Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the regulatory roles and cellular functions of mammalian ZSCAN5B and primate-specific paralogs

Particularly in the context of differentiation and development, the importance of three-dimensional chromatin architecture on gene regulation is becoming increasingly clear. The most ancient known mechanism of chromatin organization involves TFIIIC, a transcription factor (TF) that recruits RNA polymerase III (Pol III) for transcription of tRNA and other types of non-coding RNA genes. From yeast to mammals, TFIIIC also binds to scattered “extra-TFIIIC” (ETC) loci, serving to tether those loci together as anchors of chromatin loops. TFIIIC activities are modulated by MAF, MYC, and other TF proteins, many of which are likely unknown. Here we identify the ZSCAN5 TF family including mammalian ZSCAN5B and its primate-specific paralogs as proteins that occupy mammalian Pol III promoters and ETC sites. ZSCAN5B binds with high specificity to a subset of conserved tRNA genes (tDNA) in human and mouse chromatin, and modulates the expression of those and other Pol III genes. Primate-specific ZSCAN5A and ZSCAN5D also bind tDNA, although ZSCAN5D preferentially localizes to MIR SINEand LINE2-associated ETC sites. ZSCAN5A and ZSCAN5B knockdown experiments indicate important and cooperative roles in regulating tRNA and rRNA processing, cell cycle progression and differentiation in a variety of tissues. Together these data indicate that ZSCAN5 protein binding directly regulates levels of Pol III gene transcription, thereby exerting position effects on nearby Pol II genes; ultimately, this activity influences cell cycle progression and differentiation during development and in adult tissues.
Investigation of the Microbial Glyoxalase System

iii ACKNOWLEDGEMENTS.vi DEDICATION.viii TABLE OF CONTENTS.ix LIST OF FIGURES.xv LIST OF TABLES.xxxiii LIST OF ABBREVIATIONS.xxxvii CHAPTER 1: INTRODUCTION 1.1: Methylglyoxal. 1 1.2: Glyoxalase System. 3 1.2.1: Glyoxalase I. 3 1.2.2: Glyoxalase II. 7 1.2. 3: Glyoxalase III. 11 1.3: Intracellular Thiols.11 1.4: Possible Aspects for the Glyoxalase System in Gram-positive Bacteria and Evolution of the Glyoxalase Family.15 1.5: Summary of Experimental Objectives Achieved. 17 CHAPTER 2: INVESTIGATION OF THE METALLOENZYME GLYOXALASE I FROM CLOSTRIDIUM ACETOBUTYLICUM 2.1: Introduction. 19 2.2: Reagents, Materials and Instrumentation. 25
Genetic studies and identification of QTLs for sheath rot disease resistance in rice (Oryza sativa L.)

Rice genotypes BPT5204 and HP14, their direct and reciprocal F1s (DF1&RF1), F2 populations (DF2&RF2) and recombinant inbred lines (RILs) were evaluated to study the genetics of field resistance to sheath rot disease (ShR). Observed frequencies of resistant and susceptible plants in DF2 and RILs showed 27R:37S ratio and 1R:7S ratio indicating involvement of three dominant genes with complementary gene action. Significant differences between two crosses were observed between DF1&RF1, and DF2&RF2 for panicle exertion and sheath rot attributing traits indicating the role of cytoplasm in manifestation of sheath rot resistance. Plants with anthocyanin pigmentation recorded significantly higher mean for panicle exertion and higher level of resistance to sheath rot disease in both F2s and RILs. Single marker analysis indicated association of anthocyanin with sheath rot resistance making purple pigmentation as probable morpholigical marker for it. Composite interval marker analysis revealed qShR-12 located on chromosome-12 and flanked by SSR markers RM7315 and RM28118 accounting 11.78% of cumulative phenotypic variation. This is the first report on genetics, role of cytoplasm, association of anthocyanin pigmentation and SSR markers with sheath rot disease resistance.
Role of Nitric Oxide Synthase in Normal Brain Function and Pathophysiology of Neural Diseases

