Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Weed Management: The Rationale and Approach

A growing awareness of environmental issues in Canada has had a major influence on government policies. An initiative was launched by the government of Ontario to promote research toward the development of an integrated weed management (IWM) system. Research in IWM must take all aspects of the cropping system into consideration and evolve in a progressive manner. This approach must encompass the role of conservation tillage, knowledge of the critical period of weed interference, alternative methods of weed control, enhancement of crop competitiveness, modeling of crop-weed interference, influence of crop rotation and seed bank dynamics, and education and extension of the findings. The complexity involved in addressing these issues requires a multi-disciplinary approach.
Extraction of Protein from Yellowfin Tuna (Thunnus albacares) Waste by Enzymatic Hydrolysis and its Characterization

The focus of this investigation was to utilize the protein present in tuna waste by enzyme hydrolysis and characterization of protein hydrolysate (TPH). Yellowfin tuna waste was used to prepare the hydrolysate using 0.5% (w/w) bromelain enzyme. It was characterized for nutritional, functional and antioxidant properties. The protein content in the derived protein hydrolysate was 95.3 ± 3.1%. The foaming capacity as well as foam stability was maximum at pH 6.0 and the property decreased when pH deviated from neutral. Emulsifying properties viz., emulsifying activity index as well as emulsion stability index was least at 4.0 pH. DPPH radical scavenging activity of TPH revealed an IC50 value of 4.06 mg ml-1.
Deregulation and Therapeutic Potential of the Hippo Pathway in Cancer

The Hippo pathway has drawn increasing interest in the past decade for its role in the regulation of cell growth, differentiation, organ size, and tissue homeostasis. Recent studies have expanded our knowledge of known upstream regulators of the Hippo pathway and have consistently demonstrated that the Hippo pathway is critical for translating cellular cues into transcriptional responses by receiving input from a wide range of upstream signals. Dramatic overgrowth phenotypes upon deregulation of the Hippo pathway have prompted investigation into its role in cancer. Here we provide an overview of the Hippo pathway, our current understanding of its role in tumorigenesis, and potential therapeutics targeting Hippo signaling.
Regulation of Contractile Protein S-Nitrosation in Preterm Myometrium Underlies the Dysfunctional Relaxation to Nitric Oxide

Preterm labor leads to preterm delivery in over 50% of cases. Current treatment for preterm labor is inadequate and relies on findings in other smooth muscles. No treatment can prevent labor to allow a fetus to remain in the womb until term. Regulation of contraction/relaxation of the uterine smooth muscle is poorly understood. Recent work in our laboratory has revealed major disparity between term and preterm human uterine smooth muscle that suggests new approach to drug discovery.
A conserved antiviral role for a virus-induced cytoplasmic exosome complex

