Complex I is a member of the respiratory chain in both bacteria and human mitochondria. Studies have shown that many human mitochondria disorders are related to the poor assembly of Complex I, rather than simple enzymatic malfunction [1,2,3,4]. For the purpose of analyzing the assembly of the thirteen subunits (A-N) found in the Escherichia coli homolog of the Complex I enzyme, antibodies are needed to recognize the individual subunits. Since the H subunit is the only subunit without an antibody, high-affinity antibodies are needed to be produced from the HA epitope tags. The tags were introduced separately by the polymerase chain reaction (PCR) method in two different plasmids, one containing genes G-H, and the other containing H-I-J-K. DNA sequencing indicated high confidence in HA complexes. After growth of cell cultures, an induced expression of these genes by arabinose verified expression of the protein with induced tag. Then, a western blot was done to test both constructs ability to yield single proteins, of the correct size, that were recognized by the HA-antibody. Therefore, these constructs can be further tested for suitability in the analysis of Complex I assembly.
{"title":"Construction of the hemagglutinin (HA) epitope tags for Subunit H of Complex I in Escherichia coli","authors":"Q. T. Pham","doi":"10.25172/JOUR.4.1.5","DOIUrl":"https://doi.org/10.25172/JOUR.4.1.5","url":null,"abstract":"Complex I is a member of the respiratory chain in both bacteria and human mitochondria. Studies have shown that many human mitochondria disorders are related to the poor assembly of Complex I, rather than simple enzymatic malfunction [1,2,3,4]. For the purpose of analyzing the assembly of the thirteen subunits (A-N) found in the Escherichia coli homolog of the Complex I enzyme, antibodies are needed to recognize the individual subunits. Since the H subunit is the only subunit without an antibody, high-affinity antibodies are needed to be produced from the HA epitope tags. The tags were introduced separately by the polymerase chain reaction (PCR) method in two different plasmids, one containing genes G-H, and the other containing H-I-J-K. DNA sequencing indicated high confidence in HA complexes. After growth of cell cultures, an induced expression of these genes by arabinose verified expression of the protein with induced tag. Then, a western blot was done to test both constructs ability to yield single proteins, of the correct size, that were recognized by the HA-antibody. Therefore, these constructs can be further tested for suitability in the analysis of Complex I assembly.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"4 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129223349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Why does Gudea wear the roll-brimmed hat? Neo-Sumerian period statues of Gudea, king of Lagash (c. 2100 BCE), were primarily designed to convey the leader’s piety before the gods. The traditional interpretation of the roll-brimmed hat suggests that this garment added to Gudea’s pious affect, serving as a humbler alternative to the divine horned-headdress worn by Naram-Sin, the last king of the previous Akkadian period. While acknowledging the less overtly ambitious quality of the roll-brimmed hat, I nevertheless argue that other potential meanings of this headgear have been overlooked. In particular, I take a materiality and haptic approach to propose that Gudea’s hat suggests that he may have learned from, and improved upon, the grand claims of Naram-Sin. Both the Stele of Naram-Sin and the statues of Gudea share the portrayal of a strong and supple right arm, which Irene Winter has interpreted as making both leaders appear sexually alluring and “well-formed”. This paper will argue that the roll-brimmed hat had a similar effect. Exploration of earlier depictions of the roll-brimmed hat from Uruk period artworks and on rock reliefs in the Zagros mountains will demonstrate that this headgear had a history of association with the “well-formed” bodies of powerful rulers. However, those earlier depictions render the hat as a smooth surface. Thus, Gudea’s choice to emphasize his headgear’s woolly quality was deliberate. It not only gave a humble effect to the garment but also, I will propose, offered a distinct kind of allure. The pattern of the curling sheep’s wool on the hat encouraged haptic appreciation, disrupting the smooth materiality for which diorite was usually prized and creating the illusion of a soft, plush texture which contrasted with the rest of Gudea’s relatively undecorated garments. More than simply humble, I propose that this headgear was a deliberate artistic strategy designed to make Gudea powerfully attractive to both his people and his gods.
