Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of eukaryotic transcription by modification of chromatin structure

Author(s): Venkatasubrahmanyam, Shivkumar | Advisor(s): Madhani, Hiten D | Abstract: Modification of chromatin is a highly conserved and fundamental mode of transcriptional regulation in eukaryotes. Chromatin structure can be altered by covalent histone modification, variant histone incorporation and nucleosome remodeling. This thesis describes the study of these mechanisms in a model eukaryote, the budding yeast S. cerevisiae. Methylation of histone H3 on lysine 4 (K4) by Set1, the yeast homolog of human leukemia-related methyltransferases MLL1 and ALL1, is enriched along coding sequences and associated with active transcription. In contrast, the histone variant H2A.Z is found exclusively at the two nucleosomes flanking the transcription start site. H2A.Z regulates the spread of Sir-mediated silencing, which was believed to occur only in the vicinity of telomeres. Through the collaborative research detailed within, I identified members of the Set1 complex in a genetic screen for factors that cooperate with H2A.Z to antagonize Sir activity. I found that Set1 and H2A.Z share a genome-wide anti-silencing function that prevents ectopic binding and gene repression by the Sir2/3/4 complex across euchromatin. Exploring such functional redundancies between various chromatin modifiers will be important to fully understand their roles in transcription. Further collaborations led to the discovery of mechanisms that operate upstream of H2A.Z and Set1. H2A.Z interacts with a complex of 13 proteins, including the SWI/SNF-related ATPase Swr1. Swr1 is required for incorporation of H2A.Z into chromatin; loss of Swr1 or H2A.Z results in similar gene expression defects. H3 K4 methylation by Set1 requires histone H2B K123 mono-ubiquitination, which involves the E2 ubiquitin-conjugating enzyme Rad6. The RING-finger protein Bre1 is required for this modification. Rad6 acts on multiple protein targets; this putative E3 ubiquitin-ligase is likely to direct the mono-ubiquitination activity of Rad6 onto H2B. Finally, I have developed a software tool for the analysis of chromatin-profiling data from high-density tiling oligonucleotide microarrays. The use of this tool has shown that Sth1, an essential chromatin-remodeling enzyme and member of the RSC complex, slides nucleosomes around the 5' ends of coding sequences away from their predicted positions at nucleosome-positioning sequences (NPS). Thus nucleosome appear to be positioned by a combination of cis- and trans-acting factors.
Characterisation of a novel Staphylococcus aureus lineage : Clonal Complex 75 (CC75), Staphylococcus argenteus

Staphylococcus aureus is a major opportunistic human pathogen, commonly found in the nose and on the skin of healthy individuals. S. aureus can cause a broad spectrum of diseases, ranging from minor skin infections to life threatening sepsis and necrotising pneumonia. First reported in Australia in 2004, Clonal complex 75 (CC75), defined by multilocus sequence typing (MLST), is highly divergent from S. aureus at each MLST locus, and is believed to be a novel lineage of S. aureus. CC75 is common in tropical northern Australia where it is associated with skin lesions in the Indigenous population, although CC75 has also been reported elsewhere in the Asia Pacific region and South America. This thesis presents the characterisation of CC75 with the following aims: (i) determining the evolutionary position of CC75 within the genus Staphylococcus; (ii) investigating the resolving power of high-resolution melt (HRM) analysis for rapid screening to identify new CC75 MLST alleles; and (iii) investigating whether saturating dyes such as LCGreen+ are superior to non-saturating dyes such as SYBR Green for the discrimination of sequence variants utilising HRM analysis. Major findings from this thesis are: (i) the striking divergence in the multilocus sequence analysis (MLSA) and MLST housekeeping genes within the core genome between CC75 and S. aureus and the phenotypic characteristic lacking staphyloxanthin, responsible for the golden colour pigment in S. aureus, support CC75 to be a different species from S. aureus (CHAPTER 2); (ii) HRM using SYBR Green in full length MLST amplicons reliably discriminates CC75 MLST alleles at only two (tpi and gmk) out of seven loci (CHAPTER 3); (iii) the robustness of PCR (as measured by CT values) correlates inversely with the reproducibility of HRM curves (as measured by the variation of Tm values) (CHAPTER 3); (iv) HRM using SYBR Green on full length MLST amplicons lacks the resolving power to detect new CC75 MLST alleles (CHAPTER 4); and (v) saturating dyes such as LCGreen+ are not necessarily superior to non-saturating dyes such as SYBR Green for the discrimination of sequence variants (CHAPTER 5). In the presence of LCGreen+ at low MgCl2 concentration (2mM), HRM is confounded by an inverse correlation between DNA concentration and Tm. This effect is eliminated when the MgCl2 concentration is increased to 6mM (CHAPTER 5).
Development of a chemical induced dimerization approach to distinguish features of eNOS signaling at alternative subcellular loci.

