Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars

Motivated by the need to paint a more general picture of what life is—and could be—with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research—e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of “life as we don’t know it” is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it

Emergence, Construction, or Unlikely? Navigating the Space of Questions regarding Life's Origins

We survey some of the philosophical challenges and pitfalls within origins research. Several of these challenges exhibit circularities, paradoxes, or anthropic biases. We present origins approaches in terms of three broad categories: unlikely (life's origin was a chance event), construction (life's origin was a stepwise series of synthesis and assembly processes), and emergence (life was always an amalgam of many parallel processes from which the living state emerged as a natural outcome of physical driving forces). We critically examine some of the founding and possibly misleading assumptions in these categories. Such assumptions need not be detrimental to scientific progress as long as their limits are respected. We conclude by attempting to concisely state the most significant enigmas still remaining in the origins field and suggest routes to solve them

The Effects of Vertical Yoked Prism on Horizontal Heterophoria

PURPOSE: Vertical yoked prisms (VYPs) have been recommended for the remediation of vergence dysfunction, but the evidence base for their use is mostly low level. This study investigates the effect of VYP on horizontal subjective dissociated heterophoria. METHODS: Phoria measurement was performed in primary gaze with the Modified Thorington technique at 3 m and at 40 cm on 40 nonpresbyopic young adults. Subjects were seated and head position was held constant. Baseline measures (without yoked prism) of distance and near phoria were measured. Phorias were measured again through the following range of VYP, randomly presented: 2 prism diopters (Δ) base up (BU), 2Δ base down (BD), 5Δ BU, and 5Δ BD. Twenty-six subjects also had their phorias measured with control lenses of +0.125 DS OU (because of unavailability of Plano trial lenses) randomly presented along the other conditions. RESULTS: There was no significant difference overall between phoria measured in any of the yoked prism conditions, including the baseline measure, at distance or near. Neither was there evidence of a predictable esophoric or exophoric shift with either BU or BD prism. CONCLUSIONS: Vertical yoked prisms did not exert any immediate effect on horizontal phoria in young adults when posture was controlled. This suggests that, if VYPs do indeed improve horizontal vergence problems, they do not do so by a direct or immediate impact on horizontal phoria

An improved system to measure leaf gas exchange on adaxial and abaxial surfaces

Measurement of leaf carbon gain and water loss (gas exchange) in planta is a standard procedure in plant science research for attempting to understand physiological traits related to water use and photosynthesis. Leaves carry out gas exchange through the upper (adaxial) and lower (abaxial) surfaces at different magnitudes, depending on the stomatal density, stomatal aperture, cuticular permeability, etc., of each surface, which we account for in gas exchange parameters such as stomatal conductance. Most commercial devices measure leaf gas exchange by combining the adaxial and abaxial fluxes and calculating bulk gas exchange parameters, missing details of the plant's physiological response on each side. Additionally, the widely used equations to estimate gas exchange parameters neglect the contribution of small fluxes such as cuticular conductance, adding extra uncertainties to measurements performed in water-stress or low-light conditions. Accounting for the gas exchange fluxes from each side of the leaf allows us to better describe plants' physiological traits under different environmental conditions and account for genetic variability. Here, apparatus and materials are presented for adapting two LI-6800 Portable Photosynthesis Systems to work as one gas exchange system to measure adaxial and abaxial gas exchange simultaneously. The modification includes a template script with the equations to account for small fluxes. Instructions are provided for incorporating the add-on script into the device's computational sequence, display, variables, and spreadsheet results. We explain the method to obtain an equation to estimate boundary layer conductance to water for the new setup and how to embed this equation in the devices' calculations using the provided add-on script. The apparatus, methods, and protocols presented here provide a simple adaptation combining two LI-6800s to obtain an improved system to measure leaf gas exchange on adaxial and abaxial surfaces

Improved reperfusion following alternative surgical approach for experimental stroke in mice

Background: Following ischemic stroke, recanalisation and restoration of blood flow to the affected area of the brain is critical and directly correlates with patient recovery. In vivo models of ischemic stroke show high variability in outcomes which may be due to variability in reperfusion. We previously reported that a surgical refinement in the middle cerebral artery occlusion (MCAO) model of stroke, via repair of the common carotid artery (CCA), removes the reliance on the Circle of Willis for reperfusion and reduced infarct variability. Here we further assess this refined surgical approach on reperfusion characteristics following transient MCAO in mice.Methods: Mice underwent 60 min of MCAO, followed by either CCA repair or ligation at reperfusion. All mice underwent laser speckle contrast imaging at baseline, 24h and 48h post-MCAO.Results: CCA ligation reduced cerebral perfusion in the ipsilateral hemisphere compared to baseline (102.3 ± 4.57 %) at 24h (85.13 ± 16.09 %; P [less than] 0.01) and 48h (75.04 ± 12.954 %; P [less than] 0.001) post-MCAO. Repair of the CCA returned perfusion to baseline (94.152 ± 2.44 %) levels and perfusion was significantly improved compared to CCA ligation at both 24h (102.83 ± 8.41 %; P [less than] 0.05) and 48h (102.13 ± 9.34 %; P [less than] 0.001) post-MCAO. Conclusions: Our findings show CCA repair, an alternative surgical approach for MCAO, results in improved ischemic hemisphere perfusion during the acute phase

Information-based methods for predicting gene function from systematic gene knock-downs

<p>Abstract</p> <p>Background</p> <p>The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA interference phenotypes have been recorded for the nematode <it>Caenorhabditis elegans</it>. Although previous studies have demonstrated the merit of using knock-down phenotypes to predict gene function, it is unclear how the data can be used most effectively. An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role.</p> <p>Results</p> <p>We compared several methods for detecting gene-gene functional similarity from phenotypic knock-down profiles. We found that information-based measures, which explicitly incorporate a phenotype's genomic frequency when calculating gene-gene similarity, outperform non-information-based methods. We report the presence of newly predicted modules identified from an integrated functional network containing phenotypic congruency links derived from an information-based measure. One such module is a set of genes predicted to play a role in regulating body morphology based on their multiply-supported interactions with members of the TGF-<it>β </it>signaling pathway.</p> <p>Conclusion</p> <p>Information-based metrics significantly improve the comparison of phenotypic knock-down profiles, based upon their ability to enhance gene function prediction and identify novel functional modules.</p