Miracle-dz/UniFAR-FTUs huggingface dataset:
Splicing-dependent NMD requires Prp17 in Saccharomyces cerevisiae

Nonsense mediated mRNA decay (NMD) denotes that nonsense mutations, or errors in gene expression which introduce a premature translation termination codon (PTC), can lead to a reduction of mRNA level in any organism. Remarkably, whether a PTC will lead to NMD often depends on the presence of a downstream intron, splicing of which marks a spliced mRNA by deposition of the exon junction complex (EJC) in mammalian cells so as to affect its translation and degradation in the cytoplasm. Saccharomyces cerevisiae, which has introns only in 5% of its genes and lacks proteins essential for the EJC assembly, was not expected to undergo splicing-dependent NMD. Conversely, here we report that the presence of an intron can also enhance NMD in this organism. Following screening for genes that might be specifically involved in splicing-dependent NMD, we identified splicing factor Prp17 and surprisingly found that a portion of it co-sediments with ribosomal fractions. Together, our results indicate that whilst splicing-dependent NMD is a universal feature of eukaryotes this appears to be distinct from cytoplasmic NMD and depends on interactions between the spliceosome and ribosome that are unconnected to an EJC-like marking mechanism. Topic: Prp17, splicing, EJC, NMD, translation, S. cerevisiae, yeast, RNA
The ERK MAPK pathway modulates Gq-dependent locomotion in Caenorhabditis elegans

The heterotrimeric G protein Gq regulates neuronal activity through distinct downstream effector pathways. In addition to the canonical Gq effector phospholipase Cβ, the small GTPase Rho was recently identified as a conserved effector of Gq. To identify additional molecules important for Gq signaling in neurons, we performed a forward genetic screen in the nematode Caenorhabditis elegans for suppressors of the hyperactivity and exaggerated waveform of an activated Gq mutant. We isolated two mutations affecting the MAP kinase scaffold protein KSR-1 and found that KSR-1 modulates locomotion downstream of or in parallel to the Gq-Rho pathway. Through epistasis experiments, we found that the core ERK MAPK cascade is required for Gq-Rho regulation of locomotion, but that the canonical ERK activator LET-60/Ras may not be required. Through neuron-specific rescue experiments, we found that the ERK pathway functions in acetylcholine neurons to control Gq-dependent locomotion. Additionally, expression of activated LIN-45/Raf in acetylcholine neurons is sufficient to cause an exaggerated waveform phenotype and hypersensitivity to the acetylcholinesterase inhibitor aldicarb, similar to an activated Gq mutant. Taken together, our results suggest that the ERK MAPK pathway modulates the output of Gq-Rho signaling to control locomotion behavior in C. elegans.
EFFECT OF SUB-LETHAL DOSES OF SYNTHETIC AND NATURAL ACARICIDES ON HONEY BEE (Apis mellifera L.) HEALTH, MEMORY, BEHAVIOUR AND ASSOCIATED GENE EXPRESSION

EFFECT OF SUB-LETHAL DOSES OF SYNTHETIC AND NATURAL ACARICIDES ON HONEY BEE HEALTH, MEMORY, BEHAVIOUR AND ASSOCIATED GENE EXPRESSION Hanan A. Gashout Advisors: University of Guelph, 2016 Professor Ernesto Guzman Professor Paul H. Goodwin Acaricides are applied in honey bee (Apis mellifera L.) colonies to control parasitic mites, including Varroa destructor. However, acaricides may cause adverse effects to honey bees. In three studies here reported, bees were exposed to lethal and sublethal doses of five of the most commonly used hive acaricides, and their impact on honey bee health, memory and behaviour, as well as on the immune and neural systems of bees was evaluated. Calculated LD50s showed that tau-fluvalinate is the most toxic among the tested acaricides (0.45 μg/bee), followed by amitraz (1.99 μg/bee), coumaphos (6.23 μg/bee), thymol (51.25 μg/bee) and formic acid (152.45 μg/bee). In term of hazard ratios (estimates of hive level risk), tau-fluvalinate was the most hazardous acaricide (3.6), followed by formic acid (0.9), and then amitraz, coumaphos and thymol, with the same hazard ratio (0.5). The expression of health and detoxification genes was analyzed and it was found that vitellogenin was not affected by any of the acaricides and that formic acid was the only acaricide that down-regulated cytochrome P450, suggesting that detoxification mechanisms of the exposed bees were in part compromised. Conversely, all acaricides except tau-fluvalinate increased the expression of the gene encoding acetylcholinesterase. The effect of sublethal doses (LD05) of acaricides on memory was evaluated. Formic acid significantly affected the bees’ short, mid and long-term memory, while the rest of the acaricides affected memory only in the long term. Memory related genes were analyzed and it was found that neurexin, neuroligin-1 and major royal jelly protein-1 were not affected by any of the acaricides at sublethal doses. However, thymol, formic acid, amitraz and coumaphos increased defensin-1 expression, suggesting induction of immune responses, which also could have detrimental effects in bees’ brains. The hygienic behaviour of bees was inhibited only when exposed to sublethal doses of coumaphos but not to the other acaricides, whereas taufluvalinate, coumaphos and formic acid reduced their foraging behaviour. Overall, it can be concluded that sub-lethal exposure to acaricides affects the health, memory and behaviour of honey bees differently, and that amitraz and thymol, appear to be the safest acaricides to bees among the five tested.
Stochastic Methods for Inferring States of Cell Migration

Cell migration refers to the ability of cells to translocate across a substrate or through a matrix. To achieve net movement requires spatiotemporal regulation of the actin cytoskeleton. Computational approaches are neceary to identify and quantify the regulatory mechanisms that generate directed cell movement. To address this need, we developed computational tools, based on stochastic modeling, to analyze time series data for the position of randomly migrating cells. Our approach allows parameters that characterize cell movement to be efficiently estimated from time series data. We applied our methods to analyze the random migration of Mouse Embryonic Fibroblasts (MEFS). Our analysis revealed that these cells exist in two distinct states of migration characterized by differences in cell speed and persistence. Further analysis revealed that the Rho-family GTPase RhoG plays a role in establishing these two states. An important feature of our computational approach is that it provides a method for predicting the current migration state of an individual cell from time series data. Using this feature, we demonstrate that HeLa cells also exhibit two states of migration, and that these states correlate with differences in the spatial distribution of active Rac1.
Strain and Sex Differences in the Hepatotoxicity of 4-Aminobiphenyl in the Mouse

Recent studies from our laboratory on the aromatic amine carcinogen, 4-aminobiphenyl (ABP) have shown a significantly lower prevalence of ABP-induced liver tumors in male mice lacking the N-acetyltransferases, and a dramatically lower prevalence in females than in males, but no association of tumor prevalence with strain or sex differences in levels of acute ABP-induced DNA damage. This thesis aimed to investigate the possible involvement of acute cytotoxic effects of ABP in the development of a tumor-promoting inflammatory environment. We found that wild-type male mice showed higher acute hepatotoxicity to ABP, as well as, a possible trend towards higher serum levels of the pro-inflammatory cytokine interleukin 6. This correspondence between acute ABP cytotoxicity and inflammatory response with ultimate tumor growth is consistent with a model whereby ABP not only initiates cells by damaging DNA but also promotes tumor growth in a gender-selective fashion that may be governed by gonadal hormone
Anti-hyphal properties of potential bioactive compounds for oral rinse in suppression of Candida growth

