Biology subjects

Makalowski, W.

Publications and source records attributed to Makalowski, W..

10 recordsLinked to original sources

bioRxiv2024

Application of a new data management system to the study ofthe gut microbiome of children who are small for theirgestational age

Microbiome studies aim to answer the following questions: which organisms are in the sample and what is their impact on the patient or the environment? To answer these questions, investigators have to perform comparative analyses on their classified sequences based on the collected metadata, such as treatment, condition of the patient, or the environment. The integrity of sequences, classifications, and metadata is paramount for the success of such studies. Still, the area of data management for the preliminary study results appears to be neglected. Here, we present the development of a central data management system with an accessible web interface for the study of the gut microbiome in children who are small for their gestational age. We have called this system MetagenomicsDB. The web interface allows users, regardless of their bioinformatics expertise, to operate the system. The interface contains links to external resources in order to facilitate literature search, statistical analyses, and assessments of the potential pathogenicity of taxa. Preliminary study results are automatically quality-controlled and subsequently imported into a relational database. After exploration and optional filtering by the user, data are exported in a format directly suitable for follow-up analyses. Compared to a more conventional approach of storing the data in plain files, the automated quality control and database storage offered by MetagenomicsDB provides an enhanced quality assurance of the produced study results. This is especially true in a collaborative setting. Also, the automation of the data transfer from the format of the input data to the format needed for downstream analyses makes basic statistical and bioinformatic analyses accessible. The web interface not only allows us to perform our internal analyses, but will also facilitate transparent sharing of the complete study results at publication time with reviewers and the general public. We demonstrated the viability of this approach by making a subset of our preliminary study results already publicly accessible: https://www.bioinformatics.uni-muenster.de/tools/metagenomicsDB In the context of our study, our system provided more flexibility to conduct study- specific analyses and to integrate specific external resources than existing and necessarily more generic solutions. Our system is not yet ready to be widely applicable out-of-the-box for any microbiome study. However, we expect that due to the modular concept, the tests, and the extensive description of the underlying rationale, large parts of our implementation can be adapted for future projects in a fraction of the time needed to develop a new data management system from scratch. Thus, we report our endeavors in order to motivate the application of data management systems at the scale of single studies in microbiome research.

bioinformatics↗

bioRxiv2024

Exploring Alu-Driven DNA Transductions in the Primate Genomes

Long terminal repeats (LTRs) and non-LTRs retrotransposons, aka retroelements, collectively occupy a substantial part of the human genome. Certain non-LTR retroelements, such as L1 and SVA, have the potential for DNA transduction, which involves the concurrent mobilization of flanking non-transposon DNA during retrotransposition. These events can be detected by computational approaches. Despite being the most abundant short interspersed sequences (SINEs) that are still active within the genomes of humans and other primates, the transduction rate caused by Alu sequences remains unexplored. Therefore, we conducted an analysis to address this research gap and utilized an in-house program to probe for the presence of Alu-related transductions in the human genome. We analyzed 118,489 full-length AluY subfamilies annotated within the first complete human reference genome, T2T-CHM13. For comparative insights, we extended our exploration to two non-human primate genomes, the chimpanzee and the rhesus monkey. After manual curation, our findings did not confirm any Alu-mediated transductions, whose source genes are, unlike L1 or SVA, transcribed by RNA polymerase III, implying that they are infrequent or possibly absent not only in the human but also in chimpanzee and rhesus monkey genomes. Although we identified loci in which the 3 Target Site Duplication (TSD) was located distantly from the retrotransposed AluYs, a transduction hallmark, our study could not find further support for such events. The observation of these instances can be explained by the incorporation of other nucleotides into the poly(A) tails in conjunction with polymerase slippage.

genetics↗

bioRxiv2023

First cleavage is a manifestation of the geometry of the unfertilized oocyte: implications for monozygotic twinning in mice.

A long-standing question in mammalian embryology is whether regional differences of oocyte composition matter for the properties of blastomeres receiving those regions after fertilization. A hitherto untested hypothesis is that allocation depends on the orientation of 1st cleavage. However, the orientation is influenced by the site of sperm entry, which can be almost anywhere on the membrane of oocytes when these are inseminated. This variability undermines consistency and reproducibility of studies. Therefore, we harnessed the intracytoplasmic sperm injection to impose the site of fertilization in three specific ooplasmic regions (animal pole, vegetal pole, equator) in mice. Notwithstanding this categorical distinction, after 1st cleavage, the sister blastomeres differed from each other nearly the same way, as measured by gene expression and twin blastocysts formation following 2-cell embryo splitting. We reasoned that either the oocyte territories did not matter, or their effect was obscured by other factors. To shed light on these possibilities, we immobilized the oocytes on the micromanipulation stage during sperm injection and for 24 h thereafter. Imaging revealed that the orientation of 1st cleavage, instead of varying with the fertilization site, followed the shorter diameter of the unfertilized oocyte. This led in most cases to the segregation of animal and vegetal hemispheres into the sister blastomeres of 2-cell embryos. Since one blastomere received more of the animal materials and the other blastomere more of the vegetal materials, this offers a rationale to explain the distinct properties of monozygotic twins derived from 2-cell embryos in mice.