Nitric oxide (NO) is a highly reactive signaling molecule that plays diverse and important bioregulatory roles. In endothelial cells, NO is synthesized by eNOS, a member of the NO synthase (NOS) family, whose activity is tightly regulated at the posttranslational level by acylation, phosphorylation, S-nitrosylation and protein-protein interactions. The biological actions of NO arise as a direct consequence of chemical reactions between NO, or NO-derived species, and protein targets. S-nitrosylation of specific cysteine residues in target proteins is emerging as an important mechanism of NO signaling. Although eNOS is known to undergo a complex pattern of trafficking within endothelial cells, the distinct activities, modes of regulation, and protein targets of NO at eNOS-containing organelles are largely unexplored. We hypothesize that eNOS is differentially regulated at alternative subcellular loci and NO is preferentially transferred to protein acceptors that neighbor NO synthases. To test these hypotheses, we sought to develop a conditional heterodimerization approach that can target eNOS, on-demand, to discrete subcellular loci (via specific targeting sequences e.g. nuclear, mitochondrial, Golgi and cell membrane) and assess the consequences for eNOS activity, regulation and protein S-nitrosylation patterns. Furthermore, we sought to devise a proteomic strategy for unbiased identification of S-nitrosylation sites on proteins that mediate NO bioactivities. Use of these new tools should enable the resolution of controversies regarding the role of diffusion in NO biology, as well as the identification of novel protein targets and mechanism that regulate NO biosynthesis at distinct loci within endothelial cells. In this thesis research, I describe the development and application of "eNOS CID" and "SNOSID" as powerful new tools to address the impact of eNOS compartmentalization on NO signalling in endothelial cells.
Comparison of indices to estimate abundance of dusky-footed woodrats

Indices often are applied without calibrating to the number of animals present, or determining a ratio of animals present, to the attribute used as an index. In this study, we developed a new index (tail-rattles) and tested it and a conventional index (houses) against a robust estimate of abundance (mark-recapture) to assess their usefulness as indicators of abundance of dusky-footed woodrats (Neotoma fuscipes). We live-trapped woodrats in 24 redwood (Sequoia sempervirens) forest stands from 4 seral stages during 1992-1993. We applied the 2 indices over a 1.2-ha trapping grid, and both estimates were modeled as a function of the minimum number of woodrats captured in 5 nights of trapping. Counts of physical sign, inhabited woodrat houses (r 2 =0.40), and counts of tail-rattles (r 2 =0.85) were related to mark-recapture estimates of minimum abundance. Tail-rattling was a superior index of dusky-footed woodrat abundance because tail-rattles were more precise than counts of dusky-footed woodrat houses along transects. The tail-rattling index was easy to apply and standardize, and it was sensitive to variation in robust estimates of abundance. We recommend an approach verifying the relationship between our index and dusky-footed woodrat abundance in other geographic areas and habitat types before it is applied.
Origin and early evolution of Ceropegieae (Apocynaceae-Asclepiadoideae)

