Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineered Cytoskeletal Arrays Reveal Mechanisms of Membrane Transport and Tubulation

Within the cell, cytoskeletal molecular motors transport and remodel membrane-bound cargos along microtubule and actin filament tracks. Typically, there are multiple actin and microtubule motors attached to the same cargo, which must coordinate to navigate a complex cytoskeletal environment and deliver their cargos to specific locations. We used an engineering, in vitro reconstitution, approach to investigate the interplay between a processive, microtubule-based motor, kinesin-1, and a non-processive, actin filamentbased motor, Myo1c, in a simplified environment with increasing physiological complexity. First, we examined the interplay between purified motors attached to a membrane-coated bead at individual actin filament/microtubule intersections on the surface of a coverslip. We found that Myo1c is capable of initiating and terminating microtubule-based, kinesin-1-driven runs at actin filament/microtubule intersections. This ability of Myo1c to affect kinesin-1 motility at actin intersections is inhibited by the presence of nonmuscle tropomyosin Tm2 at the actin intersection. This suggests that tropomyosin may regulate Myo1c tethering of kinesin-1-driven cargo within cells by preventing termination of motility until reaching the highly dynamic actin just beneath the plasma membrane, sorting cargo to distinct subcellular domains. Next, we investigated the interplay between Myo1c and kinesin-1 on deformable giant unilamellar vesicles (GUVs) at physiologically relevant micropatterned arrays of sparse microtubules crossing dense actin filaments. We found that the lipid composition of GUVs regulates its frequency of tubulation along microtubules by kinesin-1 and actin filaments by Myo1c. GUVs containing a PtdIns(4,5)P2-rich lipid composition (PIP2-GUVs) tend to deform at actin/microtubule intersections along the microtubule, yet, the BAR domain protein endophilin is necessary for robust tubulation. Alternatively, in the presence of a physiological lipid mixture (LM-GUVs), kinesin-1 can readily tubulate Myo1c-tethered cargo at actin/microtubule intersections, with no significant change upon addition of endophilin. Myo1c can also transport both PIP2-GUVs and LMGUVs along actin, yet significantly more deformation and tubulation occurs with LM-GUVs. In both cases, the presence of endophilin increases the frequency of tubulation along actin filaments by Myo1c. Overall, the ability of Myo1c and kinesin-1 to transport, sort, and deform vesicles along microtubules and actin filaments depends on the type of actin track, scaffolding-type membrane deformation-factors like endophilin, and the lipid composition of the vesicle. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor E. M. Ostap This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2463 Second Advisor Erika L. Holzbaur
INTEGRATING MACROECOLOGY AND QUANTITATIVE GENETICS: EVOLUTION OF BODY SIZE AND BRAIN SIZE UNDER ISLAND RULE

Island rule proposes that a negative correlation between ancestral body size in continents and the descendent body size in islands exists, and this pattern have been widely studied in a macroecological and comparative perspectives. However, there are doubts about what mechanisms underlie body size evolution in islands. Here we review methodological and theoretical framework on evolutionary quantitative genetics, showing their application on body and brain size evolution in islands, using Hippopotamus dwarfism as example. In our analyses we started by generating 10,000 combinations of model parameters (generation time, effective size and heritability) and tested by Mutation-Drift Equilibrium model if body size dwarfism is a consequence of neutral drift or directional selection. We found that 99.9 % of simulations rejected neutral model. Then, we estimated the strength of directional selection necessary to differentiate the island species and found that a relatively low proportion of population (0.01 - 0.2%) should be selectively killed to decrease body size. Our results also showed that one unit decrease in body size would increase, on average, fitness by 4% in each generation, so directional selection is a plausible explanation to island rule. Finally, we also simulated the evolution of brain size of dwarfed Hippopotamus as a consequence of body size evolution alone. Our estimates of Expected Brain Size (EBS = 484 A 64 cc) were larger than the observed brain size (equal to 380 cc), which suggests the need to estimate directional selection acting on brain size independently of body size evolution. This supports the overall idea that brain size reduction is advantageous in island environments under a scenario reduction in resources, due to the high energetic budget of brain. Our analyses using evolutionary quantitative genetic support that Island Rule as a parsimonious adaptive explanation for the reduction in brain and body sizes and illustrates how to couple evolutionary analyses at population level to better understand macroecological patterns.
Jujube Cultivar Vitamin C Profile and Nutrient Dynamics during Maturation

