Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Germ-line Expression of the Caenorhabditis elegans Gene Fem-1 by Maternal Transcripts

In addition to previously identified roles for RNA, several new ways in which RNA serves as a regulator of gene expression have recently been described. RNA molecules are involved in both transcriptional and post-transcriptional forms of regulation, sometimes heritably affecting gene activity. Whereas most previously characterized regulatory roles of RNA involve downregulation, I describe a role for maternal transcripts of a gene in promoting zygotic activity of that gene, which I term the licensing of genetic activity. This regulation occurs in the germ line, a tissue notable for its abundance of genetic surveillance mechanisms. The maternal-effect regulation described here was identified using alleles of a sex-determining gene in Caenorhabditis elegans called fem-1. Females homozygous for fem-1 deletions produce heterozygous offspring that exhibit germ-line feminization and have reduced fem-1 activity and transcript accumulation. This phenotype can be rescued by injecting fem-1 RNA into the maternal germ line. The reduction in activity of the zygotic fem-1 locus is heritable, suggesting that the gene is becoming epigenetically silenced. Thus the maternal fem-1 RNA licenses the activity of the zygotic locus by preventing its silencing. By restricting germ-line activity to genes that were expressed in the germ line of the previous generation, this process may contribute to protecting the identity and integrity of the germ line. I performed an RNAi screen of candidate genes to ask whether they are required for maternal-effect silencing or licensing. Several enhancers and suppressors of germ-line feminization in the descendants of fem-1 deficiency homozygotes were identified. Chromatin regulation may be involved, and small-RNA pathways are important for both the silencing and licensing components of fem-1 regulation. Based on my characterization of this phenomenon, I proposed models of how maternal-effect regulation of fem-1 may be mediated. To test predictions of certain models, I examined whether specific characteristics of fem-1 make it susceptible to this silencing. Results of these experiments limit the possible models of maternal-effect regulation and suggest directions for future investigation. %%%%PhD
Systematics, Biogeography, and Species Delimitation of the Malagasy Psorospermum (Hypericaceae)

2 Table of contents. 3 Acknowledgements . 4 Chapter 1: Systematics and Biogeography of the African-Malagasy Psorospermum (Hypericaceae) with emphasis on the Malagasy species. 5 Chapter 2: Integrative taxonomy: investigating the species boundaries in Malagasy Psorospermum using morphometrics and molecular phylogenetic methods. 49 Chapter 3: Towards the taxonomic revision of the Malagasy Psorospermum: what can we retrieve from ancient literature? 164
Detection of enterotoxins and genotyping of Staphylococcus aureus strains isolated from Isfahan Educational Hospital, Iran

Background and aims: Staphylococcus aureus is known as one of the most important nosocomial pathogens, which may lead to several infections. The aim of this study was determining the enterotoxins A, C, and TSST-1 and molecular characterization of S. aureus strains with PFGE and MLST typing methods. Materials and methods: In the present study during the sixmonths sampling, fifty S. aureus strains were isolated from patients admitted to Al-Zahra university hospital. Antimicrobial susceptibility testing, Multiplex PCR for detection of enterotoxin A, C and TSST-1, pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for molecular typing. Results : In antibiogram the highest and lowest percentage of resistance was belonged to tetracycline and rifampin respectively. Multiplex PCR indicated that 30% of the strains harbored sea and 34% harbored sec genes. However, only 4% of our collected isolates had tsst gene. In PFGE method analysis on all S. aureus strains, a total of 19 different patterns were identified. Nine various sequence types in 27 selected S. aureus isolates were identified by MLST. Conclusions : Present study indicates a possible higher variability among our S. aureus strains by two different molecular typing methods; nevertheless four main common types (CT1, CT7, CT9, and CT11) with at least one toxin genes were determined.
Diet of small mammals from the Karoo. South Africa