Nitric oxide synthase has three isoforms; according to their roles and tissues or cells they are involved. Neuronal NOS (nNOS) takes place in neuronal signalling, endothelial NOS (eNOS) takes place in vasodilation and inducible NOS (iNOS) takes place in immune responses. nNOS and eNOS are dominant but all isoforms have various roles in the central nervous system. nNOS and eNOS separately or together works in healthy brain during cognitive processes and in unhealthy brain during the pathology of related diseases. These roles were shown by inhibitor applied or by transgenic animal model studies and also by investigating the diseases at the molecular level. Besides, it is possible to say that iNOS has roles in some neurological pathologies creating immune responses. Three different isoforms mainly serve in different systems so there are lots of researchers from various disciplines working collaterally not knowing the others related works about NOSs. Because of this, a comprehensive chapter will be valuable for neuroscientists working with either healthy or unhealthy brains. The purpose of this chapter is to gather an overview of NOSs duties during the normal processes of the brain like learning and memory formation and abnormal processes such as depression, schizophrenia and brain cancers.
AMPK in the control of hepatic glucagon signalling and protein synthesis

AMP-activated protein kinase (AMPK) is a key regulator of energy homeostasis via effects on multiple downstream targets. Firstly, we discovered the mechanism by which AMPK antagonizes hepatic glucagon signalling, which is elevated in type 2 diabetes and participates in the establishment of hyperglycaemia. We identified cyclic nucleotide phosphodiesterase 4B (PDE4B) as a novel AMPK substrate in liver. AMPK phosphorylates PDE4B at several sites leading to its activation, decreasing cyclic AMP levels and downstream PKA signalling induced by glucagon. Secondly, we clarified how AMPK activation leads to decreased protein synthesis. It is known that AMPK downregulates protein translation by inhibition of mammalian target of rapamycin complex 1 (mTORC1) and activation of elongation factor 2 kinase (eEF2K), a kinase that phosphorylates and inhibits the essential translation factor eEF2. We showed how eEF2K is controlled by cytosolic Ca2+, mTORC1 and AMPK. We identified a new phosphorylation .
Striatal fast-spiking interneurons drive habitual behavior

Habit formation is a behavioral adaptation that automates routine actions. Habitual behavior correlates with broad reconfigurations of dorsolateral striatal (DLS) circuit properties that increase gain and shift pathway timing. The mechanism(s) for these circuit adaptations are unknown and could be responsible for habitual behavior. Here we find that a single class of interneuron, fast-spiking interneurons (FSIs), modulates all of these habit-predictive properties. Consistent with a role in habits, FSIs are more excitable in habitual mice compared to goal-directed and acute chemogenetic inhibition of FSIs in DLS prevents the expression of habitual lever pressing. In vivo recordings further reveal a previously unappreciated selective modulation of SPNs based on their firing patterns; FSIs inhibit most SPNs but paradoxically promote the activity of a subset displaying high fractions of gamma-frequency spiking. These results establish a microcircuit mechanism for habits and provide a new example of how interneurons mediate experience-dependent behavior.
The multiplicative weight updates method for evolutionary biology

Recently there is much interest in the application of methods from the Theory of computation to evolutionary biology. Starting with the work of Christos Papadimitriou and Adi Livnat, there has been a concerted eﬀort to use these techniques to analyze such diverse phenomena as: the algorithmic role of recombination to increase mixability, the evolution of modularity, and the evolution of complex adaptations. There is also work by Les Valiant and his students using tools primarily from learning theory to more broadly analyze evolutionary processes. In parallel, computer science theory has developed a novel method which has been applied in diverse areas of algorithms and complexity: the Multiplicative Weight Updates (MWU) method. The MWU method simply applies the MWU general-purpose online learning al-gorithm on problem-speciﬁc loss functions. The contribution of this thesis is to apply the MWU method and the algorithmic lens to make models in evolutionary biology. The ﬁrst contribution is a surprising equivalence between the MWU al-gorithm playing a coordination game and inﬁnite-population genetics models with recombination and no mutation. By so doing, we resolve analytically a question asked by Papadimitriou and Livnat: whether mixability is increased in the short-term by recombination. Other models introduced using MWU as a basic dynamics include a model of the Evolution of Animal personality and of tool use. Finally, the thesis presents a novel connection between universal semantic communication and the Rivoire-Leibler model of population genetics, in addition to inﬁnite population asexual selection models. with MWU as the key to proving the latter connection.
Distinguishing Yellowstone Cutthroat Trout, Rainbow Trout, and Hybrids by Use of Field‐Based Phenotypic Characteristics