Vitamin C proﬁles of 46 jujube cultivars were assessed from 2012 to 2015, and fruit nutrient dynamics of 10 cultivars during maturation were examined from 25 Aug. to 7 Oct. 2014 at 2-week intervals at New Mexico State University’s Alcalde Sustainable Agriculture Science Center and Los Lunas Agricultural Science Center. This is the ﬁrst report in the United States proﬁling Vitamin C in jujube cultivars. The vitamin C content of mature fruit of 45 (of 46) cultivars ranged from 225 to 530 mg/100 g fresh weight (FW) plus ‘Youzao’ having the highest content of 820 mg/100 g FW at early mature stage. In general, drying cultivars had higher vitamin C content than fresh-eating cultivars whereas ‘Jinsi’ series (multipurpose) had relatively higher vitamin C content than others (>400 mg/100 g FW). Fruit vitamin C and moisture content decreased signiﬁcantly during the maturation process. The average vitamin C
Targeted Reduction of Pathogenic Heteroplasmy Through Binding of G-Quadruplex DNA

Pathogenic mitochondrial DNA (mtDNA) variants are typically heteroplasmic, with coexistence of variant and wild type genomes. Because heteroplasmy dictates phenotype, the reduction of heteroplasmy is potentially therapeutic. We identified pathogenic variants that increased the potential for formation of non-canonical G-quadruplexes (GQ) within mtDNA. The Leigh Syndrome (LS)-associated mt.10191T>C variant has a high probability of local GQ formation that was enhanced by the variant. Structural studies of mt.10191C-containing oligonucleotides confirmed the formation of GQ, and its interaction with the small molecule GQ-binding agent berberine increased GQ stability. The GQ formed at mt.10191 impeded polymerase processivity, and inhibition was enhanced by the mt.10191C variant. We applied a cyclical treatment of two GQ binding compounds, berberine or RHPS4, to primary fibroblasts from LS patients with heteroplasmic mt.10191T>C mutation. This treatment induced alternating mtDNA depletion and repopulation and was effective in shifting heteroplasmy towards the nonpathogenic allele, leading to an increase in complex I protein levels. This study demonstrates the potential for using small-molecule GQ-binding agents to induce beneficial shifts in mitochondrial heteroplasmy.
Endoderm lineage labelling using BAC reporter constructs in ES cells and mouse embryos

The endoderm is one of the three embryonic germ layers that gives rise to inner organs like lung, liver and pancreas. BAC recombineering was used to generate transgenic embryonic stem cells and mouse lines containing fluorescent reporters under the control of important endodermal genes like Foxa2, Sox17, Hhex, Nkx2.1 and Pdx1. This allowed the analysis of the specific expression patterns of those genes during endoderm and organ formation. In particular, the analysis of the Hhex reporter expression showed new insights during endoderm development and organogenesis. Moreover, the use of whole mount antibody stainings showed the contemporaneous downregulation of BMP-signalling during these events. Therefore, this analysis offered useful new tools for the study of early endodermal developmental events.
Phenolic extracts from grape stems inhibit Listeria monocytogenes motility and adhesion to food contact surfaces

Abstract This study evaluated the effect of grape stems extracts on motility, surface energy and adhesion of L. monocytogenes to stainless steel and polypropylene surfaces. Stem extracts from Red Globe grapes showed a higher content of total phenolics than Carignan stems. Moreover, both extracts reduced adhesion of Listeria to stainless steel (0.77–2.22 log CFU cm−2) and polypropylene (0.71–2.38 log CFU cm−2) and completely inhibited bacterial motility at 4.5 and 5 mg mL−1 of Red Globe and Carignan extracts, respectively. Similarly, both extracts affected the surface energy of bacteria and modified the adhesion potential of L. monocytogenes to both surfaces. Otherwise, caffeic, ferulic and gallic acids, catechin and rutin, presented in both extracts, reduced adhesion of L. monocytogenes to stainless steel (0.39–2.04 log CFU cm−2) at 10 mM. In conclusion, Red Globe and Carignan grape stem extracts inhibited adhesion of L. monocytogenes to stainless steel and polypropylene surfaces by inhibiting motility and modifying its adhesion potential.
Vertical stratification influences global patterns of biodiversity