The feeding habits of seven rodent, and an elephant shrew species from the semi-arid Karoo, South Africa were determined by microscopic examination of stomach contents. The elephant shrew Macroscelides proboscideus was found to consume significant amounts of vegetation, making it a functional herbivore/ insectivore. Two of the rodents (Otomys unisulcatus and Parotomys brantsii) formed a herbivorous guild, while the remainder (Gerbillurus paeba, Mus minutoides, Rhabdomys pumilio, Desmodillus auricularis and Saccostomus campestris) were omnivorous. The paucity of granivorous small mammals in the Karoo contrasts the patterns of trophic specialization for North American and Israeli semi-arid communities, but is similar to that of South American and Australian semi-arid communities.
Species composition, diversity, and stand structure of tropical lower montane forests resulting from various human impacts on the Shan Plateau, eastern Myanmar

We observed species composition, diversity, and stand structure in the tropical lower montane forests of a hilly region in eastern Myanmar and examined the impacts of anthropogenic disturbances on the forest stands. From our survey of 58 sample plots (30 m × 30 m), we categorized four stand types using nonmetric multi-dimensional scaling (NMS) ordination. The four stand types exhibited signiﬁcant contributions of various anthropogenic impacts, reﬂecting differences in local livelihoods within different varying landscapes. Anthropogenic disturbances, especially the extraction of ﬁrewood, can signiﬁcantly affect the stand structure of forests and, in turn, the species composition and tree diversity. Some early successional species such as Phyllanthus albizzioides and Albizia odoratissima became indicator species of highly disturbed forests. As ﬁrewood is mainly extracted from privately owned forests rather than communal forests, land tenure was also an important factor governing the intensity of anthropogenic disturbances. Species richness and diversity values decreased in stand types exposed to more severe anthropogenic disturbances. Stem density was signiﬁcantly higher in highly disturbed forests. This was a result of higher numbers of multi-stemmed individuals, which revealed the effect of cutting larger stems for ﬁrewood extraction. In old secondary forests, the lack of young trees under the canopy may threaten future forest regeneration. Depending on varying forest conditions and the local population ʼ s input, different forest management activities should be applied to forests to optimize production and protection for the local community.
Effect of Whole Quail (Coturnix japonica) Egg Consumption on some Reproductive Parameters and Lipid Profile of Male Albino Rat (Rattus norvegicus)

The present study evaluated the effect of whole egg consumption on the liver, testes, cauda epididymal sperm reserve and lipid profile of male rats. These evaluations were carried out on adult twenty (20) male albino rats, which were randomly selected into four groups of 5 rats each, designated groups A, B, C and D. Group A was the control group and received only equivalent volume of distilled water, while groups B, C and D received 0.25mg/kg, 0.5mg/kg; and 1.0mg/kg body weight of the quail egg respectively. Standard procedures were carried out in the tissue processing, cauda epididymal sperm reserve and in lipid profile determinations. On days 35 and 49, the mean serum total cholesterol value of group D was significantly lower than that of the control group. On day 35, the mean serum low density lipoprotein and high density lipoprotein (LDL and HDL cholesterol) values of all the treatment groups were significantly lower and higher than that of the control group, respectively. However, on days 49 and 63, the mean serum very low density lipoprotein (VLDL cholesterol) and triglyceride values of all the treatment groups were significantly higher than that of the control group. A significant increase in cadual epididymal sperm count (CESR) was recorded on day 63 at the mid and high doses. No obvious pathological lesions were observed in the histomorphology of the testes and liver when compared to the control. Therefore, whole quail egg consumption caused an increase in serum triglyceride and very low density lipoprotein concentration, and also improved fertility. In other words, prolonged consumption of quail egg should be done with caution as it may predispose one to cardiovascular disease.
Regulation of mitochondrial dynamics by Aurora A kinase

Aurora A kinase (AURKA) is a major regulator of mitosis and an important driver of cancer progression. The roles of AURKA outside of mitosis, and how these might contribute to cancer progression, are not well understood. Here we show that a fraction of cytoplasmic AURKA is associated with mitochondria, co-fractionating in cell extracts and interacting with mitochondrial proteins by reciprocal co-immunoprecipitation. We have also found that the dynamics of the mitochondrial network are sensitive to AURKA inhibition, depletion or overexpression. This can account for the different mitochondrial morphologies observed in RPE1 and U2OS cell lines, which show very different levels of expression of AURKA. We identify the mitochondrial fraction of AURKA as influencing mitochondrial morphology, since an N-terminally truncated version of the kinase that does not localize to mitochondria does not affect the mitochondrial network. We identify a cryptic mitochondrial targeting sequence in the AURKA N-terminus and discuss how alternative conformations of the protein may influence its cytoplasmic fate.
The asexual morph of Trichomerium gloeosporum

