Biology subjects

Schmelling, N. M.

Publications and source records attributed to Schmelling, N. M..

3 recordsLinked to original sources

bioRxiv2023

CATHI: An interactive platform for comparative genomics and homolog identification

AO_SCPLOWBSTRACTC_SCPLOWBioinformatics has established itself as a central pillar of modern biology. Specifically, comparative genomics enables scientists to study a vast number of genomes efficiently. These comparative analyses shed light on the evolution and potential function of genomes and genes, but are also increasingly used as a key tool for metabolic engineering and synthetic biology by identifying appropriate targets for modification. While numerous sophisticated tools for comparative genomics and homolog identification exist, those tools predominantly target highly skilled bioinformatics users. Consequently, many biologists either defer such analyses to their more versed bioinformatic collaborators or resort to suboptimal tools. Here, we present an intuitive solution available on all major operating systems, easily accessed through common web browsers. CATHI - Comparative Analysis Tool for Homolog Identification - integrates a suite of best-practice bioinformatic tools, encompassing BLAST for homology searches, MAFFT for multiple sequence alignment, FastTree2 for phylogeny reconstruction, and clinker for synteny analysis. Specifically tailored to biologists, CATHI orchestrates predefined settings and automated pipelines, obviating the need for programming expertise. This platform empowers researchers to confidently engage in detailed comparative genomics studies by streamlining the analytical process. The interactive framework provides users with a plethora of options. This includes real-time execution and progress monitoring, facilitates dynamic result tracking, and a set of search functions across NCBI databases like CDD or ProtFam. Users can interactively engage in data exploration, filtering, and visualization through CATHIs intuitive interface. Furthermore, the seamless export of project data in standard formats (FASTA, Newick, CSV, and HTML) facilitates the integration with further third-party tools such as TreeViewer and Jalview. To benchmark CATHI, we revisited the comparative analysis of cyanobacterial circadian clock proteins conducted by Schmelling et al. in 2017, revealing consistent global patterns among identified homologs, while also highlighting individual variations attributed to the expansion of available databases.

bioinformatics↗

bioRxiv2023

Too many big promises: What is holding back cyanobacterial research and applications?

Climate change as a global crisis demands a shift from a fossil fuel-based economy to-wards sustainable solutions. Cyanobacteria are promising organisms for the truly sustainable, carbon-neutral production of various chemicals. However, so far, proof of concepts for large-scale cyanobacterial productions that produce industrial-relevant amounts of desired products are lacking. To systematically address this topic, a comprehensive overview that identifies current obstacles and solutions is missing. We conducted a quantitative survey among researchers in the cyanobacterial community. This work investigates individual experiences and challenges in the field of cyanobacteria, as well as information about specific protocols. Additionally, qualitative interviews with academic experts were conducted. Their answers were compared, and highlights were summarised. In this work, we provide for the first time a comprehensive overview of current trends and challenges as perceived by researchers in the field of cyanobacteria. Based on the results of the survey and interviews, we formulate a set of recommendations on how to improve the working conditions within the cyanobacteria research community.

microbiology↗

bioRxiv2021

A chimeric KaiA-like regulator extends the nonstandard KaiB3-KaiC3 clock system in bacteria

Organisms from all kingdoms of life have evolved diverse mechanisms to address the predictable environmental changes resulting from the Earths rotation. The circadian clock of cyanobacteria is a particularly simple and elegant example of a biological timing mechanism for predicting daily changes in the light environment. The three proteins KaiA, KaiB, and KaiC constitute the central timing mechanism that drives circadian oscillations in the cyanobacterium Synechococcus elongatus PCC 7942. In addition to the standard oscillator, Synechocystis sp. PCC 6803, another model organism for cyanobacterial research, harbors several divergent clock homologs. Here, we describe a potential new chimeric KaiA homolog that we named KaiA3. At the N-terminus, KaiA3 is similar to the NarL-type response regulator receiver domain. However, its similarity to canonical NarL transcription factors drastically decreases in the C-terminal domain, which resembles the circadian clock protein, KaiA. In line with this, we detected KaiA3-mediated stimulation of KaiC3 phosphorylation. Phosphorylation of KaiC3 was rhythmic over 48 h in vitro in the presence of KaiA3 and KaiB3 as well as in Synechocystis cells under free-running conditions after light/dark entrainment. This results in the presence of two different oscillators in a single-celled prokaryotic organism. Deletion of the kaiA3 gene leads to KaiC3 dephosphorylation and results in growth defects during mixotrophic growth and in the dark. In summary, we suggest that KaiA3 is a nonstandard KaiA homolog, thereby extending the KaiB3-KaiC3 system in Cyanobacteria and potentially other prokaryotes.

microbiology↗