Prioritization of Potential Targets in a Massive Multiplex CRISPR Screen

First Place award in the Medical Technology and Informatics Category at the 26th Denman Undergraduate Research ForumHematologic cancers, broadly categorized as leukemias, lymphomas, and myelomas, are diagnosed in 3.3 million people globally and account for 10% of new cancer cases in the U.S. every year. In the last decade, newer treatments that directly target aberrant molecular processes, rather than the entire cell, have provided a less toxic alternative to traditional chemotherapy, however, identification of targets for molecular inhibitors is a major rate-limiting step. Recent studies have demonstrated the efficacy of utilizing Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) as a mechanism to conduct forward genetic screens and combining the results with existing drugs to significantly improve the identification of probable therapeutics. The following study explores an algorithm to process data from pooled CRISPR forward genetic screens to rapidly prioritize potential targets. Currently, targets of interest are manually curated by comparing pooled CRISPR data to existing gene, protein, and drug databases. This is a Sisyphean task as individual gene products vary among individuals, while gene pathway products are consistently similar. Thus, our algorithm will rapidly aggregate genes of interest for a pre-determined synergistic value (p-value, false discovery rate (FDR-value)), while simultaneously performing an efficient gene pathway-level analysis by automatically comparing against known databases including pathway analysis, drug/protein interaction databases, and biomedical literature. The algorithm will quickly display the common gene pathways, the genes involved in respective pathways, their synergistic values in a prioritized fashion, and will include database results in an easy-to-read table to focus on potential targets for future research. The significantly reduced human labor in data processing due to the development of this algorithm will be critical in advancing research of novel drugs and improving the therapeutic outcomes for patients.College of Engineering Undergraduate Research ScholarshipNo embargoAcademic Major: Biomedical Engineerin

Fatigue Performance of Glass Fiber/Epoxy Composite at Low Temperature

Due to technological advancement in the manufacturing methods of composites, these materials find a plethora of applications which include but are not limited to wind energy projects in the form of turbine blades. These blades at times are exposed to temperatures as low as -40ᵒC. Therefore, there is a need to study low-temperature effects on such materials under different loading scenarios. This study investigates the possibility of utilizing MAC/GMC as a simulation tool to match trends of mechanical properties such as fatigue performance and stiffness variation of a given Glass fiber/Epoxy composite at 23ᵒC (room temperature) and -40 ᵒC, under fully reversed (R=-1) and tensile (R=0.1) loading cases. The results show remarkable consistency with the published data

Curiosity and learning

A toddler was playing in the sandpit for the first time, under the watchful eye of his mother. Her attention shifted as her cellphone rang and the little boy, oblivious of his surroundings, was deeply engrossed in holding sand in his hand. He seemed to be thrilled with the experience of sand slipping out of his fist as he kept repeating the action of picking up sand in his fist over and over again. Gradually curiosity took over and this time he brought his fist to his mouth and was about to get the taste of sand, when his mother pulled him up in her arms and shouted, “No..no eat, sand dirty, you bad boy”. The following few weeks the child was not allowed to play in the sand and was contained in his stroller

Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense

cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A&ndash;H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems. &nbsp;</p

Parental perceptions of the impact of neonatal unit visitation policies during COVID-19 pandemic

Objectives To ascertain parental perceptions of the impact of restricted visiting policies to neonatal intensive care units during the current COVID-19 pandemic. Design Cross-sectional survey of parents impacted by visitation policies. Setting Six tertiary level neonatal units, four from the UK and two from the USA, participated in the study. Participants Parents and families of infants hospitalised in the participating centres between 1 May 2020 and 21 August 2020. Methods Online-based and/or paper-based survey, querying the visitation policies and their impact on parents' ability to visit, care for and bond with their infants. Results A total of 231 responses were received. Visitation limited to a single visitor with no restrictions on duration was the most frequently reported policy; 140/217 (63%). Visitation policies were perceived as being restrictive by 62% (138/219) of the respondents with 37% (80/216) reporting being able to visit less often than desired, 41% (78/191) reporting being unable to bond enough and 27% (51/191) reporting not being able to participate in their baby's daily care. Mild to severe impact on breast feeding was reported by 36% (75/209) of respondents. Stricter policies had a higher impact on families and were significantly associated with a lack of bonding time, inability to participate in care and an adverse impact on breast feeding. Conclusions Visitation policies during the COVID-19 pandemic varied between centres and over time with stricter restrictions implemented earlier on in the pandemic. Parents reported significant impacts on their ability to visit, care for and bond with their infants with perceived severity of impact worse with stricter restrictions

