Ancient gene transfer from algae to animals: Mechanisms and evolutionary significance

Background Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution

CALIBRATING SLOPE-DEPENDENT ERRORS IN PROFILOMETRY

Optical profilometers, such as scanning white light interferometers and confocal microscopes, provide high resolution measurements and are widely utilized in many fields for measuring surface topography. The techniques are capable of high-speed surface measurements with nanometer-scale repeatability, and are used in industries such as data storage, automotive, MEMS, electronics, micro-optics, and bio-medical, to name a few. The instrument works best on flat, stepped structures, and slope-dependent systematic errors can be present in the measurement of steep sloped regions. These errors can be the same order of magnitude as features on the surface to be measured. Researchers have carried out many studies of these errors from first principle analyses; however the errors depend on proprietary details of the optical design and cannot be exactly calculated from first principles. The problem is further complicated by a lack of calibration artifacts to measure the errors directly. We propose a self-calibration technique, the random ball test, for calibrating slope-dependent errors of such instruments. A simulation study validates the approach and shows that the random ball test is effective in practical limits. We demonstrate the calibration on a 50x confocal microscope and a 50x white light interferometer with a specific chosen algorithm, find a surface slope- dependent bias that increases monotonically with the magnitude of the surface slope. The uncertainty of the calibration is smaller than the observed measurement bias and is dominated by residual random noise. Effects such as distortion, drift and ball radius uncertainty were investigated to understand their contribution to the calibration uncertainty

Children’s expressions of gratitude and their relations with parental values and parenting: insights from China and the United States

Gratitude, referring to a dispositional trait to appropriately show gratefulness to a benefactor for a gift or help received (Tudge, Freitas, & O’Brien, 2015), has been viewed as a moral virtue by philosophers and psychologists (e.g., Carr, Morgan, & Gulliford, 2015; McConnell, 1993, 2016). According to Tudge and colleagues, gratitude, as a moral virtue occurs when the beneficiary recognizes that a benefit is freely and intentionally provided by a benefactor, and the beneficiary autonomously repay the benefactor with something that the benefactor wants or needs if an opportunity presents itself. Gratitude, like any virtue, is not innate. Possessing virtuous gratitude requires one to understand the motivation and intentionality behind the benefits, knowing what might be the appropriate responses in a given situation, and to be able to think and act autonomously (Morgan & Gulliford, 2018; Tudge, Freitas, & O’Brien, 2015). To acquire these sociocognitive abilities and experiences, actively engaging in increasingly complex and relevant practices is necessary. Through these practices, one also gradually internalizes standards that are morally required and highly valued by the cultural group to which he/she belongs. Therefore, the development of virtuous gratitude is driven by the synergistic effects of different factors, such as sociocognitive abilities, cultural values, and everyday interactions between parents and children. The purpose of the present study is to have a better understanding of children’s expressions of gratitude and their relations with parental values and parenting in China and the United States. First, the present research investigated the expression of gratitude among 520 Chinese youth (M = 10.60 years, SD = 2.09; 56.0% female) and 489 North American youth (M = 10.28 years, SD = 2.11; 53.8% female). Consistent with what I had expected, Chinese children were less likely to express concrete gratitude, and more likely to express connective gratitude than were the North American children. Additionally, different age-related patterns of expressions of verbal, concrete, and connective gratitude were found. Across societies, older children were more likely to express connective gratitude and less likely to express concrete gratitude than were their younger counterparts. Beyond that, I examined the association between parental values for their children and children’s expressions of gratitude. However, results did not support the hypothesis that parents’ values of autonomy and relatedness would be associated with children’s expressions of connective gratitude. Findings indicated that parental values and gratitude expression were related in different ways in the Chinese and the U.S. sample. Parental values of separateness negatively predicted expression of concrete gratitude among Chinese participants, whereas in the U.S. sample, separated values were negatively associated with connective gratitude. Furthermore, by interviewing 29 North American and 19 Chinese families, I identified strategies that parents used to promote gratitude in China and the United States. In line with what had been predicted, results indicated that both the Chinese and the U.S. parents used various kinds of strategies, including role modeling, discussion about gratitude, and reinforcing gratitude expression behaviors. Moreover, Chinese parents emphasized the importance of expressing gratitude to family and relatives and regarded expressing gratefulness to family members as an effective strategy to foster gratitude in children. Additionally, I explored the relation between children’s expressions of gratitude and their wishes. Consistent with the hypothesis, findings of the present study suggested that children’s social-oriented wishes were significantly associated with connective gratitude for both the Chinese and the U.S. children. Finally, a positive relation between connective gratitude and preferences to give to charity has been found among Chinese children. However, no significant relations between gratitude and spending preferences were found among the North American youth. Findings of the present study provide important educational implications for educators and practitioners aiming to develop effective intervention programs for character development. This study also greatly advances the understanding of the ways in which culture influences the development of virtuous gratitude