ABSTRACT Most oral rinses contain active ingredients with limited antifungal activity, particularly against hyphae development. This has encouraged us to search for bioactive compounds effective against preventing morphology transition of the dimorphic Candida. The antifungal activity of the selected bioactive compounds against seven species of oral-associated Candida was screened before the evaluation of their potency to inhibit hyphal formation. The identified potent inhibitor was then further investigated on its effectiveness through a brief treatment test on germination, adhesion, cellular morphology and gene expression. Bakuchiol, hydroxychavciol and pseudolaric acid B showed antifungal activity while luteolin and sakuranetin were determined to be inactive against the oral-associated Candida species at a concentration below 1 mg/mL. Hydroxychavicol was determined as a potent inhibitor against hyphal growth of Candida albicans. Hydroxychavicol delayed the germination process of C. albicans by affecting the expression of RAS1, NRG1 and HWP1 genes up to 1 h after the treatment. In addition, the treatment caused minimal changes to the cellular morphological structure. But, hydroxychavicol showed poor anti-adherence activity against the germinated cells. In summary, hydroxychavicol is one of the identified bioactive compounds that possessed anti-candida properties against oral-associated Candida species and appeared potent in inhibition of hyphae of C. albicans by affecting its ultrastructural morphology and gene regulation. This finding could suggest development of hydroxychavicol as a bioactive compound that can potentiate the activity of oral rinse in preventing the colonization of dimorphic Candida in the oral cavity.
PARASITIC DISEASES OF FRESHWATER ORNAMENTAL FISHES COMMERCIALIZED IN FLORIANÓPOLIS, SANTA CATARINA, BRAZIL

The parasitic fauna of ornamental fish from Florianopolis, SC, Brazil was evaluated from June 2004 through June 2005. Xiphophorus maculatus (n=88), Xiphophorus helleri (n=27), Poecilia sphenops (n=20), Macropodus opercularis (n=20), Trichogaster tricopterus (n=9), Beta splendens (n=8), Puntius conchonius (n=7), Carassius auratus (n=6), Gymnocorymbus ternetzi (n=4) were analyzed. From a total of 189 examined fishes, 65 (34%) were parasitized: 15.3% with metacercariae of Ascocotyle (Digenea); 15.3% with Monogenoidea; 6.9% with Piscinoodinium pillulare (Dinoflagellida); 4.7% with Trichodina acuta (Ciliophora); 3.7% with Ichthyophthirius multifiliis (Ciliophora); 2.6% with cestodes; 2.6% with Camallanus maculatus (Nematoda); 2.1% with Lernaea cyprinacea (Crustacea) and 0.5% with Chilodonella sp. (Ciliophora). The largest mean intensities of infection were 335 and 205, respectively to X. maculatus and X. helleri infected by metacercariae in the gills.
Developing methodologies for exploring myosin-5 elasticity under strain

Motor proteins drive the movement of organelles and other types of cargo inside every eukaryotic cell type. These motors include myosins, kinesins and dyneins. Myosin-5a, a ubiquitous motor protein, has been intensively studied and its enzymatic properties and cellular functions have been described in great detail. This dimeric molecule walks processively along actin filaments, enabling it to transport a variety of cargos including mRNA, pigment granules, organelles such as the endoplasmic reticulum and endocytic vesicles. Cargos bind to the C-terminal globular tail domain of the molecule, while the N-terminal motor domain hydrolyses ATP to take regular steps on the actin filament. The structure and enzymatic properties of myosin-5 moving processively along actin under unloaded conditions have already been well characterised. However, while pulling a cargo through the viscoelastic cytoplasm, the molecule will experience variable forces. Therefore it is important to study how these forces alter the structure and kinetic behaviour of myosin-5. The purpose of this study was to design myosin-5 constructs that could be tethered, in a controlled manner, to actin via sequences introduced into the tail region of the molecule. The tethered motor protein is expected to ’stall’ while moving along the actin filament. In this way, the effects of strain on the myosin-5 structure and kinetics could then be investigated. This would simulate a case where inside the cell myosin-5 stalls due to strain, for example, whilst trying to move its cargo through spatially restricted areas of the actin cytoskeleton. To find a new way to attach the tail of myosin-5 to actin, small, artificial actin-binding proteins named Adhirons were raised with phage display assay and their properties were explored. They bind to actin with high affinity and they are also useful for staining actin in cells or for attaching actin to coverslips in various motility assays. Multiple myosin-5 constructs were explored, that had either an Avi-tag or an actin-binding Adhiron at their C-terminal ends. A construct that contained the full predicted coiled-coil motif of myosin-5, could not be attached to the same actin filament via its tail as the motors were bound to. Two further constructs that have an artificial long coiled-coil tail, were cloned and expression trials are currently in progress.
Epstein-Barr virus infection of mammary epithelial cells and risk of associated malignancy

