Life Sciences Commons^™

Dianthus Berkayii (Caryophyllaceae), A New Species From Turkey, Zeki̇ Aytaç, Ali̇ Kandemi̇r, Tuğba Ertuğrul, Ahter Fi̇şne, Mevlüde Alev Ateş

Turkish Journal of Botany

Dianthus berkayii belongs to sect. Fimbriati was described and illustrated as a new species from Erzincan Province in Eastern Anatolia, Turkey. In the current study morphological, palynological, and molecular characters were compared and discussed with its closely related species. The new species is similar to D. crinitus with fimbriate corolla, linear, acuminate, ± rigid leaves. Also similar to D. vanensis with fimbriate corolla, linear, acuminate, ± rigid, curved divaricate leaves. But distinctly different from D. crinitus by having linear and curved divaricate leaves, stem with 3?4(?5) internodes (not 5?8), a style much longer than petals, and different from D. vanensis …

Limacella Subtropicana (Amanitaceae, Agaricales), A New Species From Pakistan Based On Morphological And Molecular Phylogenetic Evidences, Aiman Izhar, Abdul Rehman Niazi, Muhammad Asif, Muhammad Haq Nawaz, Hira Bashir, Abdul Nasir Khalid

Turkish Journal of Botany

Basidiomata of a hitherto undescribed Limacella species were collected from the grasslands of Punjab, Pakistan. We describe it as Limacella subtropicana, which is characterized by its viscid, white to creamy pileus, white to the creamy stipe, changing to brown when bruised, subglobose basidiospores measuring 4.0?6.3 × 3.7?5.5 ?m, an ixotrichodermal pileipellis with subcylindric to clavate terminal elements and the common presence of clamp connections in all tissues. Maximum likelihood and Bayesian inference analyses of ITS sequences and LSU sequences of nrDNA confirmed its placement in the genus Limacella. A comprehensive description and a comparison of the new taxon with other …

Effect Of Seaweed-Based Liquid Extracts On Biomass Production And Lipid Accumulation In Nannochloropsis Oculata And Dunaliella Salina, Krishna Moorthy Abarna, Rani Velu, Padmavathy P, Jawahar P, Uma A, Kalidas C, Satya Prakash Shukla

Turkish Journal of Botany

Seaweed liquid fertilizers (SLFs) contain macronutrients, micronutrients and trace nutrients essential for microalgal growth. The study aims to evaluate the efficiency of SLFs on the biomass production, biochemical and physiological processes; and the study was carried out at different SLF concentrations of selected seaweeds i.e. Kappaphycus alvarezii, Gelidiella acerosa and Turbinaria ornata. The comparative analysis of the growth performance of two unicellular green alga on three different organic media suggest that the liquid fertilizer from red seaweed was highly efficient than the SLF prepared from brown seaweed. The growth rate of N. oculata and D. salina in K. alvarezii SLF …

Role Of More Axillary Growth2 (Max2) Protein In Regulation Of Karrikin And Strigolactone Signalling Pathways, Sarika Singh, Moin Uddin, M. Masroor A. Khan, Sobia Aman Chishti, Sangram Singh, Urooj Hassan Bhatt

Turkish Journal of Botany

MORE AXILLARY GROWTH 2 (MAX2) is an F-box protein, containing leucine-rich repeats. It is a common regulator in signalling pathways of both karrikin and strigolactone, and has several homologs such as MAX1, MAX3, and MAX4, which play a key role in the biosynthesis of strigolactone. It also interacts with various receptors and repressors of karrikin and strigolactone. Karrikins are a group of plant growth regulators found in the smoke of burning plant material and had the ability to stimulate seed germination, whereas strigolactone is a newly discovered plant hormone that regulates shoot and root branching and plays a vital role …

Modulation Of Physiological Plasticity Through Structural And Functional Modifications In Stipagrostis Plumosa L. For Adaptability To Hyper-Arid Environments, Safura Bibi, Muhammad Sajid Aqeel Ahmad, Mansoor Hameed, Ambreen Khadija Alvi

