Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteome changes following biotic and abiotic stress in forest trees

A proteomic approach was undertaken for the study of forest trees responses to biotic and abiotic stress factors. Protein extraction and two-dimensional gel electrophoresis protocols were optimised for all types of samples analysed, and the reproducibility of protein separation was investigated for different levels of biological and technical replication. The high resolution and reproducibility of protein expression patterns based on the optimised protocols guaranteed a high reliability of results. Differential display experiments were employed for the study of changes in protein expression patterns under stress conditions. In Europe, Picea abies and Fagus sylvatica are considered representative species for coniferous and broad leafed tree species respectively. These species were therefore selected as experimental models for the study of trees response to abiotic and biotic stressors. Protein expression was investigated in two Picea abies ecotypes adapted to different elevations. Direct comparison of protein expression in the needles and roots of the two ecotypes under normal growth conditions revealed differences in the constitutive expression of proteins with potential adaptive significance. The analysis of protein expression in response to and during the recovery from heat stress revealed differences in the activation of heat and oxidative stress protective mechanisms that can affect the capacity of the two ecotypes to withstand and recover from elevated temperatures. Mechanisms involved in the defence against pathogens and herbivores were investigated at local and systemic level. Fagus sylvatica - Phytophthora citricola pathosystem was selected as model system and wounding was used as elicitor of the response against herbivores. Local and systemic protein expression patterns in response to pathogen attack and root or leaf wounding exhibited overlaps consisting of co-regulated as well as differentially expressed proteins. Shared protein expression patterns indicate inter-regulation of signalling and defence pathways elicited by pathogens and herbivores while the existence of proteins exhibiting opposite regulation after infection and root wounding suggests antagonistic connections between the pathways. Overlapping and/or mutually antagonistic responses to different stress conditions indicate a complex inter-regulation of the signalling and defence pathways activated by different stressors. These pathways specifically interact to maximise chances for plant survival under different environmental conditions while minimising resource investment.
Genetic Epidemiology of Taste Perception and Cigarette Use

Cigarettes and other tobacco products contain bitter compounds including nicotine, which contribute to the chemosensory properties of tobacco and stimulate multiple sensory systems, including taste transduction pathways. Since bitter taste has evolved to identify potentially toxic compounds, and thus protect against harmful foods, our hypothesis is that aversion to this taste may prevent smoking and nicotine dependence. The goal of this research was to investigate the role of inherited differences in taste perception in smoking behaviors. We sought to determine whether such genetic variation could account for the well-known differences in flavored tobacco use among different U.S. ethnic groups. For example, around 80% of African-American smokers report that they prefer menthol cigarettes, compared to only 30% of European-American smokers who express this preference. We recruited subjects from four different populations, comprising a total of 9871 individuals, purified DNA’s from some saliva or blood samples and used a candidate gene approach to sequence taste-related genes. We identified several genetic associations between polymorphisms in taste-related genes and different smoking behaviors. We have shown that the frequency of the TAS2R38 taster haplotype differs between smokers and non-smokers in European-American populations. In addition, we identified two SNPs, one located in the menthol receptor TRPM8 and one in the menthol reactive gene TRPA1, that are strongly associated with menthol smoking in a study group of African-Americans. Moreover, we found that the taster haplotype of the TAS2R38 bitter taste receptor gene is less common in European-American smokers and that the non-taster haplotype of this gene is significantly lower in menthol smokers compared to non-menthol smokers. Overall, these findings support the hypothesis that variations in taste-related genes play a role in the choice of cigarettes when smoking. Understanding genetic differences in taste perception in tobacco use could help inform the development of more effective tobacco control policies.
Fish effluents promote root growth and suppress fungal diseases in tomato transplants

