Miracle-dz/UniFAR-FTUs huggingface dataset:
Bird Diversity in Actively and Naturally Restored Tropical Forests in an Urban-Agricultural Landscape

Secondary forests have reclaimed one sixth of deforested land worldwide, and much of this revegetated forest lies in agricultural and increasingly semi-urban landscapes. While, many studies have described faunal populations such as birds across forest-agricultural landscapes, they generally note minor changes in total species richness and more significant changes in species composition. Few studies, however, consider faunal diversity among secondary forests of different management history, such as manual restoration or natural revegetation. In this study, we surveyed bird communities in three forest sites of varying restoration and natural revegetation treatments in a tropical urban-agricultural landscape in the Ecuadorian Amazon. Our sites include manually restored and naturally revegetating forest of 20–40 years since clearing. We found that a diverse assemblage of birds visit and occupy forest fragments within the urban-agricultural landscape, including two IUCN-listed near-threatened species. Bird species richness was similar across sites of different management history; species composition varied only slightly, but differences existed in presence and occupancy for forest-dependent groups, such as large frugivores and forest insectivores. In the manually restored site, bird diversity may have been limited by under-developed forest structure, but we were unable to isolate the effects of patch size and landscape matrix. We suggest that future restoration activities consider forest structure in addition to plant species diversity when attempting to restore faunal populations, and that future studies take heed of landscape and matrix parameters when evaluating restoration projects.
Detection of structural variations during liver cancer progression

9 Introduction . 11 1.1 Overview of human liver cancer . 11 1.2 Genomic landscape of hepatocellular carcinoma . 12 1.3 External factors as oncogenic events of hepatocellular carcinoma . 14 1.4 Inflammation and cancers . 16 1.4.1 Role of inflammation in hepatocellular carcinoma . 18 1.5 Hepatocellular carcinoma induced by defects in biliary transporter genes . 20 1.5. 1 Bile salt export pump deficiency and paediatric hepatocellular carcinoma . 24 1.5. 2 Mdr2-KO mouse model of hepatocellular carcinoma . 27 1.6 Genomic copy number alterations . 29 1.6. 1 Definition and mechanisms of formation . 29 1.6. 2 Copy number variations in evolution and diseases . 35 1.6. 3 Copy number variations and cancer . 38 1.6. 4 Methods for detecting copy number variations . 42 1.7 Aim of the thesis . 46 Methods . 48 2.1 Sample description . 48 2.1.1 Samples from human liver cancer . 48 2.1.2 Samples from mouse liver cancer . 51 2.2 Experimental procedure . 51 2.2.1 DNA extraction . 52 2 2.2.2 DNA-sequencing . 52 2.2.2.1 Whole exome sequencing of human samples . 52 2.2.2.2 Targeted sequencing, whole exome sequencing and whole genome sequencing of mouse samples . 53 2.2.3 Dilution experiment for assessments of variant calling . 55 2.2. 4 SNP array for detecting copy number variations in human samples . 57 2.2. 5 TaqMan copy number assay for copy number variation validation . 58 2.2. 6 Fluorescence in situ hybridization . 59 2.2. 7 Pathway enrichment analysis . 59 2.2. 8 Expression quantification of Map2k7 in mouse liver cancer . 60 2.2. 9 Treatment of Mdr2-KO mouse with SP600125 JNK inhibitor . 60 2.3 Computational Procedure . 61 2.3.1 Alignment and variant calling from targeted re-sequencing data . 61 2.3.2 CNV analysis from SNP arrays . 63 2.3. 3 CNV and structural rearrangement analysis from whole genome sequencing data . 65 2.3. 4 GeneCNV . 66 2.3. 4.1 Workflow of the method . 67 2.3. 4.2 Dataset for exome-based method evaluation . 69 2.3. 4.3 Identification of altered genes from SNP array . 73 2.3. 4.4 Identification of modified genes from exome sequencing data . 73 2.3. 4.5 Comparison of GeneCNV with other methods . 74 Results . 76 3.1 GeneCNV: Rationale and performance evaluation . 77 3.1.1 Rationale of GeneCNV . 77 3.1.2 Comparison of GeneCNV with other methods . 85 3.1.3 Analytical and graphical outputs . 91 3 3.2 Genomic alterations in human BSEP-HCCs and mouse Mdr2-KO HCCs . 95 3.2.1 Human BSEP-HCCs do not accumulate mutations in known cancer genes . 96 3.2.2 Massive gene amplification occurs in human BSEP-HCCs . 101 3.2.3 The genomic landscape of Mdr2-KO HCCs resembles that of BSEP-HCCs . 106 3.2. 4 Somatic CNVs accumulate during Mdr2-KO HCC progression . 110 3.2. 5 JNK is deregulated in Mdr2-KO HCCs . 114 3.2. 6 JNK inhibition arrests carcinoma progression in Mdr2-KO mice . 118 Discussion . 123 Appendix: Published papers . 132 References . 133 Acknowledgements . 147
Modulation of NF-kB regulatory function in Salmonella-infected fibroblasts

