Biology subjects

Maas, A.

Publications and source records attributed to Maas, A..

8 recordsLinked to original sources

bioRxiv2025

In vivo deletion of a GWAS-identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in beta-thalassemia

Genome-wide association studies (GWAS) have identified numerous genetic variants linked to human diseases, mostly located in non-coding regions of the genome, particularly in putative enhancers. However, functional assessment of the non-coding GWAS variants has progressed at slow pace, since the functions of the vast majority of genomic enhancers have not been defined, impeding interpretation of disease-susceptibility variants. The HBS1L-MYB intergenic region harbors multiple SNPs associated with clinical erythroid parameters, including fetal hemoglobin levels, a feature impacting disease severity of beta-hemoglobinopathies such as sickle cell anemia and beta-thalassemia. HBS1L-MYB variants cluster in the vicinity of several MYB enhancers, altering MYB expression and globin switching. We and others have highlighted the conserved human MYB -84kb enhancer, known as the -81kb enhancer in the mouse, as likely candidate linked to these traits. We report here the generation of a Myb -81kb enhancer knock-out mouse model, and shed light for the first time on its impact on steady state erythropoiesis and in beta-thalassemia in vivo.

genetics↗

bioRxiv2024

Phytoplankton Photophysiology Reveals Depth Specific Zooplankton Grazing

Marine particle forensics frequently uncover information on composition, age, size, and ecological history. Zooplankton fecal pellets are also studied for process-related data, such as grazing rates and carbon sequestration potential. Here, flow cytometric analyses of fecal pellet contents revealed intact phytoplankton with photophysiological characteristics mirroring those of free-living cells. Mapping the cytometrically derived properties of cells inside fecal pellets onto vertical profiles from free-living cells revealed the potential to estimate depth specific grazing by individual zooplankton. An experiment conducted at sea confirmed that the photophysiological characteristics of free-living phytoplankton from multiple depths, consumed by zooplankton, and excreted within fecal pellets are retained for at least 24 hours after grazing is initiated. These results have implications for high resolution modeling of individual or group specific zooplankton grazing dynamics that are critical for accurately linking zooplankton grazing in the surface ocean with the mesopelagic and deep ocean food webs and carbon export. Scientific Significance StatementFecal pellet forensics have provided significant contributions to the study of zooplankton grazing and the marine carbon cycle. Gaps in knowledge about these processes remain, and continued investigations into fecal pellet contents and their fate are important for assessing connections between the surface and deeper ocean ecosystems. We describe a study conducted in the North Atlantic in the Spring of 2021 using flow cytometry to investigate fecal pellets contents. Observations that intact phytoplankton within the pellets had similar photophysiological properties to the free-living community led to a series of sample collections and experiments which provided a path forward for determining depth specific grazing by zooplankton community members. Phytoplankton survival after passing through zooplankton guts and being packaged into fecal pellets, with their potential for release far below the surface mixed layer, support prior observations of healthy phytoplankton communities at depth and validate this mechanism for the rapid transport of freshly fixed carbon to deep ocean systems. The results should be of interest to plankton ecologists and carbon cycle scientists connecting surface and deep ocean ecosystems as application of this approach at a broader scale will provide opportunities for high resolution modeling of individual and group specific zooplankton behaviors.

ecology↗

bioRxiv2023

Chromosome Pairing Through Tensioned DNA Tethers Revealed by BRCA2 Meiotic Domain Deletion

