Mechanism of DNA target site recognition by group II introns TeI3c and GsI-IIC and splicing activity of GsI-IIC reverse transcriptase

Mobile group II introns are self-catalytic ribozymes found in bacteria and eukaryotic organelles. They can mobilize within the genomes by retrohoming, which involves RNA-catalyzed splicing followed by the excised intron reverse splicing into a target site. Both RNA splicing and retrohoming are facilitated by an intron-encoded reverse transcriptase (RT). Mobile group II introns are of interest as evolutionary ancestors of spliceosomal introns in higher organisms, for their use as bacterial gene targeting vectors known as targetrons, and as a source of thermostable group II intron reverse transcriptases (TGIRTs) for RNA-seq. The focus of this master’s thesis is on two thermophilic group II introns found in bacterial thermophiles: the subgroup IIB intron TeI3c and the subgroup IIC intron GsI-IIC. The TeI3c intron is known to rely on base pairing interaction between exon-binding site sequences 1/2 (EBS1/2), within the intron RNA, and intron-binding site sequences 1/2 (IBS1/2) in the 5’ exon of its target DNA, but it is not clear what targeting rules dictate one target sequence to be better or worse than others. I studied the targeting rules of TeI3c during retrohoming by using randomized libraries and next-generation sequencing followed by computational analysis of the sequence data. Understanding the targeting rules of TeI3c can be the important step in the development of thermostable targetron, which can be useful for metabolic engineering in the biofuel industry. Unlike TeI3c, which relies primarily on base pairing for DNA target recognition, the GsI-IIC intron recognizes a 5’-exon hairpin secondary structure of the target DNA. However, the secondary structure requirements of good targets have not been studied. I studied the secondary structure requirements during GsI-IIC retrohoming by using doped target libraries and next-generation sequencing to find conserved positions within a hairpin target site followed by mobility assays on different target sites with mutated conserved positions. Finally, I studied the forward splicing of GsI-IIC intron by comparing different hairpin target sites including the same mutated target sites tested for their mobility efficiency. These experiments address whether the 5’-exon hairpin structure is recognized similarly for RNA splicing and intron mobility.Cellular and Molecular Biolog

Investigating The Implementation Of Gamification Approach To Enhance Students Learning Engagement

Students experienced online learning since the CoVid-19 pandemic started. Gradually, the students became disengage to the lesson. This issue is urgent as low learning engagement will impact students’ growth in developing critical thinking skills, learning achievement, and enduring understanding. Further, this impacts the students’ performance under iB Curriculum which integrates critical thinking throughout the lesson. This research aims to investigate the effectiveness of the gamification approach in enhancing students learning engagement through the utilizations of gamified learning application such as Quizziz. Also, to find how significance is the role of teacher while implementing the gamification approach. There were three cycles to obtain qualitative data. The study shows that the implementation of gamification demonstraded significance impact in enhancing students’ learning engagement. Student who are engaged will have higher motivation in learning, well-developed critical thinking, and also effective learning experience. This lets the students to effectively exercise their God-given attributes as human beings to learn at their best. It is recommended in future research to collaborate with other teachers from different subjects with same grade level, have longer implementation period to compare the effectiveness during online and hybrid learning, and to elaborate different gamified learning platforms that have different modes and user interface

An Optical Tweezer Array of Ultracold Molecules

Arrays of single ultracold molecules promise to be a powerful platform for many applications ranging from quantum simulation to precision measurement. Here we report on the creation of an optical tweezer array of single ultracold CaF molecules. By utilizing light-induced collisions during the laser cooling process, we trap single molecules. The high densities attained inside the tweezer traps have also enabled us to observe in the absence of light molecule-molecule collisions of laser cooled molecules for the first time

Vegetation Effects on Rhizosphere Microbial Communities in Coastal Wetlands of South Mississippi

The Mississippi vegetated coastal wetlands consist of many salt and brackish marshes. In those marshes, there are two plant species Spartina alterniflora and Juncus roemerianus that thrive in those environments. This would not be possible without the benefits of microbial communities that live in the portion of the plant's soil called the rhizosphere. The rhizosphere is crucial for plant nutrition, health, and quality. It supports the biomass and activity of microorganisms for carbon sequestration, ecosystem functioning, and nutrient cycling in natural ecosystems. To investigate the vegetation effects on rhizosphere microbial communities in coastal wetlands, plant samples and their rhizosphere soils were collected from two brackish transects and two saltwater transects at Graveline Bayou, Gautier, MS. A number of biotic and abiotic factors were measured, and their impacts on bacterial community composition and diversity were determined via Illumina MiSeq 16S rRNA gene sequence. Overall, the composition of rhizosphere bacterial community in coastal wetlands were dominated by Proteobacteria and Planctomycetes. The effects of seasonal patterns and plant developmental stages had no impacts on rhizosphere microbial communities due to similar pH level, soil moisture, and organic matter content in soil between winter and summer seasons of 2015. Salinity increased bacterial community diversity especially Proteobacteria and Bacteroidetes. There are several contrasting reports that portrayed the dominant factor in determining the diversity of rhizosphere microbial communities as either the plant species itself or the soil type of the site. In this study, the soil type was the major driving force in bacterial community diversity