AbstractNative and nonnative salmonids within the same genus sometimes hybridize, and the hybrids are often difficult to visually distinguish from parental species. We compared phenotypic delineations (based on several visual characteristics) and genotypic screening (using seven nuclear DNA loci) for 323 fish collected from an Idaho stream where Yellowstone Cutthroat Trout O. clarkii bouvieri were introgressed with Rainbow Trout O. mykiss to evaluate our ability to visually distinguish Yellowstone Cutthroat Trout from Rainbow Trout and hybrids. Assuming that the genotypes were 100% accurate, correct phenotypic classification was highest for Yellowstone Cutthroat Trout (the genotype confirmed the phenotype 94% of the time), followed by hybrids (79%) and Rainbow Trout (71%). All errors were between pure and hybrid fish. All of the measured phenotypic characteristics were useful for differentiating Yellowstone Cutthroat Trout from hybrids, but the most informative characteristics were the lack of a white lea.
The Dynamic of Soil Nitrogen in Forage Systems Based on Corn Silage Culture

The research on soil nitrogen dynamics of crop structures of the feed system studied had se purpose to reveal the amounts of N t made at the end of the vegetation periods and on the entire cumulative period of each system, both in unfertilized and fertilized variants with nitrogen. Following the obtained results there was found that the introduction into the feed of corn silage and aristed ryegrass the cumulative amount of N t in soil was 181.5 kg / ha, at the unfertilized variants and 190.2 kg/ha in the nitrogen fertilized variants.
Movement Ecology of Philippine Birds of Prey

Movement ecology of Philippine birds of prey Camille B. Concepcion Movement ecology is an emerging paradigm important to conservation biology and to the protection of global biodiversity. I used two common, but poorly known Philippine birds of prey as study tools in understanding movement ecology. One species is the migratory grey-faced buzzard (Butastur indicus), a raptor that which visits the islands in large numbers in winter. The other is the resident Philippine serpent eagle (Spilornis holospilus) which lives there at relatively high population density year-round. I used migration data at two terrestrial hawkwatch sites to assess how weather correlates influenced the movement behaviors of grey-faced buzzards. The grey-faced buzzard was the second most common raptor migrant using the Philippines as part of their migration route. My models show that they are more likely observed, either initiating or completing over-water crossings, in headwinds. I also created spatial models to understand how grey-faced buzzards overcome movement barriers (i.e. ocean). Modeled buzzard routes across the Philippines were between 1,582 and 2,970 km, and all repeatedly crossed water. Some of the routes overlapped at long and unavoidable over-water crossings. My models suggest that the optimal strategy for these birds is to find the shortest route to an exit point with the greatest possible access to stopover habitats and fewest over-water crossings under wind resistance. Additionally, I used road survey data to determine habitat associations of Philippine serpent eagle abundance across central and eastern Mindanao. My model showed that detection probability for the Philippine serpent eagle is relatively low, and the probability of occupancy was highest in near-pristine forests, especially low elevation dipterocarp forests. My road surveys helped establish the beginning of the breeding season for the Philippine serpent eagle. They also provided initial information on wintering habitats for grey-faced buzzards. This work is cutting-edge ecology and also provided natural history information about species for which there is almost no existing knowledge.
Growth and physiological responses of snapper (Pagrus auratus) and cobia (Rachycentron canadum) fed various inclusion levels of selenium supplemented lupin meal as fishmeal replacement diets