developmental biology↗

bioRxiv2023

TEclass2: Classification of transposable elements using Transformers

MotivationTransposable elements (TEs) are interspersed repetitive sequences that are major constituents of most eukaryotic genomes and are crucial for genome evolution. Despite the existence of multiple tools for their classification and annotation, none of them can achieve completely reliable results making it a challenge for genomic studies. In this work, we introduce TEclass2, a new software that uses a deep learning approach based upon a linear Transformer architecture with a k-mer to-kenizer and further adaptations to handle DNA sequences. This software has an easy configuration that allows training models on new datasets and the classification of TE models providing multiple metrics for a reliable evaluation of the results. ResultsThis work shows a successful adaptation of deep learning with Transformers for the classification of TE models from consensus sequences, and these results lay a foundation for novel methodologies in bioinformatics. We provide a tool for the training of models and the classification of consensus sequences from TE models on custom data and a web page interface with a pre-trained dataset based on curated and non-curated TE libraries allowing a fast and simple classification of TEs. Availabilityhttps://bioinformatics.uni-muenster.de/tools/teclass2/index.pl Contactwojmak@uni-muenster.de Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes. Comprehensive analyses of large, composite or arrayed repeat elements and those found in more complex regions of the genome require a complete, linear genome assembly. Here we present the first de novo repeat discovery and annotation of a complete human reference genome, T2T-CHM13v1.0. We identified novel satellite arrays, expanded the catalog of variants and families for known repeats and mobile elements, characterized new classes of complex, composite repeats, and provided comprehensive annotations of retroelement transduction events. Utilizing PRO-seq to detect nascent transcription and nanopore sequencing to delineate CpG methylation profiles, we defined the structure of transcriptionally active retroelements in humans, including for the first time those found in centromeres. Together, these data provide expanded insight into the diversity, distribution and evolution of repetitive regions that have shaped the human genome.

genomics↗

bioRxiv2021

Software Evaluation for de novo Detection of Transposons

Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. As expected, tools that build TE-models performed better than k-mer counting ones, with RepeatModeler beating competitors in most datasets. However, there is a tendency for most tools to identify TE-regions in a fragmented manner and it is also frequent that small TEs or fragmented TEs are not detected. Consequently, the identification of TEs is still a challenging endeavor and it requires a significant manual curation by an experienced expert. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

bioinformatics↗

bioRxiv2020

High-Quality Genome Assembly and Annotation of the California Harvester Ant Pogonomyrmex californicus (Buckley, 1867)

The harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America and California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in the North America. P. californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus.

genomics↗

bioRxiv2020

MetaGenomic analysis of short and long reads

Identifying single organisms in environmental samples is one of the key tasks of metagenomics. During the last few years, third generation sequencing technologies have enabled researchers to sequence much longer molecules, but at the expense of sequencing accuracy. Thus, new algorithms needed to be developed to cope with this new type of data. With this in mind, we developed a tool called MetaG. An intuitive web interface makes the software accessible to a vast range of users, including those without extensive bioinformatic expertise. Evaluation of MetaGs performance showed that it makes nearly perfect classifications of viral isolates using simulated short and long reads. MetaG also outperformed current state-of-the-art algorithms on data from targeted sequencing of the 16S and 28S rRNA genes. Since MetaGs output is also supplemented with information about hosts and antibiotic resistances of pathogens, we expect it to be especially useful to the healthcare sector. Moreover, the outstanding accuracy of the taxonomic assignments will make MetaG a serious alternative for anyone working with metagenomic sequences. MetaG can be accessed at http://bioinformatics.uni-muenster.de/tools/metag/.

bioinformatics↗

bioRxiv2019

Evolutionary stories told by one protein family: ERM phylogeny in metazoans

Ezrin, radixin, moesin, and merlin are the cytoskeletal proteins which functions are specific to metazoans. They participate in cell cortex rearrangements, including cell-cell contact formation, and play important role in cancer progression. Here we perform a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism of the protein family origin in the root of Metazoa, paralogs diversification in vertebrates and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most of vertebrates, but lost in mammals, has been described. We also highlight the set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between the ERM paralogs.

evolutionary biology↗

bioRxiv2018

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo

Early mouse embryos have an atypical translational machinery comprised of cytoplasmic lattices, poorly competent for translation. Thus, the impact of transcriptomic changes on the operational levels of proteins has likely been overestimated in the past. To find out, we used liquid chromatography-tandem mass spectrometry to detect and quantify 6,550 proteins in the oocyte and in six developmental stages (from zygote to blastocyst) collected in triplicates, and we also performed mRNA sequencing.\n\nIn contrast to the known split between the 2-cell and 4-cell stages at the transcript level, on the protein level the oocyte-to-embryo transition appeared to last until the morula stage. In general, protein abundance profiles were weakly correlated with those of their cognate mRNAs and we found little or no concordance between changes in protein and transcript expression relative to the oocyte at early stages. However, concordance increased towards morula and blastocyst, hinting at a more direct coupling of proteins with transcripts at these stages, in agreement with the increase in free ribosome abundance. Independent validation by immunofluorescence and qPCR confirmed the existence of genes featuring strongly positively and negatively correlated protein and transcript. Moreover, consistent coverage of most known protein complexes indicates that our dataset represents a large fraction of the expressed proteome. Finally, we identified 20 markers, including members of the endoplasmic reticulum pathway, for discriminating between early and late stages.\n\nThis resource contributes towards closing the gap between the predicted phenotype, based on mRNA, and the actual phenotype, based on protein, of the mouse embryo.

developmental biology↗