{"title":"An Alternative View on the Roll-Brimmed Hat","authors":"Lauren King","doi":"10.25172/JOUR.4.1.8","DOIUrl":"https://doi.org/10.25172/JOUR.4.1.8","url":null,"abstract":"Why does Gudea wear the roll-brimmed hat? Neo-Sumerian period statues of Gudea, king of Lagash (c. 2100 BCE), were primarily designed to convey the leader’s piety before the gods. The traditional interpretation of the roll-brimmed hat suggests that this garment added to Gudea’s pious affect, serving as a humbler alternative to the divine horned-headdress worn by Naram-Sin, the last king of the previous Akkadian period. While acknowledging the less overtly ambitious quality of the roll-brimmed hat, I nevertheless argue that other potential meanings of this headgear have been overlooked. In particular, I take a materiality and haptic approach to propose that Gudea’s hat suggests that he may have learned from, and improved upon, the grand claims of Naram-Sin. Both the Stele of Naram-Sin and the statues of Gudea share the portrayal of a strong and supple right arm, which Irene Winter has interpreted as making both leaders appear sexually alluring and “well-formed”. This paper will argue that the roll-brimmed hat had a similar effect. Exploration of earlier depictions of the roll-brimmed hat from Uruk period artworks and on rock reliefs in the Zagros mountains will demonstrate that this headgear had a history of association with the “well-formed” bodies of powerful rulers. However, those earlier depictions render the hat as a smooth surface. Thus, Gudea’s choice to emphasize his headgear’s woolly quality was deliberate. It not only gave a humble effect to the garment but also, I will propose, offered a distinct kind of allure. The pattern of the curling sheep’s wool on the hat encouraged haptic appreciation, disrupting the smooth materiality for which diorite was usually prized and creating the illusion of a soft, plush texture which contrasted with the rest of Gudea’s relatively undecorated garments. More than simply humble, I propose that this headgear was a deliberate artistic strategy designed to make Gudea powerfully attractive to both his people and his gods.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114242170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular dynamics (MD) simulation is a computational chemistry technique used to observe how a molecular system behaves as time passes. MD is based on solving Newton’s equations of motion. This requires the use of force fields to describe the potential energy function of each different molecule type in molecular system. In order to develop a force field, charges, bonds, angles, and dihedrals must be parameterized to fit quantum mechanics (QM) data. By basing the force field on QM data, MD simulations have higher accuracy while still using the low computational cost of molecular mechanics. This project focuses on developing well-fit force fields for β-lactam class antibiotics for future MD simulations. Full antibiotics are too large of a molecule to parameterize from scratch, so instead we broke them down into fragments. Smaller molecule fragments allow less terms to be optimized which greatly simplifies force field development. By the transferable nature of parameters in CHARMM force fields, the fragment parameters can be transferred to connecting molecules. Due to this, we can build up larger organic molecule force fields piece by piece.In this work, we developed CHARMM force fields for cephalothin, cefotaxime, ceftazidime, and aztreonam.
