Forward-directed genetic screens are extremely powerful in identifying novel genes involved in a specific biological process, including various chromatin regulatory pathways. However, the traditional ways of genetic mapping are time- and cost-demanding. Recently, the whole process was revolutionized by the development of mapping-by-sequencing (MBS) protocols. In MBS, the causal mutations and their positions within genes are identified directly by whole-genome sequencing and bioinformatics analysis of the bulk of mutant plants selected based on the mutant phenotype from a segregating population. MBS increases precision and economizes the mapping. Here, we describe a general protocol and provide practical tips on how to proceed with the mapping-by-sequencing on the example of Arabidopsis forward-directed genetic screen designed to identify mutants sensitive to a specific type of DNA damage. The described protocol is generally applicable to a wide range of genetic screens in various inbreeding species with a reference genome sequence.
- Klíčová slova
- DNA damage repair, DNA-protein crosslinks, Forward genetics, Genetic mapping, High-throughput sequencing, Mapping-by-sequencing, SNP calling, Zebularine,
- MeSH
- Arabidopsis * genetika MeSH
- fenotyp MeSH
- genom rostlinný MeSH
- mapování chromozomů * metody MeSH
- mutace MeSH
- sekvenování celého genomu metody MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
- Publikační typ
- časopisecké články MeSH
Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular in systems biology due to their ability to model long-term biological phenotypes within a qualitative, predictive framework. Boolean networks model phenotypes as attractors, which are closely linked to minimal trap spaces (inescapable hypercubes in the system's state space). In biological applications, attractors and minimal trap spaces are typically in one-to-one correspondence. However, this correspondence is not guaranteed: motif-avoidant attractors (MAAs) that lie outside minimal trap spaces are possible. MAAs are rare and poorly understood, despite recent efforts. In this contribution to the BMB & JMB Special Collection "Problems, Progress and Perspectives in Mathematical and Computational Biology", we summarize the current state of knowledge regarding MAAs and present several novel observations regarding their response to node deletion reductions and linear extensions of edges. We conduct large-scale computational studies on an ensemble of 14 000 models derived from published Boolean models of biological systems, and more than 100 million Random Boolean Networks. Our findings quantify the rarity of MAAs; in particular, we only observed MAAs in biological models after applying standard simplification methods, highlighting the role of network reduction in introducing MAAs into the dynamics. We also show that MAAs are fragile to linear extensions: in sparse networks, even a single linear node can disrupt virtually all MAAs. Motivated by this observation, we improve the upper bound on the number of delays needed to disrupt a motif-avoidant attractor.
- Klíčová slova
- Biomolecular networks, Boolean models, Boolean networks, Complex systems, Discrete dynamics, Stable motif, Trap spaces,
- MeSH
- biologické modely * MeSH
- fenotyp MeSH
- genové regulační sítě MeSH
- lidé MeSH
- matematické pojmy MeSH
- počítačová simulace MeSH
- systémová biologie statistika a číselné údaje MeSH
- výpočetní biologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.
- MeSH
- data mining * metody MeSH
- hmotnostní spektrometrie * metody MeSH
- lidé MeSH
- metabolomika * metody MeSH
- programovací jazyk * MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
One of the most common statistical analyses in experimental psychology concerns the comparison of two means using the frequentist t test. However, frequentist t tests do not quantify evidence and require various assumption tests. Recently, popularized Bayesian t tests do quantify evidence, but these were developed for scenarios where the two populations are assumed to have the same variance. As an alternative to both methods, we outline a comprehensive t test framework based on Bayesian model averaging. This new t test framework simultaneously takes into account models that assume equal and unequal variances, and models that use t-likelihoods to improve robustness to outliers. The resulting inference is based on a weighted average across the entire model ensemble, with higher weights assigned to models that predicted the observed data well. This new t test framework provides an integrated approach to assumption checks and inference by applying a series of pertinent models to the data simultaneously rather than sequentially. The integrated Bayesian model-averaged t tests achieve robustness without having to commit to a single model following a series of assumption checks. To facilitate practical applications, we provide user-friendly implementations in JASP and via the RoBTT package in R . A tutorial video is available at https://www.youtube.com/watch?v=EcuzGTIcorQ.
- Klíčová slova
- t-likelihood, t test, Bayes factor, Bayesian model-averaging, Robust inference, Unequal variances,
- MeSH
- Bayesova věta MeSH
- experimentální psychologie * metody MeSH
- interpretace statistických dat MeSH
- lidé MeSH
- statistické modely * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Plastids of diatoms and related algae with complex plastids of red algal origin are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as cell biological processes take place in the PPC; however, genome-wide predictions of the proteins targeted to this compartment were so far based on manual annotation work. Using published experimental protein localizations as reference data, we developed the first automatic prediction method for PPC proteins, which we included as a new feature in an updated version of the plastid protein predictor ASAFind. With our method, at least a subset of the PPC proteins can be predicted with high specificity, with an estimate of at least 81 proteins (0.7% of the predicted proteome) targeted to the PPC in the model diatom Phaeodactylum tricornutum. The proportion of PPC proteins varies, since 180 PPC proteins (1.3% of the predicted proteome) were predicted in the genome of the diatom Thalassiosira pseudonana. The new ASAFind version can also generate a newly designed graphical output that visualizes the contribution of each position in the sequence to the score and accepts the output of the recent versions of SignalP (5.0) and TargetP (2.0) as input data. Furthermore, we release a script to calculate custom scoring matrices that can be used for predictions in a simplified score cut-off mode. This allows for adjustments of the method to other groups of algae.