Trichomerium species are sooty molds that develop superficially on the host surface. There is little morphological and molecular data for the genus. The asexual morphs of Trichomerium have been poorly studied, with also lack molecular data. Several researchers have noted that Tripospermum is possibly the asexual morph of Trichomerium species. In this study, we collected Trichomerium-like taxa from leaves in northern Thailand. The sexual structures found on the specimen were identified as Trichomerium gloeosporum, and Tripospermum-like conidia were also associated with the sexual morph. Cultures were obtained from single Tripospermum-like conidia and sequenced. Phylogenetic analyses generated from maximum likelihood and Bayesian analyses of combined LSU and ITS sequence data demonstrate that our strains isolated from Tripospermumlike conidia clustered with strains of T. gloeosporum with high statistical support. A description of the asexual morph of T. gloeosporum with molecular data is provided.
Defences against brood parasitism in the common blackbird (Turdus merula): Plasticity, physiology and evolution

137 Introduction . 138 Recognition of parasitic eggs . 140 Ejection of parasitic eggs . 141 Ejection and risk of parasitism . 141 Aggression . 142 Ethical Note . 142 Methods . 142 Study site and species . 142 Experimental procedure and data collection . 142 Variables and statistical procedures . 145 Results . 146 Recognition of parasitic eggs . 146 Egg ejection . 147 Response towards dummies . 147 Discussion . 149 Conclusion . 155 Competing interests . 155 Authors’ contributions . 155 Acknowledgements . 155 References . 155 Chapter 7. Non-incubating blackbird males can recognize and eject experimental parasitic eggs 165 Abstract . 165 . 165 Introduction . 166 Methods . 167 General field procedure . 167 Statistical analysis . 168 Results . 168 Male and female behaviour during incubation . 168 Recognition abilities in each sex . 170 Discussion . 170 References . 173 Chapter 8. Rejection of parasitic eggs: an updated terminology for a complex process 177 Introduction . 177 Historical use of some common terms in egg-rejection studies . 178 Proposed updated terminology . 179 Discussion . 182 Is an updated terminology needed in egg-rejection studies? 182 Host judgment and the recognition-rejection dichotomy . 182 Host decision and the concept of motivation . 183 References . 184 General discussion 189 The complex process of egg rejection . 189 Endocrine consequences of brood parasitisms . 193 Evolutionary origin of egg-rejection . 194 Sex roles in egg rejection . 195
Stereospecific Degradation of Diastereomers by Plant Associated Bacteria Influences the Antifungal Performance of Dodemorph

Morpholine fungcides have certain antibacterial side effect, dodemorph being the most active among them. The diequatorial (cis-) form of dodemorph expressed higher antibacterial activity than the axial-equatorial (trans-) form, and no synergy in their joint action could be revealed in this respect. Moreover, the partition of diastereomers between cells and medium strictly correlated to their toxicity. Considerable differences were detected among degradation rates in various bacteria, and the meso-(RS)-diastereomer was deteriorated more intensively, then the trans-(SS and RR)-forms in Corynebacterium betae, Erwinia uredovora and Pseudomonasfluorescens. As a result, the stereospecific degradation of diastereomers changed their ratio in the medium, thus this metabolic step could influence the antifungal performance of dodemorph based preparations against filamentous fungi. It was demonstrated that due to synergic joint action, the fungistatic effect of morpholine derivatives noticeably increased against Botrytis cinerea by changing the ratio of diastereomers.
Therapeutic Translation in the Wake of the Genome

