Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine‐scale forest variability and biodiversity in the boreal mixedwood forest

Local spatial variation in species distributions is driven by a mix of abiotic and biotic factors, and understanding such hierarchical variation is important for conservation of biodiversity across larger scales. We sought to understand how variation in species composition of understory vascular plants, spiders, and carabid beetles is associated with concomitant spatial variation in forest structure on a 1-ha permanent plot in a never-cut mixedwood forest in central Alberta (Canada). Using correlations among dendrograms produced by cluster analysis we associated data about mapped distribution of all living and dead stems > 1 cm diameter at breast height with distributions of the three focal taxa sampled from regular grids across the plot. Variation in each of these species assemblages were significantly associated with several forest structure variables at various spatial scales, but the scale of the associations varied among assemblages. Variation in species richness and abundance was explained mostly by changes in basal area of trees across the plot; however, other variables (e.g., snag density and tree density) were also important, depending on assemblage. We conclude that fine-scale habitat variation is important in structuring spatial distribution of the species of the forest floor, even within a relatively homogeneous natural forest. Thus, assessments that ignore within-stand heterogeneity and management that ignores its maintenance will have limited utility as conservation measures for these taxa, which are major elements of forest biodiversity. This article is protected by copyright. All rights reserved.
Millipede assassins and allies (Heteroptera: Reduviidae: Ectrichodiinae, Tribelocephalinae): total evidence phylogeny, revised classification and evolution of sexual dimorphism

Evolution of sexual dimorphism in animals has long been of interest to scientists, but relatively few studies have reconstructed evolutionary patterns of extreme sexual dimorphism at a phylogenetic scale, especially in insects. Millipede assassin bugs (Heteroptera: Reduviidae: Ectrichodiinae; 736 spp.) and their sister taxon, Tribelocephalinae (150 spp.), exhibit sexual dimorphism that ranges from limited to extreme, a phenomenon apparently modulated by female morphology. Here, we reconstruct the first phylogeny for the subfamilies Ectrichodiinae and Tribelocephalinae with comprehensive generic representation (152 taxa in 72 genera) using morphological and molecular data (six gene regions). The combined phylogenetic results indicate that Tribelocephalinae are paraphyletic with respect to Ectrichodiinae, and that Ectrichodiinae themselves are polyphyletic. Based on these results, we synonymize Tribelocephalinae with Ectrichodiinae syn.n. , describe three new tribes (Ectrichodiini trib.n., Tribelocodiini trib.n., and Abelocephalini trib.n.) and two new subtribes (Opistoplatyina subtrib.n. and Tribelocephalina subtrib.n.), and revise Tribelocephalini sensu n. Ancestral state reconstruction of sexual dimorphism reconstructed limited sexual dimorphism in the ancestor of Ectrichodiinae sensu n. with at least seven evolutionary transitions to extreme sexual dimorphism within the clade.
A Genetic and Molecular Analysis of the Control of the Start of the Cell Cycle in Saccharomyces cerevisiae

Progression through the eukaryotic cell cycle is controlled by the CDC28 protein kinase and its homologs. In the budding yeast Saccharomyces cerevisiae, this kinase is required for cell cycle S T A R T (commitment to cell cycle progression late in Gl), and for entry into mitosis. Although constitutively present, CDC28 is only periodically activated. The activation of CDC28 involves its physical association with proteins called cyclins. Budding yeast have three CLN genes (CLNs 1 3), which have limited cyclin homology. At least one of the three is required for cell cycle S T A R T . Four B cyclins are known in yeast (CLBs 1-4); two have been shown to function in mitosis. This thesis reports the discovery of three genes which, when either mutated or overexpressed, relieve the requirement for CLN genes for the execution of S T A R T . The first gene was discovered as a mutation which bypasses the requirement for CLN genes, and which we have named the CLN bypass mutation (CBM). 15 distinct isolates of C B M were obtained; all were dominant, and 12 were shown to be linked or allelic with one another. T w o of the isolates caused single division meiosis as an unselected, dominant phenotype. T w o CEN plasmid clones were isolated which bypassed the CLN requirement. The first of these contained a novel B cyclin, which w e have named CLBS. CLBS transcript abundance peaks in Gl, coincident with CLN2 transcript, but earlier than CLB2 transcript. CLBS deletion does not cause lethality, either alone or in combination with other CLN or CLB deletions. However, strains deleted for CLBS require more time to complete S phase, suggesting that CLBS promotes some step in D N A synthesis. CLBS is the only yeast cyclin whose
The first recorded activity pattern for the Sunda stink-badger Mydaus javanensis (Mammalia: Carnivora: Mephitidae) using camera traps