Species distributions in terrestrial ecosystems are three-dimensional, spanning both the horizontal landscape and the vertical space provided by the physical environment. Classical hypotheses suggest that communities become more vertically stratified with increasing species richness, owing to reduced competition or finer niche subdivision. However, this assertion remains untested in the context of the broader realm of biogeography. Here, integrating traits and distribution data for amphibians globally, we show how vertical strategies interact with the physical and climatic environments to govern global patterns of species richness and community composition. Our results reveal a marked latitudinal shift in strategies of vertical habitat use, from highly arboreal assemblages in the tropics to highly fossorial assemblages in sub-tropical and temperate regions. Arboreality is strongly associated with precipitation, vegetation structure and climatic stability, whereas fossoriality is more common in dry environments with high diurnal temperature range and low vegetation structure. These analyses shed light on the importance of vertical stratification for species coexistence in species-rich regions. As certain tropical habitats become drier from climate change, the rich biological diversity that is emblematic of the tropics may transition from vertically stratified to ‘flattened’, with future communities living mostly on or beneath the ground.
The Advertisement Call and Notes on the Reproductive Ecology of the Glassfrog “Centrolene” quindianum (Anura: Centrolenidae)

Abstract. Frogs of the family Centrolenidae have been a good model system in recent studies of evolutionary ecology, biogeography, and systematics; however, the taxonomic status of some species is still uncertain. Knowing aspects about the natural history of such species can offer diagnostic characters useful for species delimitation and hence, baseline data for understanding the biology of the family Centrolenidae. We describe the advertisement call and aspects of the breeding biology of “Centrolene” quindianum, a threatened species endemic to the Andes of Colombia whose taxonomic status and phylogenetic relationships require clarification. Between July–December 2015, we performed weekly fieldtrips to monitor the breeding activity of this species in a population located in department of Quindío, western slope of the Central Andes of Colombia. The advertisement call of “C. ” quindianum consist of two types of calls. The most frequently emitted call is composed of two notes with amplitude modulation and a dominant frequency of 4,678.1 ± 156.0 Hz; the other type of call is composed of 3–5 notes with high amplitude modulation and a dominant frequency of 4,568.5 ± 61.4 Hz. Calling activity and oviposition was recorded in months with higher precipitation and lower temperature. Clutches contained 26 eggs on average, and the substrate for oviposition was mostly moss-covered tree branches. Egg yolk was usually yellow, although some eggs were green. In addition, we recorded an attempt of amplexus displacement and egg attendance by a female immediately following oviposition.
Vertical stratification in bat assemblages of the Atlantic Forest of south-eastern Brazil

Abstract: Tropical forests are three-dimensional spaces with species and resources heterogeneously distributed. The vertical stratification of tropical forest biotas has been observed for several organisms and regions, but, surprisingly, the vertical structuring of large areas of important tropical forests, such as Brazil's Atlantic Forest, remains poorly studied. Here, we addressed the use of different Atlantic Forest strata by bats, comparing ensemble composition and relative abundance between the understorey and the canopy. A total of 618 bats belonging to 31 species and four families were recorded, including 11 species of frugivores and seven species of gleaning insectivores, the two trophic guilds predominantly represented in our sampling. Fifteen species were captured exclusively in the canopy, and six exclusively in the understorey, and many of those species were represented by a low number of captures (<5). The bat species composition, richness and relative abundance between canopy and understorey strata varied. Chiroderma villosum was exclusively captured in the canopy, Artibeus lituratus was netted predominantly in the canopy and Carollia perspicillata and Desmodus rotundus were mostly captured in the understorey. Although processes such as resource partitioning between species and ecomorphological constraints may explain the differential use of forest strata, this remains little understood because of the scarcity of data for the Atlantic forest canopies.
Identification and Characterization of Y Chromosome and M Locus Genes in Anopheles and Aedes Mosquitoes Using the Chromosome Quotient Method