Gravel, V. , Dorais, M. , Dey, D. and Vandenberg, G. 2015. Fish effluents promote root growth and suppress fungal diseases in tomato transplants. Can. J. Plant Sci. 95: 427-436. Aquaculture systems generate large amounts of wastes which may constitute a beneficial amendment for horticultural crop in terms of nutrients, plant growth promoter and disease suppressiveness. This study aimed to determine (1) the nutrient value of rainbow trout farming effluents coming from two feed regimes and (2) the plant growth and disease suppressiveness effects of those fish farming effluents on tomato transplants. The effluent sludge from Skretting Orient™ (SO) had a higher content of P (38 vs. 32 mg L-1), K (23 vs. 11 mg L-1), N (19 vs. to 11 mg NO3 L-1; 186 vs. 123 mg NH4 L-1), and a higher NO3:NH4 ratio (1:9 vs. 1:13) compared with the Martin Classic (MC), while MC was richer in Mg (42 vs. 24 mg L-1) and Ca (217 vs. 169 mg L-1). For the first trial, a stimulating effect of the fish effluent was observed on plant height, leaf area and root dry biomass, while only the root biomass was increased during the second trial. Fish sludge was rich in microorganisms (97 and 142 µg fluorescein h-1 mL-1 for SO and MC, respectively) and their ability to suppress Pythium ultimum Trow and Fusarium oxysporum f.sp. lycopersici (Sacc.) Snyder & Hansen was observed. Both crude fish effluents reduced in vitro mycelial growth of P. ultimum and F. oxysporum, by 100 and 32%, respectively, while MC effluents showed a higher inhibition against F. oxysporum. When fish effluents were sterilized by filtration or autoclaving, lower in vitro inhibition of P. ultimum and F. oxysporum was observed. Mixed fish effluents reduced tomato plant root colonization by P. ultimum (by up to 5.7-fold) and F. oxysporum (by up to 2.1-fold). These results showed that fish effluent can be used as soil amendments to promote plant growth and increase soil suppressiveness, which in turn can prevent soil-borne diseases.
Novel Role of CD47 in Obesity-Associated Metabolic Dysfunctions

OF DISSERTATION NOVEL ROLE OF CD47 IN OBESITY-ASSOCIATED METABOLIC DYSFUNCTIONS Obesity and its associated comorbidities are of global concern. These complications are largely driven by perturbations in energy homeostasis, inflammation, and oxidative stress within metabolic tissues. Although these underlying pathways have been established, molecular mechanisms augmenting metabolic dysfunction have not been fully defined. CD47, a ubiquitously expressed cell membrane receptor, has been previously implicated in the development of inflammation and oxidative stress in a number of disease conditions. Previous work from our lab and others has confirmed that the most potent ligand of CD47, TSP1, plays a critical role in facilitating inflammation and metabolic dysfunction in diet-induced obesity. Whether these effects of TSP1 are mediated by CD47 has never been explored. Specifically, the functions of CD47 in white and brown adipose tissue, skeletal muscle, and the liver have never been characterized under obese conditions. Within our studies, we clearly defined distinct regulatory functions of CD47 in different metabolic tissues of a diet-induced obesity rodent model. We found that CD47 deficiency was associated with reduced adiposity and systemic inflammatory markers which preserved glucose homeostasis. In white adipose tissue, CD47 deficiency was associated with suppressed inflammation and macrophage recruitment which may be attributed to smaller adipocyte size driven by enhanced lipid mobilization. Further, whole body CD47 deficiency stimulated brown adipose tissue energy expenditure through increased FFA-mediated uncoupling and enhanced fatty acid oxidation. Interestingly, no significant changes were observed in skeletal muscle-dependent energy expenditure. In the liver, both TSP1 and CD47 deficiency protected mice from diet-induced fatty liver disease. In vitro studies demonstrated that TSP1 induces liver oxidative stress comparable to free fatty acids and that CD47 blockade partially attenuates this effect. From these studies, we concluded that increased lipid turnover fueled the enhanced energy requirements of activated brown adipose tissue resulting in a leaner phenotype despite high fat diet challenge. In addition, the increased TSP1-CD47 protein expression in the liver may augment ROS in fatty liver disease. Together, these studies provide evidence to suggest CD47 may contribute to metabolic dysfunction in a tissue-specific manner and that the pathological roles of CD47 function should expand to include obesity and its associated comorbidities.
Transcription initiation RNAs are associated with chromatin activation mark H3K4me3