Role of extracellular matrix and microenvironment in regulation of tumor growth and LAR-mediated invasion in glioblastoma

The cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical cues in the microenvironment. Recent studies have shown that miR-451 regulates downstream molecules including AMPK/CAB39/MARK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of the main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this complex process of cell proliferation and invasion and its response to conventional treatment, we propose a mathematical model that analyzes the intracellular dynamics of the miR-451-AMPK- mTOR-cell cycle signaling pathway within a cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress in response to fluctuating glucose levels. We show how up- or down-regulation of components in these pathways affects the key cellular decision to infiltrate or proliferate in a complex microenvironment in the absence and presence of time delays and stochastic noise. Glycosylated chondroitin sulfate proteoglycans (CSPGs), a major component of the extracellular matrix (ECM) in the brain, contribute to the physical structure of the local brain microenvironment but also induce or inhibit glioma invasion by regulating the dynamics of the CSPG receptor LAR as well as the spatiotemporal activation status of resident astrocytes and tumor-associated microglia. Using a multi-scale mathematical model, we investigate a CSPG-induced switch between invasive and non-invasive tumors through the coordination of ECM-cell adhesion and dynamic changes in stromal cells. We show that the CSPG-rich microenvironment is associated with non-invasive tumor lesions through LAR-CSGAG binding while the absence of glycosylated CSPGs induce the critical glioma invasion. We illustrate how high molecular weight CSPGs can regulate the exodus of local reactive astrocytes from the main tumor lesion, leading to encapsulation of non-invasive tumor and inhibition of tumor invasion. These different CSPG conditions also change the spatial profiles of ramified and activated microglia. The complex distribution of CSPGs in the tumor microenvironment can determine the nonlinear invasion behaviors of glioma cells, which suggests the need for careful therapeutic strategies.<br/

A Study of Shape Memory Polymer Based Slat-Cove Filler

Aircraft noise reduction is an application of current intense interest for which smart materials show significant potential. Specifically, the aeroacoustic noise produced by the unsteady aerodynamic flow about the leading-edge high-lift device, such as leading-edge slat, of typical transport-aircraft wings is of particular interest. Concepts with the most promise to mitigate this noise source, most notably the slat-cove filler concept, have focused on highly reconfigurable structures that change shape between different phases of the flight envelope. These shape changes often involve large deformation, which has stimulated the consideration of shape memory materials. In recent years, shape memory materials (SMMs) have drawn greater interest for applications such as smart fabrics, intelligent medical devices, self-deployable space structures, morphing structures and packaging. Compared to other shape memory materials, like shape memory alloys (SMAs) or shape memory ceramics (SMCs), shape memory polymers (SMPs) have desirable advantages such as high elastic deformation to enable large shape change, broad tailorability of mechanical properties, potential biocompatibility and biodegradability, ductility, light weight and ease of processing. However, SMPs still have some critical disadvantages such as insufficient mechanical and thermal characteristics for structural applications, low recovery stress, and long response time. The new LaRC shape memory thermosetting polymer composite (LaRC-SMPC) discussed herein was synthesized with nontoxic monomers and conductive/magnetic fillers to yield enhanced thermal/mechanical characteristics and faster response times. LaRC-SMPCs with a variety of fiber reinforcements [Kevlar, carbon fiber (standard and thin-ply), and carbon-nanotube (CNT) sheet] were fabricated to tailor the physical properties and test for suitability as a slat-cove filler (SCF). The performance of SCF prototypes fabricated with the developed LaRC-SMPCs was evaluated using a bench-top test apparatus. The SCFs made of Kevlar fiber fabric or carbon fiber fabric infused shape memory polymer composite (SMPC) exhibited kinking during simulated deployment and stowage, which can be problematic during operation. The SCF made of CNT sheet/SMP composite did not exhibit kinking, but the deployment was sluggish compared to carbon fiber fabric/SMP composite. This report documents the evolution of designing SMPCs as slat-cove fillers for aircraft noise reduction. In the course of the investigation, several 2 approaches were investigated to address shortcomings in material characteristics based on performance requirements of operational slat-cove fillers

Observation of Collisions between Two Ultracold Ground-State CaF Molecules

We measure inelastic collisions between ultracold CaF molecules by combining two optical tweezers, each containing a single molecule. We observe collisions between $^2\Sigma$ CaF molecules in the absolute ground state $|X,v=0, N=0,F=0\rangle$, and in excited hyperfine and rotational states. In the absolute ground state, we find a two-body loss rate of $7(4) \times 10^{-11} \text{cm}^{3}/\text{s}$, which is below, but close to the predicted universal loss rate.Comment: 5 pages, 4 figure