RNA degradation is a tightly regulated and highly conserved process which selectively targets aberrant RNAs using both 5’ and 3’ exonucleases. The RNAs degraded by this process include viral RNA, but the mechanisms by which viral RNA is identified and recruited to the degradation machinery are incompletely understood. To identify new antiviral genes, we performed RNAi screening of genes with known roles in RNA metabolism in Drosophila cells. We identified the RNA exosome, which targets RNA for 3’ end decay, and two components of the exosome cofactor TRAMP complex, dMtr4 and dZcchc7, as antiviral against a panel of RNA viruses. As these genes are highly conserved, I extended these studies to human cells and found that the exosome as well as TRAMP components hMTR4 and hZCCHC7 are antiviral. While hMTR4 and hZCCHC7 are normally nuclear, I found that infection by cytoplasmic RNA viruses induces their export to cytoplasmic granules, where they form a complex that specifically recognizes and induces degradation of viral mRNAs. Furthermore, I found that the 3’ UTR of bunyaviral mRNA is sufficient to confer virus-induced exosomal degradation, demonstrating cis-regulation. Several types of ribonucleoprotein (RNP) granules interact with both 5’ and 3’ decay machinery to facilitate degradation of sequestered RNAs. In order to determine whether TRAMP component-containing granules contain components of other defined RNP granules, I performed immunofluorescence for hZCCHC7 as well as components of P-bodies, stress granules, and exosome granules and found that hZCCHC7 can colocalize with proteins resident in exosome granules and stress granules during viral infection, suggesting that hZCCHC7 may bind translationally-stalled viral RNAs and bring them to exosome granules for degradation. To further characterize the regulation of TRAMP component nuclear export during infection, I investigated the viral signals necessary for this transport. I found that transfection with dsRNA is sufficient to induce relocalization, while infection with UV-inactivated viruses is not. Moreover, I tested the role of canonical innate immune adaptors in this process and found that the dsRNA sensor PKR promoted relocalization during Sindbis virus infection. Altogether, my results reveal that the presence of replicating viral RNA causes TRAMP components to be repurposed to a cytoplasmic surveillance role in several classes of RNP granules including stress granules and exosome granules. There, they selectively engage viral RNAs for degradation to restrict a broad range of viruses. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Sara Cherry This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2480
Atividade antiviral e imunomoduladora de extratos originados de Uncaria sp. em infecção in vitro de linhagem contínua de hepatócitos humanos pelo vírus Dengue

The incidence of dengue worldwide has increased in recent decades. The exacerbated immune responses play a crucial role in the infection pathophysiology, such as the induction of plasma extravasation. It is caused mainly by the production of a cascade of inflammatory cytokines that can induce coagulation disorders and alterations in vascular permeability leading, eventually, to severe hemorrhages and shock. Natural products, which have immunomodulatory properties described in ethnopharmacology, can promote the control of viral replication and a reduction of cytokines that induce endothelial permeability, which could result in milder clinical manifestations. The aim of this study was to investigate whether compounds from a medicinal plant could modulate the innate immune response associated with immunopathological characteristics in infection Dengue virus (DENV), using an in vitro model of infection with continuous lines of human hepatocytes (Huh-7). Methods and Results: After infection of Huh-7 target cells by DENV-2, cultures were treated with single lots hydroalcoholic extracts of Uncaria sp. (UGC or UGF), at different concentrations. The rate of cells containing viral antigens was determined after incubation periods by virus-specific immunofluorescence and flow cytometry. Viral non-structural protein (NS1), indicative of viral replication, was detected in cell culture supernatants and cytokines/chemokines, MIF, IL-8 and IL-6, all determined by ELISA assays In the same supernatants, the production of inflammatory factor nitric oxide was determined indirectly by nitrite (Griess reaction). Moreover, cells were analyzed by flow cytometry for cell viability changes, apoptosis and necrosis, by using LIVE/DEAD and Annexin V and Propidium iodide (PI) kits. Antiviral effects were observed by UGC and UGF, statistically significant, compared to untreated cells at concentrations that reduced the rate of viral antigen positive cells, and the amount of the secreted NS1. Significant immunomodulatory effects were shown by the reduction in secretion of MIF, IL-8 and IL-6. An increase in nitrite production in infected and treated cells was observed with the two extracts in different concentrations. In addition, reduced rates of apoptotic and necroptic cells were significant. Conclusion: There are active compounds in plant species that have antiviral and immunomodulatory capabilities. Therefore, were potential candidates for the development of a product for treatment of dengue. Supported by FIOCRUZ/RPT11D; IOC/PROEP; CNPq; FAPERJ; CAPES
A Flexible Height–Diameter Model for Tree Height Imputation on Forest Inventory Sample Plots Using Repeated Measures from the Past