Turkish Journal of Botany

The role of morpho-physiological attributes along with the antioxidant potential of Stipagrostis plumosa L. populations collected from arid regions in adaptability to aridity was evaluated. Root to shoot length, chlorophyll, carotenoids, and organic osmolytes (total free amino acids, total soluble proteins, glycinebetaine, and proline) increased with more activities of antioxidant enzymes (APX, CAT, POD, and SOD). Root and shoot fresh:dry weight ratio and leaf area decreased with increasing dryness ratio (D: 8.40?30.49) and decreasing precipitation (519 mm to 143 mm). Hyperarid populations [Noorpur Thal - NpT (D: 10.90; P: 400 mm) and Cholistan - Cho (D:30.49; P: 143 mm)] relied …

Effects Of Moderate Drought On Leaf Bulliform Cells Of Aquatic And Coastal Population Of Phragmites Australis, Olena Nedukha

Turkish Journal of Botany

Studying leaves of aquatic and terrestrial populations of Phragmites australis grown on the bank of the Venetian strait of the Dnipro River in Kyiv (Ukraine) for establishing the role of bulliform cells in the mechanisms of plant resistance to moderate soil drought were studied. Bulliform (motor) cells participate in the twisting and folding of leaves during drought and strong sunlight. The study of bulliform cells in the leaves of the aquatic and terrestrial populations of P. australis was carried out using the methods of light microscopy, cytochemical methods, laser confocal microscopy, and biochemical methods. The comparative analysis of the structure …

Marrubium Zeydanlii (Lamiaceae), A New Species From Turkey, Zeki̇ Aytaç, Bahar Kaptaner İğci̇, Tuğba Ertuğrul, Nur Münevver Pinar, Deni̇z Aygören Uluer, Bariş Özüdoğru

Turkish Journal of Botany

Marrubium zeydanlii (Lamiaceae) is described as a new species from Turkey. It is similar to M. depauperatum and M. sivasense; however, it is distinguished from M. depauperatum by having lanate hairs on the stem, oblanceolate dentate leaves, 4?6-flowered verticillasters. It is also distinguished from M. sivasense by having lanate hairs on the stem, oblanceolate leaves, and shorter petals. The pollen grains are radially symmetrical and isopolar, the shape is oblate-spheroidal with the polar axes 16.7-20 µm and the equatorial axes 17.6-19.3 µm. trnL-F region was used to identify the phylogenetic position of the newly described species. The results …

Sublethal Effects Of Two Entomopathogenic Fungi Species, Metarhizium Anisopliae And Beauveria Bassiana, On The Cabbage Aphid (Brevicoryne Brassicae), Mahdieh Mousavi, Fariba Mehrkhou, Nurper Güz, Yobert Goosta, Remzi̇ Atlihan

Turkish Journal of Agriculture and Forestry

We evaluated the sublethal (LC25) effects of the three native strains of two important entomopathogenic fungi (EPFs) species (Metarhizium anisopliae AB, M. anisopliae Iran 245, and Beauveria bassiana 106) on the cabbage aphid, Brevicoryne brassicae L. (Hemiptera: Aphididae) which is among the most destructive pests of cole crops. Studies were carried out in controlled conditions providing 25 ± 2 °C, 60% ± 5% RH and a photoperiod of 16:8 h (L:D). The age-stage, two-sex life table method was used for data analysis. The results indicated that EPF treatments affected the population growth rate of the aphids by causing prolongation of …

Crude Extracts And Essential Oil Of Platycladus Orientalis (L.) Franco: A Source Of Phenolics With Antioxidant And Antibacterial Potential As Assessed Through A Chemometric Approach, Marwa Khammassi, Rayda Ben Ayed, Sana Khedhiri, Mouna Souihi, Mohsen Hanana, Ismail Amri, Lamia Hamrouni

Turkish Journal of Agriculture and Forestry

The chemical composition, antioxidant properties and antibacterial activities of different extracts (water, ethanol, acetate ethyl and hexane) and essential oil from Platycladus orientalis leaves were analysed in this study. The essential oil was extracted by hydrodistillation, and its chemical composition was determined by gas chromatography coupled to mass spectrometry (GC-MS). The major components of the essential oil were α-pinene (40.2%), β-phellandrene (9.3), α-cedrol (9.2%) and β-caryophyllene (6.3%). Phytochemical analysis of crude extracts and essential oil revealed the richness of ethyl acetate and ethanolic extracts in total phenolic content (62.69 and 61.44 mg GAE/g DW, respectively). The antioxidant activities of all …