BRCA2 has multiple functional domains that interact with different partners, and is essential for both somatic and meiotic homologous recombination (HR). We created a Brca2{Delta}12-14 mouse model with an internal deletion of the region which we named "the meiotic domain of BRCA2", as its loss results in complete failure of meiotic HR, while somatic HR is intact. The deletion in the protein includes the HSF2BP-binding motifs (exons 12-13) and the DMC1-binding PhePP domain (exon 14). Brca2{Delta}12-14 mice showed complete infertility in both males and females, with sexually dimorphic features. Recombinase foci (both RAD51 and DMC1) were completely undetectable in mutant spermatocytes, but while DMC1 foci were also absent in mutant oocytes, RAD51 foci numbers were only partially reduced. The function of the PhePP domain for meiotic HR is unclear, but both the phenotype of Brca2{Delta}12-14, and our biochemical data indicate that, along with the BRC repeats of BRCA2, PhePP is both critical and specific for DMC1 loading in meiotic HR, analogous to the C-terminal RAD51-specific TR2/CTRB. Further investigation of DSB end processing in Brca2{Delta}12-14 meiocytes and controls, using super-resolution imaging of RPA and SYCP3 led to discovery of two novel features. First, in Brca2{Delta}12-14 oocytes, but not in the spermatocytes nor wild types, we observed RPA foci as doublets [~]200 nm apart, which could represent DSB end resolution into separate nanofoci. Second, we describe RPA structures that are completely HR-dependent and are indicative of long, double-stranded DNA connections between homologs prior to synapsis. Our observations lend support to a model for chromosome alignment via multiple HR-dependent DNA tethers that connect homologs and may be tensed. We propose that tether shortening (e.g. by dynamic adjustment of chromatin loops by meiotic cohesins) provides a plausible molecular mechanism to juxtapose homologs and initiate synapsis. Version 2 Revision SummaryThe main difference compared to version 1 (deposited on October 6 2023) is a more concise and structured description of the tensed DNA tether model of meiotic chromosome pairing, based on the discussions with colleagues and one round of peer review. In the new model presentation, we explicitly separated the inferences from the presented data from the two hypothetical propositions: (1) tether shortening contributes to pairing rather than simply accompanies it, and (2) the apparent tension, which reveals the tethers on chromosome spreads, also exists in the nuclei. We also clarified the definition of the tether, avoiding the ambiguous "RPA tether" term, and provided a more complete overview of the relevant prior literature on proteinaceous bridges and DNA connections. Biochemical data (Fig. 4, S5) has been replicated under uniform conditions and extended to mouse proteins. Manuscript has been reformatted to improve on-screen readability. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/561239v2_fig4.gif" ALT="Figure 4"> View larger version (41K): org.highwire.dtl.DTLVardef@1b95b8corg.highwire.dtl.DTLVardef@297466org.highwire.dtl.DTLVardef@198ef4borg.highwire.dtl.DTLVardef@1862be6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Biochemical characterization of the DMC1-BRCA2 interaction. (A) BRCA2 regions deleted in the mice (yellow) and studied in pull-downs (black), HSF2BP-interacting motifs, PhePP motif and the peptide used in ref. 16 are indicated. Residue numbers for human BRCA2 are shown in black, mouse in blue. (B) GST pull-down with the indicated GST-BRCA2 fragments immobilized on GSH-sepharose beads and used to precipitate recombinant DMC1 or RAD51, followed by immunoblotting with anti-RAD51 antibody (cross-reacts with DMC1) and anti-GST antibodies. Full-size GST-fragment bands are indicated by red arrows, predicted Mw listed below the blot. Experiment was performed twice with same results. (C) Co-precipitation of purified recombinant untagged DMC1 and RAD51 with purified GST-tagged BRCA2 fragment F2s3 (wild type (wt) and F2406A variant (FA)) immobilized on the beads. Bound proteins were analyzed by SDS-PAGE and stained with Coomassie. (D) ITC analysis of the interaction between untagged DMC1 and synthetic peptides corresponding to BRCA2-F2s6 fragment, its F2406A variant, and the peptide from the RAD51-binding TR2 domain, containing a similar FxPP consensus. Experiments were performed twice with the same result, replicates are shown in Figure S5. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/561239v2_figS5.gif" ALT="Figure 5"> View larger version (21K): org.highwire.dtl.DTLVardef@1ac2377org.highwire.dtl.DTLVardef@4c710eorg.highwire.dtl.DTLVardef@924e49org.highwire.dtl.DTLVardef@151a83f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure S5.C_FLOATNO (A) Repeat of the ITC experiment shown in Figure 4D. (B) GST pull-down using BRCA2-F2s3, the corresponding mouse BRCA2 fragment (I2327-Q2379), their variants with substitutions in the key phenylalanine (F2406A in human BRCA2 and F2351D in mouse BRCA2, to model the mutation introduced in the previously published mouse strain) and mouse or human his-DMC1. Proteins were expressed in E. coli, precipitated sequentially form crude lysates and detected by immunoblotting with anti-RAD51 and anti-GST antibodies. The experiment was done twice with the same result. C_FIG O_FIG O_LINKSMALLFIG WIDTH=155 HEIGHT=200 SRC="FIGDIR/small/561239v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1fcff59org.highwire.dtl.DTLVardef@e043a5org.highwire.dtl.DTLVardef@17924dcorg.highwire.dtl.DTLVardef@62fbc3_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Individualized Gaussian Process-based Prediction of Memory Performance and Biomarker Status in Ageing and Alzheimer's disease