The Sunda stink-badger Mydaus javanensis is a small carnivore inhabiting the Southeast Asian islands of Borneo, Java, Sumatra, and the Natuna Archipelago. Documented sightings are relatively common, yet the species’ behavioural ecology remains poorly understood. Whilst the species is reported to be broadly nocturnal, its detailed activity pattern has never been quantified. This study analysed photographic events from a large scale, long-term camera trapping study to assess times of activity for the Sunda stink-badger. The study took place within the lowland riparian forest corridor of the Lower Kinabatangan Wildlife Sanctuary (LKWS) in the Northeast Bornean state of Sabah. Through 2010–2015, 24,506 potential trap nights collected 2,268 Sunda stink-badger images across 470 unique events. Sunda stink-badger activity pattern was modelled using kernel density estimation, and indicated a highly nocturnal activity pattern with no detected activity during the diurnal hours, consistent with previous records. All photographs were taken between 1839 hours and 0627 hours, and modelling indicated two clear peaks in nocturnal activity, the first at 2100 hours and the second at 0500 hours. Overlap in activity patterns was found to be high (≥ 80%) between wet and dry seasons, and also between moon phases, indicating a lack of seasonal or lunar effects on Sunda stink-badger activity. An encounter rate of 1.92 unique Sunda stink-badger events per 100 potential trap nights was recorded for the LKWS. This encounter rate was lower than those found in other regional studies with lower levels of anthropogenic disturbance, suggesting extensive anthropogenic disturbance may pose a potential negative impact to the species. Whilst activity patterns derived from camera trapping are restricted to movement through the environment, these results have established a baseline for Sunda stink-badger activity patterns within a fragmented habitat subjected to high levels of anthropogenic disturbance, and have improved the basic ecological understanding of the species.
The Role of Glucocorticoid Receptor-signaling and Wnt-signaling in Avian Retinal Regeneration

ii Dedication . v Acknowledgments . vi Vita.viii List of Tables.xii List of Figures . xiii Chapters 1. General Introduction . 1 The eyea brief history.1 The structure and function of the retina.3 Retinal regeneration across speciesa general overview.4 Müller glia, stem cells and retinal progenitors. 7 MGPCs-derived retinal regeneration – definition.10 Cell-signaling pathways that influence Müller glia derived progenitors . 12 Transcription factors that influence Müller-glia derived progenitors.19 Retinal cells that influence Müller-glia derived progenitors.24 Neuroprotectionan alternative to regeneration.26 2. Glucocorticoid receptors in the retina, Müller glia and the formation of Müller glia-derived progenitors . 28 Abstract.28 Introduction . 29 Materials and methods.31 Results . 38 Discussion.61 Conclusions.66 xi 3. Wnt-signaling and the formation of Müller glia-derived progenitors in the chick retina.68 Abstract.68 Introduction . 69 Materials and methods.71 Results . 77 Discussion.99 Conclusions.104 4. Activation of glucocorticoid receptors in Müller glia is protective to retinal neurons and suppresses microglial reactivity.106 Abstract.106 Introduction . 107 Materials and methods.109 Results . 117 Discussion.136 Conclusions.141 5. Summary and Future Directions.142 Summary of findings.142 Future directions for MGPCs – derived retinal regeneration.144 Introduction.144 Future studies for GCR-signaling pathway and retinal regeneration.147 Future studies for Wnt-signaling pathway and retinal regeneration.148 Crosstalk between Wnt, GCR and other pathways.151 Future directions for studies on GCR-mediated neuronal survival.157 Concluding remarks.159 References.160
Proteomic Analysis of Pollen and Blossom Honey from Rape Seed Brassica Napus L.

