Biology subjects

Kucera, M.

Publications and source records attributed to Kucera, M..

9 recordsLinked to original sources

bioRxiv2024

Cardiac acetylcholinesterase and butyrylcholinesterase have distinct localization and function

Cholinesterase (ChE) inhibitors are under consideration to be used in the treatment of cardiovascular pathologies. A prerequisite to advancing ChE inhibitors into the clinic is their thorough characterization in the heart. The aim here was to provide a detailed analysis of cardiac ChE to understand their molecular composition, localization, and physiological functions. A battery of biochemical, microscopic, and physiological experiments was used to analyze two known ChE, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), in hearts of mutant mice lacking different ChE molecular forms. Overall, AChE activity was exceeded by BChE, while it was localized mainly in the atria and the ventricular epicardium of the heart base. AChE was anchored by ColQ in the basal lamina or by PRiMA at the plasma membrane and co-localized with the neuronal marker TUJ1. In absence of anchored AChE, heart rate was unresponsive to a ChE inhibitor. BChE, the major ChE in heart, was detected predominantly in ventricles, presumably as a precursor (soluble monomers/dimers). Mice lacking BChE were more sensitive to a ChE inhibitor. Nevertheless, the overall impact on heart physiology was subtle, showing mainly a role in cholinergic antagonism to the positive inotropic effect of {beta}-adrenergic stimulation. Our results help to unravel the mechanisms of ChE in cardiovascular pathologies and provide a foundation to facilitate the design of a novel, more effective pharmacotherapies, which may reduce morbidity and mortality of patients with various heart diseases. Abstract figure legend O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/596481v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@136068corg.highwire.dtl.DTLVardef@1e8118corg.highwire.dtl.DTLVardef@d83298org.highwire.dtl.DTLVardef@1e1cde7_HPS_FORMAT_FIGEXP M_FIG C_FIG Acetylcholinesterase (AChE) has the highest activity in the atria. It is present in the heart in molecular forms anchored by a proline-rich membrane anchor (PRiMA) and by collagen Q (ColQ) and hydrolyzes acetylcholine of neuronal origin (neuronal ACh). Butyrylcholinesterase (BChE) is predominant in the ventricles. It is secreted in the form of a soluble tetramer and hydrolyzes acetylcholine originating from cardiomyocytes (non-neuronal ACh). Key pointsO_LIInhibition of cholinesterases has therapeutic potential in cardiovascular pathologies C_LIO_LIBoth known cholinesterases are present in heart C_LIO_LIEach cholinesterase has distinct localization patterns in the heart and functions in cardiac physiology C_LIO_LISelective inhibition of acetylcholinesterase or butyrylcholinesterase may be used to alter specific cardiac functions C_LIO_LIButyrylcholinesterase polymorphism may have an impact on the outcome of the cholinesterase inhibitor treatment C_LI

physiology↗

bioRxiv2022

Integrative assessment of the transcriptome and virome of the poultry red mite Dermanyssus gallinae.

Dermanyssus gallinae is a blood-feeding mite that parasitises on wild birds and farmed poultry. The D. gallinae mite has a short life cycle of fewer than two weeks from the egg to an egg-laying female. The remarkably swift processing of blood, together with the capacity to blood-feed in most developmental stages, makes this mite a highly debilitating pest. We have constructed developmental stage-specific transcriptomes, through Illumina RNA-seq, to mine the repertoire of protein-encoding mRNA transcripts, products of which participate in key processes that ensure the success of blood digestion, rapid ontogeny, and immunity. As a result of high reproductive capacity, the prevalence of D. gallinae in egg-producing poultry farms globally causes significant economic losses. Acaricides that are used to limit the reproduction of D. gallinae mites target cys-loop ion channels, which are widely shared across the phylogeny of invertebrates. To catalogue a comprehensive list of potential invertebrate-specific ion channels, we have constructed and analysed an additional RNA-seq library of D. gallinae micro-dissected midguts, a tissue with direct exposure to host blood and potential anti-parasitics. We phylogenetically defined groups of cys-loop proteins and probed their sensitivity to selected acaricides. Ultimately, we have catalogued all assembled transcripts and their expression values in a hyper-linked excel sheet with available sequences of individual contigs. The transcriptomic data were complemented by mass-spectrometry (MS)-based metabolite identification and by viability assays using selected inhibitors applied either by microinjection or through artificial membrane feeding. Additionally, we have described the RNA-virome of D. gallinae and identified a novel virus dubbed Red Mite Quaranjavirus 1.

