Browsing by Author "Nukala, Nihitha"
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Item Design of Man-made Miniature CRISPR-Cas Proteins Using Computational and Artificial Intelligence Technologies(2023) Jayasinghe-Arachchige, Vindi; Madugula, Sita Sirisha; Nammi, Bharani; Nukala, Nihitha; Wang, Shouyi; Liu, JinPurpose: The CRISPR/Cas system is a popular genome editing technique that uses a guide RNA and specific proteins known as Cas proteins for its function. A major challenge in harnessing CRISPR-Cas technology for applications in living organisms is the lack of an efficient delivery system. Due to the larger size of available Cas proteins used in this tool, it is challenging to encapsulate the CRISPR components into a single vehicle for delivery. To address this issue, we have used computational and Artificial Intelligence (AI) tools on designing compact-size Cas proteins that have a similar function and are more efficient than available Cas proteins. Methods: The available crystal structures of the smallest CRISPR-Cas systems were utilized and further reduced. A novel method termed the "Blocks and Gaps approach” was employed to design new mini-Cas proteins with a size range of 450-500 amino acids in length. The generated protein sequences (1 million) were subsequently used in machine learning-based two classification models to filter out the non-Cas proteins from it. The resultant Cas protein sequences were used in homology-modeling-based (Swiss-Model) and AI-based (Alphafold2) protein structure prediction methods to obtain their 3D structures. Further, the global and local structural features as well as the solubility of these proteins were analyzed, and top candidates were subjected to molecular dynamics (MD) simulations including substrate DNA and gRNA. Results/Conclusions: A library of man-made miniature Cas proteins was generated, and these proteins are less than half the size of the widely used CRISPR-Cas such as Cas9 or Cas12a. 50% of these were predicted as Cas proteins by both the machine learning-based classification models used. And 90% of them show similar 3D structures as their original counterparts. 10% of these passed through the final validations. Experimental testing of the activity of these designed proteins is to be investigated at this point of the study.Item Type II Diabetes Mellitus and COVID-19: A Case Series Exploring Insulin Management in Patients from Two Family Medicine Clinics(2024-03-21) Nukala, NihithaPurpose: About 37 million Americans have diabetes and out of this population, over 90% of them have type 2 diabetes. An estimated $200 billion per year is spent on managing this disease. There is limited data on factors that could explain whether diabetic patients experienced better HgbA1C control during the COVID-19 pandemic. The relationship between diabetes medications (DM) and diabetes outcomes during the COVID era is not well-characterized. In this case series, we aimed to evaluate type II diabetes outcomes pre-COVID-19 vs. COVID-19 era. Methods: This case series was conducted in two family medicine clinics that included patients with type II diabetes. The following data from all patients at least 18 years or older on 3/1/2019 were extracted: hemoglobin A1c, medication prescriptions (insulin use patterns, non-insulin prescription patterns oral diabetes medications), and number of prescriptions discontinued. We followed a guidance statement from the American College of Physicians in terms of how outpatient diabetes is managed and used A1c of less than 8% as the threshold to assess the clinical outcomes for this outpatient population. A1c values were compared between two cohorts, a pre-COVID-19 cohort (March 1, 2019-March 13, 2020) and a COVID-19 era cohort (March 14, 2020-March 31, 2021). An analysis was performed on all patients whose A1c control status was changed, defined as the last A1c in each of the two study periods changed either from > 8% to =< 8% (got better), or from =< 8% to > 8% (got worse). For each of the patients with A1c control status change, we identified patterns of diabetic medication prescriptions during the COVID-19 era: (1) insulin and other DM medications, (2) no insulin but other DM medication, or (3) insulin-only prescriptions. Results: Eighty-one patients fulfilled the study criteria. Fifty-three patients got better, and 28 patients got worse. Of the 52 cases, 28 got better due to insulin use. Eighteen of these patients discontinued their insulin at some point during the study period. Of the 28 patients that got worse. Out of the 26 cases, 10 of them got worse while on insulin. Nine out of 10 of these patients discontinued their insulin at some point during the study period. Only 1 patient was on their insulin medication throughout the entire study. Out of the 28 cases with some form of diabetes management therapy, 16 of them were on non-insulin medications. Thirteen out of 16 of these patients discontinued at least one of their medications at some point during the study period. 23 out of 26 patients discontinued at least one prescription. Conclusion: This case series demonstrates how two family medicine clinics treated diabetic patients during a pandemic. The majority were using insulin throughout COVID-19 era and did experience changes to their medication profile with other DM medications. A1c levels did change significantly from pre-COVID-19 to COVID-19 era, while prescriptions for diabetic treatment were reduced. This study identified the importance of keeping insulin and other DM medication prescriptions through a pandemic and how COVID-19 impacted Hemoglobin A1C and overall diabetes care.