The 2003 completion of the Human Genome Project (“HGP”) led many scientists to predict a swift revolution in human therapeutics. Despite large advances, however, that revolution has been slow to materialize. Highlighting that the HGP has also led to the unveiling of a large amount of complexity in human biology, we investigate the translation of basic scientific knowledge into therapeutic drug innovation. We focus on knowledge stemming from a leading type of genetic epidemiological science, the Genome-Wide Association Studies, and the ten years that followed the HGP’s completion. For each targeted disease, we construct measures of biological complexity drawing on insights from Network Medicine (Barabási et al., 2011), and relying on implementations of the Human Disease Network (Goh et al., 2007). For less complex diseases, we find a strong and positive association between cumulative knowledge and the number of new therapies that enter the drug development process. This association weakens as complexity increases, becoming statistically insignificant at the extreme. Thus, our results suggest that complexity plays an important moderating role in translation, and portray it as a relevant factor behind the slower-than-expected unfolding of the therapeutical revolution set in motion by the HGP.
Landscape‐scale vegetation homogenization in Central European sub‐montane forests over the past 50 years

1Department of Botany, Faculty of Science, Charles University, Prague 2, Czech Republic 2Center for Theoretical Study, Charles University, Prague 1, Czech Republic 3Department of GIS and Remote Sensing, Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic 4Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague 6, Czech Republic
Shell shape and meat condition in selectively bred Sydney rock oysters, Saccostrea glomerata (Gould, 1850): the influence of grow-out methods.

The Australian edible oyster industry has been severely impacted by disease and declining yields since the 1970s. Selective breeding of Saccostrea glomerata is one measure addressing these problems by producing fast‐growing, disease‐resistant oysters. Farmers report that selected oysters have different growth characteristics than their wild counterparts using conventional grow‐out methods. This study investigated how different grow‐out methods influence commercially valuable oyster characteristics including shell length, shape, surface growth deformities and meat condition. In June 2015, selectively bred S. glomerata spat were deployed in two estuaries (Hawkesbury River and Georges River) in NSW, Australia, using three grow‐out methods (fixed trays, Stanway cylinders and floating baskets). In November 2015, oysters were transferred among grow‐out methods to test for the effects of changing grow‐out methods on oyster growth patterns. Oysters transferred from baskets to cylinders and from trays to cylinders had, on average, deeper and wider shells, a higher meat condition and fewer shell surface deformities than oysters in other grow‐out method combinations. However, these oysters were smaller than oysters not grown in cylinders. While there were some differences in growth patterns between the estuaries, overall it was the grow‐out methods that most influenced oyster characteristics. This was attributed to differences in the amount and magnitude of movement oysters experienced in the grow‐out methods, as recorded by motion sensors. This study demonstrates how grow‐out methods can be managed to achieve desired growth trajectories and therefore improve marketability among selective bred S. glomerata.
Motility of uni-flagellated bacteria: from swimming mechanics to molecular regulation

of “ Motility of uni-flagellated bacteria: from swimming mechanics to molecular regulation ” by Michael Morse, Ph.D., Brown University, May 2016 Swimming bacteria are able to move through their environment using one or more helical flagella, each of which are rotated by a flagellar motor. These rotating helical flagella generate hydrodynamic propulsive forces which offset the drag force acting on the moving cell body. The direction in which the motor rotates the flagellum and the resulting fluid flows determine a cell’s swimming trajectory. Much research on motile bacteria focuses on the multi-flagellated bacterial species E. coli, which is studied as a model system. In this dissertation, I focus on the swimming of uni-flagellated bacteria, primarily using Caulobacter crescentus as a model. Previous studies have reported various bacterial species swimming in circular trajectories near solid surfaces due to increased fluid drag near stationary boundaries. I examine Caulobacter crescentus swimming near an air-water interface and observe trajectories with both clockwise and counterclockwise average curvature. Near a clean air-water interface, cells should only swim with a slight clockwise curvature, as the interface acts as a free surface. I show that the counterclockwise trajectories are a result of high surface viscosity due to adsorption of large molecules at the airwater interface. Small amounts of surfactant added to the bacterial medium reduces surface contamination through competitive adsorption and causes cells to swim in exclusively clockwise trajectories similar to their behavior near a clean air-water interface. Studies on E. coli have shown contradictory results concerning the distribution of time intervals over which flagellar motors rotate in the clockwise and counterclockwise directions. Since Caulobacter crescentus only has one flagellum, the rotation direction of its flagellar motor can be determined at any time by the swimming pattern of a single cell. By observing this distribution of rotation times, I show that the process controlling switching between rotation directions is not a Poisson process. Instead the intervals of time between switching can be described using first passage time theory. Finally, by utilizing a three parallel channel microfluidic device, I am able to determine how changing oxygen levels alter these switching rates. Caulobacter crescentus displays aerotactic behavior by extending the length of clockwise motor rotation when moving up oxygen gradients. These effects have a large impact on the motile behavior of Caulobacter crescentus and other uni-flagellated swimmers, especially near naturally occurring and abundant air-water interfaces.
Identify Important SUMOylation Site of Influenza Virus Protein Using FRET Technology and New Strategy for Fluorescence Protein Expression

