Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterising dopaminergic plasticity in the mouse olfactory bulb

Experience can shape the brain through multiple interacting forms of neuronal plasticity. In the mouse olfactory bulb, a heterogenous population of dopaminergic neurons is known to be particularly plastic, regulating their gene expression and lifelong generation in an activity-dependent manner. However, how their electrophysiological function can change is not well understood. This thesis aimed to understand how olfactory bulb dopaminergic neurons respond functionally following perturbation of odour experience. I live labelled olfactory bulb dopaminergic neurons using the DAT transgenic mouse. I characterised the labelled population at postnatal day (P)28, showing that the majority of neurons are dopaminergic. Approximately 22% of the labelled population is calretinin-positive, which can be distinguished from the dopaminergic population by immunohistochemistry and electrophysiology. I used an odour deprivation manipulation, unilateral naris occlusion, for 1 and 3 days to study experience-dependent plasticity in the labelled neurons. I show with immunohistochemistry that the activity of these neurons is reduced and there is downregulation of the dopamine-synthesising enzyme, tyrosine hydroxylase, as quickly as 1 day after occlusion. To investigate electrophysiological functional plasticity, I used acute slice electrophysiology to study a subpopulation of olfactory bulb dopaminergic neurons that lack an axon. I demonstrate that the firing properties of these neurons are not affected by these durations of occlusion. However, I show that after 3 days of occlusion there is a significant increase in the sag potential, medium afterhyperpolarisation and amplitude and charge of mini excitatory postsynaptic currents in anaxonic olfactory bulb dopaminergic neurons. I investigated GABAA-mediated auto-inhibition in both subpopulations of olfactory bulb dopaminergic neurons – axonic and anaxonic. I show that, unlike presumed anaxonic cells, presumed axonic dopaminergic neurons do not have auto-inhibition, except following pharmacological enhancement of L-type calcium channels. Whilst studying auto-inhibition, I found a calcium-dependent current that was present in the majority of presumed axonic dopaminergic neurons and only a minority of the presumed anaxonic subpopulation. This work provides further insight into experience-dependent plasticity of olfactory bulb dopaminergic neurons and reveals important functional differences between subtypes of this population.
Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hyper-variable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 million years. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e. secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e. primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees. Author summary A long-standing question in evolution is whether or not new species can arise in the presence of gene flow, which is expected to inhibit the formation of reproductive isolating barriers. We investigated the genomics underlying the origin of a Hawaii Island-endemic riparian tree and purported case of incipient sympatric speciation due to disruptive selection across a sharp forest-riparian ecotone. We find extensive evidence of ongoing gene flow between the riparian tree and its closest relative along with local genomic regions resistant to admixture that likely formed through selection on genes for ecological adaptation and/or reproductive isolation. These results strongly suggest that where disruptive selection is strong, incipient speciation with gene flow is possible even in long-lived, highly dispersible trees.
Distinct Proximal and Distal Corticospinal Signals Embed Limb Dynamics Through the Modulation of Stiffness

The complexities of the human musculoskeletal system and its interactions with the environment creates a difficult challenge for the neural control of movement. The consensus is that the nervous system solves this challenge by embedding the dynamical properties of the body and the environment. However, the modality of control signals and how they are generated appropriately for the task demands are a matter of active debate. We used transcranial magnetic stimulation over the primary motor cortex to show that the excitability of the corticospinal tract is modulated to compensate for limb dynamics during reaching tasks in humans. Surprisingly, few profiles of corticospinal modulation in some muscles and conditions reflected Newtonian parameters of movement, such as kinematics or active torques. Instead, the overall corticospinal excitability was differentially modulated in proximal and distal muscles, which corresponded to different stiffness at proximal and distal joints. This suggests that the descending corticospinal signal determines the proximal and distal impedance of the arm for independent functional control of reaching and grasping. Significance Statement The nervous system integrates both the physical properties of the human body and the environment to create a rich repertoire of actions. How these calculations are happening remains poorly understood. Neural activity is known to be correlated with different variables from the Newtonian equations of motion that describe forces acting on the body. In contrast, our data show that the overall activity of the descending neural signals is less related to the individual Newtonian variables and more related to limb impedance. We show that the physical properties of the arm are controlled by two distinct proximal and distal descending neural signals modulating components of limb stiffness. This identifies distinct neural control mechanisms for the transport and manipulation actions of reach.
Saharan dust deposition initiates successional patterns among marine microbes in the Western Atlantic

