA in polymerases. RNA and protein are codependent, and trade proficiencies. Protein has proficiency in folding into complex three-dimensional states, contributing enzymes, fibers, adhesives, pumps, pores, switches, and receptors. RNA has proficiency in direct molecular recognition, achieved by complementary base pairing interactions, which allow it to maintain, record, and transduce information. The large phylogenetic distance that characterizes partnerships in organismal mutualism has close analogy with large distance in chemical space between RNA and protein. The RNA backbone is anionic and self-repulsive and cannot form hydrophobic structural cores. The protein backbone is neutral and cohesive and commonly forms hydrophobic cores. Molecules in Mutualism extends beyond RNA and protein. A cell is a consortium of molecules in which nucleic acids, proteins, polysaccharides, phospholipids, and other molecules form a mutualism consortium that drives metabolism and replication. Analogies are found in systems such as stromatolites, which are large consortia of symbiotic organisms. It seems reasonable to suggest that 'polymers in mutualism relationships' is a useful and predictive definition of life

Dramatic Loss of Ube3A Expression during Aging of the Mammalian Cortex

Neurobiological studies of aging are beginning to link functional changes with a loss of experience-dependent plasticity. In the visual system, age-related functional changes include decreases in visual acuity, orientation selectivity, motion perception, and ocular dominance plasticity. A recent paper has shown that Ube3A, an E3 ubiquitin ligase that is absent in Angelman's syndrome, is required for experience-dependent plasticity during development of the visual cortex. Knocking out Ube3A during development leads to rigidity of ocular dominance plasticity that is strikingly similar to the reduced plasticity seen in older animals. Furthermore, ubiquitin ligases have been linked with age-related neurodegenerative disorders and longevity. Ubiquitin ligases selectively mark proteins for degradation, and a balance between synaptic proteins and their degradation is important for neural transmission and plasticity. This led us to ask whether normal aging is characterized by a loss of Ube3A in the cortex. We used Western blot analysis in order to quantify Ube3A expression across the life span of humans, macaque monkeys, and cats. We found that Ube3A expression declines across the lifespan in human, monkey, and cat cortex. The losses were substantial (50–80%) in all areas studied which includes V1, V3, V4, frontal, and auditory cortex. In addition, when compared with other synaptic proteins there was a selective loss of Ube3A in human cortex. The progressive loss of Ube3A expression during cortical aging is an important new finding. Furthermore, the selective loss of Ube3A in human cortex highlights a specific vulnerability in human brain aging that may signify a dramatic shift in cortical function and plasticity

Birds and beaches, dogs and leashes : dog owners\u27 sense of obligation to leash dogs on beaches in Victoria, Australia

Domesticated dogs threaten the conservation of beach-nesting birds in Australia through disturbance, and destruction of eggs and chicks. Leashing of dogs can improve conservation outcomes, but few dogs are leashed on beaches. We surveyed dog owners to explore their sense of obligation to leash dogs on beaches. Dog owners were more likely to feel obliged to leash their dog when they believed other people expected dogs to be leashed, and when they believed their dog was a threat to wildlife or people. Dog owners were less likely to feel obliged to leash their dog if they considered unleashed dog recreation to be important. Improved compliance may be achieved through community-based approaches to foster social norms for dog control, tailoring information products to emphasize the risk that all unleashed dogs may pose to beach-nesting birds and raising awareness of designated off-leash exercise dog recreation areas. <br /

First records of Hyalomma rufipes and Ixodes neitzi (Acari: Ixodidae) found on large carnivores in South Africa

Ixodid ticks (Acari: Ixodidae) are important disease vectors for large carnivores, but the composition of the tick communities that parasitize carnivores is poorly understood. We collected ticks from leopards (Panthera pardus) and brown hyenas (Hyaena brunnea) in the Soutpansberg Mountains, South Africa, to determine which species feed on these carnivores. We identified a total of eight tick species belonging to six genera, and recorded Ixodes neitzi and Hyalomma rufipes on P. pardus for the first time

Sensory and repetitive behaviors among children with autism spectrum disorder at home

Atypical sensory and repetitive behaviors are defining features of autism spectrum disorder (ASD) and are thought to be influenced by environmental factors; however, there is a lack of naturalistic research exploring contexts surrounding these behaviors. The current study involved video recording observations of 32 children with ASD (2 – 12 years of age) engaging in sensory and repetitive behaviors during home activities. Behavioral coding was used to determine what activity contexts, sensory modalities, and stimulus characteristics were associated with specific behavior types: hyperresponsive, hyporesponsive, sensory seeking, and repetitive/stereotypic. Results indicated that hyperresponsive behaviors were most associated with activities of daily living and family-initiated stimuli, whereas sensory seeking behaviors were associated with free play activities and child-initiated stimuli. Behaviors associated with multiple sensory modalities simultaneously were common, emphasizing the multi-sensory nature of children’s behaviors in natural contexts. Implications for future research more explicitly considering context are discussed

A practical guide and perspectives on the use of experimental pain modalities with children and adolescents

Use of experimental pain is vital for addressing research questions that would otherwise be impossible to examine in the real world. Experimental induction of pain in children is highly scrutinized given the potential for harm and lack of direct benefit to a vulnerable population. However, its use has critically advanced our understanding of the mechanisms, assessment and treatment of pain in both healthy and chronically ill children. This article introduces various experimental pain modalities, including the cold pressor task, the water load symptom provocation test, thermal pain, pressure pain and conditioned pain modulation, and discusses their application for use with children and adolescents. It addresses practical implementation and ethical issues, as well as the advantages and disadvantages offered by each task. The incredible potential for future research is discussed given the array of experimental pain modalities now available to pediatric researchers

Intracranial EEG fluctuates over months after implanting electrodes in human brain.

OBJECTIVE: Implanting subdural and penetrating electrodes in the brain causes acute trauma and inflammation that affect intracranial electroencephalographic (iEEG) recordings. This behavior and its potential impact on clinical decision-making and algorithms for implanted devices have not been assessed in detail. In this study we aim to characterize the temporal and spatial variability of continuous, prolonged human iEEG recordings. APPROACH: Intracranial electroencephalography from 15 patients with drug-refractory epilepsy, each implanted with 16 subdural electrodes and continuously monitored for an average of 18 months, was included in this study. Time and spectral domain features were computed each day for each channel for the duration of each patient\u27s recording. Metrics to capture post-implantation feature changes and inflexion points were computed on group and individual levels. A linear mixed model was used to characterize transient group-level changes in feature values post-implantation and independent linear models were used to describe individual variability. MAIN RESULTS: A significant decline in features important to seizure detection and prediction algorithms (mean line length, energy, and half-wave), as well as mean power in the Berger and high gamma bands, was observed in many patients over 100 d following implantation. In addition, spatial variability across electrodes declines post-implantation following a similar timeframe. All selected features decreased by 14-50% in the initial 75 d of recording on the group level, and at least one feature demonstrated this pattern in 13 of the 15 patients. Our findings indicate that iEEG signal features demonstrate increased variability following implantation, most notably in the weeks immediately post-implant. SIGNIFICANCE: These findings suggest that conclusions drawn from iEEG, both clinically and for research, should account for spatiotemporal signal variability and that properly assessing the iEEG in patients, depending upon the application, may require extended monitoring