ii Public abstract . iii Acknowledgements . iv Attributions . v Table of contents . vii List of figures . ix List of tables . xi Chapter 1: Introduction . 1 1.1 Sexual reproduction and sex determination . 1 1.2 The canonical theory of the degeneration of Y chromosomes . 8 1.3 The Anopheles Y chromosome . 10 1.4 Difficulties in assembling Y, W, and M locus sequences.14 1.5 The chromosome quotient (CQ) method . 16 1.6 References . 24 Chapter 2: Insights into the preservation of the homomorphic sex-determining chromosome of Aedes aegypti from the discovery of a male-biased gene tightly-linked to the M-locus . 34 2.1 Abstract . 36 2.2 Introduction . 37 2.3 Methods.39 2.4 Results . 46 2.5 Discussion . 52 2.6 References . 69
How to measure homologous recombination deficiency in ovarian cancer

VOL. 5, N. 1, 2017 1Department of Obstetrical-Gynecological Sciences and Urological Sciences, “Sapienza” University of Rome, Rome, Italy. 2Institute of Cancer Sciences, University of Glasgow, Glasgow, UK. Correspondence to: Claudia Marchetti, Department of Obstetrics and Gynecology, “Sapienza” University of Rome, Viale del Policlinico 155, 00161 Roma, Italy. Phone: + 39 338 4652 744 − Fax: + 39 06 4997 2564 E-mail: clamarchetti@libero.it CANCER BREAKING NEWS 2017;5(1):15-20 DOI: 10.19156/cbn.2017. 0034 How to measure homologous recombination deficiency in ovarian cancer
Leaf-cutting ant populations profit from human disturbances in tropical dry forest in Brazil

Abstract: Anthropogenic disturbance often results in the proliferation of native species of particular groups that leads to biotic homogenization. Leaf-cutting ants are an example of such winner organisms in tropical rain forests, but their response to disturbance in dry forests is poorly known. We investigated Atta colony density in areas of tropical dry forest in Brazil with different distance to roads and vegetation cover. Atta colonies were surveyed in 59 belt transects of 300 × 20 m, covering a total area of 35.4 ha. We found 224 Atta colonies, 131 of which were active and belonged to Atta opaciceps (87 colonies, 2.45 ha−1), A. sexdens (35 colonies, 0.98 ha−1) and A. laevigata (9 colonies, 0.25 ha−1). The density of active colonies sharply decreased from 15 ± 2.92 ha−1 in the 50-m zone along roads to only 2.55 ± 1.65 ha−1 at distances up to 300 m. The reverse pattern was observed for inactive colonies. Active Atta colonies preferentially occur in areas with low vegetation cover, while inactive colonies prefer areas with high vegetation cover. We demonstrate for the first time that anthropogenic disturbances promote the proliferation of leaf-cutting ants in dry forest in Brazil, which may affect plant regeneration via herbivory and ecosystem engineering as demonstrated for rain forests.
How to incorporate information on propagule pressure in the analysis of alien establishment success

Identifying the factors that determine the success of biological invasions has major consequences for both ecological theory and conservation decision‐making. Reliably inferring these factors depends on adequately accounting for the known effects of propagule pressure on establishment success, but detailed information on the size and number of introduced populations is often lacking. Here, we conduct simulations to explore the effects of incomplete knowledge of propagule pressure on inferences regarding the correlates of establishment success. We compare situations where we have complete information on propagule number and propagule size across species, allowing success to be modelled at the population scale (population‐level analysis), with those where data for propagule size (species‐level analysis) and both propagule size and number (location‐level analysis) are unavailable. We assess the ability to correctly infer the effects of a covariate on establishment success when this covariate exhibits varying degrees of correlation with propagule pressure. We show that when establishment success is modelled at the level of species, rather than populations, this leads to an elevated tendency to incorrectly infer the effects of species‐level traits on establishment success (higher type 1 error and lower power), particularly when traits in question are strongly associated with propagule pressure. These biases are magnified when using proxies for propagule pressure, such as the number of locations where species have been introduced, and are magnified further when these proxies are converted to binary variables. Our results validate the current best practice for the analysis of establishment success in alien species at the population level, when the effects of propagule size and a covariate predicting establishment probability can both be reliably inferred. However, given the growing interest in understanding correlates of biological invasions, they strongly urge caution in interpreting results based on incomplete knowledge of propagule pressure.
Reproductive success of mule deer in a natural gas development area

