Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences

In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students' self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.

"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19

The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from students' perspectives. Strengths included the quality of mentorship, opportunities for learning and professional development, and a feeling of connection with a larger community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote Research Experiences for Undergraduates (REUs) that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

Conversion of nontumorigenic dormant MOLT3 by lactate into a glycolytic cancer via epigenetic changes and lymphangiognesis

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Background: Lactate considered a "waste product" lactate is a multifunctional modulator. Processes modulated by lactate are: 1. initiation of the transformation of the microenvironment 2.production of hyaluronan which interacts with RHAMM to cause cell motility, stabilize mitotic spindle, and supports stem cells. With these many processes, we hypothesized that lactate might interrupt the dormant state of the MOLT3 dormant cell line. Previous authors Indraccola et al, PNAS, 2006 reported that the dormant MOLT3 cell line implanted in SCID mice could be interrupted to become tumorigenic by co-implantation with VEGF,FGF, or irradiated (dead) Kaposi Sarcoma. We used this model to determine if lactate could stimulate tumorigenesis in a similar manner. Methods: In multiple cohorts of SCID mice, lactate was coimplanted with MOLT3 cells. In approximately 40 days, tumors grew rapidly in an exponential manner. Arterial perfusion was measured by contrast enhanced dual energy CT and MRI perfusion. Immunohistochemistry was performed for vascular stains CD21,VEGFR3, Notch 1, Ephrin B, VEGFA,VEGFD, Macrophages, VEGFD. Rna sequencing was performed on six samples, 3 Molt3 cell plugs, 3 MOLT3/lactate tumors (sequencing done at UCLA, data processed at Broad Street Institute MIT). Results: The data confirmed lactates's modulator role. Perfusion studies showed no arterial flow. The IHC showed many cancer cell with many mitotic figures and apoptosis.IHC confirmed presence of numerous macrophages, increased VEGFD, lymphatics and no arteries. Indraccola's reported their tumors showed no mitotic figures. 1114 genes were up/down regulated. In general rna showed: 1.mitochondrial dysfunction 2.Down regulated tumor suppressors 3) Up regulated oncogenes 4)Increased Stem cell markers 5) increased NFK-b and other pathways. Conclusions: Lactate induced an avascular "cancer" with features similar to natural pancreatic ductal and triple negative breast cancer. Results question the universality of the angiogenic switch. We hypothesize Lactate from marophages may be the cause of inflammation induced cancer.

Functional interactions between microRNAs and RNA binding proteins

Ensuring the appropriate spatial-temporal control of protein abundance requires careful control of transcript levels. This process is regulated at many steps, including the rate at which transcripts decay. microRNAs (miRNAs) and RNA Binding Proteins (RBPs) represent two important regulators of transcript degradation. We review here recent literature that suggests these two regulators of transcript decay may functionally interact. Some studies have reported an excess of miRNA binding sites surrounding the positions at which RBPs bind. Experimental reports focusing on a particular transcript have identified instances in which RBPs and miRNAs compete for the same target sites, and instances in which the binding of a RBP makes a miRNA recognition site more accessible to the RISC complex. Further, miRNAs and RBPs use similar enzymes for degradation of target transcripts and the degradation of the target transcripts occurs in similar subcellular compartments. In addition to miRNA-RBP interactions involving transcript decay, RBPs have also been reported to facilitate the processing of pri-miRNAs to their final form. We summarize here several possible mechanisms through which miRNA-RBP interactions may occur.

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.

Mutational spectrometry without phenotypic selection: human mitochondrial DNA

By first separating mutant from nonmutant DNA sequences on the basis of their melting temperatures and then increasing the number of copies by high-fidelity DNA amplification, we have developed a method that allows observation of point mutations in biological samples at fractions at or above 10-6. Using this method, we have observed the hotspot point mutations that lie in 100 base pairs of the mitochondrial genome in samples of cultured cells and human tissues. To date, 19 mutants have been isolated, their fractions ranging from 4x10-4 down to the limit of detection. We performed specific tests to determine if the observed signals were artefacts arising from contamination, polymerase errors during PCR or DNA adducts created during the procedure. We also tested the possibilities that DNA replication mismatch intermediates, or endogenous DNA adducts that were originally present in the cells, were included with true mutants in our separation steps and converted to mutants during PCR. We show that while most of the mutants behave as double-stranded point mutants in the cells, some appear to arise at least in part from mismatch intermediates or cellular DNA adducts. This technology is therefore sufficient for the observation of the spectrum of point mutations in human mitochondrial DNA and is a tool for discovering the primary causes of these mutations.

Efficiency of separation of DNA mutations by constant denaturant capillary electrophoresis is controlled by the kinetics of DNA melting equilibrium

Constant denaturant capillary electrophoresis (CDCE) separation takes place in the heated portion of the capillary where faster-moving, unmelted DNA fragments are in equilibrium with slower-moving, partially melted forms. Within a certain temperature range, the position of the melting equilibrium and thus the average electrophoretic mobility of each mutant is different. The resulting differences in mobility allow sequences containing single base pair point mutations to be separated from each other. We report the results of experiments in which we explored the rules defining separation efficiency by varying the parameters of CDCE. We discovered an unusual peak broadening mechanism. In contrast to most other DNA electrophoresis systems, peak width in CDCE steadily decreases with the square root of the separation speed. Moreover, the peak width displays a sharp maximum at a specific temperature. To account for these observations, we use a model which describes CDCE separation as a random walk. According to this model, peaks in CDCE are broad because the kinetics of the melting equilibrium are slow and therefore the number of random walk steps represented by melting/renaturation transitions is relatively small. In addition to providing a satisfactory interpretation of the data, the model also predicts that separation efficiency will increase as the ionic strength of the running buffer is increased and as the concentration of denaturant in the buffer is decreased. These predictions were verified and were used to establish conditions for high-resolution CDCE suitable for separating complex mixtures of single base pair mutants.