Abstract In the study, honey from oilseed rape Brassica napus L. , and both hand-collected (winter rape Visby and Cult) and bee-collected pollen of oilseed rape were analyzed for their proteome content, in order to see if any plant proteins were present to allow the proteo-typing of the oilseed rape honey. Proteins were fractionated by two-dimensional gel electrophoresis (2DE), stained by Coomassie blue and then analyzed by mass spectrometry. All identified proteins were divided into few groups due to their biological function. In 2DE gels with separated proteins from blossom honey, only bee (Apis mellifera) main proteins (Major royal jelly protein 1-5 and Glucosidase) were found. So we analyzed all proteins using gel-free based analysis with the SYNAPT G2 high definition mass spectrometry. We identified proteins that were present in both oilseed rape pollen and honey (Bna, Polygalacturonase, Non-specific lipid-transfer protein, GAPDH and others). We believe that these proteins are important for the nutritional value of plant pollen-enriched honey and further research is required on honey and honeybee pollen protein.
Anaerobic Biodegradation of Polyaromatic Hydrocarbons by a Sulfate Reducing Bacteria C1Fd Strain

1Laboratory of Molecular Biology, Department of Food Science and Technology, School of Chemistry, 2Laboratory of Molecular Biology and Genetic Engineering, School of Chemistry, School of Chemistry, University Autonomous of Coahuila, Blvd. V. Carranza and Jose Cardenas V. s/n Col. Republica Ote. , 25280 Saltillo, Coahuila, Mexico. 3Laboratory of Bioremediation, School of Biological Sciences, University Autonomous of Coahuila, Carretera TorreónMatamoros Km. 7.5, 27000 Torreon, Coahuila, Mexico.
Patterns of Food Consumption and Production of Mountainous Community in Sinjai District, South Sulawesi Province, Indonesia

Food availability of one area affects its community food consumption patterns. The area will use its natural resources to satisfy all needs of its society. This study aimed to explain the patterns of consumption and production of food in a mountainous area. This research is a descriptive study using both qualitative and quantitative approaches. In qualitative approach, the data obtained by indepth-interview and Focus Group Discussion (FGD), whereas quantitative data obtained through household surveys of 40 households as samples. Field data collection is done systematically through questionnaires and interviews. There are two data sources namely primary data and secondary data. Primary data were obtained from people in the local area either as informants selected using snowball techniqueor respondents selected purposively. Furthermore, the secondary data were obtained from the literature that correlates with research areas. The result shows that the pattern of food production in the mountainous region is divided into two types based on the land used that is wetland and dry land. The wetland is used by mountainous community to produce food such as rice and corn with a frequency of twice a year. As for the dry land, it is cultivated to produce vegetables that are produced throughout the year as daily necessities. The pattern of consumption in the community correlates with the amount, type and consumptive frequency of the food. In general, people in mountainous areas still consume rice as a staple food by eating vegetables and fish as complementary with a frequency of 2-3 times a day. This is because the access is still relatively easy to obtain these foods.
Isolation and Identification of Bioactive Constituents of Plant Pathogenic Fungi and Targeted Synthesis of Isochromanone Analogs

An unknown fungal species was cultured from necrotic Brachiaria eruciformis leaves found in Oxford, Mississippi. The fungus was identified via molecular techniques as Pyricularia grisea. This fungus was grown on Czapek Dox broth culture medium for 21 days under continuous light at 24 0C. The culture filtrate was extracted with ethyl acetate and concentrated. The major bioactive compound, namely pyrichalasin H, was isolated using TLC-guided fractionation and identified via spectroscopic techniques. The compound was then tested for bioactivity on monocotyledons, dicotyledons and agriculturally important fungal species. Cellular leakage, chlorophyll content and root/shoot length bioassays were also performed to probe the compound’s phytotoxic mechanism of action. In addition to this project, targeted synthesis of structural analogs of a previously-isolated isochromanone compound was carried out in the laboratory. Structures were characterized by spectroscopic techniques and biological activity was evaluated, with significant phytotoxicity observed in monocots.
Direct interaction between troponin and myosin enhances the ATPase activity of heavy meromyosin