The first-branching lineages of the tribe Ceropegieae, Anisotominae, Leptadeniinae, and Heterostemminae, are the focus of the present study. In the ingroup we molecularly analysed 34 samples from southern and (north)eastern Africa and Asia for the nuclear internal transcribed spacer (ITS) region, and five plastid markers (trnT-L, trnL-F and trnH-psbA intergenic spacers, trnL, and rps16 introns). Maximum Parsimony and Bayesian analyses were conducted for phylogenetic reconstruction and Bayesian binary MCMC (BBM) analysis as implemented in RASP for testing biogeographic inference. Sister to the well-known hyperdiverse subtribe Stapeliinae (around 700 species) are the Anisotominae, an African subtribe of c. 30 species, with the tropical Neoschumannia in sister-group position to the remaining genera, Anisotoma, Emplectanthus, Riocreuxia, and Sisyranthus. Emplectanthus is sequenced in full for the first time, and its monophyly as sister to Anisotoma is documented. As in Sisyranthus, new sequences in Riocreuxia, especially in Riocreuxia torulosa s.l. , reveal very low genetic variation pointing to an actively radiating and speciating group, possibly in adaptation to pollinator pressure. Molecular and morphological data necessitate the transfer of Brachystelma natalense to Anisotoma, and the new combination Anisotoma natalensis is proposed. Leptadeniinae are sister to the Stapeliinae–Anisotominae clade. The position of the strictly Asian, rheophytic Pentasachme could be resolved as sister to the remaining genera of Leptadeniinae, Conomitra, Leptadenia, and Orthanthera. The position of the S Asian/Australasian wet forest lianas of the genus Heterostemma as sister to the remaining Ceropegieae is confirmed, indicating a humid Asian origin for this tribe known for its arid-adapted African succulents.
Habitat Suitability Modeling of the Federally Endangered Poweshiek Skipperling in Michigan

Abstract The Poweshiek skipperling Oarisma poweshiek (Lepidoptera: Hesperiidae) is a historically common prairie butterfly with a range extending throughout the mesic prairies and prairie fens of the upper Midwestern United States and southern Manitoba, Canada. Rapid, range-wide declines have reduced the number of verified Poweshiek skipperling locations to seven, four of which occur in Michigan. To assist with monitoring and, ultimately, conservation efforts, we developed a habitat model using the software Maxent with ecological and geographical factors. Using a lowest-presence threshold methodology, our habitat suitability model indicated potentially high suitability in 26 of 138 prairie fens with no documentation of Poweshiek skipperling occurrence. The strongest predictors of suitable habitat in our model were prairie fen area and surrounding natural land cover. Wildlife managers can use results from this analysis to expand monitoring to include sites with suitable habitat where Poweshiek skipperling .
Metapopulation management of an Endangered species with limited genetic diversity in the presence of disease: the Tasmanian devil Sarcophilus harrisii

There has been much discussion relating to the current biodiversity crisis, with the loss of species now at an unprecedented rate. Using augmentation and/or reintroduction to minimize the loss of species in the wild is becoming more prominent. Zoological institutions have been traditionally involved in the management of insurance populations providing a range of species for release to the wild. Insurance populations can be costly, both in resources and behavioural changes, and so should aim to be maintained for as short a time as possible, with a maximum of 40 years. A Tasmanian devil Sarcophilus harrisii insurance population was established in 2006 with the arrival of devil facial tumour disease, and was founded with 120 individuals sourced predominantly from the west coast of Tasmania. Here the challenges of establishing and managing an insurance population in an already genetically depauperate species in the presence of a contagious cancer are discussed. The Tasmanian devil insurance metapopulation now includes a continuum of management scenarios (from intensive zoo-based facilities, through free-range enclosures, to an island and fenced peninsula) and consists of over 700 devils representing at least 180 founders. The lessons learned in regard to this programme are presented, including the issues surrounding reduced genetic diversity and how we are striving to improve the long-term management of the insurance metapopulation through a combination of molecular genetics, modelling and on-the-ground management. The tools and technologies that have been developed in this programme are directly applicable to the recovery and management of a suite of other threatened fauna.
Phenotypic plasticity in Cardiocondyla obscurior

