Laura A. Diaz-Martinez

ZNF16 (also known as HZF1 and KOX9) is a multi-C2H2 zinc finger protein first identified via its expression in human T-cells and shown to have a role in blood cell differentiation. ZNF16 was later shown to be ubiquitously expressed in a variety of fetal and adult tissues, suggesting a broader function. In this study, we confirm the ubiquitous expression of ZNF16 in a variety of cancer and non-cancer cell lines and show that ZNF16 depletion reduces cell viability in all cell lines tested. Furthermore, we show that ZNF16 localizes to the nucleolus in a transcription-dependent manner, interacts with the intergenic spacer region of the rDNA and promotes rDNA transcription. Additionally, RNA-sequencing experiments after ZNF16 depletion revealed that ZNF16 also has roles in a variety of pathways including extracellular matrix-receptor interaction, focal adhesions, cytokine-cytokine receptor interactions, human papillomavirus infection and cancer pathways. These findings are consistent with broader roles for ZNF16, including the regulation of nucleolar function, a process that is essential for all cells, and provide evidence at the cellular/molecular level of its role in the regulation of cancer-associated genes (e.g. NRAS, BIRC3, EGFR).

ZNF16 (also known as HZF1 and KOX9) is a multi-C2H2 zinc finger protein first identified via its expression in human T-cells and shown to have a role in blood cell differentiation. ZNF16 was later shown to be ubiquitously expressed in a variety of fetal and adult tissues, suggesting a broader function. In this study, we confirm the ubiquitous expression of ZNF16 in a variety of cancer and non-cancer cell lines and show that ZNF16 depletion reduces cell viability in all cell lines tested. Furthermore, we show that ZNF16 localizes to the nucleolus in a transcription-dependent manner, interacts with the intergenic spacer region of the rDNA and promotes rDNA transcription. Additionally, RNA-seq experiments after ZNF16 depletion revealed that ZNF16 also has roles in a variety of pathways including ECM-receptor interaction, focal adhesions, cytokine-cytokine receptor interactions, human papillomavirus (HPV) infection and cancer pathways. These findings are consistent with broader roles for ZNF16, including the regulation of nucleolar function, a process that is essential for all cells, and provide evidence at the cellular/molecular level of its role in the regulation of cancer-associated genes (e.g., NRAS, BIRC3, EGFR).

Solidarity and critical hope support faculty and staff who wish to accompany students, read the current reality of their experience, and imagine new practices that can rectify injustices and promote access and belonging. Here, we describe an example of this praxis by responding to student concerns about injustices in a course registration process. With some exceptions, undergraduates at this institution register for classes according to their earned college credits. At first glance, this meritocratic system shows care to students by recognizing their hard work. However, our analysis shows that it also discriminates against underserved groups of students. Using 10 years of course registration data, we compared assigned course registration periods between different student populations. The current registration process privileges white-identifying students over those identifying as African American/Black, Hispanic/Latino(a), Native American/Alaskan Native/Pacific islander, Asian, or two or more races. Pell grant-eligible and first-generation students also registered later compared to their peers; these inequities persisted throughout their college career. These results demonstrate an example of critical hope praxis for Jesuit institutions in which we accompany students and investigate policies that appear to preference cura apostolica (care for the institution in maintaining the status quo) at the expense of cura personalis.

Biomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In centralized and aggregated inter-lab studies, biocytometry demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples.

Course-based undergraduate research experiences (CUREs) are increasingly becoming the first, and perhaps only, research experience for many biology students. Responsible and ethical conduct of research (RECR) is crucial for the integrity of scientific research and essential for students to have an understanding of the scientific process at any academic level. However, there is a current lack of RECR education in biology CUREs. To understand the level of RECR knowledge and skills in undergraduate students, we created a diagnostic survey that uses case scenarios designed to illustrate RECR issues in the CURE classroom. Analysis of students’ responses indicated that the overall percentage of students who are able to effectively use RECR terminology and identify the impact of RECR violations on science integrity and ultimately on society is low. Furthermore, some students equated RECR violations to academic dishonesty, indicating difficulties separating the research and academic aspects of CUREs. This diagnostic tool can aid instructors in identifying gaps in student RECR knowledge for the subsequent development of RECR educational interventions, particularly to ensure the integrity of the research performed in CURE settings.