Natural gas development is increasing across North America and causing concern over the potential impacts on wildlife populations and their habitat, particularly for ungulate species. Understanding how this development impacts reproductive success metrics that are influential for ungulate population dynamics is important to guide management of ungulates. However, the influences of natural gas development on reproductive success metrics of mule deer Odocoileus hemionus have not been studied. We used statistical models to examine the influence of natural gas development and temporal factors on reproductive success metrics of mule deer in the Piceance Basin, northwest Colorado during 2012–2014. We focused on study areas with relatively high or low levels of natural gas development. Pregnancy and in utero fetal rates were high and statistically indistinguishable between study areas. Fetal survival rates increased over time and survival was lower in the high versus low development study areas in 2012 possibly influenced by drought coupled with habitat loss and fragmentation associated with development. Our novel results suggest managers should be concerned with the influences of development on fetal survival, particularly during extreme environmental conditions (e.g. drought) and our results can be used to guide development planning and/or mitigation. Developers and wildlife managers should continue to collaborate on development planning, such as implementing habitat treatments to improve forage availability and quality, minimizing disturbance to hiding and foraging habitat particularly during parturition, and implementing directional drilling to minimize pad disturbance density to increase fetal survival in developed areas.
Influence of mycorrhizal inoculation on carrot growth, metabolites and nutrition

ABSTRACT Mycorrhizae are fungal symbionts forming mutualistic relationships with plant roots. This study was undertaken to evaluate the overall influence of arbuscular mycorrhizal fungi (AMF) on the overall growth and development of carrot plant. Surface-sterilized seeds of carrot were sown in earthen pots filled with sterile soil. Half of the pots were inoculated with AMF spores; the other half without any AMF inoculation represented control. After germination inoculated plants, along with the controls, were sampled at 20, 40, 60 and 80 days of growth after seedling emergence. There is a progressive net increase in growth with each 20-day interval after seedling emergence. Storage roots of carrot had a higher level of metabolites and nutrients like nitrogen, phosphorus and potassium in mycorrhiza colonized plants than the control. High performance liquid chromatography analysis indicated an increase in the carbohydrate fractions in AMF-inoculated roots. Thus, mycorrhiza has been found increasing the growth, metabolites and nutrition of carrot plant.
Contribution of Activating Transcription Factor 3 to development of acinar-to-ductal cell metaplasia

i Co-Authorship Statement . ii Acknowledgments . iii Table of Contents . v List of Tables . viii List of Figures . ix List of Appendices . xi List of Abbreviations . xii Chapter 1 . 1 1 Introduction . 1 1.1 Overview . 1 1.2 Pancreatitis . 2 1.2. 1 Cell Responses to Injury . 3 1.2. 2 Cellular and Molecular Events in ADM . 5 1.3 Signalling Pathways in Acinar-to-Duct Metaplasia . 8 1.4 The Unfolded Protein Response . 12 1.4. 1 General Overview . 12 1.4. 2 Involvement of UPR in Pancreatitis and PDAC . 14 1.5 Activating Transcription Factor 3 . 17 1.5. 1 General Overview . 17 1.5. 2 ATF3 Transcriptional Activity . 21 1.5. 3 Physiological protective roles of ATF3 . 22 1.5. 4 ATF3 in pathology . 23
Deciphering causal genetic determinants of red blood cell traits

Genome-wide association studies (GWAS) have ascertained numerous trait-associated common genetic variants, frequently localized to regulatory DNA. We find that common genetic variation at BCL11A associated with fetal hemoglobin (HbF) level lies in noncoding sequences decorated by an erythroid enhancer chromatin signature. Fine-mapping uncovers a motifdisrupting common variant associated with reduced transcription factor binding, modestly diminished BCL11A expression and elevated HbF. The surrounding sequences function in vivo as a developmental stage-specific lineage-restricted enhancer. Genome engineering reveals the enhancer is required in erythroid but not B-lymphoid cells for BCL11A expression. These findings illustrate how GWAS may expose functional variants of modest impact within causal elements essential for appropriate gene expression. We propose the GWASmarked BCL11A enhancer represents an attractive target for therapeutic genome engineering for the β-hemoglobinopathies.