Neuroimaging markers based on Magnetic Resonance Imaging (MRI) combined with various other measures (such as informative covariates, vascular risks, brain activity, neuropsychological test etc.,) might provide useful predictions of clinical outcomes during progression towards Alzheimers disease (AD). The Bayesian approach aims to provide a trade-off by employing relevant features combinations to build decision support systems in clinical settings where uncertainties are relevant. We tested the approach in the MRI data across 959 subjects, aged 59-89 years and 453 subjects with available neuropsychological test scores and CSF biomarker status (amyloid-beta (A{beta})42/40 & and phosphorylated tau (pTau)) from a large sample multi-centric observational cohort (DELCODE). In order to explore the beneficial combinations of information from different sources, we presented a MRI-based predictive modelling of memory performance and CSF biomarker status (positive or negative) in the healthy ageing group as well as subjects at risk of Alzheimers disease using a Gaussian process multikernel framework. Furthermore, we systematically evaluated predictive combinations of input feature sets and their model variations, i.e. (A) combinations of brain tissue classes and feature type (modulated vs. unmodulated), choices of filter size of smoothing (ranging from 0 to 15 mm full width at half maximum), and image resolution (1mm, 2mm, 4mm and 8mm); (B) incorporating demography and covariates (C) the impact of the size of the training data set (i.e., number of subjects); (D) the influence of reducing the dimensions of data and (E) choice of kernel types. Finally, the approach was tested to reveal individual cognitive scores at follow-up (up to 4 years) using the baseline features. The highest accuracy for memory performance prediction was obtained for a combination of neuroimaging markers, demographics, genetic information (ApoE4) and CSF-biomarkers explaining 57% of outcome variance in out of sample predictions. The best accuracy for A{beta}42/40 status classification was achieved for combination demographics, ApoE4 and memory score while usage of structural MRI improved the classification of individual patients pTau status.

neuroscience↗

bioRxiv2020

A cryptic BRCA2 repeated motif binds to HSF2BP oligomers with no impact on meiotic recombination

BRCA2 plays a prominent role in meiotic homologous recombination (HR). Loss of BRCA2 or several of its meiotic partners causes fertility defects. One of these partners, HSF2BP, was recently discovered as expressed physiologically in germline and ectopically produced in cancer cells. It has an N-terminal coiled coil motif involved in direct binding to the protein BRME1, and both HSF2BP and BRME1 are essential for meiotic HR during spermatogenesis. It also interacts through its C-terminal Armadillo (ARM) domain with a conserved region of BRCA2 of unknown function. We analyzed the structural properties and functional consequences of the BRCA2-HSF2BP interaction and tested the emerging model of its involvement in meiosis. We solved the crystal structure of the complex between the BRCA2 fragment that is disordered in solution and the HSF2BP dimeric ARM domain. This revealed two previously unrecognized BRCA2 repeats that each interact with one ARM monomer from two different dimers. BRCA2 binding triggers ARM tetramerization, resulting in a complex containing two BRCA2 fragments connecting two ARM dimers. The 3D structures of the BRCA2 repeats are superimposable, revealing conserved contacts between the BRCA2 residues defining the repeats and the HSF2BP residues lining the groove of the ARM. This large interface is responsible for the nanomolar affinity of the interaction, significantly stronger than any other measured interaction involving BRCA2. Deleting exon 12 from Brca2, encoding the first repeat, disrupted BRCA2 binding to HSF2BP in vitro and in cells. However, Brca2{Delta}12/{Delta}12 mice with the same deletion were fertile and did not show any meiotic defects, contrary to the prediction from the model positing that HSF2BP acts as a meiotic localizer of BRCA2. We conclude that the high-affinity interaction between BRCA2 and HSF2BP and the resulting HSF2BP oligomerization are not required for RAD51 and DMC1 recombinase localization to meiotic double strand breaks and for productive meiotic HR.

