bioRxiv Science⌕ Search

Biology subjects

Ziegler, M.

Publications and source records attributed to Ziegler, M..

34 records · Page 2Linked to original sources

Short periods of decreased water flow may modulate long-term ocean acidification in reef-building corals

Ocean acidification (OA) poses a major threat to reef-building corals. Although water flow variability is common in coral reefs and modulates coral physiology, the interactive effects of flow and OA on corals remain poorly understood. Therefore, we performed a three-month OA experiment investigating the effect of changes in flow on coral physiology. We exposed the reef-building corals Acropora cytherea, Pocillopora verrucosa, and Porites cylindrica to control (pH 8.0) and OA (pH 7.8) conditions at moderate flow (6 cm s-1) and monitored OA effects on growth. Throughout the experiment, we intermittently exposed all corals to low flow (2 cm s-1) for 1.5 h and measured their photosynthesis:photosynthesis (P:R) ratio under low and moderate flow. On average, corals under OA calcified 18 % less and grew 23 % less in surface area than those at ambient pH. We observed species-specific interactive effects of OA and flow on coral physiology. P:R ratios decreased after 12 weeks of OA in A. cytherea (22 %) and P. cylindrica (28 %) under moderate flow, but were unaffected by OA under low flow. P:R ratios were stable in P. verrucosa. These results suggest that short periods of decreased water flow may modulate OA effects on some coral species, indicating that flow variability is a factor to consider when assessing long-term effects of climate change.

physiology↗

GEMCAT - A new algorithm for gene expression-based prediction of metabolic alterations

The conclusive interpretation of multi-omics datasets obtained from high throughput approaches is an important prerequisite to understand disease-related physiological changes and to predict biomarkers in body fluids. We here present a Gene Expression-based Metabolite Centrality Analysis Tool, GEMCAT, a new genome scale metabolic modelling algorithm. GEMCAT enables integration of transcriptomics or proteomics data to predict changes in metabolite concentrations which can be verified by targeted metabolomics. In addition, GEMCAT allows to trace measured and predicted metabolic changes back to the underlying alterations in gene expression or proteomics and thus enables functional interpretation and integration of multi-omics data. We demonstrate the predictive capacity of GEMCAT on two datasets, one using RNA sequencing data and metabolomics from an engineered human cell line with a functional deletion of the mitochondrial NAD-transporter and another using proteomics and metabolomics measurements from patients with inflammatory bowel disease.

bioinformatics↗

Common types of microdebris affect the physiology of reef-building corals

Marine debris, particularly microdebris (< 1 mm) poses a potential threat to marine life, including reef-building corals. While previous research has mainly focused on the impact of single polymer microplastics, the effects of natural microdebris, composed of a mixture of materials, have not been explored. Therefore, this study aimed to assess the effects of different microdebris, originating from major sources of pollution, on reef-building corals. For this, we exposed two scleractinian coral species, Pocillopora verrucosa and Stylophora pistillata, known to frequently ingest microplastics, to four types of microdebris in an 8-week laboratory experiment: fragmented environmental plastic debris, artificial fibers from clothing, residues from the automobile sector consisting of tire wear, brake abrasion, and varnish flakes, a single polymer microplastic treatment consisting of polyethylene particles, and a microdebris-free control treatment. Specifically, we (I) compared the effects of the different microdebris on coral growth, necrosis, and photosynthesis, (II) investigated the difference between the microdebris mixtures and the exposure to the single polymer treatment, and (III) identified potential mechanisms causing species-specific effects by contrasting the feeding responses of the two coral species on microdebris and natural food. We show that the fibers and tire wear had the strongest effects on coral physiology, with P. verrucosa being more affected than S. pistillata. Both species showed increased volume growth in response to the microdebris treatments, accompanied by decreased calcification in P. verrucosa. Photosynthetic efficiency of the symbionts was enhanced in both species. The species-specific physiological responses might be attributed to feeding reactions, with P. verrucosa responding significantly more often to microdebris than S. pistillata. These findings highlight the effect of different microdebris on coral physiology and the need for future studies to use particle mixtures to better mimic naturally occurring microdebris and assess its effect on corals in more detail. HighlightsO_LIThe effects of major sources of microdebris pollution on coral physiology were compared. C_LIO_LIOverall, microdebris had only minor impacts on coral physiology. C_LIO_LIArtificial fibers and tire wear caused the strongest effect on coral physiology. C_LIO_LISingle polymer and complex microdebris caused similar, yet species-specific effects. C_LIO_LISpecies-specific effects might be due to different feeding behaviors. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/569976v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1ba7ba8org.highwire.dtl.DTLVardef@c5795org.highwire.dtl.DTLVardef@4a10deorg.highwire.dtl.DTLVardef@9983e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

The bacterial microbiome of symbiotic and menthol-bleached polyps of Galaxea fascicularis

AO_SCPLOWBSTRACTC_SCPLOWCoral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of the G. fascicularis microbiome to menthol bleaching--the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleached G. fascicularis originating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results--although preliminary--contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.

microbiology↗

Algal symbioses with fire corals demonstrate host genotype specificity and niche adaptation at subspecies resolution

Corals share an intimate relationship with photosynthetic dinoflagellates that contribute to the biology of the emerging metaorganism. While many coral-algal associations exhibit high host fidelity, the extent of this specificity under environmental change remains to be fully understood and is a prerequisite to forecasting the adaptive potential of this obligate symbiosis. Here, we disentangled the contribution of host genotype and environment on governing coral-algae associations by working at subspecies resolution. We used fine-scale genotyping of algal symbionts from 198 fire coral colonies (Millepora cf. platyphylla) that map to ten distinct sexually produced clonal host genotypes across three environmentally distinct reef habitats. Based on microalgal ITS2 genotyping, we show that algal-host specificity extends down to the Symbiodiniaceae subspecies level in a natural reef environment. Closely related Symbiodinium (A7)-dominated algal assemblages almost perfectly mapped to fire coral host genotype. Furthermore, identification of host genotype- and habitat-specific Symbiodinium alga suggest the presence of algal phenotypic diversity even at this taxonomic resolution (i.e., within Symbiodinium A7), which may aid environmental niche adaptation of the metaorganism. Our results suggest that the here-identified Millepora-Symbiodinium associations are co-evolved to match their prevailing environment. Thus, despite the presence of rarer host generalist Cladocopium algae, scope for environmentally induced modification of the cnidarian-algal association is likely constrained by host genotype.

evolutionary biology↗

POLG genotype influences degree of mitochondrial dysfunction in iPSC derived neural progenitors, but not the parent iPSC or derived glia

Diseases caused by POLG mutations are the most common form of mitochondrial disease and associated with phenotypes of varying severity. Clinical studies have shown that patients with compound heterozygous POLG mutations have a lower survival rate than patients with homozygous mutations, but the molecular mechanisms behind this remain unexplored. Using an induced pluripotent stem cell (iPSC) model, we investigate differences between homozygous and compound heterozygous genotypes in different cell types, including patient-specific fibroblasts, iPSCs, and iPSC-derived neural stem cells (NSCs) and astrocytes. We found that compound heterozygous lines exhibited greater impairment of mitochondrial function in NSCs than homozygous NSCs, but not in fibroblasts, iPSCs, or astrocytes. Compared with homozygous NSCs, compound heterozygous NSCs exhibited more severe functional defects, including reduced ATP production, loss of mitochondrial DNA (mtDNA) copy number and complex I expression, disturbance of NAD+ metabolism, and higher ROS levels, which further led to cellular senescence and activation of mitophagy. RNA sequencing analysis revealed greater downregulation of mitochondrial and metabolic pathways, including the citric acid cycle and oxidative phosphorylation, in compound heterozygous NSCs. Our iPSC-based disease model can be widely used to understand the genotype-phenotype relationship of affected brain cells in mitochondrial diseases, and further drug discovery applications. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/526021v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@ce1761org.highwire.dtl.DTLVardef@610ed3org.highwire.dtl.DTLVardef@1460b0org.highwire.dtl.DTLVardef@1d7fd53_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