microbiology↗

bioRxiv2021

Decadal trend of plankton community change and habitat shoaling in the Arctic gateway recorded by planktonic foraminifera

The Fram Strait plays a crucial role in regulating the heat and sea-ice dynamics in the Arctic. In response to the ongoing global warming, the marine biota of this Arctic gateway is experiencing significant changes with increasing advection of Atlantic species. The footprint of this "Atlantification" has been identified in isolated observations across the plankton community, but a systematic, multi-decadal perspective on how regional climate change facilitates the invasion of Atlantic species and affects the ecology of the resident species is lacking. Here we evaluate a series of 51 depth-resolved plankton profiles collected in the Fram Strait during seven surveys between 1985 and 2015, using planktonic foraminifera as a proxy for changes in both the pelagic community composition and species vertical habitat depth. The time series reveals a progressive shift towards more Atlantic species, occurring independently of changes in local environmental conditions. We conclude that this trend is reflecting higher production of the Atlantic species in the "source" region, from where they are advected into the Fram Strait. At the same time, we observe that the ongoing extensive sea-ice export from the Arctic and associated cooling-induced decline in density and habitat shoaling of the subpolar Turborotalita quinqueloba, whereas the resident Neogloboquadrina pachyderma persists. As a result, the planktonic foraminiferal community and vertical structure in the Fram Strait shifts to a new state, driven by both remote forcing of the Atlantic invaders and local climatic changes acting on the resident species. The strong summer export of Arctic sea ice has so far buffered larger plankton transformation. We predict that if the sea-ice export will decrease, the Arctic gateway will experience rapid restructuring of the pelagic community, even in the absence of further warming. Such a large change in the gateway region will likely propagate into the Arctic proper.

ecology↗

bioRxiv2020

Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community

Isotopic and trace-element signals in the calcite shells of the planktonic foraminifera Neogloboquadrina pachyderma represent key proxies to reconstruct past climatic conditions in northern high latitudes. A correct interpretation of these chemical signals requires knowledge of the habitat and trophic interactions of the species. Direct observations on the biological interactions of N. pachyderma in polar environments are lacking and to date no consensus exists on the trophic behaviour of this species. Here we use single-cell metabarcoding to characterise the interactions of 39 specimens of N. pachyderma from two sites in the Baffin Bay with the local eukaryotic pelagic community. Our results show that the eukaryotic interactome of the foraminifera is dominated by diatoms, accounting for > 50% of the reads in 17 of the samples, but other groups such as Crustacea and Syndiniales are also present. The high abundance Syndiniales suggests that these parasites could infect N. pachyderma and may play an important role in its population dynamics. Moreover, the strong but taxonomically non-specific association with algae, existing irrespective of depth and occurring in specimens collected far below the photic zone indicates that opportunistically grazed diatom-fuelled marine aggregates likely represent the main interaction substrate of N. pachyderma.

molecular biology↗

bioRxiv2020

Anaerobic metabolism of Foraminifera thriving below the seafloor

Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. The relative abundance of Foraminifera gene expression in anoxic sediment depths increased an order of magnitude, which was confirmed in a ten-day incubation experiment where the development of anoxia coincided with a 27-fold increase in the relative abundance of Foraminifera protein encoding transcripts. This indicates that many Foraminifera were not only surviving, but thriving under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, dissimilatory nitrate reduction, fumarate reduction, and dephosphorylation of creatine phosphate. This was co-expressed alongside genes involved in production of reticulopodia, phagocytosis, calcification, and clathrin-mediated-endocytosis (CME). Thus, Foraminifera may use CME under anoxic conditions to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These mechanisms help explain how some Foraminifera can thrive under anoxia, which would help to explain their ecological success documented in the fossil record since the Cambrian period more than 500 million years ago.