{"title":"Force Field Development of β-lactam Class Antibiotics","authors":"Trevor Heinzmann","doi":"10.25172/JOUR.5.1.2","DOIUrl":"https://doi.org/10.25172/JOUR.5.1.2","url":null,"abstract":"Molecular dynamics (MD) simulation is a computational chemistry technique used to observe how a molecular system behaves as time passes. MD is based on solving Newton’s equations of motion. This requires the use of force fields to describe the potential energy function of each different molecule type in molecular system. In order to develop a force field, charges, bonds, angles, and dihedrals must be parameterized to fit quantum mechanics (QM) data. By basing the force field on QM data, MD simulations have higher accuracy while still using the low computational cost of molecular mechanics. This project focuses on developing well-fit force fields for β-lactam class antibiotics for future MD simulations. Full antibiotics are too large of a molecule to parameterize from scratch, so instead we broke them down into fragments. Smaller molecule fragments allow less terms to be optimized which greatly simplifies force field development. By the transferable nature of parameters in CHARMM force fields, the fragment parameters can be transferred to connecting molecules. Due to this, we can build up larger organic molecule force fields piece by piece.In this work, we developed CHARMM force fields for cephalothin, cefotaxime, ceftazidime, and aztreonam.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126431747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flagella can be used to make magnetically-controlled microfluidic and nanoscale devices for biomedical applications in both vitro and vivo environments. They are capable of operating with high precision on the cellular and subcellular level. So far, scientists and engineers have successfully used monolithic inorganic materials or photoactive polymers [1] to mimic the helical bacterial flagella whose rotary-propulsion mechanism effectively overcomes the dominant viscous forces that prevail in a low Reynolds-number environment. Here, we focus on bacterial flagella and their rotary motion. The bacterial flagellum is an ideal biomaterial for constructing self-propelling nanoswimmers because it can reversibly change its geometry in response to different environmental stimuli such as pH, the local concentration of certain organic solvents, and mechanical force on the flagella. The bacterial flagellum is very easy to manipulate because it is composed of flagellin which can be mechanically isolated through vortexing and centrifugation, which enables flagella to be used as nanoscale sensors and mechanical transducers. Our project focuses on fabricating a bacterial flagella forest which consists of an ordered array of flagella on a glass substrate. Flagella are attached to magnetic nanobeads via biotin-avidin bonding for actuation by oscillating magnetic field.
{"title":"Engineering a Bacterial Flagella Forest for Sensing and Actuation – A Progress Report","authors":"Xihe Liu, Shulin Ye, Isaac Oti, L. Metzinger","doi":"10.25172/JOUR.4.1.4","DOIUrl":"https://doi.org/10.25172/JOUR.4.1.4","url":null,"abstract":"Flagella can be used to make magnetically-controlled microfluidic and nanoscale devices for biomedical applications in both vitro and vivo environments. They are capable of operating with high precision on the cellular and subcellular level. So far, scientists and engineers have successfully used monolithic inorganic materials or photoactive polymers [1] to mimic the helical bacterial flagella whose rotary-propulsion mechanism effectively overcomes the dominant viscous forces that prevail in a low Reynolds-number environment. Here, we focus on bacterial flagella and their rotary motion. The bacterial flagellum is an ideal biomaterial for constructing self-propelling nanoswimmers because it can reversibly change its geometry in response to different environmental stimuli such as pH, the local concentration of certain organic solvents, and mechanical force on the flagella. The bacterial flagellum is very easy to manipulate because it is composed of flagellin which can be mechanically isolated through vortexing and centrifugation, which enables flagella to be used as nanoscale sensors and mechanical transducers. Our project focuses on fabricating a bacterial flagella forest which consists of an ordered array of flagella on a glass substrate. Flagella are attached to magnetic nanobeads via biotin-avidin bonding for actuation by oscillating magnetic field.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116700394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Refugees have a variety of mental health needs due to their experiences, including trauma, anxiety, and depression. Psychotherapy, one of the main modalities for treatment, presents limitations including language barriers and negative stigmas. Music therapy might help to overcome these limitations due to its reliance upon music, rather than verbal language, as the therapeutic medium, and due to music’s ubiquitous cultural prevalence. Music therapy has been shown to have positive effects on sleep quality, well- being, trauma symptoms, social function, and mood. Music therapy training and research results have demonstrated ways to connect with clients through music and overcome cross-cultural barriers. The objective of this case study was to determine the effects of group music therapy on levels of anxiety, depression, well-being, functional disability, and distress in two adult Congolese refugees. Further, the study explored the themes which the participants reported they preferred and were most likely to use on their own regarding the music interventions. A mixed-methods approach was used to gather both quantitative and qualitative data. The study involved eight weekly, one hour-long music therapy sessions following a protocol that included four themes: socialization, emotional expression, English-learning, and personalized use of music. Levels of anxiety, depression, well-being, and functional disability were assessed using psychometric tests before the first session, after the fourth session, and after the eighth session. The data found overall decreased levels of anxiety, depression, and distress, increased levels of well-being, and little change in level of functional disability. Prevalent themes from the self-report questionnaire were instrument playing, singing, listening, and the hello song. Conclusions and recommendations for future research are included.
