Sorghum bicolor is an essential cereal crop that is extensively parasitized by plants of the Striga genus, leading to yield loss and exacerbating food insecurity in sub-Saharan Africa.  Previous research has suggested that soil microbes may reduce the degree of Striga penetration into host roots. This study focused on examining the effect of natural soil microbes on the formation of root aerenchyma by studying possible patterns of formation in different cultivars of S. bicolor under various conditions, including soil sterility and Striga treatment. Seeds of Striga-resistant genotype SRN39 and Striga-susceptible genotype Shanqui Red (SQR) were germinated in vitro and grown in a greenhouse environment. After two weeks, cross-sections of the plant roots were taken and analyzed. Images of root cross-sections were electronically processed and quantified based on the amount of aerenchyma formation.  An initial analysis found that SQR grown in natural soil saw significantly more aerenchyma formation than those grown in sterile conditions. Meanwhile, a second comparison found that aerenchyma was completely absent in SRN39 regardless of soil sterility. In addition, this analysis found that the crown and seminal root tips of S. bicolor grown in sterile soil had significantly less aerenchyma compared to those grown in non-sterile soil. This suggests that soil microbe therapy may prove useful to certain sorghum cultivars, such as SRN39, that already exhibit natural Striga tolerance properties. The insight gained through these findings can be potentially applied to building a Striga-resistant yet affordable and productive sorghum cultivar. 

Fragile X syndrome occurs in subjects with >200 CGG repeats in the 5’ untranslated region of the FMR1 gene. Premutation carriers (55-200 CGG repeats) were originally thought to be asymptomatic but some have psychological and metabolic issues among others, and with age some develop the neurodegenerative disease called Fragile X-associated tremor/ataxia syndrome (FXTAS). Studies have been done which have shown that people with FXTAS tend to have mitochondrial functionality problems. However, the exact reason for why this occurs is still elusive. The overall goal of our research was to evaluate the mitochondrial DNA copy numbers (mtDNA) and deletions in fibroblasts from individuals with the FMR1 premutation by qPCR utilizing dual-labeled probes. To measure the mtDNA and deletions, we evaluated the Ct values for each DNA sample provided from Real Time Quantitative-PCR (qPCR).  Our data shows that there was not a significant difference between the mitochondrial DNA copy numbers in fibroblasts from individuals with FXTAS and without it. Our data also shows that non-affected FXTAS carriers had a lower mitochondrial gene ratio, signifying that they had more deletions.

Three tyrosine sulfation sites are known in complement C4, and sulfation of C4 influences its activity in the complement cascade. Since tyrosine sulfation usually occurs within a group of proteins, this research focuses on whether there are additional tyrosine sulfation sites in complement proteins. The Position-Specific Scoring Matrix (PSSM) reports high scores at tyrosine sites in all of the complement proteins. Some of the complement proteins, such as complement C5, have tyrosine residues located on the exterior of the protein, showing an increased likelihood of becoming sulfated. An increased understanding of tyrosine sulfation contributes to the development of pharmaceutical drugs that could treat diseases related to mutations of complement-mediated immune responses. These diseases include macular degeneration, angioedema, systemic lupus erythematosus, and other complement deficiencies that greatly impact the lives of affected people.

Background: Intron mediated enhancement (IME) is the phenomenon in eukaryotic organisms in which an intron improves gene expression. Creating new introns that boost gene expression beyond observed introns would be useful in biotechnology applications.
Results: Introns near the promoter are compositionally distinct from those farther down the transcript. This difference in composition is used in an algorithm called the IMEter, which can be used to predict the effectiveness of an intron. Creating artificial introns that simply maximize the IMEter score results in introns that are almost entirely GC. In order to create more natural introns we propose a genetic algorithm, MIA, that simultaneously maximizes IMEter score and the relative entropy compared to average introns. We also propose MIA+, which adds a motif-scoring function to the fitness function.
Conclusions: MIA creates high scoring introns as well as introns with repeated motifs which have previously been shown to be effective in increasing IME. Command line options allow the user to tune the algorithm for IMEter score or motif density. Based on previous experimental data, introns created by MIA are expected to increase gene expression 20-fold or more.

Ibuprofen is a nonsteroidal anti-inflammatory drug that is used worldwide to inhibit pain and inflammation. Ibuprofen has been shown to have negative side effects in the cardiovascular system, but there has been significantly less research on the side effects in the kidney. The goal of this research is to determine if ibuprofen causes proteasomal dysfunction in the kidney. The proteasome is a complex that is critical for removal of unwanted and oxidized proteins. Proteasome levels were observed through western blotting and proteasome assays, and no significant difference was found in proteasome levels between the ibuprofen and control samples. The proteasome activity was significantly decreased in samples treated with ibuprofen. It was also determined that automated western blot machines are not as effective as manual western blotting methods.

Mesoporous silica nanocages (MSNs) are inorganic-based nanocarriers containing porous channels. These channels can be filled with medicinal compounds and utilized to target various diseases in the respiratory system. The purpose of this study is to determine the frequency of MSN uptake, retention and fate in macrophages after deposition in the lungs following a single, acute period of inhalation. Macrophages, highly phagocytic cells of the lungs, appear to uptake MSNs at different rates and to different degrees following inhalation into the lungs. The actual MSN uptake by these cells over time was done by calculating the volume of MSN in alveolar macrophages at 1, 7, and 21 days post-inhalation. In previous studies, mice were exposed to MSNs and harvested after 1, 7, and 21 days to show macrophages as the dominant cell type in the lungs to sequester MSN following inhalation. Using cells recovered from the lungs by bronchoalveolar lavage (BAL), as well as examining lung tissues to determine the location of these cells in lungs, MSN with either a positive or negative surface charge to determine its effect on uptake were used to determine the relative frequency of uptake in the macrophages. The results show that the area of MSNs within the macrophages both slightly decrease over time. However, overall it indicates that the MSNs are not clearing out from the lungs or the macrophages.

With a deeper knowledge and understanding of the effects of point mutations on amino acid interactions and protein functions, the objective is to create a database to store the collected data and add on to computational learning. Currently, through the FoldIt software, a Rosetta score is provided to serve as a frame of reference for the stability of a mutation. However, only a small amount of designs and mutations engineered achieve the desired function. The database would allow for an increased accuracy and level of knowledge on the prediction on how different point mutations would affect protein stability and efficiency through altered amino acid interactions. The current project focuses on the already well understood β-glucosidase B (BglB) enzyme with a known crystal structure and reports the Michaelis-Menten kinetics and thermal stability of purified mutants. [Insert part about important results]. Through the analysis of the results and the accumulation of data points within the database on BglB, there can be an improved understanding toward point mutations that can be applied to other proteins. The research currently does not have immediate short term results but the data that is collected continues to grow and better the predictive algorithm and protein redesign.