LASER INDUCED LOCAL STRUCTURAL AND PROPERTY MODIFICATIONS IN SEMICONDUCTORS FOR ELECTRONIC AND PHOTONIC SUPERSTRUCTURES SIC TO GRAPHENE CONVERSION

Graphene is a single atomic layer two-dimensional (2D) hexagonal crystal of carbon atoms with sp2-bonding. Because of its various special or unique properties, graphene has attracted huge attention and considerable interest in recent years. This PhD research work focuses on the development of a novel approach to fabricating graphene micro- and nano-structures using a 532 nm Nd:YAG laser, a technique based on local conversion of 3C-SiC thin film into graphene. Different from other reported laser- induced graphene on single crystalline 4H- or 6H- SiC, this study focus on 3C-SiC polycrystal film grown using MBE. Because the SiC thin film is grown on silicon wafer, this approach may potentially lead to various new technologies that are compatible with those of Si microelectronics for fabricating graphene-based electronic, optoelectronic, and photonic devices. The growth conditions for depositing 3C-SiC using MBE on Si wafers with three orientations, (100), (110), and (111), were evaluated and explored. The surface morphology and crystalline structure of 3C-SiC epilayer were investigated with SEM, AFM, XRD, µ-Raman, and TEM. The laser modification process to convert 3C-SiC into graphene layers has been developed and optimized by studying the quality dependence of the graphene layers on incident power, irradiation time, and surface morphology of the SiC film. The laser and power density used in this study which focused on thin film SiC was compared with those used in other related research works which focused on bulk SiC. The laser-induced graphene was characterized with µ-Raman, SEM/EDS, TEM, AFM, and, I-V curve tracer. Selective deposition of 3C-SiC thin film on patterned Si substrate with SiO2 as deposition mask has been demonstrated, which may allow the realization of graphene nanostructures (e.g., dots and ribbons) smaller than the diffraction limit spot size of the laser beam, down to the order of 100 nm. The electrical conductance of directly written graphene micro-ribbon (< 1 µm) was measured via overlaying two micro- electrodes using e-beam lithography and e-beam evaporation. The crystalline quality (stacking order, defect or disorder, strain, crystallite size, etc.) of laser-induced graphene was analyzed using Raman spectroscopy through the comparison with pristine natural graphite and CVD-grown monolayer graphene on SiO2/Si and other substrates. The experimental results reveal the feasibility of laser modification techniques as an efficient, inexpensive, and versatile (any shape and location) means in local synthesis of graphene, especially in patterning graphene nanostructures. Different from other laser induced graphene research works, which were concentrated on bulk SiC wafers, this PhD research work focuses on thin film SiC grown on Si (111) for the first time

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

The pharmacological regulation of cellular mitophagy

Small molecules are pharmacological tools of considerable value for dissecting complex biological processes and identifying potential therapeutic interventions. Recently, the cellular quality-control process of mitophagy has attracted considerable research interest; however, the limited availability of suitable chemical probes has restricted our understanding of the molecular mechanisms involved. Current approaches to initiate mitophagy include acute dissipation of the mitochondrial membrane potential (ΔΨm) by mitochondrial uncouplers (for example, FCCP/CCCP) and the use of antimycin A and oligomycin to impair respiration. Both approaches impair mitochondrial homeostasis and therefore limit the scope for dissection of subtle, bioenergy-related regulatory phenomena. Recently, novel mitophagy activators acting independently of the respiration collapse have been reported, offering new opportunities to understand the process and potential for therapeutic exploitation. We have summarized the current status of mitophagy modulators and analyzed the available chemical tools, commenting on their advantages, limitations and current applications

Functional traits and phenotypic plasticity modulate species coexistence across contrasting climatic conditions

Functional traits are expected to modulate plant competitive dynamics. However, how traits and their plasticity in response to contrasting environments connect with the mechanisms determining species coexistence remains poorly understood. Here, we couple field experiments under two contrasting climatic conditions to a plant population model describing competitive dynamics between 10 annual plant species in order to evaluate how 19 functional traits, covering physiological, morphological and reproductive characteristics, are associated with species’ niche and fitness differences. We find a rich diversity of univariate and multidimensional associations, which highlight the primary role of traits related to water- and lightuse- efficiency for modulating the determinants of competitive outcomes. Importantly, such traits and their plasticity promote species coexistence across climatic conditions by enhancing stabilizing niche differences and by generating competitive trade-offs between species. Our study represents a significant advance showing how leading dimensions of plant function connect to the mechanisms determining the maintenance of biodiversity