microbiology↗

bioRxiv2019

Extinctions in marine plankton preceded by stabilizing selection

Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption, increasing trait variation, or stabilisation, decreasing trait variation. In the short term, the more economical response is stabilisation, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalisation is deleterious in the face of persistently increasing stress because it reduces variability and thus decreases the ability to react to further change in stress. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptive reaction of populations facing extinction are rare. In this study, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variance in two species across a salinity rise leading to their local extinction. One species reacted by stabilisation in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remains stable or reacted by further stabilisation. These observations indicate that the default reaction of the studied Foraminifera is stabilisation and that stress escalation did not lead to the local emergence of adapted forms. Inability to breach the global adaptive threshold would explain why communities of Foraminifera, and many other groups of marine plankton, reacted to Quaternary climate change by faithfully tracking their zonally shifting environments. It also means that populations of marine species adapted to response by migration, when exposed to stress outside of the adaptive range, will be at risk of extinction.

ecology↗

bioRxiv2018

Predictability of intraspecific size variation in extant planktonic foraminifera

The size structure of plankton communities is an important determinant of their functions in marine ecosystems. However, few studies have quantified how organism size varies within species across space. Using a recently-digitised museum collection, we investigate at high intraspecific resolution how planktonic foraminifera, an important microfossil group, vary in size across the tropical and subtropical oceans of the world. We measured 3799 individuals of nine species in 53 seafloor sediments and analysed potential size biases in the museum collection. For each site, we obtained corresponding local values of mean annual sea-surface temperature (SST), net primary productivity (NPP), and relative abundance of each species. Given former studies, we expected species to reach largest shell sizes under optimal environmental conditions. At species level, we find the expected pattern; however, at population level, species greatly differ in how much size variation is explained by SST, NPP and/or relative abundance. While some species show a high predictability of size variation given one single variable (Trilobatus sacculifer, Globigerinella siphonifera, Pulleniatina obliquiloculata, Globorotalia truncatulinoides), other species showed either weak or no relationships between size and the studied covariates (Globigerinoides ruber, G. conglobatus, Neogloboquadrina dutertrei, G. menardii, Globoconella inflata). By incorporating intraspecific variation and sampling broader geographical ranges compared to previous studies, we conclude that shell size variation in planktonic foraminifera species cannot be consistently predicted by the environment. Our results caution against the general use of size as a proxy for planktonic foraminifera environmental optima, and emphasise the need for more studies analysing their within-species size variation. More generally, our findings show that contrasting results can be obtained when analysing patterns at different organisational levels, and highlights the utility of natural history collections.

ecology↗

bioRxiv2018

Surface sediment samples from early age of seafloor exploration can provide a late 19th century baseline of the marine environment

Ocean-floor sediment samples collected up to 150 years ago represent an important historical archive to benchmark global changes in the seafloor environment, such as species range shifts and invasions and pollution trends. Such benchmarking requires that the historical sediment samples represent the state of the environment at or shortly before the time of collection. However, early oceanographic expeditions sampled the ocean floor using devices like the sounding tube or a dredge, which potentially disturb the sediment surface and recover a mix of Holocene (surface) and deeper, Pleistocene sediments. Here we use climate-sensitive microfossils as a fast biometric method to assess if historical seafloor samples contain a mixture of modern and glacial sediments. Our assessment is based on comparing the composition of planktonic foraminifera (PF) assemblages in historical samples with Holocene and Last Glacial Maximum (LGM) global reference datasets. We show that eight out of the nine historical samples contain PF assemblages more similar to the Holocene than to the LGM PF assemblages, but the comparisons are only significant when there is a high local species temporal turnover (from the LGM to the Holocene). When analysing temporal turnover globally, we show that upwelling and temperate regions had greatest species turnover, which are areas where our methodology would be most diagnostic. Our results suggest that sediment samples from historical collections can provide a baseline of the state of marine ecosystems in the late 19th century, and thus be used to assess ocean global change trends.

paleontology↗

bioRxiv2017

Pathway enrichment analysis of -omics data

Pathway enrichment analysis helps gain mechanistic insight into large gene lists typically resulting from genome scale (-omics) experiments. It identifies biological pathways that are enriched in the gene list more than expected by chance. We explain pathway enrichment analysis and present a practical step-by-step guide to help interpret gene lists resulting from RNA-seq and genome sequencing experiments. The protocol comprises three major steps: define a gene list from genome scale data, determine statistically enriched pathways, and visualize and interpret the results. We focus on differentially expressed genes and mutated cancer genes, however the described principles can be applied to diverse -omics data. The protocol is designed for biologists with no prior bioinformatics training and uses freely available software including g:Profiler, GSEA, Cytoscape and Enrichment Map.

bioinformatics↗