Contemporary evolutionary concepts emphasize the importance of environment, development and genetics in shaping an organism’s phenotype. Natural selection requires phenotypic differences between individuals, which arise by interactions of environmental factors with genetic systems and are channelled by developmental constraints. This thesis on phenotypic evolution in the invasive ant C. obscurior focuses on different sources for phenotypic variation. A brief overview of genetic and environmental mechanisms underlying the evolution of phenotypic novelty is provided in Chapter 1, followed by an introduction of the study organism with an emphasis on its feasibility for laboratory studies. Chapter 2 comprises an assessment of the genomic and phenotypic divergence of two separated C. obscurior populations from Brazil and Japan. In Chapter 3, the developmental genetic basis of polyphenism is studied in C. obscurior. Chapter 4 applies the gene expression data compiled in Chapter 3 in a different context, addressing consequences of biased gene expression on gene evolution. The study presented in Chapter 5 contains the first description of the putatively mutualistic endosymbiosis between Cardiocondyla and the enterobacterium Candidatus Westeberhardia cardiocondylae (“Westeberhardia”). The general discussion in Chapter 6 begins with a critical assessment and comparison of C. obscurior and two other well-suited ant species for their potential to become widely used model systems. The chapter continues with a discussion of potential sources of rapid adaptation in C. obscurior in an attempt to synthesize different topics addressed in Chapters 2 to 5. Chapter 6 concludes with discussing possible challenges and directions of future studies on the evolutionary potential of C. obscurior.
Status of the population of Karamoja Apalis Apalis karamojae in north-eastern Uganda

The distribution of the Karamoja Apalis Apalis karamojae, an East African endemic, has been sparsely documented in Uganda. In October 2011, a survey of the species was carried out near Iriiri in north-eastern Uganda. The main aim was to find out if there is a viable population of the species and to highlight the threats to its population. Sixteen 1-km transects in four sites were surveyed. The survey recorded nine individuals including a pair at an occupied nest, which is not conclusive for determining the viability of the population. The main threats to the species were cutting of the dominant shrub Vachellia drepanolobium (Acacia drepanolobium) in the area, farming and grazing. When we attempted luring the birds using the recorded song of the Karamoja Apalis from Tanzania, these individuals did not respond. We therefore recommend (1) to undertake a more detailed GIS survey to discover the extent of the suitable habitat, (2) to repeat the survey with improved effort to better estimate the viability of this population, (3) to conduct a study to ascertain the successful breeding of the species in the area, (4) to conduct a DNA analysis to compare the Iriiri population with the Tanzanian population, and (5) to record the song of the Ugandan birds for song analysis and to determine the response of Tanzanian birds.
Pressure-sensitive adhesive properties of wheat flour dough and the influence of temperature, separation rate, and moisture content

Using the method of reduced variables, probe tack test data on wheat flour-water doughs was shifted into a series of master curves. This illustrated the equivalent influence of increasing temperature, increasing moisture content, and decreasing separation rate on adhesive behavior. An adhesive-cohesive failure transition occurred at 25-30 o C (43% moisture content). This transition occurs 50-70 o C above the T g of a pressure-sensitive adhesive and is associated with a shift in viscoelastic behavior from the rubbery state (entanglement network present) to the flow state (entanglement network disappears due to slippage). Low molecular weight plasticizers (such as water) shift the location of the rubbery-flow state transition to lower temperatures and faster rates. Thus, as the moisture content of the dough increased, the adhesive-cohesive failure transition shifted to lower temperatures and faster separation rates. Processors could prevent cohesive failure, and thus a residue-buildup on equipment, by changing either the formulations or the processing rate-temperature conditions to favor the adhesive side of the failure transition zone
Changes in dermal ossicles during somatic growth in the Caribbean littoral sea cucumbers (Echinoidea: Holothurioidea: Aspidochirotida)

