Newest Advances on the FeatureCloud Platform for Federated Learning in Biomedicine

AI in biomedicine has been a central research topic in recent years. Although there are many different techniques and strategies, the majority rely on data that is of both high quality and quantity. Despite the steady growth in the amount of data generated for patients, it is frequently difficult to make that data useful for research because of strong restrictions through privacy regulations such as the GDPR. Through federated learning (FL), we are able to use distributed data for machine learning while keeping patient data inside the respective hospital. Instead of sharing the patient data, like in traditional machine learning, each participant trains an individual machine learning model and shares the model parameters and weights. Existing FL frameworks, however, frequently have restrictions on certain algorithms or application domains, and they frequently call for programming knowledge. With FeatureCloud, we addressed these limitations and provided a user-friendly solution for both developers and end-users. FeatureCloud greatly simplifies the complexity of developing federated applications and executing FL analyses in multi-institutional settings. Additionally, it provides an app store that makes it easy for the community to publish and reuse federated algorithms. Apps can be chained together to form pipelines and executed without programming knowledge, making them ideal for flexible clinical applications. Apps on FeatureCloud can receive certification from both internal and external reviewers to guarantee safety. FeatureCloud effectively separates local components from sensitive data systems by utilizing containerization technology, making it robust to execute in any system environment and guaranteeing data security. To further ensure the privacy of data, FeatureCloud incorporates privacy-enhancing technologies and complies with strict data privacy regulations, such as GDPR.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of Proteus mirabilis

The type VI secretion (T6S) system is a molecular device for the delivery of proteins from one cell into another. T6S function depends on the contractile sheath comprised of TssB/VipA and TssC/VipB proteins. We previously reported on a mutant variant of TssB that disrupts T6S-dependent export of the self-identity protein, IdsD, in the bacterium Proteus mirabilis. Here we determined the mechanism underlying that initial observation. We show that T6S-dependent export of multiple self-recognition proteins is abrogated in this mutant strain. We have mapped the mutation, which is a single amino acid change, to a region predicted to be involved in the formation of the TssB-TssC sheath. We have demonstrated that this mutation does indeed inhibit sheath formation, thereby explaining the global disruption of T6S activity. We propose that this mutation could be utilized as an important tool for studying functions and behaviors associated with T6S systems

Strains used in this study.

<p>Strains used in this study.</p

A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of <i>Proteus mirabilis</i>

<div><p>The type VI secretion (T6S) system is a molecular device for the delivery of proteins from one cell into another. T6S function depends on the contractile sheath comprised of TssB/VipA and TssC/VipB proteins. We previously reported on a mutant variant of TssB that disrupts T6S-dependent export of the self-identity protein, IdsD, in the bacterium <i>Proteus mirabilis</i>. Here we determined the mechanism underlying that initial observation. We show that T6S-dependent export of multiple self-recognition proteins is abrogated in this mutant strain. We have mapped the mutation, which is a single amino acid change, to a region predicted to be involved in the formation of the TssB-TssC sheath. We have demonstrated that this mutation does indeed inhibit sheath formation, thereby explaining the global disruption of T6S activity. We propose that this mutation could be utilized as an important tool for studying functions and behaviors associated with T6S systems.</p></div

The TssB_wt-sfGFP fusion is partially functional in <i>P</i>. <i>mirabilis</i>.

<p>(A) Idr-dependent co-swarm assays were performed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.g001" target="_blank">Fig 1</a>. Δ<i>ids</i>::<i>tssB</i>_<i>wt</i> produces TssB_wt; Δ<i>ids</i>::<i>tssB</i>_<i>wt</i><i>-sfgfp</i> produces wild-type TssB fused to sfGFP (TssB_wt-sfGFP); and Δ<i>ids</i>::<i>tssB</i>_<i>mut</i><i>-sfgfp</i> produces the L32R mutant variant of TssB fused to sfGFP (TssB_L32R-sfGFP). The dominating strain is indicated with a dashed line on all plates. (B) Swarm assay in which a reduced swarm colony radius denotes that IdsD has been exported and transferred to an adjacent cell, where it remained unbound due to the lack of its binding partner IdsE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref035" target="_blank">35</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref058" target="_blank">58</a>]. Wild-type T6S function results in a reduced swarm colony radius; disrupted T6S function results in larger swarm colony radii. Shown is the colony expansion after 16 hours on swarm-permissive agar surfaces of monoclonal Δ<i>ids</i>-derived swarms producing IdsD and lacking IdsE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref035" target="_blank">35</a>]. Strains contain the indicated <i>tssB</i> alleles. Widths of individual swarm rings within a swarm colony are marked by different shades. Representative images of swarm colonies after 24 hours are shown below the graph. N = 3, error bars show standard deviations of individual swarm ring widths.</p

Idr-specific LC-MS/MS results of supernatant fractions from strains producing TssB_wt or TssB_L32R.

