Building a Bicycle-Powered Centrifuge

Centrifuges are very common instruments utilized in research and clinical settings. The purpose of a centrifuge is to separate the components of a mixture using centrifugal force. An example of a process that utilizes centrifugation is the acquisition of a hematocrit, where red blood cells are separated from blood plasma and the other cellular components. Industrial centrifuges are expensive and generally employed in academic or clinical contexts. A bicycle centrifuge, on the contrary, may be designed and implemented in more generalized settings. Moreover, a bicycle centrifuge affords the opportunity to relate principles in physics to concepts specific to other scientific disciplines, such as biology and kinesiology

Fluorescent Labeling of Calmodulin for Future Application

Calmodulin (CaM) is a small dumbbell-shaped, intermediary protein. CaM binds with several hundred different molecules to help control bodily functions. At Northwestern, we use fluorescently labeled CaM to understand these functions further. The goal of this project is to successfully label CaM protein using the fluorescent dye Alexa Fluor 594. After labeling CaM, we will use buffer exchange chromatography to purify the sample. Following that, we will use three processes to verify the successful labeling of CaM: UV/VIS spectroscopy, mass spectroscopy, and fluorescent microscope imaging. Once labeled and purified, our CaM samples can be used for years to come by Northwestern students and professors to understand the unknown functions of bodily enzymes it interacts with

It is Time for Zero Tolerance for Sexual Harassment in Academic Medicine

While there are more women in leadership positions in academic medicine now than ever before in our history, evidence from recent surveys of women and from graduating medical students demonstrates that sexual harassment continues in our institutions. Our ability to change the culture is hampered by fear of reporting episodes of harassment, which is largely due to fear of retaliation. We describe some efforts in scientific societies that are addressing this and working to establish safe environments at national meetings. We must also work at the level of each institution to make it safe for individuals to come forward, to provide training for victims and for bystanders, and to abolish locker room talk that is demeaning to women

Investigating the Putative RecA-Like Recombinase Gene

Our Biochemistry: Molecular Genetics class has partnered with the Immunology class to investigate the expression of JacoRen57’s gene 50. The bacteriophage JacoRen57 – found in Sioux Center, Iowa (accession: MK279840). JacoRen57’s genome has sequenced by Pittsburg SEA-PHAGES Institute and fully annotated by Northwestern College students in 2018. A region between gene 49 and 50 caught our attention as there is a large gap between these genes. Almail et al., investigated if this is a transcription regulatory region for genes 49 and/or 50 (2021). This work demonstrated the region has a regulatory function in the direction of gene 50. Based on comparison genomics, gene 50 is a putative RecA-like recombinase (Almail et al., 2019). This protein has several functions including guiding the recombination of DNA within a gene. RecA-like recombinase allows the virus to evolve into new variants which can improve infection and replication. This is crucial for creating diversity in the genome and DNA repair mechanisms (Galletto and Kowalczykowski, 2007). To continue examination of gene 50 expression, we are working towards developing antibodies for this protein. To do this, the first step is to create an expression construct (Figure 1), express the protein in bacteria, purify the protein, and then use the purified protein to inoculate mice. This poster describes the construction of the expression vector. This work will provide valuable insight into the expression of gene 50, the RecA-like recombinase

High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation

<p>Abstract</p> <p>Background</p> <p>Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer's disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments.</p> <p>Results</p> <p>We report results from a screen of 572 kinases in the human genome for effects on tau hyperphosphorylation using a loss of function, high-throughput RNAi approach. We confirm effects of three kinases from this screen, the eukaryotic translation initiation factor 2 α kinase 2 (EIF2AK2), the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and the A-kinase anchor protein 13 (AKAP13) on tau phosphorylation at the 12E8 epitope (serine 262/serine 356). We provide evidence that EIF2AK2 effects may result from effects on tau protein expression, whereas DYRK1A and AKAP13 are likely more specifically involved in tau phosphorylation pathways.</p> <p>Conclusions</p> <p>These findings identify novel kinases that phosphorylate tau protein and provide a valuable reference data set describing the kinases involved in phosphorylating tau at an AD-relevant epitope.</p