The past literature has demonstrated the beneficial effects of dietary mineral supplementation such as zinc and copper on growth and physiological performances in fish fed plant-based diets. However, the relationship between dietary selenium (Se), an essential mineral for growth and physiological functions in aquatic species, with plantderived ingredients such as lupin meal is very limited and never researched in commercially important carnivorous marine finfish species such as Australian snapper Pagrus auratus and cobia Rachycentron canadum. A series of five feeding trials were conducted to investigate the nutritional effects of dietary Se and lupin kernel meal on the responses of growth and physiology of snapper and cobia. In the first experiment, Australian snapper were fed to a reconstituted commercial diet and formulated basal diet with 0 and 0.8 mg/kg Se supplementation to evaluate the effects of dietary supplemental Se on the growth, feed utilisation, body composition and liver histology of juvenile Australian snapper. In the second experiment, five levels of Se extracted from Se-yeast were supplemented to a commercial cobia feed to determine the dietary Se requirement for juvenile cobia. The third and fourth trials evaluated the growth and physiological responses of both snapper and cobia after being fed to various inclusion levels of 0, 105, 210, 315 and 420 g/kg lupin kernel meal as fishmeal replacement which presented in a comparative study. The last experiment investigated effects of dietary Se supplementation on growth and physiological performances of juvenile cobia fed lupin-based diets. The results indicated that snapper required a lower concentration of dietary protein than the currently used diets derived from other commercial marine finfish and there is no need to provide supplementary Se to the snapper diet, as basic dietary ingredients are capable of providing adequate Se to meet the nutritional requirements of the species. Juvenile cobia fed available commercial cobia feed containing 1.15 mg/kg showed deficient-Se symptoms. The dietary Se concentration required for juvenile cobia fed pelleted formulated feed was 2.32 mg/kg based on the quadratic regression of specific growth rate, whereas dietary Se of 3.14 mg/kg may be threshold level for the species. Cobia showed less susceptibility to dietary lupin than snapper. Snapper displayed negative growth and feed efficiency with increasing inclusion lupin levels. Meanwhile, the dietary inclusion level of 105 g/kg lupin kernel meal did not impair the growth rates and feed efficiency, digestibility and health of cobia. The histopathological lesions were
Histone Crosstalks involving H3 Phosphorylation and their Role in Transcriptional Regulation

Histone phosphorylation is often a direct outcome of activated intracellular signaling pathways, and functions to translate extracellular signals into appropriate biological outputs such as changes in gene expression. Growth factors and cellular stress trigger rapid and transient expression of immediate-early genes (such as c-fos, c-jun) in mammalian cells, and their induction strongly correlates with a transient phosphorylation of S10 and S28 on histone H3. While many signaling cascades that lead to H3 phosphorylation have been mapped out, mechanistic details of the downstream events and how H3 phosphorylation contributes to transcriptional activation are still poorly defined. To investigate the direct effects of H3 phosphorylation on transcription, we targeted the H3 kinase MSK1 to endogenous c-fos promoter, and found that this is sufficient to activate its expression. Moreover, targeting MSK1 to the tissue-specific α-globin gene induces H3S28 phosphorylation and reactivates expression of this polycomb-silenced gene. Mechanistically, H3S28 phosphorylation not only disrupts binding of polycomb repressive complexes, but also induces a methyl-acetylation switch of the adjacent K27 residue. This provides the first indication that H3 phosphorylation is involved in antagonizing polycomb silencing. iii To further identify post-translational modifications (PTMs) that function together with MSK1-mediated H3 phosphorylation, I developed a novel nucleosome purification approach called Biotinylation-assisted Isolation of CO-modified Nucleosomes (BICON). This technique combines in vivo biotinylation by BirA and H3 phosphorylation by MSK1, allowing enrichment of phosphorylated nucleosomes using streptavidin. I found that MSK1phosphorylated nucleosomes are hyper-acetylated on H3 and H4, and importantly, I identified a trans-tail crosstalk between H3 phosphorylation and H4 acetylation on K12. This proof-of-principle study demonstrates that BICON can be further adapted to study PTMs and crosstalks associated with other histone-modifying enzymes. Taken together, work described in this thesis shows that histone H3 phosphorylation can initiate additional PTM changes on other residues within the nucleosome, and such crosstalk plays an important role in regulating gene expression.
Combined effects of compost containing Sulfamethazine and zinc on pakchoi (Brassica chinensis L.) growth, soil sulfonamide resistance genes, and microbial communities