<p>Idr-specific LC-MS/MS results of supernatant fractions from strains producing TssB_wt or TssB_L32R.</p

The L32R mutation disrupts Idr function.

<p>(A) Schematic of the Idr-dependent co-swarm assay. Strains are inoculated either as monocultures or as 1:1 mixed cultures onto swarm-permissive media as previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref034" target="_blank">34</a>]. The dominating strain in the mixed culture will occupy the outer swarm edges; boundary formation assays [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref039" target="_blank">39</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref055" target="_blank">55</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref057" target="_blank">57</a>] are then used to determine the identity of the dominating strain. The test strain dominated the mixed swarm if the mixed swarm colony forms a visible boundary with strain HI4320. Conversely, strain HI4320 dominated the mixed swarm if the mixed swarm does not form a boundary with strain HI4320. The dominating strain is indicated by a dashed line. (B) The Idr-dependent co-swarm assay using the indicated strains. BB2000-derived Δ<i>ids</i>::<i>tssB</i>_<i>wt</i> produces TssB_wt; it lacks the entire <i>ids</i> operon [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref039" target="_blank">39</a>]. BB2000-derived <i>icmF*</i>::<i>tssB</i>_<i>wt</i> produces TssB_wt; it contains a chromosomal transposon insertion in the gene encoding the core T6S membrane component, TssM/IcmF [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref034" target="_blank">34</a>]. Δ<i>ids</i>::<i>tssB</i>_<i>mut</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref035" target="_blank">35</a>] produces the mutant variant TssB_L32R.</p

Sheath formation is inhibited by the L32R mutation.

<p>(A) Swarm agar pads were inoculated with indicated strains and incubated at 37°C in a humidity chamber. After 4.5–5.5 hours, agar pads were imaged using phase contrast and epifluorescence microscopy to visualize cell bodies and TssB-sfGFP variants, respectively. BB2000-derived Δ<i>ids</i>::<i>tssB</i>_<i>wt</i><i>-sfgfp</i> produces wild-type TssB fused to sfGFP (TssB_wt-sfGFP); it lacks the entire <i>ids</i> operon [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref039" target="_blank">39</a>]. Δ<i>ids</i>::<i>tssB</i>_<i>mut</i><i>-sfgfp</i> produces the L32R mutant variant of TssB fused to sfGFP (TssB_L32R-sfGFP). <i>icmF*</i>::<i>tssB</i>_<i>wt</i><i>-sfgfp</i> produces TssB_wt-sfGFP; it is derived from BB2000 and contains a chromosomal transposon insertion in the gene encoding the core T6S membrane component, TssM/IcmF [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.ref034" target="_blank">34</a>]. Scale bars, 10 μm. (B) Whole cell extracts from swarming colonies of Δ<i>ids</i>::<i>tssB</i>_<i>wt</i><i>-sfgfp</i>, Δ<i>ids</i>::<i>tssB</i>_<i>mut</i><i>-sfgfp</i> and <i>icmF*</i>::<i>tssB</i>_<i>wt</i><i>-sfgfp</i> were collected after 16–20 hours on swarm-permissive plates. Samples were analyzed using western blot analysis and probed with an anti-GFP antibody to detect TssB-sfGFP and anti-σ⁷⁰ as a loading control. Bands corresponding to the sizes of TssB-sfGFP and σ⁷⁰ are indicated with black arrowheads, while bands corresponding to the size of monomeric sfGFP are indicated with a grey arrowhead. A negative control sample of a swarm colony not producing any TssB-sfGFP fusion can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184797#pone.0184797.s001" target="_blank">S1 Fig</a>.</p

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology