Open scholarship at Cornell
eCommons is a service of Cornell University Library that provides long-term access to a broad range of Cornell-related digital content of enduring value. Learn more about eCommons.
Make a deposit
Submit your document, research paper, image, data, code, and more into Cornell's digital repository. Learn how to submit.
Recent Submissions
Defining Organic Dairy Quality: A Study on Thermoduric Bacteria
Lee, Renee (2024-12)
Thermoduric bacteria can be divided in two main subgroups, non-sporeforming and sporeforming, and both are a major challenge for the dairy industry as they can survive higher temperatures, which they are subjected to during pasteurization. Sporeforming bacteria, a subgroup of thermoduric bacteria, are able to survive other processing hurdles, such as drying and sanitation, in addition to pasteurization. Non-sporeforming thermoduric bacteria and sporeforming bacteria originate from different places on organic farms with improperly sanitized farm equipment often linked with non-sporeforming thermoduric bacteria and contamination from the environment, feed, and bedding being the major driver of sporeforming bacteria. It is important to accurately enumerate and characterize thermoduric bacteria in order to better formulate control measures, however there is little understanding of the thermoduric bacterial populations in contemporary organic dairy supplies in the United States. This research aims to (i) evaluate the diversity of aerobic and anaerobic thermoduric bacteria in organic dairy using a farm-to-table approach, (ii) assess the association between higher laboratory pasteurization counts and certain subgroups of thermoduric bacteria, and (iv) identify whether climate is a driver of aerobic sporeforming bacterial diversity. Overall, the outcomes of these studies may help facilitate the development of a system to apply the appropriate prevention measures for non-sporeforming and sporeforming thermoduric bacteria at farms and processing plants in order to improve organic dairy product quality.
BILAYER 2-DMINESIONAL MOLYBEDNUM DISULFIDE CROWN ETHER POLYMER THIN FILM MEMORY TRANSISTOR
Zhou, Haolei (2024-12)
Neuromorphic electronics have been developed and innovated in recent years due to their critical contributions to the future intelligent computing systems. The human brain has outstanding information processing functions with neural networks which can operate at a low energy consumption. Potentiation and depression are brain activities that refer to the process by which synaptic connections between neurons become stronger or weaker with frequent and periodic stimulating pulses. This concept is correlated with the learning and memory functions and can be simulated with various electronics nowadays. Among them, organic electro-double-layer transistors provide an opportunity since they are biologically compatible, well tunable and low power consumption for switching. 2-D monolayer Molybdenum disulfide (MoS_2) have recently been applied on the organic FET due to its high effective mass, large direct band gap around 1.8 eV, ultra-low power dissipation and a high on/off ratio. It is an ideal material designed for the semiconductor part of the device. Although there are several research of MoS_2 on the transistors currently, the exploration of MoS_2 application on the transistors is still in an incipient stage. To accomplish potentiation and depression activities, hysteresis is the crucial characteristic we are seeking in the devices. 2-D polymer materials have the proper microstructure for membrane applications which is capable to cage the ions inside the electrolyte. The porous structure can also fulfill membrane ion selectivity. 2-D polymers have not been applied wildly on the transistors yet, but we think it is intriguing and provides an unprecedented opportunity to modify the neuromorphic memory transistors. We study the potential of combining MoS_2 and crown ether, a 2-D polymer thin film, to construct a bilayer memory transistor. Through a comprehensive investigation of the synthesize process, characterization and device integration of 2D polymers, our work tends to unravel some principal mechanisms including dielectric constant of solvents, concentration-dependent dynamics and ion-selectivity of membranes. This research aims to facilitate the rational design of a bilayer structure memory transistor for neuromorphic computing.
Branched peptide-based targeted protein degraders for the modulation of ternary complex geometry
Almonte, Joshua (2024-12)
Proteolysis Targeting Chimeras (PROTACs) are heterobifunctional targeted protein degraders that selectively degrade a protein of interest (POI) by recruiting innate protein degradation machinery. The current PROTAC design landscape is limited by the use of small molecules as ligands which are difficult to design and modify and have a limited range of potential targets. Peptide-based PROTACs (PepTACs) address these limitations through their modularity, standardized synthesis, and the availability of tools—such as phage display, yeast display, and increasingly powerful computational techniques—for designing peptide ligands against nearly any protein target. Here, we aim to expand on the design of PepTACs by proposing a method to modify the linker attachment point utilizing selectively branched, peptide ligands and solid-phase peptide synthesis. As a proof-of-concept, two model branched PepTACs were synthesized and characterized against the oncoprotein known as Cell Cycle-Related and Expression-Elevated Protein in Tumor (CREPT). Lipid nanoparticle delivery of PepTACs was explored, revealing peptide hydrophobicity as a driving force for encapsulation. LNP delivery of the branched constructs into HeLa cells showed dose-dependent cellular uptake. However, a CREPT-luciferase degradation assay yielded inconclusive results regarding their intracellular activity. Circular dichroism indicates branching destabilizes central binding features. Further studies are needed to elucidate the structure-activity relationships of branched PepTACs.
DEVELOPMENT AND IMPLEMENTATION OF FOOD SAFETY AND QUALITY INDUSTRY INTERVENTIONS IN ACADEMIA: THE NEED FOR PRACTICALITY FROM A BUSINESS PERSPECTIVE
Motzer, Caroline (2024-12)
Food safety and quality are integral departments of any successful food business, and while research is constantly identifying possible tools (e.g. artificial intelligence or novel microbiological testing methods) to further efforts in these departments, tools created by academia need to be practical from a business perspective in order to be most effective and adopted into industry. To address this, three investigations were conducted. The first investigation explored whether novel AI and digital technologies are suitable for human pathogen control in Controlled Environment Agriculture (CEA) and the associated challenges and opportunities that could come with implementation in the industry. To achieve this, AI, food safety, and CEA experts gathered to conduct a gap and opportunities workshop for AI implementation for human pathogen control in CEA. Additionally, a site visit to a CEA business was conducted to view operations. Outcomes from this investigation highlight how tools created by academia for food industry, in order to be effective, need to take into account i) the industry’s current level of food safety maturity, ii) current industry practices and norms and, iii) how to effectively communicate the quantitative financial benefit (i.e., in this case, reduction in recall risk) to business leaders. The second study involved the development of a food quality related tool specifically for the dairy industry: a microbiological test to enumerate quality defect causing thermoduric bacteria in dairy with a special focus on non-sporeforming bacteria. To address this, 38 isolates from non-sporeforming genera were inoculated into skim milk broth and independently subjected to four different heat treatments (A: 63°C for 30 minutes, B: 65°C for 15 minutes, C: 68°C for 7 minutes and D: 70°C for 5 minutes), followed by plating using two different media types (Standard Methods Agar and Aerobic Count Petrifilms), each of which were incubated and enumerated after three different incubation periods (24h, 48h, and 72h) at 32°C. All combinations were compared to our gold standard test, the Laboratory Pasteurization Count (i.e., heat treatment of 63°C for 30 minutes followed by plating with Standard Methods Agar and incubation of plates for 48h at 32°C). This study attempted to utilize knowledge gained from the first investigation such as use of current industry standard practices (i.e., we made sure to use standard dairy industry media [Standard Methods Agar] and an incubation temperature [32°C]). Interestingly, our results suggest that i) Aerobic Count Petrifilms are not a suitable media to enumerate some thermoduric bacteria and, ii) 72h incubation time presented a significantly smaller log reduction (i.e., there was more bacterial growth at 72h) compared to the gold standard incubation time of 48h. However, due to the small effect size in cell count reduction between the 48h incubation and 72h incubation (i.e., estimated mean pairwise difference in cell count reductions between 48h and 72h of only 0.28 log CFU/mL), the final method suggested for further exploration in this study utilized an incubation time of 48h. The researchers selected the 48h incubation time because, from a business perspective, waiting the additional 24h for marginally more exact results did not seem valuable for industry. Finally, the third study worked to address a gap highlighted in the first investigation; the need for identification of costs associated with implementing food safety tools for industry. Furthermore, it aims to understand what drives small and medium-sized businesses to invest into food safety programs as they may face unique challenges. This study involved using 9 small and medium-size dairy processing plants (SMDPPs), which all had been part of a prior ~1 year-long Listeria Environmental Monitoring Program (EMP) implementation study. Each plant was emailed an EMP cost questionnaire which was used to obtain each plant’s (i) self-reported EMP associated costs (e.g., estimated total value of product in a plant at any given time [EVTFP], corrective actions costs) and, (ii) perceived ability to control pathogens in their processing environment. Finally, plants were evaluated by the research team on their food safety culture resulting in a food safety culture score. Results showed that variables including plant size, EVTFP, overall Listeria prevalence in a plant, and food safety culture scores are not reliable predictors for how much a plant invested into its Listeria EMP indicating that investment into EMP for SMDPPs may be influenced by other, outside or non-food safety related factors. Overall, the outcomes from these three investigations illustrate that food safety and quality tools, in order to be most effective, need to take into account the industry’s current food safety and quality maturity, work to utilize pre-existing foundations/standard practices in the industry, and communicate costs and financial returns to business leaders.
DISSECTING TRANSCRIPT-SPECIFIC REGULATION OF PRE-MRNA SPLICING EFFICIENCY BY CIS-ELEMENTS AT EACH CHEMICAL STEP
Jin, Bozhou (2024-12)
Pre-mRNA splicing is a highly conserved step in regulating eukaryotic gene expression levels and transcript identities. Non-coding intronic sequences must be precisely removed from nascent transcripts through 2 sequential transesterification reactions. In every splicing event, a large ribonucleoprotein complex named the spliceosome must assemble anew and catalyze the reactions through a chain of intermediate steps. The efficiency of each of these steps is transcript-specific and regulates gene expression. However, what cis-elements determine these efficiencies is not well understood. Our lab has previously developed MPE-seq, a targeted RNA-seq method that allows the simultaneous detection of rare splicing isoforms from all introns in the genome. Coupling this method with metabolic labeling enables the quantification of splicing efficiency at each of the two transesterification steps. In this thesis, I demonstrate my work to further develop this method to allow large-scale comparative studies on strains carrying different variations of the same gene. With this method, I worked towards setting up a system using two distinct classes of transcripts in Saccharomyces cerevisiae to identify and understand the cis-elements that lead to their different splicing regulations.