The transcriptional regulator “nuclear factor kappa B” (NF-κB) regulates many processes in eukaryotic cells, including the response to infections. In this work, we have used new experimental set-up to analyze the NF-κB response in fibroblasts infected with Salmonella enterica serovar Typhimurium. Fibroblasts were selected as host cell prototype in our experiments due to the ability of S. Typhimurium to establish persistent infections in this cell type using a dedicated regulatory program. NF-κB normally displays an oscillatory behavior that can be measured as cytosol- nuclear translocation dynamics. In this work, we studied NF-κB subcellular location in live cells overtime. Our studies, performed at single cell level, could differentiate NF-κB dynamics in infected (ST+) and uninfected (ST—) fibroblasts that co-exist in culture. These experiments revealed that in a cytokine-free environment, S. Typhimurium induces NF-κB nuclear translocation in the bacteria-containing fibroblasts. Conversely, in culture conditions where signaling molecules released by the cells in the culture accumulate in the medium, the ST— cells are those showing increased NF-κB nuclear translocation. Moreover, ST+ fibroblasts show less NF-κB activation when cells are challenged with external stimuli such as TNF-α, IL-1β or a second S. Typhimurim infection. These observations are consistent with refractoriness of the ST+ cells to extracellular stimuli. We also applied sorting techniques to fibroblast cultures incubated with S. Typhimurium, which were separated into ST+ and ST— cell populations. These two fibroblast populations were analyzed for gene and protein expression. The analyses showed that expression of NF-κB regulated genes was enriched in the ST— fibroblasts. These data supported an active role of intracellular S. Typhimurium in dampening the NF-κB response in the ST+ cells. Although the precise mechanism by which S. Typhimurium attenuates the NF-κB response in fibroblasts remains uncovered, we demonstrate that protein effectors secreted by type III secretion systems encoded in the Salmonella pathogenicity islands 1 and 2 (SPI1-T3SS and SPI2-T3SS) are involved in such attenuation. Collectively, these data demonstrate that intracellular S. Typhimurium attenuate NF-κB in fibroblasts and this effect is noticeable only when infected and bystander uninfected cells are examined separately. Such modulation of NF-κB activation at the organism level could potentially result in infected cells that would remaine hidden and safe from the host immune system attack.
Chromatin and cryptic transcription

he eukaryotic chromatin struc-ture is essential in correctly defin-ing transcription units. Impairing this structure can activate cryptic promoters, and lead to the accumulation of aberrant RNA transcripts. Here we discuss criti-cal pathways that are responsible for the repression of cryptic transcription and the maintenance of genome integrity.
Exploring Species Diversity and Molecular Evolution of Arachnida through DNA Barcodes

EXPLORING SPECIES DIVERSITY AND MOLECULAR EVOLUTION OF ARACHNIDA THROUGH DNA BARCODES Monica Rose Young Advisor: University of Guelph, 2012 Professor P.D. N. Hebert This thesis investigates species diversity and patterns of molecular evolution in Arachnida through DNA barcoding. The first chapter assesses mite species richness through comprehensive sampling at a subarctic location in Canada. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species with high rates of turnover between major habitat types, demonstrating the utility of DNA barcoding for biodiversity surveys of understudied taxa. The second chapter explores nucleotide composition, indel occurrence, and rates of amino acid evolution in Arachnida. The results suggest a significant shift in nucleotide composition in the arachnid subclasses of Pulmonata (GC = 37.0%) and Apulmonata (GC = 34.2%). Indels were detected in five apulmonate orders, with deletions being much more common than insertions. Finally, rates of amino acid evolution were detected among the orders, and were negatively correlated with generation length, suggesting that generation time is a significant contributor to variation in molecular rates of evolution in arachnids.
Hurricane Disturbance Benefits Nesting American Oystercatchers (Haematopus palliatus)

