Biology subjects

Cammarota, C.

Publications and source records attributed to Cammarota, C..

4 recordsLinked to original sources

bioRxiv2024

Biology exams rarely use visual models to engage higher-order cognitive skills

Visual models are a necessary part of molecular biology education because submicroscopic compounds and processes cannot be directly observed. Accurately interpreting the biological information conveyed by the shapes and symbols in these visual models requires engaging visual literacy skills. For students to develop expertise in molecular biology visual literacy, they need to have structured experiences using and creating visual models, but there is little evidence to gauge how often undergraduate biology students are provided such opportunities. To investigate students visual literacy experiences, we surveyed 66 instructors who taught lower division undergraduate biology courses with a focus on molecular biology concepts. We collected self-reported data about the frequency with which the instructors teach with visual models and we analyzed course exams to determine how instructors incorporated visual models into their assessments. We found that most instructors reported teaching with models in their courses, yet only 16% of exam items in the sample contained a visual model. There was not a statistically significant relationship between instructors self-reported frequency of teaching with models and extent to which their exams contained models, signaling a potential mismatch between teaching and assessment practices. Although exam items containing models have the potential to elicit higher-order cognitive skills through model-based reasoning, we found that when instructors included visual models in their exams the majority of the items only targeted the lower-order cognitive skills of Blooms Taxonomy. Together, our findings highlight that despite the importance of visual models in molecular biology, students may not often have opportunities to demonstrate their understanding of these models on assessments.

scientific communication and education↗

bioRxiv2024

Optimal sequencing depth for measuring the concentrations of molecular barcodes

In combinatorial genetic engineering experiments, next-generation sequencing (NGS) allows for measuring the concentrations of barcoded or mutated genes within highly diverse libraries. When designing and interpreting these experiments, sequencing depths are thus important parameters to take into account. Service providers follow established guidelines to determine NGS depth depending on the type of experiment, such as RNA sequencing or whole genome sequencing. However, guidelines specifically tailored for measuring barcode concentrations have not yet reached an accepted consensus. To address this issue, we combine the analysis of NGS datasets from barcoded libraries with a mathematical model taking into account the PCR amplification in library preparation. We demonstrate on several datasets that noise in the NGS counts increases with the sequencing depth; consequently, beyond certain limits, deeper sequencing does not improve the precision of measuring barcode concentrations. We propose, as rule of thumb, that the optimal sequencing depth should be about ten times the initial amount of barcoded DNA molecules before any amplification step.

bioinformatics↗

bioRxiv2024

Fas2: A Tale of Two Chromosomes

The cell-cell adhesion molecule Fasciclin II (Fas2) has long been studied for its evolutionarily-conserved role in axon guidance. It is also expressed in the follicular epithelium, where together with a similar protein, Neuroglian (Nrg), it helps to drive the reintegration of cells born out of the tissue plane. Remarkably, one Fas2 protein null allele, Fas2G0336, demonstrates a mild reintegration phenotype, whereas work with the classic null allele Fas2EB112 showed more severe epithelial disorganization. These observations raise the question of which allele (if either) causes a bona fide loss of Fas2 protein function. The problem is not only relevant to reintegration but fundamentally important to understanding what this protein does and how it works: Fas2EB112 has been used in at least 37 research articles, and Fas2G0336 in at least three. An obvious solution is that one of the two chromosomes carries a modifier that either suppresses (Fas2G0336) or enhances (Fas2EB112) phenotypic severity. We find not only the latter to be the case, but identify the enhancing mutation as Nrg14, also a classic null allele.

genetics↗

bioRxiv2020

An Axon-Pathfinding Mechanism Preserves Epithelial Tissue Integrity

Dividing cells often move apically within epithelial tissue layers, likely to escape the spatial confinement of their neighbors. Because of this movement, daughter cells may be born displaced from the tissue layer. Reintegration of these displaced cells helps support tissue growth and maintain tissue architecture. In the Drosophila follicular epithelium, reintegration relies on the immunoglobulin-superfamily cell-adhesion molecules (IgCAMs) Neuroglian and Fasciclin 2, which line cell-cell borders1. These molecules have been described in epithelia, but are well-studied for their roles in neural development2-8. We show here that reintegration works in the same way as IgCAM-mediated axon growth and pathfinding; it relies not only on extracellular adhesion but also mechanical coupling between IgCAMs and the lateral Spectrin-Based Membrane Skeleton. Our work indicates that reintegration is mediated by a distinct epithelial cell-cell junction that is compositionally and functionally equivalent to junctions made between axons.

cell biology↗