Deposition of aerosolized desert dust can affect marine microbial community structure and function through pulsed addition of limiting micro‐ and macronutrients. However, few studies have captured responses to dust deposition in situ following trans‐oceanic transport. We conducted a 26‐d time series evaluating biogeochemical and microbial community response to Saharan dust deposition in surface waters in the subtropical western Atlantic (Florida Keys National Marine Sanctuary, U.S.A.). Following periods of elevated atmospheric dust concentrations, particulate and dissolved iron concentrations increased in surface waters. Autotrophic picoeukaryote abundance increased rapidly, followed by increases in the abundance of heterotrophic bacteria and Synechococcus. Concomitant to cell count changes, we observed successional shifts in bacterial community composition. The relative abundances of Prochlorococcus and Pelagibacter declined with dust arrival, while relative abundance of heterotrophic bacteria increased, beginning with Vibrionales and followed sequentially by Chrysophyceae, Rhodobacteriaceae, and Flavobacteriaceae. Finally, a peak in Synechococcus cyanobacteria was observed. These results provide new insight into microbial community succession in response to Saharan dust deposition, their association with temporal dynamics in surface water dissolved and particulate iron concentrations, and a potential role for bioprocessing of dust particles in shaping marine microbial responses to deposition events.
Leguminosas forestales: aspectos relacionados con su nutrición y uso en la recuperación de suelos degradados

Characterized as aggressive pioneer species that produce large amounts of biomass, forest legumes have shown exceptional qualities in studies of rehabilitation of degraded soils. When associated with atmospheric nitrogen­ fixing bacteria and mycorrhizal fungi, these species show superior nutrient utilization and growth capacity in adverse soil conditions. The objective of this paper is to present the principal results obtained in the Research Program on Use on Nodulated and Mycorrhizal association Legume Species in Rehabilitation of Degraded Areas, developed by Embrapa/CNPAB in conjunction with the Federal University of Viçosa, Brazil. Greenhouse experiments have shown that these species have great tolerance to A l 3+ toxicity and efficient use of K, Ca and Mg. On the other hand, all the evaluated species proved responsive to phosphate fertilization.
Genetic diversity among Asparagus species using morphological characteristics and RAPD markers in Pakistan

The aim of present research was to study the genetic diversity among Asparagus species and its cultivars using morphological characteristics and RAPD markers. In-vitro and field experiments of 14 germplasm sources of Asparagus species and its cultivars were conducted at the Kohat University of Science and Technology to estimate the comparative performance. Highest genotypic variance, phenotypic variance, genotypic and phenotypic coefficient of variance were observed in shoot height in shoot related traits were 318.40, 320.30, 939.34 and 944.96, respectively, whereas highest values for root related traits were observed in root length that were 21.84, 22.35, 141.60 and 144.91 respectively. Among the shoot related traits maximum heritability, genetic advance and genetic gain were calculated for shoot length, while in root related traits these characters were highest for root dry weight. RAPD markers were used to evaluate genetic diversity analysis of 14 germplasm sources of Asparagus species and its cultivars. RAPD markers generated a total of 247 bands, of these 239 bands were polymorphic with average of 34.1 bands per primer. Cluster analysis based on Neighbor Joining methods showed that wild species (A. adsendens, A. densiflorus, A. capitatus, A. gracelus, A. plumosus, A. racemosus and A. setaceus) were genetically distant from A. officinalis and its cultivars (Abril, Apollo, Gersengum, Huchel, Para seletion and Taranga). The results of the present investigations could be particularly used for authentic identification and would be useful for evaluation of genetic improvement of Asparagus species and its cultivars. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 13-24
Glycaemic, gastrointestinal, hormonal and appetitive responses to pearl millet or oats porridge breakfasts: a randomised, crossover trial in healthy humans