Transcription initiation RNAs (tiRNAs) are small, predominantly 18 nt, RNAs whose biogenesis is associated with nucleosomes adjacent to active transcription initiation sites. These loci usually contain modified histones associated with transcription initiation, including histone H3 trimethylated at lysine 4 (H3K4me3). To further characterize the relationship of tiRNAs and H3K4me3 marked nucleosomes, H3K4me3-targeted RNA:chromatin immunoprecipitations were performed in a murine macrophage cell line, and small RNA sequence libraries were constructed and subjected to deep sequencing. The H3K4me3 libraries exhibited a distinct profile of read lengths with a noticeable enrichment of sequences 17-26 nt in length, with a peak at ∼18nt that included tiRNAs. These RNAs show clear enrichment of sequences that map to genomic features known to be associated with transcription initiation, including CAGE transcription initiation sites (TSSs), sites of RNAPII occupancy, and H3K4me3 sites. The distribution of sequences that map in the vicinity of TSSs is consistent with previous descriptions of tiRNAs; viz. a major peak at approximately 40 nt downstream of the TSS, and a minor broader peak approximately 150-200 nt upstream of, and on the opposite strand to, the TSS. These results show that tiRNAs are physically associated with H3K4me3-marked chromatin. tiRNAs may be markers of RNAPII pausing and it remains a possibility that their association with H3K4me3 is part of an epigenetic signaling system.
The unrealized potential of herbaria for global change biology

Plant and fungal specimens in herbaria are becoming primary resources for investigating how plant phenology and geographic distributions shift with climate change, greatly expanding inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a wealth of additional data—including nutrients, defensive compounds, herbivore damage, disease lesions, and signatures of physiological processes—that capture ecological and evolutionary responses to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium data, global change topics to which they have been applied, and new hypotheses they could inform. We find that herbarium data have been used extensively to study impacts of climate change and invasive species, but that such data are less commonly used to address other drivers of biodiversity loss, including habitat conversion, pollution, and overexploitation. In addition, we note that fungal specimens are under-explored relative to vascular plants. To facilitate broader application of plant and fungal specimens in global change research, we outline the limitations of these data and modern sampling and statistical tools that may be applied to surmount challenges they present. Using a case study of insect herbivory, we illustrate how novel herbarium data may be employed to test hypotheses for which few data exist, despite potentially large biases. With the goal of positioning herbaria as hubs for global change research, we suggest future research directions and curation priorities.
Chloroplast genome of the wild tuber-bearing diploid potato relative Solanum chacoense

Abstract Solanum chacoense is a wild tuber-bearing species belonging to Solanaceae family. The chloroplast genome of the species was completed by de novo assembly using a small amount of whole genome sequencing data. The genome is the circular DNA molecule with a length of 155,532 bp containing 159 predicted genes totally, including 105 protein-coding, 45 tRNA and eight rRNA genes. Maximum-likelihood phylogenetic analysis with 26 species in Solanaceae revealed that S. chacoense is the most closely grouped with S. commersonii.
Siphonophores from surface waters of the Colombian Pacific Ocean

Siphonophores are colonial hydrozoans that feed on zooplankton including fish larvae, and occur throughout the world's oceans from surface waters to ocean depths. Here we describe the composition of hyponeustonic siphonophores (0–3 m depth) from the tropical Colombian Pacific Ocean based on 131 plankton samples collected between June–October from 2001–2004. Samples were dominated by species of Calycophorae, with only three species of Physonectae identified, consistent with their deeper depth distribution. Muggiaea atlantica, Chelophyes contorta, Diphyes dispar, and Eudoxoides mitra were the most common of the 21 species identified. We found moderate structuring of the siphonophore community by the salinity gradient from inshore to offshore, and greater richness during the night because of diel vertical migration. Temperature did not play a significant role in structuring siphonophore communities, perhaps because of the narrow temperature range observed (3.5 °C). We extend the known temperature and salinity range of several species, including M. atlantica up to temperatures of 28.6 °C and salinities down to 24.7. Interestingly, only polygastric stages of M. atlantica were found, suggesting the reproductive stage of M. atlantica in tropical waters might be found in deeper waters. Chelophyes appendiculata was rare in our study and C. contorta was common, providing evidence they have a potential allopatric relationship, with C. contorta replacing C. appendiculata in warm water. Finally, we found siphonophore abundance was positively related to the abundance of copepods and fish eggs, with the top 13 most abundant species all having positive correlations, suggesting siphonophore abundances are tightly controlled by their food.
The microbiology of lean and obese soil

The bacterial genus Bradyrhizobium is biologically important within soils, with different representatives found to perform a range of functions including nitrogen fixation through symbioses, photosynthesis and denitrification. The Highfield experiment at Rothamsted provides an opportunity to study the impact of plants on microbial communities as it has three long-term contrasting regimes; permanent grassland, arable and bare fallow (devoid of plants). The bare fallow plots have a significant reduction in soil carbon and microbial biomass. Bradyrhizobium has been shown by metagenomic studies on soil to be one of the most abundant and active groups including in bare fallow soil indicating that some phenotypes are adapted to survive in the absence of plants. A culture collection was created with isolates obtained from contrasting soil types from Highfield in addition to woodland soil, gorse (Ulex europeaus) and broom (Cytisus scoparius) root nodules. The collection’s phylogeny has been explored by sequencing housekeeping genes to determine whether soil treatment affects the core genome. One grassland and one bare fallow isolate had their genome sequenced and differences have been assessed to establish their potential for a range of functions and to direct future experiments. The functional diversity of the collection has been investigated using carbon metabolism assays to identify key substrates and determine whether the isolates group according to soil treatment. Symbiosis capacity and role in nitrogen cycling has been examined using nodulation tests, anaerobic growth on nitrate and nitrous oxide production and reduction through denitrification. A high level of diversity can be seen throughout the collection with differences being linked to niche adaptation. Understanding more about Bradyrhizobium could give clues on how above ground management impacts a key group within the soil community. Furthermore, the first assembled genomes of two non-symbiotic Bradyrhizobium strains isolated from soil provide an important resource for microbiology and soil ecology.
Attribute Non-attendance as an Information Processing Strategy in Stated Preference Choice Experiments: Origins, Current Practices, and Future Directions

Stated preference discrete choice experiments (CE) are increasingly being used by researchers seeking to understand people’s preferences and values in environmental economics, transportation, health, and marketing. An active CE research area relates to behaviors that break from the assumptions of full rationality assumed in standard discrete choice models. In particular, considerable attention in recent years has been on attribute non-attendance (ANA), a type of choice behavior where individuals ignore one or more attributes in CE questions. In this article, we delve into the origins and motivations for the study of ANA as an information processing strategy, delineate the variety of approaches that have developed in the growing literature to identify and account for ANA behavior, and discuss several promising directions for this literature that could enhance our understanding of decision-making in CE studies.
Deciphering eukaryotic cis-regulatory logic with 100 million random promoters