Abstract Contractility of the heart muscle is a result of sliding movements between thick and thin filaments, produced by interactions between actin and myosin during the cross-bridge cycle. Activation of the myofilament is triggered by Ca2+ binding to cardiac troponin C and is regulated through an “on/off” switching process occurring in the thin filament. Beside Ca2+ regulation, strongly bound cross-bridges exert a positive feedback on myofilament regulation. Despite the importance of this positive feedback mechanism, its full molecular basis has so far remained elusive. Ca2+-regulated interactions between thick and thin filaments are widely regarded as an allosteric system, which means that multiple protein-protein interactions at their interface may exert alternative feedback effects on myofilament activation. To advance knowledge about these regulatory feedback mechanisms, we investigated a previously unstudied, hypothetical interaction between cardiac troponin and myosin, and how this interaction affects the function of myosin. Our results strongly suggest that myosin does indeed interact with the N-terminus of cardiac troponin I and the C-terminus of cardiac troponin T, suggesting a possible direct interaction between myosin and the IT-arm of troponin. We also conducted an in vitro heavy meromyosin (HMM) ATPase assay, and found that troponin significantly enhanced the actin-activated ATPase activity of HMM, both in the absence of tropomyosin and at the activated state of thin filament.
Surf zones regulate larval supply and zooplankton subsidies to nearshore communities

Surf zone hydrodynamics vary along shorelines potentially affecting the delivery of larvae and zooplankton subsidies to intertidal communities, and, hence, the intensity of postsettlement interactions, growth and reproduction of filter‐feeding foundation species and planktivorous fishes. We investigated the ability of zooplankton assemblages to enter the wide surf zone of the rip‐channeled, more dissipative beach at Sand City, California, and the narrow surf zone of the steep reflective beach at nearby Carmel River State Beach. Every day for a month, we surveyed zooplankton inside and outside the surf zone and concomitant larval settlement of the dominant invertebrate onshore at each site in this upwelling regime. At the more dissipative surf zone, all zooplankters were far more concentrated inside than outside the surf zone. Many taxa increased in the surf zone and the predominant invertebrate on beaches, Emerita analoga, settled abundantly when prevailing northwesterly winds relaxed and waves were small. At the reflective surf zone, concentrations of zooplankters of most taxa were far greater outside than inside the surf zone, and many taxa increased in the surf zone when waves were small. Twice as many taxa were positively correlated inside and outside the surf zone at the dissipative than the reflective surf zone, indicating that zooplankters were more freely exchanged although behavior also played a role. Thus, spatial and temporal variation in surf zone hydrodynamics may regulate subsidies of zooplankton food and larval recruits to nearshore communities with potential cascading effects on community dynamics and structure.
Chronic Mitochondrial Translation Inhibition Alters Metabolic Phenotype and Stemness Properties of a Leukemic Cell Line

Recently, we demonstrated that the anti-bacterial agent tigecycline preferentially induces death in leukemia cells through the inhibition of mitochondrial protein synthesis. To better understand the mechanisms of sensitivity and resistance to mitochondrial translation inhibition, we treated TEX leukemia cells with increasing concentrations of tigecycline over 4 months, and selected a population of cells resistant to tigecycline (RTEX+TIG). Compared to their wild type counterparts, the resistant RTEX+TIG cells had an altered metabolic profile with diminished oxidative phosphorylation and a greater reliance on glycolysis. Upon removal of tigecycline from RTEX+TIG cells, the cells re-established aerobic metabolism and oxidative phosphorylation to wild type levels. At the molecular level, these cells had increased levels of HIF1α. Strikingly, tigecycline-resistant cells had decreased expression of CD34 and CD117, clonogenic growth potential and engraftment capabilities in vivo. Thus, chronic inhibition of mitochondrial translation leads to the establishment of rho-zero-like metabolic phenotype, and is associated with differentiation of leukemia cells.
Growth races in The Mallee: Height growth in woody plants examined with a trait-based model