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

Abstract Background Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear. Methods Diabetic gastroparetics, diabetic non-gastroparetic controls, idiopathic gastroparetics and non-diabetic non-gastroparetic controls underwent full-thickness gastric body biopsies. Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®. A subset of differentially expressed genes in diabetic gastroparesis was validated in a separate cohort using QT-PCR. Results 111 genes were differentially expressed in diabetic gastroparesis and 181 in idiopathic gastroparesis with a log2fold difference of | ≥ 2| and false detection rate (FDR) < 5%. Top canonical pathways in diabetic gastroparesis included genes involved with macrophages, fibroblasts and endothelial cells in rheumatoid arthritis, osteoarthritis pathway and differential regulation of cytokine production in macrophages and T helper cells by IL-17A and IL-17F. Top canonical pathways in idiopathic gastroparesis included genes involved in granulocyte adhesion and diapedesis, agranulocyte adhesion and diapedesis, and role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Sixty-five differentially expressed genes (log2fold difference | ≥ 2|, FDR < 5%) were common in both diabetic and idiopathic gastroparesis with genes in the top 5 canonical pathways associated with immune signaling. 4/5 highly differentially expressed genes (SGK1, APOLD1, CXCR4, CXCL2, and FOS) in diabetic gastroparesis were validated in a separate cohort of patients using RT-PCR. Immune profile analysis revealed that genes associated with M1 (pro inflammatory) macrophages were enriched in tissues from idiopathic gastroparesis tissues compared to controls (p < 0.05). Conclusions Diabetic and idiopathic gastroparesis have both unique and overlapping transcriptomic signatures. Innate immune signaling likely plays a central role in pathogenesis of human gastroparesis.https://deepblue.lib.umich.edu/bitstream/2027.42/145193/1/12920_2018_Article_379.pd

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

Abstract Background Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear. Methods Diabetic gastroparetics, diabetic non-gastroparetic controls, idiopathic gastroparetics and non-diabetic non-gastroparetic controls underwent full-thickness gastric body biopsies. Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®. A subset of differentially expressed genes in diabetic gastroparesis was validated in a separate cohort using QT-PCR. Results 111 genes were differentially expressed in diabetic gastroparesis and 181 in idiopathic gastroparesis with a log2fold difference of | ≥ 2| and false detection rate (FDR) < 5%. Top canonical pathways in diabetic gastroparesis included genes involved with macrophages, fibroblasts and endothelial cells in rheumatoid arthritis, osteoarthritis pathway and differential regulation of cytokine production in macrophages and T helper cells by IL-17A and IL-17F. Top canonical pathways in idiopathic gastroparesis included genes involved in granulocyte adhesion and diapedesis, agranulocyte adhesion and diapedesis, and role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Sixty-five differentially expressed genes (log2fold difference | ≥ 2|, FDR < 5%) were common in both diabetic and idiopathic gastroparesis with genes in the top 5 canonical pathways associated with immune signaling. 4/5 highly differentially expressed genes (SGK1, APOLD1, CXCR4, CXCL2, and FOS) in diabetic gastroparesis were validated in a separate cohort of patients using RT-PCR. Immune profile analysis revealed that genes associated with M1 (pro inflammatory) macrophages were enriched in tissues from idiopathic gastroparesis tissues compared to controls (p < 0.05). Conclusions Diabetic and idiopathic gastroparesis have both unique and overlapping transcriptomic signatures. Innate immune signaling likely plays a central role in pathogenesis of human gastroparesis.https://deepblue.lib.umich.edu/bitstream/2027.42/145193/1/12920_2018_Article_379.pd

An evaluation of the applicability of pseudospectral methods to problems in transport phenomena

Call number: LD2668 .T4 1986 J66Master of ScienceChemical Engineerin