Author(s): Jiang, Jin | Advisor(s): Liao, Jiayu | Abstract: Influenza, which is also commonly known as "the flu", is an infectious disease caused by an influenza virus. The symptoms of influenza could be mild to severe, including fever, headache, sore throat, feeling tired, headache, coughing, and muscle pains. The influenza virus infects and kills over 100,000 people in the world every year. Due to the fast pace in which influenza virus mutates, the virus itself would develop resistances to the current FDA approved drugs. The influenza non-structural protein (NS1) is related to the SUMOylation pathway, a post-translational modification involved in various cellular processes. The first part of this thesis is mainly focus on finding out the SUMOylation site of the NS1 influenza protein by using site-directed mutagenesis and Forster Resonance Energy Transfer (FRET) based technology. Since the SUMO protein is conjugated to the lysine residue of the NS1 protein, by mutate each lysine to Alanine and using FRET-based SUMOylation assay to test every mutants of NS1, the Lysine residue K131 was founded to be the SUMOylation site of NS1. This result was further proved by Plaque assay, which showed the mutation of Lysine 131 would affect the viral replication in MDCK cells. Identification of essential SUMOylation site(s) of NS1 can provide supporting evidence to develop new medicine for treating Influenza virus.The second part of this thesis is focus on designing a new strategy for fluorescence protein expression. Nowadays, using E.coli bacteria as the host for protein production is a very common strategy. However, there are several challenges that needs to be overcome by using E.coli protein production, such as the degradation of the target protein, the toxic of protein towards the host, the misfolding and instability of the protein, and the complex purification procedures. By expression the proteins in inclusion bodies (IBs) would help alleviating these problems. This thesis conducted a signal sequence TMAO-reductase (ssTorA) to drive the target protein Ypet-Uba2, into the inclusion bodies and overcame the degradation of the protein. Also, a buffer screening method was designed to purify the protein from inclusion bodies. As a result, trehalose was proved to be a high efficient additive for the Ypet-Uba2 protein purification.
Co-expression of MDM2 and CDK4 in transformed human mesenchymal stem cells induces dedifferentiated liposarcoma potency

Amplification and overexpression of MDM2 and CDK4 are well-known diagnostic criteria of well-differentiated liposarcoma (WDLPS)/dedifferentiated liposarcoma (DDLPS). Although it was reported that depletion of MDM2 or CDK4 decreased proliferation in DDLPS cell lines, it remains unclear whether MDM2 and CDK4 induce WDLPS/DDLPS tumorigenesis. We examined whether MDM2 and/or CDK4 produce WDLPS/DDLPS using transformed human bone marrow stem cells (BMSCs), 2H and 5H, with five oncogenic hits (overexpression of hTERT, TP53 degradation, RB inactivation, c-MYC stabilization, and overexpression of HRASv12). In vitro functional experiments revealed that co-overexpression of MDM2 and CDK4 plays key roles in tumorigenesis by increasing cell growth and migration and inhibiting adipogenic differentiation potency compared to sole expression of MDM2 or CDK4. Using mouse xenograft models, we found that co-overexpression of MDM2 and CDK4 in 5H cells with five additional oncogenic mutations can develop proliferative DDLPS in vivo. Our results suggest that co-overexpression of MDM2 and CDK4 induces DDLPS tumour potency in transformed human BMSCs by accelerating cell growth and migration and blocking adipogenetic potential incooperation with multiple genetic factors.