molecular biology↗

bioRxiv2020

Inducible expression of human C9ORF72 36x G4C2 hexanucleotide repeats is sufficient to cause RAN translation and rapid muscular atrophy in mice

The hexanucleotide G4C2 repeat expansion in the first intron of the C9ORF72 gene explains the majority of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) cases. Numerous studies have indicated the toxicity of dipeptide repeats (DPRs) which are produced via repeat-associated non-AUG (RAN) translation from the repeat expansion and accumulate in the brain of C9FTD/ALS patients. Mouse models expressing the human C9ORF72 repeat and/or DPRs show variable pathological, functional and behavioral characteristics of FTD and ALS. Here, we report a new Tet-on inducible mouse model that expresses 36x pure G4C2 repeats with 100bp upstream and downstream human flanking regions. Brain specific expression causes the formation of sporadic sense DPRs aggregates upon 6 months dox induction but no apparent neurodegeneration. Expression in the rest of the body evokes abundant sense DPRs in multiple organs, leading to weight loss, neuromuscular junction disruption, myopathy and a locomotor phenotype within the time frame of four weeks. We did not observe any RNA foci or pTDP-43 pathology. Accumulation of DPRs and the myopathy phenotype could be prevented when 36x G4C2 repeat expression was stopped after 1 week. After 2 weeks of expression, the phenotype could not be reversed, even though DPR levels were reduced. In conclusion, expression of 36x pure G4C2 repeats including 100bp human flanking regions is sufficient for RAN translation of sense DPRs and evokes a functional locomotor phenotype. Our inducible mouse model highlights the importance of early diagnosis and treatment for C9FTD/ALS patients. Summary statementOnly 36 C9ORF72 repeats are sufficient for RAN translation in a new mouse model for ALS and FTD. Reducing toxic dipeptides can prevent but not reverse the phenotype.

neuroscience↗

bioRxiv2019

The origin and diversification of pteropods predate past perturbations in the Earth’s carbon cycle

Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification (OA). Their thin aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in Earths carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset incorporating 21 new species and new fossil evidence. In agreement with traditional taxonomy, we recovered the first molecular support for a division between sea butterflies (Thecosomata: mucus-web feeders) and sea angels (Gymnosomata: active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled and unshelled groups, diverged in the mid to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene Eocene Thermal Maximum (PETM), which is the closest analogue to modern-day ocean acidification and warming. Our findings indicate that aragonitic calcifiers have been resilient to extreme perturbations in the Earths carbon cycle over evolutionary timescales.

evolutionary biology↗

bioRxiv2018

The mouse Klf1 Nan variant impairs nuclear condensation and erythroid maturation

Kruppel-like factor 1 (KLF1) is an essential transcription factor for erythroid development, as demonstrated by Klf1 knockout mice which die around E14 due to severe anemia. In humans, >65 KLF1 variants, causing different erythroid phenotypes, have been described. The Klf1 Nan variant, a single amino acid substitution (p.E339D) in the DNA binding domain, causes hemolytic anemia and is dominant over wildtype KLF1. Here we describe the effects of the Nan variant during fetal development. We show that Nan embryos have defects in erythroid maturation. RNA-sequencing of the Nan fetal liver cells revealed that Exportin 7 (Xpo7) was among the ~780 deregulated genes. This nuclear exportin is implicated in terminal erythroid differentiation; in particular it is involved in nuclear condensation. Indeed, KLF1 Nan fetal liver cells had larger nuclei and reduced chromatin condensation. Knockdown of XPO7 in wildtype erythroid cells caused a similar phenotype. We conclude that reduced expression of XPO7 is partially responsible for the erythroid defects observed in Nan erythroid cells.

developmental biology↗