Biology subjects

Anjur-Dietrich, M.

Publications and source records attributed to Anjur-Dietrich, M..

5 recordsLinked to original sources

bioRxiv2025

ProSynTaxDB: A curated protein database and workflow for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes

Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.

bioinformatics↗

bioRxiv2023

Clustering of cortical dynein regulates the mechanics of spindle orientation in human mitotic cells

The forces which orient the spindle in human cells remain poorly understood due to a lack of direct mechanical measurements in mammalian systems. We use magnetic tweezers to measure the force on human mitotic spindles. Combining the spindles measured resistance to rotation, the speed it rotates after laser ablating astral microtubules, and estimates of the number of ablated microtubules reveals that each microtubule contacting the cell cortex is subject to [~]1 pN of pulling force, suggesting that each is pulled on by an individual dynein motor. We find that the concentration of dynein at the cell cortex and extent of dynein clustering are key determinants of the spindles resistance to rotation, with little contribution from cytoplasmic viscosity, which we explain using a biophysically based mathematical model. This work reveals how pulling forces on astral microtubules determine the mechanics of spindle orientation and demonstrates the central role of cortical dynein clustering. HighlightsO_LICytoplasmic viscosity does not determine the spindles resistance to rotation C_LIO_LIEach astral microtubule that contacts the cell cortex is pulled on by a single dynein motor C_LIO_LIPulling forces on astral microtubules determine the mechanics of spindle orientation C_LIO_LIThe mechanics of spindle orientation is regulated by clustering of dynein motors at the cell cortex C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/557210v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@56e8daorg.highwire.dtl.DTLVardef@1d16449org.highwire.dtl.DTLVardef@f3006org.highwire.dtl.DTLVardef@119f6aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

Self-organization of kinetochore-fibers in human mitotic spindles

During eukaryotic cell division, chromosomes are linked to microtubules (MTs) in the spindle by a macromolecular complex called the kinetochore. The bound kinetochore microtubules (KMTs) are crucial to ensuring accurate chromosome segregation. Recent electron tomography reconstructions (Kiewisz et al. 2021) captured the positions and configurations of every MT in human mitotic spindles, revealing that many KMTs in these spindles do not reach the pole. Here, we investigate the processes that give rise to this distribution of KMTs using a combination of analysis of the electron tomography reconstructions, photoconversion experiments, quantitative polarized light microscopy, and biophysical modeling. Our results indicate that in metaphase, KMTs grow away from the kinetochores along well-defined trajectories, continually decreasing in speed as they approach the poles. The locations of KMT minus ends, and the turnover and movements of tubulin in KMTs, are consistent with models in which KMTs predominately nucleate de novo at kinetochores and are inconsistent with substantial numbers of non-KMTs being recruited to the kinetochore in metaphase. Taken together, this work leads to a mathematical model of the self-organization of kinetochore-fibers in human mitotic spindles.

biophysics↗

bioRxiv2020

Bacterial evolution in high osmolarity environments

Bacteria must maintain a cytosolic osmolarity higher than that of their environment in order to take up water. High osmolarity environments therefore present a formidable stress to bacteria. To explore the evolutionary mechanisms by which bacteria adapt to high osmolarity environments, we selected Escherichia coli in media with a variety of osmolytes and concentrations for 250 generations. Adaptation was osmolyte-dependent, with sorbitol stress generally resulting in increased fitness in conditions with higher osmolarity, while selection in high concentrations of proline resulted in increased fitness specifically on proline. Consistent with these phenotypes, sequencing of the evolved populations showed that passaging in proline resulted in specific mutations in an associated metabolic pathway that increases the ability to utilize proline for growth, while evolution in sorbitol resulted in mutations in many different genes that generally improve growth in high osmolarity conditions at the expense of growth at low osmolarity. High osmolarity decreased growth rate but increased mean cell volume compared with growth on proline as the sole carbon source, demonstrating that osmolarity-induced changes in growth rate and cell size follow an orthogonal relationship from the classical Growth Law relating cell size and nutrient quality. Isolates from a sorbitol-evolved population that capture the likely temporal sequence of mutations revealed by metagenomic sequencing demonstrate a tradeoff between growth at high and low osmolarity. Our study highlights the utility of experimental evolution for dissecting complex cellular networks and environmental interactions, particularly in the case of behaviors that can involve both specific and general metabolic stressors. ImportanceFor bacteria, maintaining higher internal solute concentrations than the environment allows cells to take up water. As a result, survival is challenging in high osmolarity environments. To investigate how bacteria adapt to high osmolarity environments, we evolved Escherichia coli in a variety of high osmolarity solutions for hundreds of generations. We found that evolved populations adopted different strategies to improve their growth depending on the osmotic passaging condition, either generally adapting to high osmolarity conditions or better metabolizing the osmolyte as carbon source. Single-cell imaging demonstrated that enhanced fitness was coupled to faster growth, and metagenomic sequencing revealed mutations that reflect growth tradeoffs across osmolarities. Our study demonstrates the utility of long-term evolution experiments for probing adaptation during environmental stress.

microbiology↗

bioRxiv2017

Variation in traction forces during cell cycle progression

Tissue morphogenesis results from the interplay between cell growth and mechanical forces. While the impact of forces on cell proliferation has been fairly well characterized, the inverse relationship is much less understood. Here we investigated how traction forces vary during cell cycle progression. Cell shape was constrained on micropatterned substrates in order to distinguish variations in cell contractility from cell size increase. We performed traction force measurements of asynchronously dividing cells expressing a cell-cycle reporter, to obtain measurements of contractile forces generated during cell division. We found that forces tend to increase as cells progress through G1, before reaching a plateau in S phase, and then decline during G2. This biphasic behaviour revealed a previously undocumented specific and opposite regulation of cell contractility during each cell cycle stage.

cell biology↗