- Klíčová slova
- chloroplast, diatoms, evolution, gene transfer, genome annotation, mitochondria, organelle, periplastidic compartment, protein transport, secretory pathway, technical advance,
- MeSH
- bílkoviny řas * metabolismus MeSH
- plastidy * metabolismus MeSH
- proteom MeSH
- Rhodophyta metabolismus MeSH
- rozsivky * metabolismus genetika MeSH
- software * MeSH
- výpočetní biologie * metody MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- bílkoviny řas * MeSH
- proteom MeSH
Gout and hyperuricemia increase cardiovascular disease risk, highlighting the need for improved risk stratification. In this pilot study, we evaluated the Coronary Event Risk Test (CERT) in 94 hyperuricemic and 196 gout patients, and 53 controls. Plasma ceramides were determined by liquid chromatography-mass spectrometry. Elevated CERT scores (≥7) occurred in 11.7 % (2-fold increase) of hyperuricemic and 31.12 % (5.5-fold increase) of gout patients compared to controls. Additionally, both hyperuricemic and gout patients with increased CERT also exhibited higher levels of inflammation and atherogenic index of plasma, both of which were significantly associated with CERT. Incorporating CERT into routine care may enhance risk stratification and guide targeted interventions in this patient population.
- Klíčová slova
- Cardiovascular risk, Ceramides, Coronary event risk test, Gout, Hyperuricemia, Lipidomics,
- MeSH
- biologické markery krev MeSH
- ceramidy * krev MeSH
- chromatografie kapalinová MeSH
- dna (nemoc) * krev diagnóza komplikace MeSH
- dospělí MeSH
- hodnocení rizik MeSH
- hyperurikemie * krev diagnóza komplikace MeSH
- kardiovaskulární nemoci * diagnóza krev etiologie epidemiologie MeSH
- kyselina močová * krev MeSH
- lidé středního věku MeSH
- lidé MeSH
- metody pro podporu rozhodování * MeSH
- pilotní projekty MeSH
- prediktivní hodnota testů MeSH
- prognóza MeSH
- rizikové faktory kardiovaskulárních chorob MeSH
- senioři MeSH
- studie případů a kontrol MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- biologické markery MeSH
- ceramidy * MeSH
- kyselina močová * MeSH
BACKGROUND: Current experimental data on RNA interactions remain limited, particularly for non-coding RNAs, many of which have only recently been discovered and operate within complex regulatory networks. Researchers often rely on in-silico interaction detection algorithms, such as TargetScan, which are based on biochemical sequence alignment. However, these algorithms have limited performance. RNA-seq expression data can provide valuable insights into regulatory networks, especially for understudied interactions such as circRNA-miRNA-mRNA. By integrating RNA-seq data with prior interaction networks obtained experimentally or through in-silico predictions, researchers can discover novel interactions, validate existing ones, and improve interaction prediction accuracy. RESULTS: This paper introduces Pi-GMIFS, an extension of the generalized monotone incremental forward stagewise (GMIFS) regression algorithm that incorporates prior knowledge. The algorithm first estimates prior response values through a prior-only regression, interpolates between these prior values and the original data, and then applies the GMIFS method. Our experimental results on circRNA-miRNA-mRNA regulatory interaction networks demonstrate that Pi-GMIFS consistently enhances precision and recall in RNA interaction prediction by leveraging implicit information from bulk RNA-seq expression data, outperforming the initial prior knowledge. CONCLUSION: Pi-GMIFS is a robust algorithm for inferring acyclic interaction networks when the variable ordering is known. Its effectiveness was confirmed through extensive experimental validation. We proved that RNA-seq data of a representative size help infer previously unknown interactions available in TarBase v9 and improve the quality of circRNA disease annotation.
