MACUB (2021) Conference

Abstract:

The vascular flora at Riverdale Park, Bronx, New York were sampled during the growing season of 2021, April 14 to October 26, 2021. One hundred fifty-four species in 122 genera in 72 families were identified. Sixty non-native vascular plant species composed 39% of the flora. The largest families in the flora were the Asteraceae, 16 species and Rosaceae, 13 species. The largest genera were Acer 6 species, Quercus and Carex each with 5 species. The circumference and trunk diameter of Riverdale Park’s big trees were measured with a diameter tape 1.37 meters above the ground. A double trunked Q. alba had a circumference of 515 cm, Q. rubra 338 cm, Q. velutina 335 cm while Acer saccharinum, Platanus occidentalis, Carya ovata, and Liriodendron tulipifera with circumferences over 300 cm. The parks protected status will enable researchers to conduct comparative floras in the future.

 

Abstract:

Thyroid hormone has profound effects on the heart and cardiovascular system. In thyroid hormone deficiency, cardiac function is impaired. The thyroid gland produces two hormones, T4 (~85%) and T3 (~15%). T4 is a prohormone that is deiodinated to T3, the active hormone. Reduced serum T3 levels can result from thyroid disease, (hypothyroidism), or indirectly as a result of decreased T4 to T3 conversion. In some hypothyroid patients, and in severe illness, surgery or trauma, there is decreased activity of the mono-deiodinase enzyme resulting in decreased serum T3, often with normal levels of serum T4 and the regulatory hormone, TSH (thyroid stimulating hormone). There is evidence that inflammatory cytokines play a role in this low T3 syndrome, sometimes referred to as nonthyroidal illness. The virus that causes COVID-19, the SARS-CoV-2 coronavirus, can damage heart muscle and affect cardiac function. Furthermore, in critical illness, including heart failure, there is evidence that low T3 states further impair cardiac function and have been shown to be a reliable prognostic marker. The low T3 state in critical illness and in heart failure has been associated with increased all-cause mortality.
To assess the current use of thyroid function testing, and the prevalence of nonthyroidal illness in a critically ill patient population, we retrospectively reviewed thyroid function testing in 720 COVID-19 patients at NYU Langone’s Tisch Hospital between March and May 2020. Of those patients, T3 testing was included in only 37 patients, (average age 60.86 years, range 19.7 – 86 years; 52.7% male; average days after positive COVID-19 test 20.04). All but 2 patients (94.6%) had serum T3 levels below the reference range [reference range 1.2 to 2.8 nmol/L]. Of those patients with reduced serum T3 levels, only two appeared to be hypothyroid with elevated TSH. Therefore, 89.2% of the patients who were tested for serum total T3 meet the criteria for nonthyroidal illness.
These data are significant in demonstrating the high occurrence of nonthyroidal illness in a large COVID-19 population with very severe illness. Low T3 states may have adverse effects in critical illness and serve as an independent predictor of increased risk of mortality. Additionally, experimental COVID treatment protocols with hydroxychloroquine would put this patient population at greater risk of cardiac effects. Hypothyroidism and hydroxychloroquine both prolong the QT interval, which predisposes to ventricular arrhythmias and sudden cardiac death.
In summary, in 720 COVID-19 patients, only 37 (0.05%) were assessed for serum total T3, despite the growing understanding in the medical community that the low T3 syndrome may have adverse effects in critical illness and is a reliable independent prognostic indicator of mortality. In those 37 patients, 94.6% had reduced serum T3, with 89.2% meeting the criteria for non-thyroidal illness. Replacement with liothyronine sodium injection (Triostat) has been shown to be safe and effective in treating the low T3 syndrome after cardiac surgery, and may prove to be beneficial in this setting.

Abstract:

Innate immunity is characterized by host defenses involving anatomical barriers, sensor systems that recognize patterns associated with microbes or tissue damage, phagocytic cells, the inflammatory response and fever. Macrophages are a very important component of innate immunity. They are sentinel cells that can immediately detect foreign invasion or tissue abnormalities and trigger appropriate innate immune responses to clear the problem. Macrophages are present in nearly all human organs and tissues. A critical aspect of macrophages is that they are phagocytic cells, which engulf and degrade microbial pathogens, foreign objects, dead cell debris, and cancer cells. Upon stimulation and activation, macrophages regulate innate immune responses, as well as adaptive immune responses involving lymphocytes, by recruiting other immune cells to the local of invasion or damage.
In response to a microenvironment that has microbial cells or products, stimulated lymphocytes, or damaged cells, macrophages undergo final differentiation into one of two distinct activated or functional populations. The M1 macrophages are characterized by the generation of high levels of pro-inflammatory cytokines, antimicrobial properties, increased production of reactive nitrogen and oxygen species, and induction of helper lymphocyte responses. In contrast, M2 macrophages are characterized by their involvement in tissue remodeling and immune regulation.
The mechanistic target of rapamycin (mTOR) is a conserved serine/threonine protein kinase that responds to environmental signals, such as nutrient availability and presence of specific growth factors or hormones, to control cell growth, proliferation, metabolism, survival and differentiation. The mTOR pathway plays a critical role in mammalian cell, organ and organism homeostasis. The current model of mTOR activation suggests that a cytoplasmic mTOR translocates to the lysosome in response to nutrients. Once on the lysosome mTOR encounters its activator and becomes fully activated. Once activated, mTOR phosphorylates its targets to trigger protein translation initiation, lipid synthesis, ribosome biogenesis, and inhibition of macroautophagy.
Not much in currently known about the role of mTOR in macrophage polarization, and macrophage-mediated innate immune responses. Recent findings show that the mTOR pathway is required for macrophage differentiation from bone marrow derived progenitor cells. Moreover, recent studies suggest that mTOR triggers macrophage differentiation by inhibiting macroautophagy in the cell. Here, we propose to investigate the role of mTOR in macrophage polarization and activation. We hypothesize that mTOR translocates to the lysosome in response to pathogen signals, inhibits macroautophagy, and triggers during M1 polarization, but not M2 polarization, to ensure rapid phagocytosis of pathogenic invaders.
To investigate our hypothesis we are going to use monocytes isolated from peripheral blood. The monocytes will be differentiated into inactive macrophages in culture by the addition of phorbol 12-myristate 13-acetate (PMA). After that, we will trigger M1 or M2 polarization by using lipopolysaccharide (LPS, M1) or interleukin4 (IL-4, M2), in the absence or presence of the mTOR allosteric inhibitor rapamycin. We will then measure M1 or M2 cytokine production by specific ELISA assays, followed by fluorescence microscopy evaluation of mTOR subcellular localization and autophagosome formation.

Abstract:

The humble and lowly kitchen sponge often sits neglected in a dish by the sink, marinating in the pool of water, soap, dirt, oil, and leftover food-- a perfect home for a rich microbial ecosystem. Following recent studies that explored the bacterial composition of kitchen sponges, we hypothesized that these sponges should harbor bacteriophages as well. A team of undergraduate students as part of a research course isolated bacteria from their own dirty kitchen sponges and used the isolated bacteria to find bacteriophages residing in the same sponge. All students had numerous bacteria from their sponges to choose for isolation, but only two successfully found a bacteriophage in the sponge that infected their isolated bacteria. Subsequent microscopy, biochemical and genomic characterization of the bacteria revealed that these two isolated strains are members of the Enterobacter cloacae subgroup. What was originally thought to be two isolated phages ended up being a single novel phage that is able to infect both of the isolated hosts from the two different sponges. Further host range testing with standard-related lab strains found that the phage can also infect Cronobacter muytjensii. Electron microscopy shows that phage is myoviridae. The genome of the phage does not show any strong similarity to other sequenced bacteriophages, and most of the identified genes have no known predicted function. Subsequent work has identified additional bacteriophages that infect these two bacterial isolates. Ongoing efforts continue to characterize these bacteriophages and the two related enteric bacteria. Many Gram-negative enteric bacterial strains are opportunistic pathogens that readily acquire resistance to antibiotics. These bacteriophages will help us understand the therapeutic potential of bacteriophages in treating infections caused by enteric bacteria.

Abstract:

The global COVID-19 pandemic left universities with few options but to turn to remote learning. With much effort, STEM courses made this change in modality; however, many laboratory skills, such as measurement and handling equipment, are more difficult to teach in an online learning environment. A cohort of instructors who are part of the NSF RCN-UBE funded Sustainable, Transformative Engagement across a Multi-Institution/Multidisciplinary STEM (STEM2) Network (a working group of faculty from two community colleges and three 4-year universities) analyzed introductory biology and chemistry courses to identify essential laboratory skills that students will need in advanced courses. Seven essential laboratory proficiencies were derived from reviewing disciplinary guiding documents such as AAAS Vision and Change in Undergraduate Biology Education, American Society for Microbiology Recommended Curriculum Guidelines for Undergraduate Microbiology Education and American Chemical Society Guidelines for Chemistry: data analysis, scientific writing, proper handling and disposal of laboratory materials, discipline-specific techniques, measurement, lab safety and personal protective equipment, and interpersonal/collaborative skills. Our analysis has determined that some of these skills are difficult to develop in a remote/online setting but could be recovered with appropriate interventions. Skill recovery procedures suggested are a skill “boot camp,” department/college coordinated club events, and a triage course. The authors recommend that one of these three recovery mechanisms be offered to bridge this skill gap and better prepare STEM students for upper-level science courses and the real world.