© 2017 Ecological Society of Australia Plant height and growth are fundamental to the understanding of species ecological strategies, to the description and prediction of ecosystem dynamics and to vegetation management, such as plant species' fire responses. However, a convenient way to characterize the height growth strategies for multiple species have been elusive. We examine the height growth trajectories in 18 woody plant species in a light-saturated, fire-prone, semi-arid environment as well as the influence of functional traits on those trajectories. We test trait-growth relationships by examining the influence of specific leaf area, woody density, seed size and leaf nitrogen content on three aspects of plant growth; maximum relative growth rate, age at maximum growth and asymptotic height. Woody plant species in the semi-arid mallee exhibit fast growth trajectories. Small seeded species were likely to be the fastest to reach maximum height, while large-seeded species with high leaf nitrogen were likely the slowest. Tall species had low stem densities and tended to have low specific leaf area. We modelled plant growth using a hierarchical multi-species model that formally incorporates plant functional traits as species-level predictors of growth, which provides a method for predicting species height growth strategies as a function of their traits. We extend this approach by using the modelled relationships from our trait-growth model to predict: growth trajectories of species with limited data; real species with only trait data and; hypothetical species based only on trait coordination. We hope this highlights the potential to use trait information for ecological inference and to generate predictions that could be used for management.
The Absorption of Sodium Ions by the Crayfish, Astacus Pallipes Lereboullet : I. The Effect of External and Internal Sodium Concentrations

1. The effects of external and internal sodium concentrations on the uptake of sodium ions by the crayfish, Astacus pallipes , has been studied. 2. The normal sodium influx, measured with 24 Na, from O.3 mM /l. NaCl solution is 1.5 µM. /10 g. body weight/hr. The rate of loss of sodium to de-ionized water has roughly the same value. 3. Net loss of sodium reduces the external sodium concentration required for sodium balance. The minimum equilibrium concentration is about 0.04 mM. /l. NaCl. 4. The relation between the external sodium concentration and the sodium influx is non-linear. The influx has a maximum of about 10 µM. /10 g. /hr. at an external concentration of approx. 1 mM. /l. 5. The 24 Na influx is a true measure of the sodium uptake rate at low external concentrations. At higher concentrations the influx may exceed the uptake rate by some 20%. 6. Net loss of sodium increases the influx by three to five times. Loss of 5-10% of the total internal sodium increases the influx from the normal to the maximum level. A 1% change has a significant effect on the influx. Changes in the internal sodium content reflect changes of the blood sodium concentration. 7. A scheme is suggested whereby the external and internal sodium concentrations interact together on the influx to produce a self-regulating system which maintains the animal in sodium balance.
Engagement of spinal- vs prefrontal-projecting locus coeruleus neurons parses analgesia from aversion & anxiety in rats

The locus coeruleus (LC) projects throughout the brain and spinal cord and is the major source of central noradrenaline. It remains unclear whether the LC acts functionally as a single global effector or as discrete modules. Specifically, while spinal-projections from LC neurons can exert analgesic actions, it is not known whether they can act independently of ascending LC projections. Using viral vectors taken up at axon terminals, we expressed chemogenetic actuators selectively in LC neurons with spinal (LC:SC) or prefrontal cortex (LC:PFC) projections. Activation of the LC:SC module produced robust, lateralised analgesia while activation of LC:PFC produced aversion. In a neuropathic pain model, LC:SC activation reduced hind-limb sensitization and induced conditioned place preference. By contrast, activation of LC:PFC exacerbated spontaneous pain, produced aversion and increased anxiety-like behaviour. This independent, contrasting modulation of pain-related behaviours mediated by distinct noradrenergic modules provides evidence for a discrete functional organisation of the LC.