Abstract Whole-grain cereal breakfast consumption has been associated with beneficial effects on glucose and insulin metabolism as well as satiety. Pearl millet is a popular ancient grain variety that can be grown in hot, dry regions. However, little is known about its health effects. The present study investigated the effect of a pearl millet porridge (PMP) compared with a well-known Scottish oats porridge (SOP) on glycaemic, gastrointestinal, hormonal and appetitive responses. In a randomised, two-way crossover trial, twenty-six healthy participants consumed two isoenergetic/isovolumetric PMP or SOP breakfast meals, served with a drink of water. Blood samples for glucose, insulin, glucagon-like peptide 1, glucose-dependent insulinotropic polypeptide (GIP), peptide YY, gastric volumes and appetite ratings were collected 2 h postprandially, followed by an ad libitum meal and food intake records for the remainder of the day. The incremental AUC (iAUC2h) for blood glucose was not significantly different between the porridges (P > 0·05). The iAUC2h for gastric volume was larger for PMP compared with SOP (P = 0·045). The iAUC2h for GIP concentration was significantly lower for PMP compared with SOP (P = 0·001). Other hormones and appetite responses were similar between meals. In conclusion, the present study reports, for the first time, data on glycaemic and physiological responses to a pearl millet breakfast, showing that this ancient grain could represent a sustainable alternative with health-promoting characteristics comparable with oats. GIP is an incretin hormone linked to TAG absorption in adipose tissue; therefore, the lower GIP response for PMP may be an added health benefit.
Effects of contemporary agricultural land cover on Colorado potato beetle genetic differentiation in the Columbia Basin and Central Sands

Abstract Landscape structure, which can be manipulated in agricultural landscapes through crop rotation and modification of field edge habitats, can have important effects on connectivity among local populations of insects. Though crop rotation is known to influence the abundance of Colorado potato beetle (CPB; Leptinotarsa decemlineata Say) in potato (Solanum tuberosum L.) fields each year, whether crop rotation and intervening edge habitat also affect genetic variation among populations is unknown. We investigated the role of landscape configuration and composition in shaping patterns of genetic variation in CPB populations in the Columbia Basin of Oregon and Washington, and the Central Sands of Wisconsin, USA. We compared landscape structure and its potential suitability for dispersal, tested for effects of specific land cover types on genetic differentiation among CPB populations, and examined the relationship between crop rotation distances and genetic diversity. We found higher genetic differentiation between populations separated by low potato land cover, and lower genetic diversity in populations occupying areas with greater crop rotation distances. Importantly, these relationships were only observed in the Columbia Basin, and no other land cover types influenced CPB genetic variation. The lack of signal in Wisconsin may arise as a consequence of greater effective population size and less pronounced genetic drift. Our results suggest that the degree to which host plant land cover connectivity affects CPB genetic variation depends on population size and that power to detect landscape effects on genetic differentiation might be reduced in agricultural insect pest systems.
Parity and dietary energy allowance during gestation influence piglet energy status and serum insulin-like growth factor 1 at birth

Abstract: Over- or under-supplying energy by 15% to gestating sows had minimum consequences for piglet chemical body composition or energy storage (liver and muscle glycogen) at birth, when estimated amino acid requirements were met. Providing gestating sows with energy 15% below versus 15% above requirements increased piglet serum insulin-like growth factor 1 (IGF-1) concentrations at birth (P < 0.05). Piglets from first versus second parity sows had lower serum IGF-1 but greater liver glycogen and body fat. Precisely matching the estimated energy and nutrient requirements throughout gestation and across parities likely improves piglet quality; over-supplying energy appears most detrimental for piglet IGF-1 serum concentrations at birth.
Towards development of a statistical framework to evaluate myotonic dystrophy type 1 mRNA biomarkers in the context of a clinical trial

Myotonic dystrophy type 1 (DM1) is a rare genetic disorder, characterised by muscular dystrophy, myotonia, and other symptoms. DM1 is caused by the expansion of a CTG repeat in the 3’-untranslated region of DMPK. Longer CTG expansions are associated with greater symptom severity and earlier age at onset. The primary mechanism of pathogenesis is thought to be mediated by a gain of function of the CUG-containing RNA, that leads to trans-dysregulation of RNA metabolism of many other genes. Specifically, the alternative splicing (AS) and alternative polyadenylation (APA) of many genes is known to be disrupted. In the context of clinical trials of emerging DM1 treatments, it is important to be able to objectively quantify treatment efficacy at the level of molecular biomarkers. We show how previously described candidate mRNA biomarkers can be used to model an effective reduction in CTG length, using modern high-dimensional statistics (machine learning), and a blood and muscle mRNA microarray dataset. We show how this model could be used to detect treatment effects in the context of a clinical trial.
An in vitro Actinidia Bioassay to Evaluate the Resistance to Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa) is by far the most important pathogen of kiwifruit. Sustainable expansion of the kiwifruit industry requires the use of Psa-tolerant or resistant genotypes for the breeding of tolerant cultivars. However, the resistance of most existing kiwifruit cultivars and wild genotypes is poorly understood, and suitable evaluation methods of Psa resistance in Actinidia have not been established. A unique in vitro method to evaluate Psa resistance has been developed with 18 selected Actinidia genotypes. The assay involved debarking and measuring the lesions of cane pieces inoculated with the bacterium in combination with the observation of symptoms such as callus formation, sprouting of buds, and the extent to which Psa invaded xylem. Relative Psa resistance or tolerance was divided into four categories. The division results were consistent with field observations. This is the first report of an in vitro assay capable of large-scale screening of Psa-resistance in Actinidia germplasm with high accuracy and reproducibility. The assay would considerably facilitate the breeding of Psa-resistant cultivars and provide a valuable reference and inspiration for the resistance evaluation of other plants to different pathogens.
Edit-Time Tactics in Idris