Dermal ossicles in holothuroids are important taxonomic characters, but they can change during somatic growth. Ossicles in very young individuals may be so different from those in adults as to indicate separate species. Since juveniles are rarely found, growth changes in ossicles have previously been studied in only a few species worldwide. During 25 years of collecting in Puerto Rico, series of juveniles of many common littoral species of Caribbean holothuroids have been obtained. In this paper, ossicles of 12 of the 17 valid Caribbean species in the Order Aspidochirotida are described. The pattern of changes varies between species. In some it is mainly a change in size, the ossicles becoming gradually either larger, as in Holothuria (Platyperona) parvula (the tables and rods increase in size but the buttons stay about the same length), or smaller and simpler (e.g., the rods in Holothuria (Selenkothuria) glaberrima). In other species, a type of ossicle lacking in small juveniles is added during somatic growth (e.g., buttons in H. (Thymiosycia) arenicola; rosettes in H. (Halodeima) mexicana), or ossicles present in juveniles are absent in adults (e.g., all tables in Astichopus multifidus; tables with quadruped disks in H. (Thymiosycia) impatiens and H. (Theelothuria) princeps; tables with wide, delicate disks and tall spires in H. (H.) mexicana and Isostichopus badionotus). In H. (Cystipus) cubana, the ossicles (tables, rods, buttons) all change almost totally in appearance. The changes in the ossicles are affected by continual dissolution and redeposition of the calcite. Ossicle changes in the species covered in this paper are documented in line drawings and tables of measurements. Changes in external morphology of the species during somatic growth also are noted. There are photographs of some of the juveniles.
Eliminating thrips from in vitro shoot cultures of apple with insecticides

The insecticides acephate, dichlorvos, and imidacloprid were assayed, using in vitro shoot cultures of apple (Malus xdomestica Borkh.), to determine their phytotoxicity at several concentrations and their effectiveness for eradication of the Western Flower Thrip (Frankliniella occidentalis, Pergande) from infested apple shoot cultures. Commercial formulations of acephate (Orthene), dichlorvos (VaportapeII), and imidacloprid (Admire) and a technical grade of imidacloprid were used in the experiments. For acephate and imidacloprid, concentrations of 1 to 80 mg.L -1 a.i. in shoot culture medium were used, while for dichlorvos, a fumigant, particles of the formulated product containing concentrations of 0.7 to 6.4 mg a.i. were suspended in the head space of the 500-mL glass culture jar. Acephate, dichlorvos, and the technical grade of imidacloprid did not cause phytotoxicity and growth of shoot cultures was unaffected at all treatment concentrations tested after a 6-week treatment period. Imidacloprid (20 to 80 mg.L -1 of the commercial formulation) caused chlorosis at the end of the 6-week treatment period. None of the treatments tested resulted in the death of shoots. Thrips were eradicated by acephate or imidacloprid treatments of 5 mg.L -1 and by dichlorvos treatment of 0.7 mg per 500-mL culture jar. Shoot cultures grew normally after the treatment period. Chemical names used: O,S-dimethyl acetylphosphoramidothioate (acephate), 2,2- dichlorovinyl dimethyl phosphate (dichlorvos),1-(6-chloro-3-pyridylmethyl)-N-nitroimidazolidin-2-ylideneamine (imidacloprid).
The Analysis of Under Graduate Students’ Translation Work of News Text from English to Indonesia

: News as a part of formal text almost translated in a different language. It needs the different translation method to build the best quality of translation work. The purposes of this study are to find the quality of the students‟ translation work of English news text to Indonesia and to describe the English education department students‟ method of translating English news text to Indonesia. This study was conducted at one of a university in Indonesia. The study uses the qualitative method; the samples are 12 under graduate students of English education department. The quality of students‟ translation work gathered from the document analysis and the assessment adopted from Larsons‟ criterion. Meanwhile, the students‟ translation method that compiled by Newmark was analysed from the interview. After doing the analysis, the English Education Department students‟ translation work quality is dominated by the fair level for the accuracy, clarity and naturalness. Then, the methods that were used by the students are word for word method, free translation method, faithful translation method, adaptation translation method, and literal translation.
EXTRACELLULAR BIOSYNTHESIS OF SILVER NANOPARTICLES USING ASPERGILLUS FLAVUS AND THEIR ANTIMICROBIAL ACTIVITY AGAINST GRAM NEGATIVE MDR STRAINS

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Virus-based MicroRNA Silencing

1School of Life Sciences, Tsinghua University, Beijing, China; 2MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; 3State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection (Ministry of China), Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China *For correspondence: yuleliu@mail.tsinghua. edu.cn