Comparison of Outcomes of Preterm Infants Who Received Human Milk-Based vs. Bovine-Milk Based Human Milk Fortifier

Background: Bovine (BOV) or human milk-based fortifier (HUM) is used to add necessary macronutrients to mother's own breastmilk. HUM has been shown to improve growth outcomes and decrease morbidities in infants<1250 grams (g) birth weight (BW). Data is scant about outcomes for neonates 1250-1500g BW. Aim: Compare neonatal outcomes of infants 1250-1500g BW fed HUM vs BOV. Methods: This retrospective cohort study examined data from 150 babies 1250-1500g BW born Jan. 2016-Dec. 2018. Nutrition outcomes included days to full feeds (130 mL/kg/day), parenteral nutrition days, weight, length, and head circumference data. Nutritional z-scores were calculated using Fenton 2013 curves. Clinical outcomes included common neonatal morbidities. Outcomes were analyzed through statistical testing. Comparisons were adjusted for BW. Results: HUM-fed infants were born earlier, had a lower BW, and lower % of small for gestational age (SGA) infants at birth. The postmenstrual age (PMA) at discharge was not significantly different. HUM-fed infants had higher discharge weight z-score and growth velocity. Conclusions: Despite being more premature and smaller at birth, HUM-fed infants went home at a similar PMA and had less postnatal growth failure. This study demonstrates a HUM diet is associated with improved growth outcomes for infants 1250-1500 g BW. This project was completed with contributions from Jana Unger, Joseph Hagan, Muralidhar Premkumar, and Amy B. Hair from the Texas Children's Hospital.Biology and Biochemistry, Department ofHonors Colleg

A non-toxic approach for treatment of breast cancer and its metastases: capecitabine enhanced photodynamic therapy in a murine breast tumor model

Aim: Breast cancer (BCA) in women is a leading cause of mortality and morbidity; distant metastases occur in ~40% of cases. Here, as an alternative to ionizing radiation therapy and chemotherapy and their associated side effects, we explored a new combination approach using capecitabine (CPBN) and aminolevulinate-based photodynamic therapy (PDT). We had previously developed a combination PDT approach in which 5-fluorouracil (5FU), a differentiation-promoting agent, increases the levels of protoporphyrin IX (PpIX) in cancer cells when given as a neoadjuvant prior to aminolevulinic acid (ALA). However, 5FU can be toxic when administered systemically at high levels. We reasoned that CPBN, a known chemotherapeutic for BCA and less toxic than 5FU (because CPBN is metabolized to 5FU specifically within tumor tissues), might work equally well as a PDT neoadjuvant.Methods: Murine 4T1 BCA cells harboring a luciferase transgene were injected into breast fat pads of female nude mice. CPBN (600 mg/kg/day) was administered by oral gavage for 3 days followed by intraperitoneal ALA administration and PDT with red light (633 nm) on day 4. Tumor growth and regression were monitored in vivo using bioluminescence imaging. Histological changes in primary tumors and metastases were assessed by immunohistochemistry after necropsy.Results: CPBN pretreatment of 4T1 tumors increased cellular differentiation, reduced proliferation, raised PpIX levels, enhanced tumor cell death, and reduced metastatic spread of 4T1 cells post-PDT, relative to vehicle-only controls.Conclusion: The use of CPBN as a non-toxic PDT neoadjuvant for treatment of BCA represents a novel approach with significant potential for translation into the clinic