Biology subjects

Hübner, A.

Publications and source records attributed to Hübner, A..

7 recordsLinked to original sources

bioRxiv2026

DeepPhage: leveraging the power of NGS phage display data, an in-depth analysis for the identification of Eu3+-binding peptides

Summary: Phage Surface Display (PSD) is a widely used molecular technique for identifying peptides and antibodies with applications in therapeutics, diagnostics, and materials science. The use of highly diverse phage libraries enables the screening of millions of ligand variants, while the integration of Next-Generation Sequencing (NGS) provides high-throughput access to the sequence composition of selected phage populations. Despite these advances, the identification of genuine target-binding ligands remains challenging due to biases introduced during library construction, biological selection and propagation, as well as the enrichment of target-unrelated peptides (TUPs). These factors distort sequence distributions and complicate the interpretation of PSD-NGS experiments, particularly when comparing multiple libraries or selection rounds. Consequently, robust computational methods are required to distinguish biologically relevant enrichments from technical artifacts. We demonstrate DeepPhage using PSD-NGS datasets from Eu3+ biopanning experiments, in which differences in peptide composition between experimental conditions were identified and a systematic comparison of several conditions was made possible. It was developed to address the lack of comparative analysis tools for large-scale PSD-NGS experiments by combining statistical analyses with comprehensive visualisation. These features form the basis for a more reliable interpretation of phage display selection experiments. DeepPhage provides a reproducible framework for comparative PSD-NGS analysis, which supports the identification of sequence bias, library heterogeneity and potential target-binding peptides across multiple experiments. The software is freely available as an open-source command-line application, so that it can be deployed on a high computer cluster for particularly large volumes of data. Availability and implementation: DeepPhage is entirely open source and is available on GitLab https://codebase.helmholtz.cloud/phagelabs-hif/DeepPhage/-/tree/stable_release_v0.1 under the GPL v3 licence. The repository contains documentation, installation instructions, a user guide and example data. The sample data used for the demonstration is available at the online repository RODARE (https://doi.org/10.14278/rodare.4647).

bioinformatics↗

bioRxiv2026

AncientMetagenomeDir dating metadataset highlights need for standardised radiocarbon reporting in ancient DNA

Ancient DNA is a valuable data source for the understanding of our past. However, to effectively interpret this data, it is essential to know the age of the samples from which the DNA is obtained. Although the field of palaeogenomics has been recognised for its robust open data sharing practices, dating information associated with analysed samples is not reported consistently across palaeogenomic studies, nor is it included as metadata in most genetic data repositories. Here, we describe the addition of standardised precise dating information for ancient microbial genomes into the AncientMetagenomeDir metadata repository of published ancient metagenomic samples. This extension currently includes dating information for over 700 ancient microbial genomic datasets, of which 333 are dated using historical, contextual, or stratigraphic methods, and 405 are radiocarbon dated. We quantitatively assess the quality of radiocarbon date reporting and find that, despite established reporting conventions, radiocarbon dating information is often reported inconsistently across ancient metagenomic studies. This new resource provides ancient microbial researchers with standardised dating information that facilitates more accurate and consistent analysis of metagenomic sequencing data. The dataset also highlights the need for greater standardisation of radiocarbon date reporting in original publications in order to allow effective reuse of this and future ancient microbial data.

bioinformatics↗

bioRxiv2021

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this regions demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

genomics↗

bioRxiv2020

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

bioinformatics↗

bioRxiv2018

Triple A patient cells suffering from mitotic defects fail to localize PGRMC1 to mitotic kinetochore fibers

HIGHLIGHT SUMMARYO_LIInvestigating cell division in human adrenal cells we show that proliferation is decreased upon overexpression of ALADIN, PGRMC1 or PGRMC2.\nC_LIO_LIIn immunofluorescence experiments using human adrenal cells and triple A patient fibroblasts we observed that during cell division PGRMC1 localizes to the microtubule kinetochore-fibers in metaphase and to the mid-body in telophase.\nC_LIO_LIDepletion of ALADIN results in mis-localization of Aurora A and PGRMC1 in metaphase cells of the human adrenal cell line and fibroblasts derived from patients with triple A syndrome.\nC_LIO_LIIn real time PCR using RNA of fibroblasts of triple A syndrome patients and healthy controls we measured an increased expression of PGRMC2 in cells with ALADIN mis-function compared to the control cells.\nC_LIO_LIWe hypothesize that a loss of the regulatory interaction between ALADIN and PGRMC2 leads to an over-regulation and over-expression of PGRMC2 and displaces PGRMC1 at the metaphase spindle. This diminishing of PGRMC1 concentration at kinetochore fibers may lead to mitotic errors and pro - liferation arrest.\nC_LI\n\nABSTRACTMembrane-associated progesterone receptors are restricted to the endoplasmic reticulum and are shown to regulate the activity of cytochrome P450 enzymes which are involved in steroidogenesis or drug detoxification. PGRMC1 and PGRMC2 belong to this group of microsomal receptors and are of interest due to their suspected role during cell cycle. PGRMC1 and PGRMC2 are thought to bind to each other thereby suppressing entry into mitosis. We could previously report that PGRMC2 interacts with the nucleoporin ALADIN which when mutated results in the autosomal recessive disorder triple A syndrome. ALADIN is a novel regulator of mitotic controller Aurora kinase A and depletion of this nucleoporin leads to microtubule instability. In the current study, we present that proliferation is decreased when ALADIN, PGRMC1 or PGRMC2 are over-expressed. Furthermore, we find that depletion of ALADIN results in mis-localization of Aurora kinase A and PGRMC1 in metaphase cells. Additionally, PGRMC2 is over-expressed in triple A patient fibroblasts. Our results emphasize the possibility that loss of the regulatory interaction between ALADIN and PGRMC2 gives rise to a depletion of PGRMC1 at kinetochore fibers and to mitotic errors. This observation may explain part of the symptoms seen in triple A syndrome patients.

cell biology↗

bioRxiv2018

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kxa, Khoe-Kwadi and Bantu languages. Although present-day Bantu-speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun) and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu NRY lineages among Bantu-speaking groups, except for small amounts of \"Khoisan\" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for NRY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

genetics↗

bioRxiv2017

Genetic structure and sex-biased gene flow in the history of southern African populations

ObjectivesWe investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa.\n\nMaterial and MethodsWe analyzed previously published complete mtDNA genome sequences and ~900 kb of NRY sequences from 23 populations from Namibia, Botswana and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b.\n\nResultsOur results support an eastern African origin for Y-chromosome haplogroup E1b1b; however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting a more complex origin for pastoralism in this region. We confirm that the Bantu expansion had a notable genetic impact in southern Africa, and that in this region it was probably a rapid, male-dominated expansion. Furthermore, we find a significant increase in the intensity of sex-biased gene flow from north to south, which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.\n\nConclusionsOur study shows that the population history of southern Africa has been very complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

genetics↗