Most studies on the benefits of participation in undergraduate research (UGR) use data from student participants in undergraduate research programs (URPs), which offer a limited number of positions. In reality, however, the majority of UGR students participate in undergraduate research not in programs (URNPs). The authors conducted an institution-wide study at a Hispanic-serving institution to examine the relationship between academic success and participation in these two UGR modalities. Although there were some differences between URPs and URNPs, participation in research at this institution was largely equitable and inclusive, with UGR demographics that reflected those of the institution, and it was positively associated with increased benefits along multiple academic metrics, regardless of UGR modality. Importantly, these increases were observed for both first time in college and transfer students.

Rhodoquinone (RQ) is an electron carrier that participates in the metabolic pathways of select species capable of anaerobic growth. Due to its importance in cellular metabolism, an understanding of the biosynthesis and regulation of RQ may precede novel anti‐parasitic or anti‐microbial drugs. An essential enzyme for RQ biosynthesis in some bacteria and protists is RquA, which converts the precursor ubiquinone (UQ) to RQ. To explore the alternative functions of RQ in metabolism and photosynthesis, Rhodospirillum rubrum served as a model organism for growth studies in liquid media. Wild‐type R. rubrum was compared with a ΔrquA knockout. Semi‐aerobic and anaerobic (dark and light) growth conditions were investigated using media enriched with the substrates succinate, fructose, pyruvate and acetate in the presence of bicarbonate or DMSO. These studies demonstrated that the ΔrquA strain was capable of dark anaerobic growth in the presence of select nutrients, but incapable of anaerobic growth in the light. To further characterize the RquA protein, RquA was tagged with a green fluorescent protein (GFP). When transformed with a plasmid containing the rquA gene, W303 yeast cells gain the ability to produce RQ.Yeast containing GFP‐tagged RquA were imaged with fluorescent confocal microscopy with the goal of discerning the location of recombinant RquA in the yeast cells. These studies revealed alternative roles of RQ in bioenergetics and further elucidated the function of RquA.

Cohesin is a multiprotein ring complex that regulates 3D genome organization, sister chromatid cohesion, gene expression, and DNA repair. Cohesin is known to be ubiquitinated, although the mechanism, regulation, and effects of cohesin ubiquitination remain poorly defined. We previously used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in human HCT116 cells. Here we report that mass spectrometry analysis of dual-affinity purifications identified the USP13 deubiquitinase as a novel cohesin-interacting protein. Subsequent immunoprecipitation/Western blots confirmed the endogenous interaction in HCT116, 293T, HeLa, and RPE-hTERT cells; demonstrated that the interaction occurs specifically in the soluble nuclear fraction (not in the chromatin); requires the ubiquitin-binding domains (UBA1/2) of USP13; and occurs preferentially during DNA replication. Reciprocal dual-affinity purification of endogenous USP13 followed by mass spectrometry demonstrated that cohesin is its primary interactor in the nucleus. Ectopic expression and CRISPR knockout of USP13 showed that USP13 is paradoxically required for both deubiquitination and ubiquitination of cohesin subunits in human cells. USP13 was dispensable for sister chromatid cohesion in HCT116 and HeLa cells, whereas it was required for the dissociation of cohesin from chromatin as cells transit through mitosis. Together these results identify USP13 as a new cohesin-interacting protein that regulates the ubiquitination of cohesin and its cell cycle regulated interaction with chromatin.

Keywords: Mitochondria dynamics, cell cycle, mitochondria heterogeneity, genomic heterogeneity