{"title":"The Effects of Group Music Therapy on Levels of Anxiety, Depression, Well-Being, Functional Disability, and Distress in Adult Congolese Refugees","authors":"Elise Hawkes","doi":"10.25172/JOUR5.1.8","DOIUrl":"https://doi.org/10.25172/JOUR5.1.8","url":null,"abstract":"Refugees have a variety of mental health needs due to their experiences, including trauma, anxiety, and depression. Psychotherapy, one of the main modalities for treatment, presents limitations including language barriers and negative stigmas. Music therapy might help to overcome these limitations due to its reliance upon music, rather than verbal language, as the therapeutic medium, and due to music’s ubiquitous cultural prevalence. Music therapy has been shown to have positive effects on sleep quality, well- being, trauma symptoms, social function, and mood. Music therapy training and research results have demonstrated ways to connect with clients through music and overcome cross-cultural barriers. The objective of this case study was to determine the effects of group music therapy on levels of anxiety, depression, well-being, functional disability, and distress in two adult Congolese refugees. Further, the study explored the themes which the participants reported they preferred and were most likely to use on their own regarding the music interventions. A mixed-methods approach was used to gather both quantitative and qualitative data. The study involved eight weekly, one hour-long music therapy sessions following a protocol that included four themes: socialization, emotional expression, English-learning, and personalized use of music. Levels of anxiety, depression, well-being, and functional disability were assessed using psychometric tests before the first session, after the fourth session, and after the eighth session. The data found overall decreased levels of anxiety, depression, and distress, increased levels of well-being, and little change in level of functional disability. Prevalent themes from the self-report questionnaire were instrument playing, singing, listening, and the hello song. Conclusions and recommendations for future research are included.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124016383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNA binding proteins control post-transcriptional aspects of gene regulation. While transcriptional control over the aging process has been well-established, less is known about post-transcriptional control over the aging process. We have used CRISPR/Cas9 genetics to study combinations of RNA binding proteins in C. elegan, a transparent nematode or roundworm one millimeter in length, and their role in aging. The manner in which the research was conducted was through experimental laboratory work in which the lifespan of the nematodes was monitored until their death. The three mutations affecting RNA binding proteins that assays were performed with are exc-7, fox-1, and mbl-1. We found that double mutants have stronger effects on lifespan than single mutants. Thus, RNA binding protein mutations, although separate, appeared to be functionally connected. These observations, though being considered in C. elegans, could have a substantive impact on the study of gene regulation in humans and in turn, provide insight into the human aging processes.
{"title":"Combinatorial Genetics of RNA Binding Proteins for Lifespan Regulation in C. elegans","authors":"Nikita Tapiawala","doi":"10.25172/JOUR.4.1.6","DOIUrl":"https://doi.org/10.25172/JOUR.4.1.6","url":null,"abstract":"RNA binding proteins control post-transcriptional aspects of gene regulation. While transcriptional control over the aging process has been well-established, less is known about post-transcriptional control over the aging process. We have used CRISPR/Cas9 genetics to study combinations of RNA binding proteins in C. elegan, a transparent nematode or roundworm one millimeter in length, and their role in aging. The manner in which the research was conducted was through experimental laboratory work in which the lifespan of the nematodes was monitored until their death. The three mutations affecting RNA binding proteins that assays were performed with are exc-7, fox-1, and mbl-1. We found that double mutants have stronger effects on lifespan than single mutants. Thus, RNA binding protein mutations, although separate, appeared to be functionally connected. These observations, though being considered in C. elegans, could have a substantive impact on the study of gene regulation in humans and in turn, provide insight into the human aging processes.","PeriodicalId":221628,"journal":{"name":"SMU Journal of Undergraduate Research","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128087152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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