Abstract. Coastal ecosystems are under increasing pressure from human activity, introduced species, sea level rise, and storm activity. Hurricanes are a powerful destructive force, but can also renew coastal habitats. In 2003, Hurricane Isabel altered the barrier islands of North Carolina, flattening dunes and creating sand flats. American Oystercatchers (Haematopus palliatus) are large shorebirds that inhabit the coastal zone throughout the year. Alternative survival models were evaluated for 699 American Oystercatcher nests on North Core Banks and South Core Banks, North Carolina, USA, from 1999–2007. Nest survival on North Core Banks increased from 0.170 (SE = 0.002) to 0.772 (SE = 0.090) after the hurricane, with a carry-over effect lasting 2 years. A simple year effects model described nest survival on South Core Banks. Habitat had no effect on survival except when the overall rate of nest survival was at intermediate levels (0.300–0.600), when nests on open flats survived at a higher rate (0.600; SE = 0.112) than nests in dune habitat (0.243; SE = 0.094). Predator activity declined on North Core Banks after the hurricane and corresponded with an increase in nest survival. Periodic years with elevated nest survival may offset low annual productivity and contribute to the stability of American Oystercatcher populations.
When does perceived coach autonomy support help reduce athlete burnout? The role of athletes’ experiential avoidance.

Researchers have found that perceived coach autonomy support is negatively related to athlete burnout. However, whether offering such support would be helpful for all athletes or only athletes with certain characteristics is unknown. Following the notion of autonomous goal regulation suggested in self-determination theory, the authors propose that having autonomy support from coaches will be more strongly associated with a decrease in athlete burnout among athletes with lower experiential avoidance than among those with higher experiential avoidance. Experiential avoidance is a tendency to escape, avoid, or modify the frequency of uncomfortable experiences. A total of 141 collegiate student athletes completed surveys at two time points over three months. The results indicate that perceived coach autonomy support is negatively related to athlete burnout. Furthermore, the negative relationship between perceived coach autonomy support and decreased athlete burnout is stronger when experiential avoidance is low rather than high. When the three dimensions of burnout were analyzed individually (i.e., emotional and physical exhaustion, reduced sense of accomplishment and sport devaluation), only emotional and physical exhaustion and overall score were significant. The implications and applications of these results are discussed from an interactionist perspective.
Functional and structural studies of AAA+ proteases

AAA+ proteases are found in all domains of life. They degrade misfolded proteins as well as specific regulatory factors and thus play critical roles in protein quality control and numerous cellular processes. These enzymes share a conserved architecture in which a hexameric AAA+ ATPase recognizes, unfolds, and translocates substrates into an associated self-compartmentalized peptidase for degradation. In addition to participating in proteolysis, AAA+ ATPases, by themselves, can unfold and/or remodel macromolecular complexes. However, rigorous characterization of these unfolding reactions in the absence of proteolysis has been difficult. In Chapter 2, I develop a robust assay that uses FRET to monitor unfolding of a dimeric substrate. I use this assay to compare and contrast the unfolding activities of the E. coli AAA+ ClpX and ClpA unfoldases, revealing significant functional differences for these enzymes in the presence and absence of ClpP, their cognate peptidase. Substrate recognition is another important aspect of function but is poorly understood for many AAA+ enzymes, including the HslU unfoldase, which partners with the dodecameric HslV peptidase. HslU contains a unique auxiliary domain, called the I domain, which is thought to aid in substrate recognition and to couple ATP hydrolysis to substrate processing. However, the precise mechanism by which the I domain functions remains unclear. In Chapter 3, I use structural and biochemical approaches to characterize a point mutation in the I domain that elevates HslU ATPase activity and alters the preferred direction of substrate unfolding and degradation. These studies shed light on how substrates are recognized and processed by the HslUV protease. In Chapter 4, I develop and use a disulfide-crosslinking approach to generate mixed HslU hexamers containing different numbers and arrangements of hydrolytically active and inactive subunits in an effort to understand how the ATPase cycle of HslU is coupled to function. Contrary to models suggested by the majority of HslUV structures, I find that HslU appears to function using a probabilistic mechanism of ATP hydrolysis. Thesis Supervisor: Robert T. Sauer Title: Salvador E. Luria Professor of Biology Thesis Co-supervisor: Tania A. Baker Title: E.C. Whitehead Professor of Biology
Complete mitochondrial DNA sequence of Brachysomophis crocodilinus (Anguilliformes: Ophichthidae)