The reef-building coral Galaxea fascicularis: a new model system for coral symbiosis

Reef-building corals owe their evolutionary success to their symbiosis with unicellular algae (Symbiodiniaceae). However, increasingly frequent heat waves lead to coral mass-bleaching events and pose a serious threat to the survival of reef ecosystems. Despite significant efforts, a mechanistic understanding of coral-algal symbiosis functioning, what leads to its breakdown and what can prevent it, remains incomplete. The main obstacles are low amenability of corals to experimental handling and, owing to its obligatory nature, the difficulties of manipulating the coral-algal association. Indeed, many studies on the symbiotic partnership are conducted on other cnidarian model organisms and their results may therefore not be fully transferable to tropical reef-building corals. Here, we identify the tropical stony coral species Galaxea fascicularis as a novel candidate coral model system. Individual polyps of this species can be separated, enabling highly replicated genotype studies, and are well suited to experimental investigation of the symbiosis as they can be easily and effectively rid of their algal symbionts (bleached). We show that bleached adult individuals can reestablish symbiosis with non-native symbionts, and we report the completion of the gametogenic cycle ex-situ, with the successful spawning in aquaria over multiple years. These achievements help overcome several of the major limitations to direct research on corals and highlight the potential of G. fascicularis as an important new model system for investigations of symbiosis functioning and manipulation.

systems biology↗

Interactive effects of microplastic pollution and heat stress on reef-building corals

Plastic pollution is an emerging stressor that increases pressure on ecosystems such as coral reefs that are already challenged by climate change. However, the effect of plastic pollution in combination with global warming is largely unknown. Thus, the goal of this study was to determine the cumulative effect of microplastic pollution with that of global warming on reef-building coral species and to compare the severity of both stressors. For this, we conducted a series of three controlled laboratory experiments and exposed a broad range of coral species (Acropora muricata, Montipora digitata, Porites lutea, Pocillopora verrucosa, and Stylophora pistillata) to microplastic particles in a range of concentrations (2.5-2,500 particles L-1) and mixtures (from different industrial sectors) at ambient temperatures and in combination with heat stress. We show that microplastic can occasionally have a negative effect on the corals thermal tolerance. In comparison to heat stress, however, microplastic constitutes a minor stressor. While heat stress led to decreased photosynthetic efficiency of algal symbionts, and increased bleaching, tissue necrosis, and mortality, treatment with microplastic particles had only minor effects on the physiology and health of the tested coral species at ambient temperatures. These findings underline that while efforts to reduce plastic pollution should continue, they should not replace more urgent efforts to halt global warming, which are immediately needed to preserve remaining coral reef ecosystems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/454458v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@c2eeb0org.highwire.dtl.DTLVardef@1c49ea6org.highwire.dtl.DTLVardef@18bab59org.highwire.dtl.DTLVardef@9e952b_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

A comparative baseline of coral disease across the central Red Sea

The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Disease surveys were conducted along 22 reefs in the central Red Sea along the Saudi Arabian coast in October 2015, which coincided with a bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (<0.5%), based on the examination of >75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases were Acropora white syndrome (59.1% of the survey sites), Porites growth anomalies (40.9%), and Porites white syndrome (31.8%). Over half of the coral genera within transects had lesions and corals from the genera Acropora, Millepora and Lobophyllia were the most commonly affected. Cell-associated microbial aggregates were found in four coral genera resembling patterns found in the Indo-Pacific. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average DHW values but absence of bleaching and the highest average disease prevalence was recorded. Our study provides a foundation and baseline data for coral disease prevalence in the Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.

ecology↗

Stem cell derived astrocytes with POLG mutations and mitochondrial dysfunction including abnormal NAD+ metabolism is toxic for neurons

The inability to reliably replicate mitochondrial DNA (mtDNA) by mitochondrial DNA polymerase gamma (POLG) leads to a subset of common mitochondrial diseases associated with neuronal death and depletion of neuronal mtDNA. Defining disease mechanisms remains difficult due to the limited access to human tissue. Astrocytes are highly abundant in the brain, playing a crucial role in the support and modulation of neuronal function. Astrocytes also respond to insults affecting the brain. Following damage to the center neural system, which can be hypoxia, inflammation or neurodegeneration, astrocytes become activated and lose their supportive role and gain toxic functions that induce rapid death of neurons and oligodendrocytes. The role of astrocyte reactivation and the consequences this has for neuronal homeostasis in mitochondrial diseases has not been explored. Here, using patient cells carrying POLG mutations, we generated iPSCs and then differentiated into astrocytes. We demonstrated that POLG-astrocytes exhibited both mitochondrial dysfunctions, including loss of mitochondrial membrane potential, energy failure, complex I and IV defects, disturbed NAD+/NADH metabolism, and mtDNA depletion. Further, POLG derived astrocytes presented an A1-like reactive phenotype with increased proliferation, invasion, upregulation of pathways involved in response to stimulus, immune system process, cell proliferation and cell killing. Under direct and indirect co-culture with neurons, POLG-astrocytes exhibited a toxic effect leading to the death of neurons. Our findings demonstrate that mitochondrial dysfunction caused by POLG mutations leads not only to intrinsic defects in energy metabolism affecting both neurons and astrocytes, but also to neurotoxic damage driven by astrocytes. Our studies provide a robust astroglia-neuronal interaction model for future investigation of mitochondrial involvement in neurogenesis and neurodegenerative diseases. Highlights{blacksquare} Patient-specific astrocytes harbouring a POLG mutation showed lower mitochondrial membrane potential and mtDNA depletion. {blacksquare}POLG-astrocytes generated elevated L-lactate as the end glycolytic product. {blacksquare}Patient-specific astrocytes with POLG mutations exhibited mitochondrial respiratory chain disruption accompanied with abnormal UCP2/SirT1/SirT3 mediated NAD+ metabolism. {blacksquare}Suppressed complex I and IV-driven respiration contributed to the pathological mechanisms in POLG-related disease. {blacksquare}POLG-astrocytes exhibit A1-reactive phenotype and neurotoxic potential. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/423652v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@18995fdorg.highwire.dtl.DTLVardef@1d615d4org.highwire.dtl.DTLVardef@334aa8org.highwire.dtl.DTLVardef@16a84ba_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Natural isotope correction improves analysis of protein modification dynamics

Stable isotope labelling in combination with high resolution mass spectrometry approaches are increasingly used to analyse both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.

bioinformatics↗

AP-4 mediates vesicular transport of the 2-AG endocannabinoid producing enzyme DAGLB

The adaptor protein complex AP-4 mediates anterograde axonal transport and is essential for axon health. AP-4-deficient patients suffer from a severe neurological disorder, which encompasses neurodevelopmental and neurodegenerative features. While impaired autophagy has been suggested to account for axon degeneration in AP-4 deficiency, axon growth defects occur through an unknown mechanism. Here we use orthogonal proteomic and imaging methods to identify DAGLB (diacylglycerol lipase-beta) as a cargo of AP-4 vesicles. DAGLB is a key enzyme for the generation of 2-AG (2-arachidonoylglycerol), the most abundant endocannabinoid in brain. During normal development, DAGLB is targeted to the axon, where 2-AG signalling drives axonal growth. We show that DAGLB accumulates at the TGN of AP-4-deficient cells, including in iPSC-derived neurons from a patient with AP-4 deficiency syndrome. Our data thus support that AP-4 mediates axonal targeting of DAGLB, and we propose that axon growth defects in AP-4 deficiency may arise through spatial dysregulation of endocannabinoid signalling.

cell biology↗

Authentic field experiences for STEM teachers: Collecting Florida fossils

The extensive sedimentary sequence of Florida preserves evidence of prehistoric life spanning some 40 million years into the past. This paper describes the results of a three-pronged professional development (PD) program conducted in November 2019 in which Florida teachers from eight counties gained knowledge and experience about the process and content of paleontology at an active field research site in northern Florida. Working alongside scientists, 15 elementary, middle, and high school teachers collected 5-million-year-old fossil vertebrates and made scientifically important discoveries that advance understanding of Floridas prehistoric life. The PD included three components: (1) a pre-trip webinar; (2) a morning tour of our museum exhibits to scaffold teachers understanding of the kinds of fossils they would find; and (3) the actual day-long field experience collecting fossils. A post-PD evaluation revealed gains in knowledge about, and experience with, fossils and paleontology. We also found that overall satisfaction with the PD underscored the importance of each of the three components supporting one-another--resulting in a more informative and rewarding learning experience for the participants. Fossils and the science of paleontology are a gateway for STEM learning and this subject and its extensions are applicable to existing standards in earth and life sciences at many grade levels.

scientific communication and education↗

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

genomics↗

The knockout of the HMG-Domain of the porcine SRY-gene by CRISPR/Cas RNP microinjection causes sex reversal in gene-edited pigs

1The sex-determining region on the Y chromosome (SRY) is thought to be the central genetic element of male sex development. Mutations within the SRY gene are associated with a male-to-female sex reversal syndrome in humans and other mammalian species such as mice and rabbits. However, the underlying mechanisms are largely unknown. To understand the biological function of the SRY gene, a site-directed mutational analysis is required to investigate associated phenotypic changes at the molecular, cellular and morphological level. In our study, we successfully generated a knockout of the porcine SRY gene by microinjection of two clustered regularly interspaced short palindromic repeats (CRISPR) - associated protein - 9 nuclease (Cas9) ribonucleoprotein (RNP) complexes targeting the centrally located "high mobility group" (HMG) domain of the SRY gene. Mutations within this region resulted in the development of complete external and internal female genitalia in genetically male pigs. The internal female genitalia including uteri, ovaries, and oviducts, revealed substantial size differences in 9-months old SRY-knockout pigs compared to age-matched female wild type controls. In contrast, a deletion within the 5 flanking region of the HMG domain was not associated with sex reversal. Results of this study demonstrates for the first time the central role of the HMG domain of the SRY gene in male sex determination in pigs. Moreover, quantitative analysis by digital PCR revealed evidence for a duplication of the porcine SRY locus. Our results pave the way towards the generation of boars exclusively producing phenotypically female offspring to avoid surgical castration without anesthesia in piglets. Moreover, the study establishes a large animal model that is much more similar to humans in regard of physiology and anatomy and pivotal for longitudinal studies.

developmental biology↗

Growth potential of Listeria monocytogenes in twelve different types of RTE salads: impact of food matrix, storage temperature and shelf life

Listeriosis is a food borne disease associated with high hospitalization and fatality rates; in 2014, EU member states reported 2194 cases with 98.9% hospitalization rates and 210 fatalities. Proper risk analysis and the development of effective food safety strategies critically depend on the knowledge of the growth characteristics of L. monocytogenes on the product in question. Ready-to-eat (RTE) salads present a challenge in this context due to the absence of a heat treatment step before consumption and the interaction of pathogens with the plant microbial microbiota. This study provides challenge-test based data of the growth characteristics of L. monocytogenes on twelve RTE salads. The food matrix, storage time and storage temperature were factors with a significant impact on the growth of L. monocytogenes. While most tested salads permitted a significant increase of L. monocytogenes in at least one of the tested conditions, no growth was observed on celeriac, carrot and corn salad products. There was a considerable increase in growth at 8 {degrees}C compared to 5 {degrees}C. Our data indicate that the reduction of the storage temperature at retail level to 5 {degrees}C and product shelf life could help mitigate the risk of L. monocytogenes in RTE salads.

microbiology↗