Genome-Wide Analysis Of Peroxidase Genes In Passion Fruit (Passiflora Edulis Sims.) And Their Expression Patterns Induced By Root Colonization Of Piriformospora Indica Under Cold Stress, Dangdi Liang, Muhammad Moaaz Ali, Shariq Mahmood Alam, Xuping Huang, Ahmed Fathy Yousef, Walid F. A. Mosa, Emi̇ne Orhan, Zhimin Lin, Faxing Chen

Turkish Journal of Agriculture and Forestry

Peroxidases (PODs) have various physiological and biochemical roles in plant growth, development and stress response. The POD genes were identified in various plant species, but in passion fruit has not yet been thoroughly characterized. Here, we discovered 30 putative POD genes from the genome of Passiflora edulis Sims. For further elucidation, comprehensive bioinformatics analysis was utilized to determine the physicochemical properties, gene organization, conserved motifs, gene duplication and phylogenetic relationships of PePOD genes. Most of the POD proteins were predicted to be located in extracellular region. Gene organization and motif analysis showed that the number of exons and motifs in …

Selected Phenolics And Antioxidant Capacities: From Boğazkere (Vitis Vinifera L.) Grape To Pomace And Wine, Hande Tahmaz, Gökhan Söylemezoğlu

Turkish Journal of Agriculture and Forestry

In this research, the amounts of trans-resveratrol, (+)-catechin, (-)- epicatechin, and malvidin-3-glucoside which are among phenolic compounds as well as the total phenolic compound, total anthocyanin, and antioxidant capacity changes were examined in the Boğazkere (Vitis vinifera L.) grape, pomace before press, pomace after press and wine. In all parameters examined, a decrease was seen when proceeding from grape to wine, only (+)- catechin and (-)- epicatechin levels were detected to be higher in the prepress pomace. Total phenolic compound, total anthocyanin, and antioxidant capacity levels were found highest in grape samples, respectively, 8018 mg GAE/kg; 1606 mg/kg; 16.05 μmol …

Evaluation Of Cone And Seed Quality Of Siberian Stone Pine (Pinus Sibirica Du Tour) For Plus-Tree Selection, Svetlana Velisevich, Alexander Popov

Turkish Journal of Agriculture and Forestry

Siberian stone pine (Pinus sibirica Du Tour) is a cone-bearing species with outstanding nutritious seeds, health-supporting properties, and nut oil. Currently, the main volume of pine nuts is harvested in natural forests, which causes damage to ecosystems. The best solution to this problem would be harvesting nuts on special pine nut plantations established on the basis of high-seeding clones. However, it is hampered by the low efficiency of the existing methods for assessing plus-tree productivity. This work focused on cone analysis in two sites used for plus-tree selection: a 42-year-old sparse forest plantation and a 186-224-year-old closed natural forest. The …

Phytophthora-Citrus Interactions And Management Strategies: A Review, Anas Fadli, Hamid Benyahia, Sajjad Hussain, Rashid Iqbal Khan, Muhammad Junaid Rao, Talaat Ahmed, Veronica Ancona, Muhammad Fasih Khalid

Turkish Journal of Agriculture and Forestry

Citrus production is declining worldwide due to several biotic and abiotic factors. The diseases caused by Phytophthora spp. present major economic risks since they are soil-borne and spread quickly if environmental conditions are favorable, or irrigation is poorly managed. Phytophthora species are present in all citrus-producing areas around the world causing significant losses in crop yield and affecting tree health. Bark infection, damping-off, root rot, gummosis, brown rot, and cortical root rot are among the typical symptoms caused by Phytophthora spp. The pathogenicity of Phytophthora spp. depends mainly on the specific interactions between the isolates and citrus cultivars. The use …

Plant Growth-Promoting Bacteria Improve Triticum Aestivum L. Growth And Photosynthetic Activity In Sulfonamide-Contaminated Soil, Ammara Saleem, Asma Zulfiqar, Soha A. Alamoudi, Mada F. Ashkan, Eman Alhomaidi

Turkish Journal of Agriculture and Forestry

Antibiotics are disseminated by grazing animals or their feces throughout agricultural areas. These antibiotics, as environmental pollutants, have a negative impact on plant growth and physiology. Sulfonamides are frequently used to protect livestock production, but they also have a considerable negative impact on plant growth and rhizospheric bacteria. Plants are sensitive to their surroundings, and they employ their internal biological systems to deal with the threats to their growth and development. Soil microbes, which are the most common inhabitants, have amazing metabolic capacities that enable them to overcome abiotic constraints. The effects of sulfonamide stress on wheat cultivar Chakwal-50 were …