The human tumor virus, Epstein-Barr virus (EBV), is a γ-herpesvirus associated with human epithelial and B-cell malignancies. The association of EBV infection with breast cancer has been reported in many recent studies (1). EBV can be divided into two major types, EBV type 1 and EBV type 2. Type 1 is dominant throughout most of the world, but the two types are equally prevalent in Africa (2). The EBV infection pattern is classified as either lytic, or latent 0, I, II and III (3). LMP1 is the well-documented oncoprotein of the EBV latent gene products (4). EBV strongly constitutes a risk factor for malignant transformation because it can infect mammary epithelial cells “MECs” and its DNA fragments can induce immortalization in these cells (5,6). EBV is incriminated as a carcinogenic agent by the World Health Organization (7) so; a childhood immunization against EBV might have a great impact on public health. This editorial is on a research article by Hu et al. (8) entitled “Epstein-Barr Virus Infection of Mammary Epithelial Cells Promotes Malignant Transformation”. This editorial will focus on the evidence that delayed EBV infection causes latent infection of “MECs” leading to phenotypic changes which is a part of a multistep process of breast carcinogenesis together with other genetic and environmental factors.
Characterizing the Community Dynamics of the Leaf Microbiome

The phyllosphere microbiome of seasonal plants is influenced by biological, environmental and ecological factors. To explore the influence of these factors simultaneously and to determine the forces that drive community composition, we sampled leaf communities from common bean (Phaseolus vulgaris), soybean (Glycine max) and Canola (Brassica napus), planted at three different locations at the Koffler Scientific Reserve, over the course of a growing season. Temporal changes had the most significant affect on the community, regardless of host species or location. Precipitation had the most dramatic effect on the Canola microbiome, while soybean and bean communities followed a more predictable pattern of development throughout the summer and were only minimally affected by rainfall. Leaf communities at the beginning of the season were strongly influenced by soil communities. As time passed, the leaf communities differentiated from the soil, becoming less diverse and containing a greater proportion of leafadapted and leaf-specific taxa.
OV-MZ-6 ovarian cancer cells overexpressing kallikrein-related peptidases KLK4, 5, 6 and 7: effects on expression of cancer-related genes

In this study, the effects of kallikrein-related peptidases KLK4-7 overexpression on gene regulation in OV-MZ-6 ovarian cancer cells were investigated. KLK4-7 overexpression led to significant upregulation of moesin and keratin 19 and downregulation of keratin 7 and jun-B on both mRNA and protein level in OV-MZ-6 cells. Furthermore, KLK5 exerted the strongest impact on gene regulation in OV-KLK4-7 cells. These findings may lead to clinical use of some KLKs and their inhibitors for the diagnosis and treatment of ovarian cancer patients.
Comparative analyses of layer males, dual purpose males and mixed sex broilers kept for fattening purposes regarding their floor space covering, weight-gain and several animal health traits

As a major part of world poultry production is specialised in meat or egg production, millions of day-old male layer chicks are culled in Europe each year. Within the present study, about 500 birds each of three genetic lines, Lohmann Brown (LB), Lohmann Dual (LD) and Ross 308 were fattened separately in a poultry floor management system over an eleven-week period. At regular intervals 55 birds per line were weighed and the floor space covered by their bodies was calculated using planimetric measurements. Furthermore, several animal health traits were assessed within the final two weeks of fattening. The mean floor area occupied by one-week old Ross 308 broilers was approximately 1.5‑fold higher compared to those of LB and LD at the same age and extended up to more than twice the space with increasing age. The highest mean body weight was measured for Ross 308, followed by LD and LB. While uniformity of the LB flock was high at any time body weights of LD and Ross 308 encompassed a wide range, resulting in a low uniformity within these groups. None of the examined LB and LD chickens showed keel bone deformities, breast plumage pollution or foot pad dermatitis. In contrast, all of the Ross 308 broilers had moderate to severe pollution of breast plumage and up to 27% showed lesions on at least one foot pad at the end of the fattening period. About 91% of the LD and 56% of the LB chickens showed lesions at the comb and/or wattle at the end of the fattening period, indicating aggressive male-male interactions within these groups. The mean eviscerated carcass weight was almost four times higher for Ross 308 (4.11 kg) than for LB (1.05 kg) and LD (1.03 kg).
E-nose for basal stem rot detection