Abstract:

Undergraduate biology students often graduate without exposure to authentic research experiences. Laboratory courses follow a one or two week fail-proof experiment resembling a cookbook recipe, lacking the uncertainty of genuine research. Techniques in molecular biology cover an array of skills essential to succeed in a biotechnological laboratory today. This lab course is based on the teaching of concepts while imparting the skills and applications of modern techniques, providing students with theoretical concepts and laboratory skills. We prepare students to carry-out scientific protocols that can be applied to a future workforce setting. Students are immersed in a 10-week series of labs with the objective to use molecular cloning to make a novel gene therapy vector; therapies are designed to inhibit the expression of genes of the virus that causes Covid-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Students are introduced to PubMed and Genbank to research the background of SARS-CoV-2 and its target genes; the Spike gene (S), the membrane gene (M) the nucleocapsid gene (N) and the envelope gene (E). Students use the DNA software, Serial Cloner, as a tool to evaluate DNA sequences and mFOLD to analyze RNA structure. Students generate and visualize the design of an antisense gene therapy directed against one of the target viral genes. Using our gene therapy platform, students generate a vector with a unique target. Subsequently student-generated vectors were transfected into mammalian tissue culture cells that express the target genes (S, M, N or E) and RNA and protein was collected to measure the efficacy of the gene therapy vector to reduce the expression of the target viral gene.

Abstract:

Undergraduate Research is a powerful high impact practice, I use it in my honors General Biology 2 course, where students are engaged in analysis of bacteriophage genomes. The class is a part of HHMI Sea-Phages program. Spring 2020 was the semester that started a challenging stretch of semesters. The Undergraduate Research class started its Bioinformatics project in person and finished online. I decided to compare the outcomes of the online classes to those of the in person. For the Spring 2020 the students' performance was comparable to an in-person modality. This can be attributed to the fact that students received ample in person instruction prior to conducting their independent investigations. They got a chance to build a community of learners, knew each other and could help each other. Starting from Fall 2020 the real challenge begun. Initially, I thought that it should not make too much of a difference for the computational research to be conducted online rather than in person. However, from the start I learned that it was more challenging. Students seemed more confused and less confident about the research objectives. Explaining the use of various software was more difficult and building student support groups was more difficult. To compare the outcomes, I decided to look at the artifacts produced y students. Students were required to write research reports and present their findings to their peers at the end of semester. I developed rubrics to assess the presentations and the final reports. The results were compared to the oral presentations and written reports from the semester's taught fully in person. Spring 2020 semester was not compared as it was neither fully online nor fully in-person. The major challenges were the participation in synchronous sessions and keeping the time line. Overall, the analysis of students’ presentations showed that the level of understanding of project was comparable to the in-person delivery. The amount misconceptions propagated in the reports was a bit higher. One of surprising observations was that students were more likely to ask for clarifications and help when meeting in person. Online delivery resulted in hesitancy to seek help and ask questions both from instructor and from other students. I am going to discuss here the ways to engage students in their bioinformatics research. I will also describe the challenges, achievements and failures on my par while instructing students online in their bioinformatics projects.

Abstract:

After COVID-19 pandemic in 2020 Spring, we all higher education instructors have been forced to change the delivery method of lectures as well as lab courses. Besides hybrid courses, there would be two different ways to deliver lectures; either synchronously or asynchronously. Although there is a study reporting that students in fully online programs showed more positive attitudes than traditional classroom settings (Perera et al. (2017) Life Sci. Edu., 16, ar60), it is very common to hear that there have been many struggles among higher education instructors for successful engagement of students in fully online settings, especially during COVID-19 pandemic. Here, we sought to compare the effectiveness of synchronous live streaming and asynchronous on students’ learning outcome in Microbiology lecture. Both courses were taught by the same instructor, using the same material. Although the asynchronous mode does not allow live, interactive activities, interactive video quizzes using H5P and discussion board-based participation were done. When the score distribution of the first exam were compared, synchronous course (S; n=18) showed average 72.42 (S.D. 16.15) and median 73.5. On the other hand, one asynchronous course (AS1; n=18) showed the similar range (average 73.52, S.D. 9.73 and median 70.55), the other asynchronous course (AS2; n=18) showed significantly lower value (average 64.88, S.D. 17.25 and median 55.90). When two asynchronous sections are combined (n=36), the average is 69.20 (S.D.=14.48) and the median is 68.03. More interestingly, there are very clear, two peaks were observed in AS2 group’s score distribution (higher peak: average 84.64, S.D.=5.75, median 85.8 vs lower peak: average 52.30, S.D.=6.19, median 54.30). As the asynchronous courses are still ongoing (2021 Fall), we cannot make the overall conclusion yet. Nevertheless, this preliminary data set would be very interesting to analyze the effect of the delivery modes in post-pandemic online teaching.