Metaprogramming allows users to write programs that write programs. In dependently-typed languages such as Idris, recent work on elaborator reflection paved theway for newapplications of metaprogramming by showing that a tactic-based proof language can be substituted with a monadic interface that exposes the internal elaborator. The goal of our work is to use elaborator reflection to write editor interaction actions in Idris. Currently in Idris modes of editors such as Emacs, users can perform actions like type-checking holes, case-splitting, and lemma extraction. Implementations of all of these Idris editor actions are hard-coded in the compiler, and they are written in Haskell. Ourwork will allowus to rewrite them in Idris as metaprograms and to move them into an Idris library, instead of having them embedded into the compiler. Furthermore, Idris users can write our own tactics through elaborator reflection and run them from the editor, i.e. in edit-time. This would extend the abilities of the editor interaction mode from the current built-in features to anything that can be done with tactics. In our work, we present the design and implementation of this feature in the Idris compiler. We also implement an intuitionistic theorem prover tactic, which is meant to be an better alternative to the built-in proof search editor action, and an add-clause tactic that exemplifies how we can move some of the hard-coded features from the compiler to a library.
Genetic basis of susceptibility to Diplodia sapinea and Armillaria ostoyae in maritime pine

Forest ecosystems are increasingly challenged by extreme events, e.g. pest and pathogen outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems. Adaptive phenotypes, including susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), height and needle phenology were assessed in a range-wide common garden of maritime pine (Pinus pinaster Aiton), a widespread conifer in the western Mediterranean Basin and parts of the Atlantic coast. Broad-sense heritability was significant for height (0.497), needle phenology (0.231-0.468) and pathogen symptoms (0.413 for D. sapinea and 0.066 for A. ostoyae) measured after inoculation under controlled conditions, but not for pine processionary moth incidence assessed in the common garden. Genetic correlations between traits revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae. Maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. An association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait. This study provides important insights to develop genetic conservation and breeding strategies integrating tree responses to pathogens.
NOVEL TEMPORARY AQUATIC HABITATS AND DESERT INVERTEBRATE COMMUNITIES

The addition of desert water developments alleviates water stress for a variety of organisms and is likely necessary for some species as water availability from other isolated water sources declines with climate change. However, constructed water catchments are different structurally and do not cycle water the same way as natural sites. We assessed whether these novel habitats, the constructed catchments of the Sonoran Desert, function as ecological equivalents of the natural waters and evaluated their effects on macroinvertebrate biodiversity, community composition, and trophic function. We documented an accumulation of ammonia and less diversity and different taxa assemblages in the novel habitat. We also documented a more heterotrophic food web in the natural water basins that are more dependent on resource pulses, and a more autotrophic food web in novel habitats that are more dependent on primary production from the open catchment basin. As natural resource managers continue to add constructed waters to mitigate for climate change induced declines in water availability, organisms are more likely to encounter these novel habitats as they disperse. Consequently, by increasing the density of these novel habitats we are having a measurable effect on the types of species and trophic groups present as well as the ecosystem cycling of energy and nutrients across the desert landscape. The consequences of these shifts in invertebrate community composition and ecosystem cycling on the larger desert ecosystem is unknown.
Forest community assembly is driven by different strata‐dependent mechanisms along an elevational gradient

The mechanisms driving forest community assembly along elevational gradients remain elusive. The distinct strata in heterogeneous forest are subject to differing assembly mechanisms. This study aims to evaluate how different ecological mechanisms driving forest community assembly across strata and spatial scales, and to identify how these assemblages respond to different abiotic or biotic variables along an elevational gradient.