Abstract Brachysomophis crocodilinus belongs to the family Ophichthidae, the complete mitochondrial genome of which was sequenced in this study. The mitochondrial genome of B. crocodilinus is of 17,818 bp in length, with overall base composition of 32.11% A, 24.69% T, 16.22% G, and 26.98% C. The genome content includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. The result of phylogenetic analysis indicates that B. crocodilinus mitogenome is close to that of Ophisurus macrorhynchos, which are nested within the family Ophichthidae.
Metabolome analysis - mass spectrometry and microbial primary metabolites

Mass spectrometry (MS) has been a major driver for metabolomics, and gas chromatography (GC)MS has been one of the primary techniques used for microbial metabolomics. The use of liquid chromatography (LC)-MS has however been limited, but electrospray ionization (ESI) is very well suited for ionization of microbial metabolites without any previous derivatization needed. To address the capabilities of ESI-MS in detecting the metabolome of Saccharomyces cerevisiae, the in silico metabolome of this organism was used as a template to present a theoretical metabolome. This showed that in combination with the specificity of MS up to 84% of the metabolites can be identified in a high mass accuracy ESIspectrum. A total of 66 metabolites were systematically analyzed by positive and negative ESI-MS/MS with the aim of initiating a spectral library for ESI of microbial metabolites. This systematic analysis gave insight into the ionization and fragmentation characteristics of the different metabolites. With this insight, a small study of metabolic footprinting with ESI-MS demonstrated that biological information can be extracted from footprinting spectra. Statistical analysis of the footprinting data revealed discriminating ions, which could be assigned using the in silico metabolome. By this approach metabolic footprinting can advance from a classification method that is used to derive biological information based on guilt-by-association, to a tool for extraction of metabolic differences, which can guide new targeted biological experiments.
Behavioural, modeling, and electrophysiological evidence for domain-generality in human metacognition

Metacognition, or the capacity to introspect on one’s own mental states, has been mostly characterized through confidence reports in visual tasks. A pressing question is to what extent the results from visual studies generalize to other domains. Answering this question allows determining whether metacognition operates through shared, domain-general mechanisms, or through idiosyncratic, domain-specific mechanisms. Here, we report three new lines of evidence for decisional and post-decisional mechanisms arguing for the domain-generality of metacognition. First, metacognitive efficiency correlated between auditory, tactile, visual, and audiovisual tasks. Second, confidence in an audiovisual task was best modeled using supramodal formats based on integrated representations of auditory and visual signals. Third, confidence in correct responses involved similar electrophysiological markers for visual and audiovisual tasks that are associated with motor preparation preceding the perceptual judgment. We conclude that the domain-generality of metacognition relies on supramodal confidence estimates and decisional signals that are shared across sensory modalities.
Interacting effects of climate and landscape physiography on piñon pine growth using an individual‐based approach