ABSTRACT To understand the ecotoxicity of antibiotics and heavy metals in soil, 5% (w/w) composts containing different concentrations of sulfamethazine (SMZ) and/or zinc (Zn) were applied to soil to investigate their effects on pakchoi (Brassica chinensis L.) growth, soil sulfonamide resistance genes (SRGs: sul1, sul2, and dfrA7), and soil microbial communities. Composts containing less than 1.0 mg SMZ kg–1 or less than 2.8 g Zn kg–1 promoted pakchoi growth and the metabolic activity of soil microbial communities. Compared with the control, the absolute abundances (AAs) of soil SRGs significantly increased by 0.85–4.54 times with 50.6 μg kg–1 SMZ treatment (P < 0.05), the AA of sul2 increased by 166% with 248.8 mg Zn kg–1 treatment. The combination treatments with 19.8 μg SMZ kg–1 and 179.9 mg Zn kg–1 in soil had synergistic stimulatory effects on pakchoi growth, soil SRGs and microbial metabolism, whereas 53.5 μg SMZ kg–1 and 262.1 mg Zn kg–1 had an opposite effect. Pearson’s correlation analysis showed that carbon metabolism by soil microorganisms had significant positive correlations with shoot height of pakchoi (r = 0.84, P < 0.05) and AAs of SRGs (r > 0.80, P < 0.05).
KDM1A maintains genome-wide homeostasis of transcriptional enhancers

Transcriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of mono-methylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature that distinguishes enhancers from gene promoters. Lysine Specific Demethylase 1 (LSD1, aka KDM1A), an enzyme specific for demethylating H3K4me2/me1, has been shown to “decommission” stem cell enhancers during the differentiation of mouse embryonic stem cells (mESC). However, the roles of LSD1 in undifferentiated mESC remain obscure. Here, we show that LSD1 occupies a large fraction of enhancers (63%) that are primed with binding of transcription factors (TFs) and H3K4me1 in mESC. In contrast, LSD1 is largely absent at latent enhancers, which are not yet primed by TF binding. Unexpectedly, LSD1 levels at enhancers exhibited a clear positive correlation with its substrate, H3K4me2 and enhancer activity. These enhancers gain additional H3K4 methylation upon the loss of LSD1 in mESC. The aberrant increase in H3K4me at enhancers was accompanied with increases in enhancer H3K27 acetylation and expression of enhancer RNAs (eRNAs) and their target genes. In post-mitotic neurons, loss of LSD1 resulted in premature activation of enhancers and genes that are normally induced after neuronal activation. These results demonstrate that LSD1 is a versatile suppressor of primed enhancers, and is involved in homeostasis of enhancer activity.
shRNA mediated inhibition of Cdc42 gene expression in Calu-6, lung cancer cells

Background Information RNAi technique as a new strategy in gene therapy is the effective gene silencing method. Cdc42 is a member of Rho GTPases involving in lung cancer cells migration and proliferation. In the present study, targeting and inhibiting the Cdc42 expression in Calu-6 cells was investigated. Recombinant lentiviral particles were produced by co-transfection of pMD2.G, psPAX2 and pGFP-C-shLenti plasmid in 293T packaging cells. Calu-6 cells were transduced by recombinant lentiviruses using polybrene. GFP-fluorescence microscopy and MTT assay were used to assess the Calu-6 target cell transduction and rate of lentiviral transduced cells proliferation, respectively. Real time PCR was performed to compare the expression of Cdc42 gene before and after shRNA delivery. Results GFP-fluorescence microscopy analysis showed that Calu-6 cells were successfully transduced with recombinant lentiviral expressing shRNA-Cdc42. The viability of transduced cells was reduced within 72, 96 and 120 hours of transduction process. Real time PCR analyze showed the significant reduction of Cdc42 gene expression. Conclusions: Lentiviral vectors may be reasonable tools for this gene delivery due to stable expression of silencing RNA. Inhibition of Cdc42 expression by lentiviral mediated shRNA delivery could be an effective method to inhibit proliferation of lung cancer cells. Significance: Over expression of Cdc42 gene have been seen in lung cancer. This make Cdc42 gene a key target in treatment of cancer. On the other hand, gene therapy is a proper method to modulate gene expression. It seems modulation of cdc42 gene expression by gene therapy accompany with proper vehicles creating hopes in treatment of lung cancer.