Biology subjects

Brandt, P.

Publications and source records attributed to Brandt, P..

4 recordsLinked to original sources

bioRxiv2026

A Multiplex Droplet Digital PCR Assay for Chromosome Copy Number Determination in Candida albicans

Chromosome copy number variation (CNV) is a major contributor to genome plasticity and adaptation in Candida albicans, a leading fungal pathogen of humans. Aneuploidy, defined as deviations from the normal diploid chromosome set, rapidly alters gene dosage, enabling tolerance to host-imposed and antifungal stress. Accurate detection and quantification of chromosomal copy number changes are thus essential to dissect the mechanisms by which C. albicans adapts and evolves. Here, we describe the development, optimization, and validation of a six-color, 16-plex droplet digital PCR assay for simultaneous quantification of all C. albicans chromosome arms in a single reaction. Each target is detected by a unique dual-color or single-color combination of probes, enabling high-order multiplexing through binary fluorescence encoding. Following optimization of probe concentrations, PCR cycling parameters, genomic DNA extraction and pre-treatment with restriction enzymes, the assay provides accurate, reproducible chromosome-level copy number estimates that correlate closely with WGS results across euploid and aneuploid isolates. Compared to whole-genome sequencing, the assay is rapid, cost-effective, and scalable, requiring minimal DNA input and allowing high-throughput analysis of large isolate collections. The 16-plex assay thus provides a platform for dissecting genome instability and adaptive evolution in C. albicans. Article SummaryWe developed and validated a 16-plex droplet digital PCR assay that estimates chromosome dosage across the entire genome of the human fungal pathogen C. albicans in a single reaction. The assay uses six fluorescent colors and unique color combinations to track one marker on each chromosome arm, enabling rapid detection of aneuploidy (extra or missing chromosomes). Results closely matched whole-genome sequencing for isolates with simple aneuploid forms and detected low-frequency trisomic clones in mixed populations. With optimized DNA preparation, this method provides a practical tool for screening genome instability in research and clinical settings.

microbiology↗

bioRxiv2024

Synergistic cross-kingdom host cell damage between Candida albicans and Enterococcus faecalis

The fungus Candida albicans and the Gram-positive bacterium Enterococcus faecalis share mucosal niches in the human body. As opportunistic pathogens, both are found to expand population size during dysbiosis, and can cause severe systemic infections in susceptible individuals. Here, we show that the presence of C. albicans results in increased host cell damage by E. faecalis. Furthermore, E. faecalis aggravates oropharyngeal candidiasis in mice. Increased damage is mediated by enterococcal cytolysin, and involves both physical interaction and altered glucose availability. Physical interaction promotes accumulation of bacteria on host cells, facilitating contact of cytolysin with host cells. Glucose depletion by the metabolic activity of the fungus sensitized host cells to cytolysin. This work illustrates how a complex interplay between fungi and bacteria can result in detrimental consequences for the host.

microbiology↗

bioRxiv2020

Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis

PhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and non-profit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the BEST awardee institutions included career panels, skill-building workshops, job-searching workshops, site visits, and internships. An initial concern was since doctoral training is lengthy and requires focused attention on dissertation research, having students participate in additional complementary training activities might lengthen time to degree and hamper student research productivity. To address this concern, using time to degree and publication records as measures of efficiency and productivity, metrics were analyzed from ten BEST awardee institutions. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Furthermore, a few institutions even demonstrated a positive correlation between participation in career and professional development activities and productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce. Significance StatementOur study is unique in that it compiled doctoral degree durations at ten different universities, recorded individual participation in career and professional development activities in terms of dosage, and tracked individual engagement in real-time rather than relying on surveys sent to trainees after graduation. Participation in career and professional development activities, including internships, did not decrease efficiency or productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce.

scientific communication and education↗

bioRxiv2018

Applying Inter-rater Reliability to Improve Consistency in Classifying PhD Career Outcomes

In the past year, there has been an exciting groundswell of national efforts to integrate multiple taxonomies for the transparent dissemination and analysis of PhD career outcomes. In this study, we leveraged the unique resources of the Broadening Experiences in Scientific Training Consortium to examine the reliability of the three-tiered Unified Career Outcomes Taxonomy (UCOT v.2017) that was collaboratively developed at a meeting convened by Rescuing Biomedical Research in August 2017. Using an amended version of the UCOT v.2017 (UCOT v.2017-rev1) and a new Supplementary Guidance document, we categorized over 570 PhD alumni records from three different universities. Utilizing Krippendorffs alpha to measure the interrater reliability from nine different individuals, we determined moderate to robust reproducibility within the first two tiers of the taxonomy (Workforce Sector and Career Type); however, the reliability for the third tier (Job Function) did not meet established standards. The team identified significant sources of error, revised category definitions, improved coder training materials and processes, and tested for improved reliability through coding 219 PhD alumni records using the revised taxonomy, UCOT v.2017-rev2. Our results revealed that the changes introduced in UCOT v.2017-rev2 improved inter-rater reliability in all three tiers, and either met or exceeded the acceptable standards for reliability. A final set of clarifications were made to UCOT v.2017-rev2, resulting in UCOT v.2018 and a Finalized Guidance document. Our findings underscore the importance of carefully developing guidance documents to aid coders in the reliable and consistent categorization of alumni career outcomes. We propose periodic assessment of the UCOT v.2018 to address the natural evolution of PhD careers in the global workforce. Ultimately, we hope that UCOT v.2018 will aid in the classification and dissemination of alumni career outcomes that is essential to educating trainees, institutions, and agencies about the diversity of career options for PhDs, and therein empower all PhDs to pursue the careers of their choice.

scientific communication and education↗