Graphene Oxide: A Promising Material For The Germination Of Melon Seeds Under Salinity Stress, Haluk Çağlar Kaymak, Meli̇ke Sevi̇m, Önder Meti̇n

Turkish Journal of Agriculture and Forestry

It is well-known that salinity is an important adverse environmental factor (abiotic stresses) that limits plant growth, development, and productivity all over the world. Herein, we report for the first time the use of graphene oxide (GO) as a promising material against the salinity stress using melon (Cucumis melo L.) seeds as the model crop. GO as a priming material possesses various advantages such as being highly water-soluble, nontoxic, producible on a large scale from graphite, and low-cost over the existing materials. In this study, we identified the effect of different GO doses (0, 0.25, 0.50, 0.75, and 1.0 mg/mL) …

Herbicide Resistance In Avena Sterilis Subsp Ludoviciana Populations From The Wheat Fields Of Turkey, Süleyman Gürdal Türkseven, Ahmet Uludağ, Mehmet Demi̇rci̇, Ahmet Tansel Seri̇m

Turkish Journal of Agriculture and Forestry

Avena sterilis L. subsp ludoviciana (Durieu) Gillet and Magne (AVELU) is among the most common and economically important grass weed species, especially in wheat fields of Turkey; therefore, the herbicides with the same mode of action (ACCase and ALS/AHAS inhibitors) are used to control have been successively applied without incessant by farmers. A study was conducted to find out the extent of wild oat problems throughout Turkey including herbicide resistance. This paper includes results of determining the herbicide resistance status of AVELU populations to ACCase and ALS inhibitors that are fenoxaprop (Fen), pinoxaden (Pin), tralkoxydim (Tra), mesosulfuron+iodosulfuron (MeI), and proxycarbazone+mesosulfuron …

Biochar Mitigates Salt Stress By Regulating Nutrient Uptake And Antioxidant Activity, Alleviating The Oxidative Stress And Abscisic Acid Content In Cabbage Seedlings, Melek Eki̇nci̇, Meti̇n Turan, Ertan Yildirim

Turkish Journal of Agriculture and Forestry

A pot experiment was conducted to investigate the growth, physiology, and biochemistry of cabbage seedlings in response to salinity stress with biochar. The study was conducted as factorial completely randomized design with two factors; salinity levels (0 and 150 mM NaCl) and biochar doses (weighed at the rate of 0%, 2.5%, and 5% by soil weight). Growth parameters such as stem diameter, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, and root dry weight of cabbage seedlings treated with 150 mM NaCl were lower than the control. Biochar amendments improved the growth parameters of cabbage seedlings under …

Inter-Primer Binding Site (Ipbs) Retrotransposon Markers Provide Insights Into Thegenetic Diversity And Population Structure Of Carrots (Daucus, Apiaceae), Mehtap Yildiz, Carlos Arbizu

Turkish Journal of Agriculture and Forestry

Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) …

Study Of Anatomical And Acc (1-Aminocyclopropane-1-Carboxylate) During Flower Budabscission Indicate An Important Role Of Alternate Bearing, Muhammet Ali̇ Gündeşli̇, Sali̇h Kafkas, Şenay Karabiyik, Si̇nan Eti̇, Nesi̇be Ebru Kafkas

Turkish Journal of Agriculture and Forestry

This study investigates whether, and how, 1-aminocyclopropane-1-carboxylic acid (ACC) is concerned in flower bud abscission of pistachio (Pistacia vera L.). Abscission was studied about the activation of the abscission zone, located between shoot and flower bud, from Uzun pistachio cultivar where the abscission profiles and the scanning electron micrographs pictorial differences in the abscission program, under natural conditions of flower bud. ACC content was investigated in the flower bud abscission zone during growth and abscission using liquid chromatography coupled with electrospray tandem mass spectrometry (UPLC/ESI-MS/MS). Results showed that abscission layers were started at first 45 days after full blooming (DAFB) …

Comparative Study Of Phenolic Compounds In Olive Oils From Differentgeographic Regions, Şeyma Şi̇şi̇k Oğraş