INTRODUCTION An electronic nose is an intelligent device, able to mimic human olfaction functions and may be used for detection, recognition and classification of volatile compounds and odours. An e-nose consists of an array of sensors, signal collecting unit(s) and suitable pattern recognition algorithm. The possible implementations of these devices are wide ranging, from agricultural applications to solving environmental issues. In terms of agricultural applications, e-nose systems have been used successfully to assist product quality monitoring, fruit ripeness determination as well as inspection of fish. The e-nose has also been used to detect the causal agent or element of plant disease such as fungi and bacteria. Fungi produce mycotoxins on agricultural commodities during plant growth or after harvest during storage and shipment, which could be detrimental to living organisms when ingested. Also, the growth of the moulds in grains reduces their nutritional quality and subsequent decrease in germination results in economic loss. The disease is a threat to the oil palm industry causing an estimated annual lost of RM80 million. Hence a novel feasibility study to use an e-nose to detect plant disease, specifically the basal stem rot (BSR) disease, is executed, with a commercial e-nose, Cyranose 320 incorporated artificial neural networks.
Seasonal metabolism and carbon export potential of a key coastal habitat: The perennial canopy‐forming macroalga Fucus vesiculosus

The important role of macroalgal canopies in the oceanic carbon (C) cycle is increasingly being recognized, but direct assessments of community productivity remain scarce. We conducted a seasonal study on a sublittoral Baltic Sea canopy of the brown alga Fucus vesiculosus, a prominent species in temperate and Arctic waters. We investigated community production on hourly, daily, and seasonal timescales. Aquatic eddy covariance (AEC) oxygen flux measurements integrated ~ 40 m2 of the seabed surface area and documented considerable oxygen production by the canopy year‐round. High net oxygen production rates of up to 35 ± 9 mmol m−2 h−1 were measured under peak irradiance of ~ 1200 μmol photosynthetically active radiation (PAR) m−2 s−1 in summer. However, high rates > 15 mmol m−2 h−1 were also measured in late winter (March) under low light intensities < 250 μmol PAR m−2 s−1 and water temperatures of ~ 1°C. In some cases, hourly AEC fluxes documented an apparent release of oxygen by the canopy under dark conditions, which may be due to gas storage dynamics within internal air spaces of F. vesiculosus. Daily net ecosystem metabolism (NEM) was positive (net autotrophic) in all but one of the five measurement campaigns (December). A simple regression model predicted a net autotrophic canopy for two‐thirds of the year, and annual canopy NEM amounted to 25 mol O2 m−2 yr−1, approximately six‐fold higher than net phytoplankton production. Canopy C export was ~ 0.3 kg C m−2 yr−1, comparable to canopy standing biomass in summer. Macroalgal canopies thus represent regions of intensified C assimilation and export in coastal waters.
On the importance of time scales when studying adaptive evolution

Long‐term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effects on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like variation in recombination rate along the chromosomes. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio‐temporal variation in great tit bill length, which was related to the recent use of bird feeders. We discuss how this case study illustrates the importance of considering different temporal scales and evolutionary mechanisms both while analyzing trait temporal trends and when searching for and interpreting the signals of putative genomic footprints of selection. More generally this commentary discusses interesting challenges for unraveling the time scale at which adaptive traits evolve and their genomic bases.