The breastfeeding biochemist parent: planning, pumping and perfectionism

The very fact that having an article about breastfeeding in The Biochemist seems peculiar may, in fact, demonstrate why it is important that we think and talk about the topic. In this feature, I want to discuss why people choose to breastfeed their children, how this is possible when returning to work as a bench scientist, and the steps we can all take supporting people in making that choice, as part of an inclusive working environment. Hopefully, there’s a bit of science in there too.

SCHNAPPs - Single Cell sHiNy APPlication(s)

ABSTRACTMotivationSingle-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. On one hand, the data produced by scRNASeq is technically complex, with analytical workflows that are still very much an active field of bioinformatics research, and on the other hand, a wealth of biological background knowledge is often needed to guide the investigation. Therefore, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis, so that they can focus on the Science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools.ResultsWe present SCHNAPPs, a computer program designed to enable bench-scientists to autonomously explore and interpret single cell RNA-seq expression data and associated annotations. The Shiny-based application allows selecting genes and cells of interest, performing quality control, normalization, clustering, and differential expression analyses, applying standard workflows from Seurat (Stuart et al., 2019) or Scran (Lun et al., 2016) packages, and most of the common visualizations. An R-markdown report can be generated that tracks the modifications, and selected visualizations facilitating communication and reproducibility between bench-scientist and bioinformatician. The modular design of the tool allows to easily integrate new visualizations and analyses by bioinformaticians. We still recommend that a data analysis specialist oversees the analysis and interpretation.AvailabilityThe SCHNAPPs application, docker file, and documentation are available on GitHub: https://c3bi-pasteur-fr.github.io/UTechSCB-SCHNAPPs; Example contribution are available at the following GitHub site: https://github.com/baj12/SCHNAPPsContributions.

Competing Discourses of Scientific Identity among Postdoctoral Scholars in the Biomedical Sciences

The postdoctoral period is generally one of low pay, long hours, and uncertainty about future career options. To better understand how postdocs conceive of their present and future goals, we asked researchers about their scientific identities while they were in their postdoctoral appointments. We used discourse analysis to analyze interviews with 30 scholars from a research-intensive university or nearby research institutions to better understand how their scientific identities influenced their career goals. We identified two primary discourses: bench scientist and principal investigator (PI). The bench scientist discourse is characterized by implementing other people’s scientific visions through work in the laboratory and expertise in experimental design and troubleshooting. The PI discourse is characterized by a focus on formulating scientific visions, obtaining funding, and disseminating results through publishing papers and at invited talks. Because these discourses represent beliefs, they can—and do—limit postdocs’ understandings of what career opportunities exist and the transferability of skills to different careers. Understanding the bench scientist and PI discourses, and how they interact, is essential for developing and implementing better professional development programs for postdocs.

Toward Correlation in In Vivo and In Vitro Nanotoxicology Studies

Much of the focus of the published 2011 symposium that inspired this work focused on the question, “When have you reduced risk enough to move from bench/animal studies to ‘first in-human’ studies?” Building applied research ethics related to nanotherapeutics requires bench and clinical scientists to have a clear vision about how to test nanotherapeutic safety, and it is clear that there is still much to be considered at the steps before “in-human” assessment. Herein, the perspective of the bench scientist is brought to bear on using in vivo and in vitro models to assess the safety of nanotherapeutics. Much of this work falls under the purview of the field of nanotoxicology that aims to understand the toxicological impact of engineered nanoscale materials. Engineered nanomaterials include a wide variety of materials that are manipulated and controlled on the nanoscale level where, typically, the nanoparticle or nanomaterial has some dimension that is less than 100 nm.

The Two-Way Trade—Psychiatry and Neuroscience

As scientific technologies become more sophisticated, clinicians may come to think that they must devolve into passive recipients rather than contributors to the advances in basic knowledge. This perception and accompanying modesty towards the neurosciences, however, is an error. The intellectual trade between clinician and bench scientist has always been bi-directional and nowhere is this more clearly evident than in recent interactions between psychiatry and neuroscience.