- Klíčová slova
- Bayesian network, Circular RNA, Functional annotation, Penalized regression, Structure inference,
- MeSH
- algoritmy MeSH
- genové regulační sítě MeSH
- kruhová RNA * genetika metabolismus MeSH
- lidé MeSH
- lineární modely MeSH
- messenger RNA * genetika metabolismus MeSH
- mikro RNA * genetika metabolismus MeSH
- sekvenční analýza RNA metody MeSH
- sekvenování transkriptomu * metody MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kruhová RNA * MeSH
- messenger RNA * MeSH
- mikro RNA * MeSH
BACKGROUND: Eye tumors are moving targets, but there have been no reports of radiation therapy with real-time monitoring. CASE: A 54-year-old woman with metastatic breast cancer was referred for treatment of diplopia due to choroidal metastasis after hippocampal avoiding whole brain radiotherapy. Since visual acuity was preserved and long-term survival was expected, real-time MRI-guided intensity-modulated radiation therapy (36 Gy in 20 fractions) was performed. No adverse events occurred during treatment or during the subsequent one-year follow-up period. The patient's diplopia resolved and no choroidal recurrence was observed during the follow-up period. CONCLUSION: MRI-guided radiation therapy may be a safe and effective treatment for choroidal metastases after hippocampal avoiding whole brain radiotherapy.
- Klíčová slova
- choroidal tumor, image guided radiotherapy, image-guided radiotherapy, intensity-modulated radiation therapy, retinal neoplasms,
- MeSH
- hipokampus MeSH
- lidé středního věku MeSH
- lidé MeSH
- magnetická rezonanční tomografie * MeSH
- nádory choroidey * radioterapie sekundární MeSH
- nádory mozku sekundární radioterapie MeSH
- nádory prsu * patologie MeSH
- radioterapie řízená obrazem * MeSH
- radioterapie s modulovanou intenzitou * MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
MOTIVATION: Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram (SD) describes this interplay in a discrete analog of Waddington's epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. Efficient computational tools for studying SDs are essential for the understanding of Boolean attractor landscapes and connecting them to their biological functions. RESULTS: We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist's Boolean attractor landscape mapper, biobalm. We compare biobalm to similar tools and find a substantial performance increase in SD construction, attractor identification, and attractor control. We perform the most comprehensive comparative analysis to date of the SD structure in experimentally-validated Boolean models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small SDs, indicating simple decision structures. In contrast, nonrandom models from the literature are enriched in extremely large SDs, indicating an abundance of decision points and suggesting the presence of complex Waddington landscapes in nature. AVAILABILITY AND IMPLEMENTATION: The tool biobalm is available online at https://github.com/jcrozum/biobalm. Further data, scripts for testing, analysis, and figure generation are available online at https://github.com/jcrozum/biobalm-analysis and in the reproducibility artefact at https://doi.org/10.5281/zenodo.13854760.
of the original article, 'Efficacy of Trastuzumab Deruxtecan in HER2-Expressing Solid Tumors by Enrollment HER2 IHC Status: Post Hoc Analysis of DESTINY-PanTumor02'. Trastuzumab deruxtecan (T-DXd) is an antibody-drug conjugate, which is a chemotherapy with a linker (deruxtecan) joined to an antibody (trastuzumab). Trastuzumab binds to the human epidermal growth factor receptor 2 (HER2) protein on cancer cells, where it releases the chemotherapy to kill these cells. The DESTINY-PanTumor02 clinical study tested the effectiveness of T-DXd for people with various HER2-expressing cancers and the safety of treatment. Previous results from DESTINY-PanTumor02 showed that T-DXd had antitumor activity, and the greatest effects were seen in people with the highest tumor level of HER2 [defined as immunohistochemistry (IHC) 3+]. In this previous analysis, the HER2 expression was measured at a central laboratory. In clinical practice, HER2 expression will likely be measured at a local laboratory, so understanding whether T-DXd has similar effects regardless of how HER2 expression is measured is important. Here, we looked at the effects of T-DXd based on the HER2 test result used to determine a person's eligibility for the study, which could be measured using a local or central laboratory. In people with IHC 3+ tumors (where HER2 was measured at a local or central laboratory), 51% had a decrease in the size or number of tumors, according to established criteria (referred to as an objective response), while, in people with IHC 2+ tumors, 26% had an objective response. Side effects with T-DXd were consistent with previous studies. These results confirm T-DXd has antitumor effects in HER2-expressing cancers where the HER2 expression is measured by a local or central laboratory.
- Klíčová slova
- Advanced/metastatic solid tumors, HER2 testing, HER2-expressing, Trastuzumab deruxtecan,
- MeSH
- imunohistochemie MeSH
- imunokonjugáty * terapeutické užití škodlivé účinky MeSH
- kamptothecin * analogy a deriváty terapeutické užití aplikace a dávkování škodlivé účinky MeSH
- klinické zkoušky, fáze II jako téma MeSH
- lidé MeSH
- nádory * farmakoterapie metabolismus patologie MeSH
- protinádorové látky imunologicky aktivní * terapeutické užití MeSH
- receptor erbB-2 * metabolismus MeSH
- sekundární analýza dat MeSH
- trastuzumab * terapeutické užití škodlivé účinky MeSH
- výsledek terapie MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- ERBB2 protein, human MeSH Prohlížeč
- imunokonjugáty * MeSH
- kamptothecin * MeSH
- protinádorové látky imunologicky aktivní * MeSH
- receptor erbB-2 * MeSH
- trastuzumab deruxtecan MeSH Prohlížeč
- trastuzumab * MeSH