In this study, height–diameter relations were modeled using two different mixed model types for imputation of missing heights from longitudinal data. Model Type A had a hierarchical structure of sample plot-specific and measurement occasion-specific random effects. In Model Type B, a possible temporal variance was modeled by a sample plot-specific linear time trend. Furthermore, various calibration strategies of random effects were performed on past and current data, and a combination of both. The performance of the mixed models was compared on independent data using bias and root mean square error (RMSE). The results showed that Model Type A achieved the highest precision (lowest RMSE), if sample plot-specific random effects were predicted from old data and measurement occasion-specific ones were predicted from new data. In comparison, however, Model Type B had a higher RMSE, and lower bias. Model performance was almost unaffected from the usage of past or current data for the prediction of random effects. Results revealed that a certain calibration strategy should be simultaneously applied to all random effects from the same hierarchy level. Otherwise, predictions would become imprecise and a serious bias may result. In comparison with traditional uniform height curves, the novel mixed model approach performed slightly better.
Agronomic and physiological response of giant reed (Arundo donax L.) to soil salinity

The soil salinity increase in the Mediterranean basin is one of the consequences of the climate change. The aim of this study was to evaluate the adaptability of giant reed (Arundo donax L.) to salinity, in conditions of higher temperatures, in order to hypothesise the future use of giant reed under these conditions. The trial was carried out in pots under a permanent metal structure, open on the sides and with a clear PE on the top. Four levels of soil salinity in the range 3.3-15.5 dS m–1 were imposed. The stem number of the most stressed treatment was about 45% lower than the control and also the stem height was lower than in all other treatments. The green and yellow leaf number decreased as the soil salinity increased, and their sum was significantly lower in the two most stressed treatments. Osmotic potential of the leaf sap was not affected by salinity. Leaf water potential and stomatal conductance in the saline treatments were lower than in the control. Assimilation rate showed similar pattern of stomatal conductance. Intrinsic WUE remained almost stable until July and increased during August under the most stressful conditions. PSII photochemistry was not affected by soil salinity. Biomass yield was not different from the control until to soil ECe 12.0 dS m–1: only the most stressed treatment (15.5 dS m–1) caused yield losses (50%). Tolerance threshold to salinity was 11.2 dS m–1 and the relative yield losses were 11.6% per dS m–1.
Regulation of 2-5A Dependent RNase at the Level of its Phosphorylation

Abstract : The 2-5A system is an interferon-regulated, antiviral pathway which results in the degradation of viral RNA and may also be involved in cell growth control. Interferon treatment of cells induces 2-5A synthetases which, upon activation by double stranded RNA, produce 2',5'-linked oligoadenylates (2-5A). The only well-characterized, biochemical effect of 2-5A is its activation of 2-5A dependent RNase, an interferon-inducible 80 kDa protein that cleaves single stranded RNA. Here I describe a novel level of regulation in the 2-5A pathway. Since 2-5A dependent RNase has been implicated in growth control, my objective was to determine, how activators of protein kinase C, which in several cell lines stimulate growth or inhibit differentiation would lead to qualitative as well as quantitative changes in the pattern of 2-5A dependent RNase. Murine JLS-V9R cells were treated with interferon in the presence or absence of activators or an inhibitor of protein kinase C or a phosphatase inhibitor.
Diatom performance in a future ocean: interactions between nitrogen limitation, temperature, and CO2-induced seawater acidification

nitrogen limitation, temperature, and CO2-induced seawater acidification Futian Li, John Beardall, and Kunshan Gao* State Key Laboratory of Marine Environmental Science/Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiang’an South Road, Xiamen 361102, China School of Biological Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia *Corresponding author: tel: þ86 592 2187982; fax: þ86 592 2187963; e-mail: ksgao@xmu.edu. cn
Energetic substrate availability regulates synchronous activity in an excitatory neural network

Neural networks are required to meet significant metabolic demands associated with performing sophisticated computational tasks in the brain. The necessity for efficient transmission of information imposes stringent constraints on the metabolic pathways that can be used for energy generation at the synapse, and thus low availability of energetic substrates can reduce the efficacy of synaptic function. Here we study the effects of energetic substrate availability on global neural network behavior and find that glucose alone can sustain excitatory neurotransmission required to generate high-frequency synchronous bursting that emerges in culture. In contrast, obligatory oxidative energetic substrates such as lactate and pyruvate are unable to substitute for glucose, indicating that processes involving glucose metabolism form the primary energy-generating pathways supporting coordinated network activity. Our experimental results are discussed in the context of the role that metabolism plays in supporting the performance of individual synapses, including the relative contributions from postsynaptic responses, astrocytes, and presynaptic vesicle cycling. We propose a simple computational model for our excitatory cultures that accurately captures the inability of metabolically compromised synapses to sustain synchronous bursting when extracellular glucose is depleted.
Oligosaccharides successfully thwart hijacking of the salicylic acid pathway by Phytophthora infestans in potato leaves

Potato growing is severely threatened by the late blight agent Phytophthora infestans, which is usually controlled by massive amounts of fungicides. While variety resistance is often bypassed by the pathogen, the plant innate immunity opens the way to new biological plant protection tools, e.g. the COS-OGA elicitor. This oligosaccharide composition mimics the interaction between plants and fungal pathogens as it combines chitosan oligomers (COS) with pectinderived oligogalacturonides (OGA). Two different COS-OGA elicitors were evaluated against potato late blight: FytoSave, mainly efficient against powdery mildews, and FytoSol, a new composition still under development. In addition, a comparative study of plant defence induction was performed, focusing on the effect of repeated sprayings as well as on the stimulation of salicylic acid (SA), jasmonic acid and ethylene-related pathways during the biotrophic and necrotrophic growth stages of the pathogen. The FytoSave elicitor strongly increased the SA content but failed to induce sufficient protection against late blight, while FytoSol maintained or even decreased the free SA content in the presence of P. infestans and was completely efficient. Surprisingly, the necrotrophic development of P. infestans occurred along with a strong leaf accumulation of free SA and SA-related transcripts. This may represent an attempt by P. infestans to divert plant defences for its own benefit. Preventive sprayings with FytoSol but not FytoSave completely impeded this hijacking. FytoSol seemed to keep the SA pathway under control, thereby preventing its diversion by P. infestans.
Functional Analysis of Methylomonas sp. DH-1 Genome as a Promising Biocatalyst for Bioconversion of Methane to Valuable Chemicals

Methylomonas sp. DH-1, newly isolated from the activated sludge of a brewery plant, has been used as a promising biocatalytic platform for the conversion of methane to value-added chemicals. Methylomonas sp. DH-1 can efficiently convert methane and propane into methanol and acetone with a specific productivity of 4.31 and 0.14 mmol/g cell/h, the highest values ever reported, respectively. Here, we present the complete genome sequence of Methylomonas sp. DH-1 which consists of a 4.86 Mb chromosome and a 278 kb plasmid. The existence of a set of genes related to one-carbon metabolism and various secondary metabolite biosynthetic pathways including carotenoid pathways were identified. Interestingly, Methylomonas sp. DH-1 possesses not only the genes of the ribulose monophosphate cycle for type I methanotrophs but also the genes of the serine cycle for type II. Methylomonas sp. DH-1 accumulated 80 mM succinate from methane under aerobic conditions, because DH-1 has 2-oxoglutarate dehydrogenase activity and the ability to operate the full TCA cycle. Availability of the complete genome sequence of Methylomonas sp. DH-1 enables further investigations on the metabolic engineering of this strain for the production of value-added chemicals from methane.
Insights into β-glucan biology in mutualistic plant-microbe interactions

Plants are constantly surrounded by pathogenic and mutualistic microbes, for example fungi. To defend against fungal invaders plants rely on the innate immunity of each cell which is activated in response to the perception of microbe-associated molecular patterns, so called MAMPs, by specific plant surface receptors. Fungal cell wall derived polysaccharides like branched β-1,3/1,6-glucans are perceived as MAMPs and identify a fungal cell as non-self. The fungal cell wall is a highly dynamic organelle that is constantly reshaped to tailor its structure and composition to circumvent the activation of the plant defense while ensuring cell wall integrity especially during plant colonization. This study aimed to characterize proteins of the mutualistic root endophyte Serendipita indica and its experimental host plant A. thaliana that are engaged in β-glucan biology. The WSC-domain containing lectin WSC3, a member of a multigene family in S. indica is transcriptionally induced during plant colonization and in contact with a second fungus. The fusion protein WSC3-GFP localizes to the cell wall of S. indica, reduces the exposure of β-1,3-glucan and increases cell wall stress resistance in the yeast Pichia pastoris. Isothermal titration calorimetry revealed that WSC3-His binds the MAMP laminarin, a branched β-1,3/1,6-glucan and is able to agglutinate various fungal cells. Furthermore WSC3-His efficiently competes with the unknown plant receptor and thus prevents the induction of the production of reactive oxygen species (ROS) by laminarin but does not increase colonization of barley roots by S. indica. Additionally the secreted β-1,6-glucan specific lectin FGB1 of S. indica was shown to universally suppress ROS production in barley in response to the MAMPs laminarin, chitin and flg22. The investigation of the laminarin-induced ROS production in A. thaliana revealed great natural variation among 100 tested accession. A genome wide association screen identified several genetic loci that are potentially involved in laminarin-triggered defense responses in A. thaliana. Collectively these results suggest that WSC3 might act as a structural component of the fungal cell wall to maintain cell wall integrity while FGB1 is acting as universal suppressor of MAMP-triggered ROS production. Both proteins underline the pivotal role of the fungal cell wall in general and especially of β-glucans during plant-microbe interactions. The responsiveness of A. thaliana to laminarin is subject of great natural variation and potentially represents a multigenetic trait.
Ethane-dependent synthesis of polyhydroxyalkanoates by the obligate methanotroph Methylocystis parvus OBBP

Under conditions of nutrient-limited growth, Type II obligate methanotrophs oxidize C1 compounds, such as methane or methanol and accumulate intracellular granules of poly(3-hydroxybutyrate) (P3HB). Here, we report that, under same nutrient-limited conditions, the Type II obligate methanotroph Methylocystis parvus OBBP can use ethane as its sole carbon and energy source for synthesis P3HB granules, accumulating up to 35 ± 4 wt% P3HB. 13C-NMR spectra of the P3HB confirmed incorporation of 13C from [13C2]ethane. Moreover, when valerate was added as a co-substrate with ethane, oxidation of the ethane supported synthesis of the copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). IMPORTANCE The presence of ethane in natural gas is often considered undesirable for methanotroph-based biotechnology due to the C1 specialization of obligate methanotrophs and concerns about inhibitory byproducts arising from methane monooxygenase-mediated cometabolism of ethane. This work establishes that co-oxidation of ethane and further metabolism in the absence of methane can support synthesis of the valuable polyhydroxyalkanoate bioplastics P3HB and PHBV.
Heterogeneity in attitudes underlying preferences for genomic technology producing hybrid poplars on public land

We investigate the public preference heterogeneity of planting genetically improved poplar trees for biofuel production on public land in western Canada. Using a sample of the public from British Columbia, Alberta, Saskatchewan, and Manitoba, respondents were asked to vote in a series of hypothetical referenda comparing the new, proposed forest policies with the current policy (base scenario). Proposed policies varied based on poplar breeding method (traditional, genomics, or genetic modification) and whether poplars may be used for biofuel production. A respondents’ segmentation framework with cluster analysis and probit model was applied to data of respondents to uncover the heterogeneity of public’s perception. The results of this study reveal that positive and negative perceptions about planting genetically improved poplar trees in the region create a division of respondents into Environmentalists, Knowledgeable, Challengers, and Supporters. Respondents from British Columbia and Manitoba are identified as Environmentalists and Challengers, respectively, of the new policy of planting genetically improved poplar trees on public land. Conversely, respondents from Saskatchewan and Alberta are identified as Supporters and Knowledgeable, respectively, of the new policy.