Forest and woodland ecosystems play a crucial role in the global carbon cycle and may be strongly affected by changing climate. Here, we use an individual-based approach to model pi~ non pine (Pinus edulis) radial growth responses to climate across gradients of environmental stress. We sampled pi~ non pine trees at 24 sites across southwestern Colorado that varied in soil available water capacity (AWC), elevation, and latitude, obtaining a total of 552 pi~ non pine tree ring series. We used linear mixedeffect models to assess pi~ non pine growth responses to climate and site-level environmental stress (30-year mean cumulative climatic water deficit [CWD] and soil AWC). Using a similar modeling approach, we also determined long-term growth trends across our gradients of environmental stress. Pi~ non pine growth was strongly positively associated with winter precipitation. Summer vapor pressure deficit (VPD) was strongly negatively associated with pi~ non pine growth during years of low winter precipitation, whereas summer VPD had no effect on pi~ non pine growth during years of high winter precipitation. The strength of the relationship between the annual climatic variables (winter precipitation and summer VPD) and pi~ non pine growth was also influenced by site-level environmental stress, suggesting that the sensitivity of woodland ecosystems to changing climate will vary across the landscape due to differences in local physiographic conditions. Trees at sites with lower CWDs were more responsive to summer VPD, showing greater reductions in growth rates during warmer years. Trees at sites with greater soil AWC were more responsive to winter precipitation, showing higher growth rates during years of high precipitation. Pi~ non pine growth rates declined moderately over the past century across our study area, suggesting that recent increases in aridity have resulted in long-term growth declines.
Macro-organisms influence coral reef microbial communities via shedding and induction

OF THE THESIS Macro-Organisms Influence Coral Reef Microbial Communities via Shedding and Induction by Kevin J. Walsh Master of Science in Biology with a Concentration in Ecology San Diego State University, 2016 Coral reef ecosystems are a diverse but declining habitat. Most reefs around the world have transitioned from a coral to algal dominated benthos with the exact cause for this shift remaining elusive. There is recent evidence that microbes associated with algae either directly from the algae surface or via dissolved organic carbon (DOC) stimulation are detrimental to coral health, inducing mortality and providing space for algae recruitment and growth. To address this issue I investigated how multiple reef organisms influence microbial communities in the surrounding water column. I predicted the effluence from various reef macro-organisms would alter the water column microbial community in contrasting ways. This study consisted of an experiment that looked at water column microbes induced by DOC from various reef macro-organisms and a field assessment of microbial communities, comprised of both shed and induced microbes, above replicate patches dominated by a single macro-organism. Both were conducted on the reefs in the Abrolhos Archipelago of Eastern Brazil. The controlled experiment had replicate seawater microbial communities exposed for 30 hours to the presence of the DOC from different benthic organisms including 1) coral (Mussismilia harttii), 2) crustose coralline algae, 3) algae (Stypopodium zonale), and 4) a seawater control. The microbial communities were semi-cultured and sequenced. Metagenomes showed significant changes in microbial taxa and function when grown in the presence of different macro-organisms. In the second experiment, water above replicate macro-organisms including 1) coral (Mussismilia braziliensis), 2)algae (Stypopodium, Dictota and Canistrocarpus), 3) cyanobacterial mats, and 4) zoanthids (Palythoa caribaeorum) were collected in the field and were compared to the water microbes collected 2 m above the reef. Microbial genera were identified in the water column above each macroorganism. At both a broad and specific level, metabolic pathways of microbes influenced by reef macro-organisms were distinctive. These two studies show that dominant benthic macroorganisms influence the microbes in the water column surrounding them, developing a specific “aura-biome”. The aura-biomes may reduce recruitment potential or growth of nonself macro-organisms. Therefore, as a reef changes to non-coral dominated, the microbial environment may transition to be unsuitable for coral growth, establishing a feedback loop.
Parasite fauna of three species of Antarctic whales with reference to their use as potential stock indicators

-Seventeen species of parasites representing the Cestoda, Nematoda, Acanthocephala, and Crus tacea are reported from three spe cies of Antarctic whales. Thirty-five sei whales Balaenoptera borealis, 106 minke whales B. acutorostrata, and 35 sperm whales Pkyseter cato don were examined from latitudes 30° to 64°S, and between longitudes 106°E to 108°W, during the months ofNovember to March 1976-77. Col lection localities and regional hel minth fauna diversity are plotted on distribution maps. Antarctic host-parasite records from B. borealis, B. acutorostrata, and P. catodon are updated and tabulated by commercial whaling sectors. The use of acanthocephalan para sites of the genus Corynosoma as potential Antarctic sperm whale stock indicators is discussed.