Deciphering cis-regulation, the code by which transcription factors (TFs) interpret regulatory DNA sequence to control gene expression levels, is a long-standing challenge. Previous studies of native or engineered sequences have remained limited in scale. Here, we use random sequences as an alternative, allowing us to measure the expression output of over 100 million synthetic yeast promoters. Random sequences yield a broad range of reproducible expression levels, indicating that the fortuitous binding sites in random DNA are functional. From these data we learn models of transcriptional regulation that predict over 94% of the expression driven from independent test data and nearly 89% from sequences from yeast promoters. These models allow us to characterize the activity of TFs and their interactions with chromatin, and help refine cis-regulatory motifs. We find that strand, position, and helical face preferences of TFs are widespread and depend on interactions with neighboring chromatin. Such massive-throughput regulatory assays of random DNA provide the diverse examples necessary to learn complex models of cis-regulatory logic.
[On the Speed of Transition in Central Europe]: Discussion

Atkeson, A. , and P. Kehoe. (1993a). Social insurance and transition. NBER working paper 4411. Atkeson, A. , and P. Kehoe. (1993b). Industry evolution and transition: The role of information capital. Federal Reserve Bank of Minneapolis Staff Report 162. Berg, A. , and 0. Blanchard. (1994). Stabilization and transition: Poland 1990-1991. In The transition i Eastern Europe, vol. 1, O. Blanchard, K. Froot, and J. Sachs (eds.). Chicago: University of Chicago Press. Calvo, G. , and F. Coricelli. (1991). Stagflationary effects of stabilization programs in reforming socialist economies: Supply side versus demand side factors. Mimeo, International Monetary Fund. Sachs, J. (1993). Poland's jump to the market economy. Cambridge, MA: The MIT Press.
Homoisoflavonoids from Caesalpinia spp.: A Closer Look at Chemical and Biological Aspects

Homoisoflavonoids are rare compounds distributed within a few families of plants includ‐ ing species from Fabaceae. The genus Caesalpinia, the main focus of this chapter, is a prolific source of these unique natural products. Homoisoflavonoids from Caesalpinia spp. are associ‐ ated to ethnopharmacological uses for diverse purposes. In this sense, the following chapter sheds light on the occurrence, biosynthesis, isolation, synthesis, and structural analysis of these compounds from species of the genus Caesalpinia and their biological potential.
Endocarditis caused by an oral taxon species of Bergeyella identified by partial 16S rDNA sequencing: Case report and review of the literature

Bergeyella spp bacteremia is a rare cause of infective endocarditis and is typically associated with animal contact. This case report presents a case of culture-negative endocarditis caused by Bergeyella spp oral taxon 422 in a 49-year-old man with severe periodontal disease but no animal contact. Multiple sets of blood cultures were negative, but broad-range 16S rDNA polymerase chain reaction (PCR) amplification and sequencing repeatedly detected this organism in the patient's bloodstream. Empiric broad-spectrum antibiotic treatment against Bergeyella spp resulted in resolution of clinical symptoms, resolution of bloodstream infection, and cure. This is the first human case of endocarditis caused by an oral-associated species of Bergeyella described in the literature. Culture-negative endocarditis due to Bergeyella spp from severe periodontal disease may be missed unless molecular detection methods are used.
Functional analysis of enolase in Toxoplasma gondii.

Toxoplasma gondii is an intracellular parasite of humans in the phylum Apicomplexa. In an intermediate host (including human and other mammals), T. gondii occurs in an actively dividing form (tachyzoite) and a dormant form (bradyzoite). My research is focused on the function o f enolase, which is present in two isoforms known as ENOl and EN02. Previous study showed that enolase is expressed in stage-specific manner. EN02 is expressed only in tachyzoites, and ENOl is specifically expressed in bradyzoites. Moreover, both isoforms o f enolase are be localized in nucleus as well as in cytoplasm of T. gondii. This research is aimed to dissect the role o f EN 02 in the growth o f T. gondii. I used homologous dsRNA to induce ENOl or EN 02 gene silencing. I generated two transgenic parasite lines expressing ENOl or EN 02 dsRNA, and used them in the loss-of-function study. Although the reduction o f EN02 expression was observed, I did not detect any changes in the growth of parasites, as monitored by two different methods, vacuole counting and plaque assay. I postulated that another protein or other metabolic pathway might compensate for the loss o f EN 02 function.