Turkish Journal of Agriculture and Forestry

In this study, the effect of cultivar, harvest year, and the geographic regions (Mediterranean, Aegean, Southeastern Anatolia, Marmara, and the Black Sea) on phenolic compounds of virgin olive oils were investigated. Tyrosol was the major phenolic compound in the Mediterranean, Southeastern, and Black Sea regions. Hydroxytyrosol showed the highest value (2.07 mg/kg) in the Southeastern Anatolia region and the lowest value (0.75 mg/kg) in the Marmara region. Among the phenolic acids, vanillic acid had an important place in phenolic compounds (p < 0.01). This phenolic acid gave higher values in the Marmara region compared to other regions. Flavonoids were determined as important groups of phenolic compounds in olive oils. The oils from the Southeastern Anatolia region separated from other oils with the highest levels of flavonoids such as quercetin, luteolin, and apigenin. All phenolic compounds, except transcinnamic acid and quercetin, increased in the second harvest year. Vanillic acid was the highest phenolic compound in the first year, in contrast, tyrosol had higher values than vanillic acid in the second year. Many phenolic compounds were affected by olive cultivar. Memecik has a higher content of tyrosol, vanillic acid, p-coumaric acid, ferulic acid, and quercetin in the Aegean region. However, this variety showed higher values for hydroxytyrosol, transcinnamic acid, luteolin, and apigenin in the Marmara region. Gemlik, Ayvalık, Çelebi, Domat and Memecik from Marmara regions had higher vanillic acid. Butko, Otur and Kızıl Satı showed higher tyrosol. Principal component analysis showed that phenolic compounds could play an important role in the separation of regions and cultivars.

Avian Haemosporidian Blood Parasite Diversity, Prevalence, And Distribution In Michigan’S Western Upper Peninsula, Maria M. Ferrer

Dissertations, Master's Theses and Master's Reports

Avian haemosporidian parasites, known as avian malaria (phylum Apicomplexa) can diminish an individual bird’s fitness by causing parasitemia, anemia, and reduced survival. Climate change is predicted to increase the spread of malarial parasites into more northerly latitudes where little is known about community compositions of these parasites. I assessed the prevalence and diversity of haemosporidian parasites in the first-ever community-level sampling of malaria in songbirds across the western Upper Peninsula of Michigan. In total, 179 blood samples were collected from birds representing 17 species, at five locations in the Upper Peninsula, including a mature forest, an early successional forest, and …

Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi

Dissertations, Master's Theses and Master's Reports

Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …

Links Between Electrophilic Stress And Antifungal Resistance In Pathogenic Candida Species, Amy R. Biermann

Dartmouth College Ph.D Dissertations

Collectively, Candida species are the most prevalent cause of both superficial and invasive fungal infections worldwide. Invasive Candida infections have a high mortality rate and predominantly affect individuals with underlying diseases, such as diabetes, HIV, or cancer. Unfortunately, many invasive Candida infections are recalcitrant to antifungal treatment, while intrinsically multidrug-resistant pathogens, like Candida auris, are increasing in prevalence. Although the canonical mechanisms of antifungal resistance in Candida species are well established, i.e., overexpression of efflux pumps and overexpression of or mutations in genes encoding drug targets, factors affecting the natural evolution and regulation of resistance mechanisms remain poorly understood. …

How Exercise Affects The Musculoskeletal System In The Biological Sexes: A Literature Review, Lauren Connolly

Honors Program Theses

Exercise has countless benefits for the human body. Physical activity increases overall health and reduces the risk of developing many chronic diseases. While the entire body is impacted by exercise, the musculoskeletal system is perhaps targeted most directly. Muscle contraction is required to complete any form of exercise, which helps build muscle mass and consequently strengthens bones. The physiology of musculoskeletal growth after exercise is the same for all individuals. However, the magnitude of this growth is not the same for men and women. Men have a profound ability to gain muscle mass that most women are not capable of …

Decadal Reevaluation Of Sugar Maple Dieback Etiology Across The Upper Great Lakes Region, Mattison E. Brady

Dissertations, Master's Theses and Master's Reports

Sugar maple (Acer saccharum) is a foundational tree species in northern hardwood forests of the United States and Canada. Though previous work has documented areas of substantial stress for this species in eastern North America, increasing reports of crown dieback in the Upper Great Lake states through the early 2000’s highlighted the relative lack of understanding of regional trends and causes. A 120-plot network of maple forest health monitoring sites was established and annually visited across Upper Michigan, northern Wisconsin, and eastern Minnesota between 2009 and 2012 to catalog and understand the regional phenomenon.

Results from the project’s …

Fine Scale Mapping Of Laurentian Mixed Forest Natural Habitat Communities Using Multispectral Naip And Uav Datasets Combined With Machine Learning Methods, Parth P. Bhatt

Dissertations, Master's Theses and Master's Reports

Natural habitat communities are an important element of any forest ecosystem. Mapping and monitoring Laurentian Mixed Forest natural communities using high spatial resolution imagery is vital for management and conservation purposes. This study developed integrated spatial, spectral and Machine Learning (ML) approaches for mapping complex vegetation communities. The study utilized ultra-high and high spatial resolution National Agriculture Imagery Program (NAIP) and Unmanned Aerial Vehicle (UAV) datasets, and Digital Elevation Model (DEM). Complex natural vegetation community habitats in the Laurentian Mixed Forest of the Upper Midwest. A detailed workflow is presented to effectively process UAV imageries in a dense forest environment …

Effects Of Post-Exercise Recovery Drink Composition On Subsequent Performance In Masters Class Athletes, Erica Goldstein

Electronic Theses and Dissertations, 2020-2023

Carbohydrate (CHO) and carbohydrate-protein coingestion (CHO-P) have been shown to be equally effective for enhancing glycogen resynthesis and subsequent same-day performance when CHO intake is suboptimal (≤0.8 g/kg). Few studies have specifically examined the effect of isocaloric CHO vs CHO-P consumption on subsequent high-intensity aerobic performance with limited time to recover (≤2 hours) in masters class endurance athletes. Participants (n = 22) were assigned to consume one of three beverages during a 2-hour recovery period: PLA (electrolytes and water), CHO (1.2 g/kg bm), or CHO-P (0.8 g/kg bm CHO + 0.4 g/kg bm PRO). All beverages were standardized to one …

Harnessing The Power Of The Nitro Group In Natural Product Synthesis, Katelyn Bobek

Electronic Theses and Dissertations, 2020-2023

The high reactivity and electron-withdrawing ability of the nitro group makes it a powerful tool in synthesizing a diverse range of bioactive natural products. The potential of the nitro group was employed via two main methodologies: iron (III)-mediated oxidative dearomatization and oxime carbonate butyrolactone formation to reach three important heterocyclic scaffolds; spiro, tropone and γ-butyrolactone. Nitro precursors were enantioselective synthesized by key nitro-aldol (Henry) and nitro-Michael reactions. A library of polysubstituted butyrolactone oxime carbonates were formed under mild DMAP and Boc2O conditions from readily available δ-nitroalcohols in good to high yields with broad functional group tolerability. Six lignan γ-butyrolactone natural …

Deciphering The Role And Clinical Application Of The Fgfr4-Klb-Fgf19 Axis In Colorectal Neoplastic Progression, Michael Rohr

Electronic Theses and Dissertations, 2020-2023

Colorectal cancer (CRC) is the third most common and third deadliest cancer worldwide with rising incidence rates attributed to environmental risk factors like diet. Investigating how these factors impact carcinogenesis requires an understanding of how transcriptional events evolve with respect to neoplastic progression. We employed meta-transcriptomics and latent trajectory modeling to establish a compendium of profiled healthy, adenoma, and CRC samples scored by their position along a pseudotemporal axis. By interpolating a continuous scale from cross-sectional data, dynamic processes occurring throughout disease progression can be analyzed more accurately. For example, smaller pseudotimes represented pre-malignant dysplasia and was characterized by cellular …

Computational Methods To Analyze Next-Generation Sequencing Data In Genomics And Metagenomics, Saidi Wang

Electronic Theses and Dissertations, 2020-2023

This thesis focuses on two important computational problems in genomics and metagenomics with the public available next-generation sequencing data. One is about gene regulation, for which we explore how distal regulatory elements may interact with the proximal regulatory elements. The other is about metagenomics, in which we study how to reconstruct bacterial strain genomes from shotgun reads. Studying gene regulation, especially distal gene regulation, is important because regulatory elements, including those in distal regulatory regions, orchestrate when, where and how much a gene is activated under every experimental condition. Their dysfunction results in various types of diseases. Moreover, the current …